Diversity

21 pages, 2864 KiB

Open AccessEditor’s ChoiceArticle

Aquatic Macrophyte Vegetation Promotes Taxonomic and Functional Diversity of Odonata Assemblages in Intermittent Karst Rivers in the Mediterranean

by Marina Vilenica, Fran Rebrina, Renata Matoničkin Kepčija, Vedran Šegota, Mario Rumišek, Lea Ružanović and Andreja Brigić

Diversity 2022, 14(1), 31; https://doi.org/10.3390/d14010031 - 4 Jan 2022

Cited by 13 | Viewed by 3008

Abstract

Assemblages of adult Odonata were studied in four intermittent karst rivers encompassing macrophyte-rich (MRH) and macrophyte-poor habitats (MPH) in southern Europe, where temporary lotic habitats are the predominant freshwater type but are still understudied. With a total of 25 recorded species, the studied [...] Read more.

Assemblages of adult Odonata were studied in four intermittent karst rivers encompassing macrophyte-rich (MRH) and macrophyte-poor habitats (MPH) in southern Europe, where temporary lotic habitats are the predominant freshwater type but are still understudied. With a total of 25 recorded species, the studied habitats support species-rich Odonata assemblages, as already shown for intermittent rivers in the Mediterranean. Aquatic macrophyte abundance, conductivity, and water velocity are the most significant determinants of Odonata assemblages in the studied IRES. MRH promote higher Odonata abundance and the taxonomic and functional diversity of their assemblages compared to the MPH. Odonata assemblages in MRH are characterized by higher values of body size and a higher share of species preferring lentic and temporary hydrological conditions. Moreover, their assemblages are characterized by various patterns of nymphal development and drought resilience strategies. In contrast, MPH are preferred by lotic species, with nymphal development all year round and with no specific drought-resisting strategies. Our results contribute to the knowledge of diversity and ecological requirements of dragonflies and damselflies in IRES habitats, which could provide scientific background for future conservation activities and bioassessment protocols of such habitats and their biota. Full article

(This article belongs to the Special Issue Aquatic Insects: Biodiversity, Ecology and Conservation Challenges)

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12 pages, 1277 KiB

Open AccessEditor’s ChoiceReview

Epibiotic Communities of Common Crab Species in the Coastal Barents Sea: Biodiversity and Infestation Patterns

by Alexander G. Dvoretsky and Vladimir G. Dvoretsky

Diversity 2022, 14(1), 6; https://doi.org/10.3390/d14010006 - 23 Dec 2021

Cited by 25 | Viewed by 6547

Abstract

Crabs are important ecosystem engineers in marine habitats worldwide. Based on long-term data, we analyzed the species composition and infestation indices of epibionts and symbionts colonizing the great spider crab, Hyas araneus, and two lithodid crabs—the northern stone crab, Lithodes maja, [...] Read more.

Crabs are important ecosystem engineers in marine habitats worldwide. Based on long-term data, we analyzed the species composition and infestation indices of epibionts and symbionts colonizing the great spider crab, Hyas araneus, and two lithodid crabs—the northern stone crab, Lithodes maja, and the red king crab, Paralithodes camtschaticus—in the coastal zone of the Barents Sea. The epibiotic communities found on great spider crabs were closer to northern stone crabs (33%) compared to red king crabs (25%). The prevalence of mobile symbionts (amphipods, Ischyrocerus, and polychaetes, Harmothoe) and common epibionts, such as barnacles and hydrozoans, was low on great spider crabs and high on the body and in the gills of lithodid crabs. Epiphytes were abundant on great spider crabs but not present on both species of lithodid crabs. Egg symbionts found on H. araneus and P. camtschaticus do not affect their local populations. Differences in the fouling communities found on the three crab species are associated with host size range, surface properties of their carapaces, and behavior patterns. Full article

(This article belongs to the Special Issue Ecology and Management of Crab Species: Recent Advances and New Challenges)

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15 pages, 436 KiB

Open AccessFeature PaperEditor’s ChoiceArticle

Improving Taxonomic Practices and Enhancing Its Extensibility—An Example from Araneology

by Jason E. Bond, Rebecca L. Godwin, Jordan D. Colby, Lacie G. Newton, Xavier J. Zahnle, Ingi Agnarsson, Chris A. Hamilton and Matjaž Kuntner

Diversity 2022, 14(1), 5; https://doi.org/10.3390/d14010005 - 23 Dec 2021

Cited by 18 | Viewed by 5704

Abstract

Planetary extinction of biodiversity underscores the need for taxonomy. Here, we scrutinize spider taxonomy over the last decade (2008–2018), compiling 2083 published accounts of newly described species. We evaluated what type of data were used to delineate species, whether data were made freely [...] Read more.

Planetary extinction of biodiversity underscores the need for taxonomy. Here, we scrutinize spider taxonomy over the last decade (2008–2018), compiling 2083 published accounts of newly described species. We evaluated what type of data were used to delineate species, whether data were made freely available, whether an explicit species hypothesis was stated, what types of media were used, the sample sizes, and the degree to which species constructs were integrative. The findings we report reveal that taxonomy remains largely descriptive, not integrative, and provides no explicit conceptual framework. Less than 4% of accounts explicitly stated a species concept and over one-third of all new species described were based on 1–2 specimens or only one sex. Only ~5% of studies made data freely available, and only ~14% of all newly described species employed more than one line of evidence, with molecular data used in ~6% of the studies. These same trends have been discovered in other animal groups, and therefore we find it logical that taxonomists face an uphill challenge when justifying the scientific rigor of their field and securing the needed resources. To move taxonomy forward, we make recommendations that, if implemented, will enhance its rigor, repeatability, and scientific standards. Full article

(This article belongs to the Special Issue Phylogenomic, Biogeographic, and Evolutionary Research Trends in Arachnology)

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11 pages, 1927 KiB

Open AccessEditor’s ChoiceArticle

Microbiome Changes of Endemic Lake Baikal Sponges during Bleaching Syndrome Development

by Valeria Itskovich, Oxana Kaluzhnaya, Olga Glyzina, Ragothaman Prathiviraj, George Seghal Kiran and Joseph Selvin

Diversity 2021, 13(12), 653; https://doi.org/10.3390/d13120653 - 8 Dec 2021

Cited by 4 | Viewed by 2725

Abstract

The sponge (Porifera) microbiome is an indicator of both natural and anthropogenic stressors. Studying Baikal sponge microbial communities could help reveal if there is a connection between bacterial symbionts and a mass sponge bleaching event that was recently detected; 16S rRNA sequencing was [...] Read more.

The sponge (Porifera) microbiome is an indicator of both natural and anthropogenic stressors. Studying Baikal sponge microbial communities could help reveal if there is a connection between bacterial symbionts and a mass sponge bleaching event that was recently detected; 16S rRNA sequencing was performed among healthy and diseased freshwater sponges of Lubomirskia baikalensis and Baikalospongia intermedia, which were collected from Lake Baikal, Russia. A phylum-based taxonomic classification showed that Chlorophyta, Acidobacteria, Bacteroidetes, Actinobacteria and Cyanobacteria were most abundant across samples. When comparing healthy and diseased L. baikalensis samples, large variations in microbial composition were found at the phylum level. Comparative analyses, which were performed for the first time for B. intermedia, showed a decrease in Chlorophyta (unicellular green algae) and an increase in Bacteroidetes and Cyanobacteria in diseased specimens. At the genus level, the Opitutus (Verrucomicrobia), Planctomyces, and Nitrospira content increased in all diseased sponges, which reflected a general tendency toward an increase in Cyanobacteria in diseased sponges. Comparative analysis of the diseased and healthy sponge metagenomes showed that diseased sponges underwent various nonspecific changes in bacterial composition. The bacterial community composition is probably influenced by sponge type and degree of disease affection. Full article

(This article belongs to the Special Issue Selected Papers from 1st International Electronic Conference on Biological Diversity, Ecology, and Evolution (BDEE 2021))

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18 pages, 2968 KiB

Open AccessEditor’s ChoiceArticle

Biogeography of Long-Jawed Spiders Reveals Multiple Colonization of the Caribbean

by Klemen Čandek, Ingi Agnarsson, Greta J. Binford and Matjaž Kuntner

Diversity 2021, 13(12), 622; https://doi.org/10.3390/d13120622 - 26 Nov 2021

Cited by 7 | Viewed by 3033

Abstract

Dispersal ability can affect levels of gene flow thereby shaping species distributions and richness patterns. The intermediate dispersal model of biogeography (IDM) predicts that in island systems, species diversity of those lineages with an intermediate dispersal potential is the highest. Here, we tested [...] Read more.

Dispersal ability can affect levels of gene flow thereby shaping species distributions and richness patterns. The intermediate dispersal model of biogeography (IDM) predicts that in island systems, species diversity of those lineages with an intermediate dispersal potential is the highest. Here, we tested this prediction on long-jawed spiders (Tetragnatha) of the Caribbean archipelago using phylogenies from a total of 318 individuals delineated into 54 putative species. Our results support a Tetragnatha monophyly (within our sampling) but reject the monophyly of the Caribbean lineages, where we found low endemism yet high diversity. The reconstructed biogeographic history detects a potential early overwater colonization of the Caribbean, refuting an ancient vicariant origin of the Caribbean Tetragnatha as well as the GAARlandia land-bridge scenario. Instead, the results imply multiple colonization events to and from the Caribbean from the mid-Eocene to late-Miocene. Among arachnids, Tetragnatha uniquely comprises both excellently and poorly dispersing species. A direct test of the IDM would require consideration of three categories of dispersers; however, long-jawed spiders do not fit one of these three a priori definitions, but rather represent a more complex combination of attributes. A taxon such as Tetragnatha, one that readily undergoes evolutionary changes in dispersal propensity, can be referred to as a ‘dynamic disperser’. Full article

(This article belongs to the Special Issue Phylogenomic, Biogeographic, and Evolutionary Research Trends in Arachnology)

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46 pages, 4086 KiB

Open AccessEditor’s ChoiceArticle

Italian Vascular Flora: New Findings, Updates and Exploration of Floristic Similarities between Regions

by Adriano Stinca, Carmelo Maria Musarella, Leonardo Rosati, Valentina Lucia Astrid Laface, Wolfgang Licht, Emanuele Fanfarillo, Robert Philipp Wagensommer, Gabriele Galasso, Simonetta Fascetti, Assunta Esposito, Tiberio Fiaschi, Gianluca Nicolella, Giuseppina Chianese, Giampiero Ciaschetti, Giovanni Salerno, Paola Fortini, Romeo Di Pietro, Enrico Vito Perrino, Claudia Angiolini, Leopoldo De Simone and Giacomo Mei Show full author list Hide full author list

Diversity 2021, 13(11), 600; https://doi.org/10.3390/d13110600 - 21 Nov 2021

Cited by 50 | Viewed by 7087

Abstract

The tradition of floristic studies in Italy has made it possible to obtain a good knowledge of plant diversity both on a national and regional scale. However, the lack of knowledge for some areas, advances in plant systematics and human activities related to [...] Read more.

The tradition of floristic studies in Italy has made it possible to obtain a good knowledge of plant diversity both on a national and regional scale. However, the lack of knowledge for some areas, advances in plant systematics and human activities related to globalization, highlight the need for further studies aimed at improving floristic knowledge. In this paper, based on fieldwork and herbaria and literature surveys, we update the knowledge on the Italian vascular flora and analyze the floristic similarities between the administrative regions. Four taxa, all exotic, were recorded for the first time in Italy and Europe. In detail, Elaeodendron croceum, Kalanchoë blossfeldiana, and Sedum spathulifolium var. spathulifolium were found as casual aliens, while Oxalis brasiliensis was reported as historical record based on some herbarium specimens. Furthermore, Kalanchoë laxiflora was confirmed as a casual alien species for Italy and Europe. Status changes for some taxa were proposed at both national and regional levels, as well as many taxa were reported as new or confirmed at the regional level. Currently the Italian vascular flora comprises 9150 taxa of which 7547 are native (of which 1598 are Italian endemics) and 1603 are exotic at the national level. The multivariate analysis of updated floristic data on a regional scale showed a clear distribution along the latitudinal gradient, in accordance with the natural geographical location of the regions in Italy. This pattern of plants distribution was not affected by the introduction of alien species. Despite some taxonomic and methodological issues which are still open, the data obtained confirm the important role of floristic investigations in the field and in herbaria, as well as the collaborative approach among botanists, in order to improve the knowledge of the Italian and European vascular flora. Full article

(This article belongs to the Special Issue Biodiversity and Conservation of Vascular Flora)

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11 pages, 3180 KiB

Open AccessFeature PaperEditor’s ChoiceArticle

Evolution of Beak and Feather Disease Virus across Three Decades of Conservation Intervention for Population Recovery of the Mauritius Parakeet

by Deborah J. Fogell, Simon Tollington, Vikash Tatayah, Sion Henshaw, Houshna Naujeer, Carl Jones, Claire Raisin, Andrew Greenwood and Jim J. Groombridge

Diversity 2021, 13(11), 584; https://doi.org/10.3390/d13110584 - 16 Nov 2021

Cited by 10 | Viewed by 3802

Abstract

Emerging infectious diseases (EIDs) are key contributors to the current global biodiversity crisis. Psittaciformes (parrots) are one of the most vulnerable avian taxa and psittacine beak and feather disease (PBFD) is the most common viral disease in wild parrots. PBFD is caused by [...] Read more.

Emerging infectious diseases (EIDs) are key contributors to the current global biodiversity crisis. Psittaciformes (parrots) are one of the most vulnerable avian taxa and psittacine beak and feather disease (PBFD) is the most common viral disease in wild parrots. PBFD is caused by the beak and feather disease virus (BFDV), which belongs to the Circoviridae family and comprises a circular, single-stranded DNA genome. BFDV is considered to have spread rapidly across the world and, in 2005, an outbreak of PBFD was documented in the recovering population of the Mauritius parakeet (Alexandrinus eques). The Mauritius parakeet was once the world’s rarest parrot and has been successfully recovered through 30 years of intensive conservation management. Molecular surveillance for the prevalence of BFDV was carried out across a 24-year sample archive spanning the period from 1993 to 2017, and DNA sequencing of positive individuals provided an opportunity to assess patterns of phylogenetic and haplotype diversity. Phylogenetic analyses show variation in the extent of viral diversification within the replicase protein (Rep). Timeseries of BFDV prevalence and number of haplotypes reveal that two subsequent waves of infection occurred in 2010/2011 and 2013/2014 following the initial outbreak in 2005. Continued disease surveillance to determine the frequency and intensity of subsequent waves of infection may benefit future translocation/reintroduction planning. The continued growth of the Mauritius parakeet population despite the presence of BFDV bodes well for its long-term persistence. Full article

(This article belongs to the Special Issue Ecology and Conservation of Parrots in Their Native and Non-Native Ranges)

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20 pages, 5346 KiB

Open AccessEditor’s ChoiceArticle

Algae and Cyanobacteria Diversity and Bioindication of Long-Term Changes in the Hula Nature Reserve, Israel

by Sophia Barinova and Alla Alster

Diversity 2021, 13(11), 583; https://doi.org/10.3390/d13110583 - 14 Nov 2021

Cited by 4 | Viewed by 2597

Abstract

Lake Hula, the core of one of the most extensive wetland complexes in the Eastern Mediterranean, was drained in 1951–1958. However, about 350 hectares of papyrus marshes were allocated in the southwestern part of the previous lake and became the Hula Nature Reserve [...] Read more.

Lake Hula, the core of one of the most extensive wetland complexes in the Eastern Mediterranean, was drained in 1951–1958. However, about 350 hectares of papyrus marshes were allocated in the southwestern part of the previous lake and became the Hula Nature Reserve status, the first of two wetlands in Israel included in the Ramsar List of Wetlands of International Importance. The list of algae and cyanobacteria species of Lake Hula was compiled by us for the first time based on data from publications of 1938–1958, as well as our research in the Hula Nature Reserve, obtained within the framework of the monitoring program for 2007–2013. The list includes 225 species and intraspecies of algae and cyanobacteria belonging to eight phyla. The dynamics of the species richness of algae and cyanobacteria flora for 1938–2013 are shown. Species-bioindicators of water quality have been identified, and the change in their composition by ecological groups for a period of about a hundred years has been shown. Based on the species richness of algae communities, water quality indices were calculated with particular attention to changes in trophic status during the study period. The algae flora of Lake Hula and Hula Nature Reserve was found to be similar, but bioindication has revealed an increase in salinity and organic pollution in recent years. Full article

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33 pages, 5076 KiB

Open AccessFeature PaperEditor’s ChoiceReview

What Is an “Arachnid”? Consensus, Consilience, and Confirmation Bias in the Phylogenetics of Chelicerata

by Prashant P. Sharma, Jesús A. Ballesteros and Carlos E. Santibáñez-López

Diversity 2021, 13(11), 568; https://doi.org/10.3390/d13110568 - 6 Nov 2021

Cited by 17 | Viewed by 7694

Abstract

The basal phylogeny of Chelicerata is one of the opaquest parts of the animal Tree of Life, defying resolution despite application of thousands of loci and millions of sites. At the forefront of the debate over chelicerate relationships is the monophyly of Arachnida, [...] Read more.

The basal phylogeny of Chelicerata is one of the opaquest parts of the animal Tree of Life, defying resolution despite application of thousands of loci and millions of sites. At the forefront of the debate over chelicerate relationships is the monophyly of Arachnida, which has been refuted by most analyses of molecular sequence data. A number of phylogenomic datasets have suggested that Xiphosura (horseshoe crabs) are derived arachnids, refuting the traditional understanding of arachnid monophyly. This result is regarded as controversial, not least by paleontologists and morphologists, due to the widespread perception that arachnid monophyly is unambiguously supported by morphological data. Moreover, some molecular datasets have been able to recover arachnid monophyly, galvanizing the belief that any result that challenges arachnid monophyly is artefactual. Here, we explore the problems of distinguishing phylogenetic signal from noise through a series of in silico experiments, focusing on datasets that have recently supported arachnid monophyly. We assess the claim that filtering by saturation rate is a valid criterion for recovering Arachnida. We demonstrate that neither saturation rate, nor the ability to assemble a molecular phylogenetic dataset supporting a given outcome with maximal nodal support, is a guarantor of phylogenetic accuracy. Separately, we review empirical morphological phylogenetic datasets to examine characters supporting Arachnida and the downstream implication of a single colonization of terrestrial habitats. We show that morphological support of arachnid monophyly is contingent upon a small number of ambiguous or incorrectly coded characters, most of these tautologically linked to adaptation to terrestrial habitats. Full article

(This article belongs to the Special Issue Phylogenomic, Biogeographic, and Evolutionary Research Trends in Arachnology)

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18 pages, 851 KiB

Open AccessEditor’s ChoiceArticle

The Natural Capital Value of the Seagrass Posidonia oceanica in the North-Western Mediterranean

by Ilaria Rigo, Chiara Paoli, Giulia Dapueto, Christine Pergent-Martini, Gerard Pergent, Alice Oprandi, Monica Montefalcone, Carlo Nike Bianchi, Carla Morri and Paolo Vassallo

Diversity 2021, 13(10), 499; https://doi.org/10.3390/d13100499 - 15 Oct 2021

Cited by 18 | Viewed by 3467

Abstract

Posidonia oceanica is an endemic Mediterranean seagrass used as a ‘biological quality element’ in monitoring programmes of the EU Water Framework Directive, providing information about coastal ecosystems status. The regression of P. oceanica meadows caused a growing interest among policy makers to assess [...] Read more.

Posidonia oceanica is an endemic Mediterranean seagrass used as a ‘biological quality element’ in monitoring programmes of the EU Water Framework Directive, providing information about coastal ecosystems status. The regression of P. oceanica meadows caused a growing interest among policy makers to assess the value of seagrasses and to increase their protection. An evaluation of P. oceanica meadows located in the Ligurian-Provençal basin (NW Mediterranean) through a biophysical approach is here developed. Six meadows located in Liguria (Italy) and Corsica (France) were investigated by applying the emergy analysis to assess the natural capital (NC) stocked by leaves and rhizomes components. Results highlighted the importance of carrying out an analysis of the variations in the NC value in both components: rhizomes defined the growth stage and the capacity to store NC over time; leaves provided information on the variability due to disturbances in the water column. Emergy analysis allows defining the NC, in terms of resources needed to maintain the meadows and to provide services to coastal communities. This research is inserted into the effort of incorporating the NC evaluation into marine planning and decision making to achieve nature conservation goals, while ensuring the sustainable exploitation of marine resources. Full article

(This article belongs to the Special Issue Biodiversity Conservation in Mediterranean Sea)

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19 pages, 7208 KiB

Open AccessEditor’s ChoiceArticle

FloCan—A Revised Checklist for the Flora of the Canary Islands

by Carl Beierkuhnlein, Anna Walentowitz and Walter Welss

Diversity 2021, 13(10), 480; https://doi.org/10.3390/d13100480 - 29 Sep 2021

Cited by 20 | Viewed by 5847

Abstract

The flora of the Canary Islands has been subject to botanical studies for more than 200 years. Several biodiversity databases are available for the archipelago. However, there are various drivers of change in real biodiversity and the knowledge about it constantly needs to [...] Read more.

The flora of the Canary Islands has been subject to botanical studies for more than 200 years. Several biodiversity databases are available for the archipelago. However, there are various drivers of change in real biodiversity and the knowledge about it constantly needs to be kept track of. Island floras are both: exposed to species loss and to species introductions, either through natural processes or by anthropogenic drivers. Additionally, the evolution of endemic plant species plays a substantial role. Endemic species are sensitive to population decline due to small population sizes and possible low competitiveness against incoming species. Additionally, there is continuous progress in systematics and taxonomy. Species names or their taxonomic attribution can be modified. Here, we check published plant lists for the Canary Islands and literature, and compile currently accepted taxa into an updated checklist. For this FloCan checklist, several sources were compiled, checked for completeness and quality, and their taxonomy was updated. We illustrate how far plant names are considered in regional or global databases. This work represents the current state of knowledge on Canary Island plant diversity, including introduced and recently described taxa. We provide a comprehensive and updated basis for biogeographical and macroecological studies. Particularly, the number of non-native species is being extended substantially. The adaptation to standard international nomenclature supports integration into large-scale studies. Full article

(This article belongs to the Special Issue 2021 Feature Papers by Diversity’s Editorial Board Members)

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16 pages, 1261 KiB

Open AccessEditor’s ChoiceArticle

Exploring Plant Functional Diversity and Redundancy of Mediterranean High-Mountain Habitats in the Apennines

by Alessandro Bricca, Maria Laura Carranza, Marco Varricchione, Maurizio Cutini and Angela Stanisci

Diversity 2021, 13(10), 466; https://doi.org/10.3390/d13100466 - 26 Sep 2021

Cited by 13 | Viewed by 2981

Abstract

We analyzed plant functional diversity (FD) and redundancy (FR) in Mediterranean high-mountain communities to explore plant functional patterns and assembly rules. We focused on three above-ground plant traits: plant height (H), a good surrogate of competition for light strategies, and specific leaf area [...] Read more.

We analyzed plant functional diversity (FD) and redundancy (FR) in Mediterranean high-mountain communities to explore plant functional patterns and assembly rules. We focused on three above-ground plant traits: plant height (H), a good surrogate of competition for light strategies, and specific leaf area (SLA) and leaf dry matter content (LDMC), useful indicators of resource exploitation functional schemes. We used the georeferenced vegetation plots and field-measured plant functional traits of four widely spread vegetation types growing on screes, steep slopes, snowbeds and ridges, respectively. We calculated Rao’s FD and FR followed by analysis of standardized effect size, and compared FD and FR community values using ANOVA and the Tukey post hoc test. Assemblage rules varied across plant communities and traits. The High FR_H registered on snowbeds and ridges is probably linked to climatic filtering processes, while the high FD_H and low FD_SLA and FD_LDMC on steep slopes could be related with underlying competition mechanisms. The absence of FD patterns in scree vegetation pinpoint random assembly processes which are typical of highly unstable or disturbed ecosystems. Improved knowledge about the deterministic/stochastic processes shaping species coexistence on high mountain ecosystems should help researchers to understand and predict vegetation vulnerability to environmental changes. Full article

(This article belongs to the Special Issue Diversity, Ecology and Conservation of Alpine Plants)

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21 pages, 1019 KiB

Open AccessEditor’s ChoiceArticle

Concurrent Butterfly, Bat and Small Mammal Monitoring Programmes Using Citizen Science in Catalonia (NE Spain): A Historical Review and Future Directions

by Ignasi Torre, Adrià López-Baucells, Constantí Stefanescu, Lídia Freixas, Carles Flaquer, Carme Bartrina, Alba Coronado, David López-Bosch, Maria Mas, Sílvia Míguez, Joaquim Muñoz, Ferran Páramo, Xavier Puig-Montserrat, Carme Tuneu-Corral, Andreu Ubach and Antoni Arrizabalaga

Diversity 2021, 13(9), 454; https://doi.org/10.3390/d13090454 - 21 Sep 2021

Cited by 17 | Viewed by 3617

Abstract

The Biodiversity and Bioindicators research group (BiBIO), based at the Natural Sciences Museum of Granollers, has coordinated four long-term faunal monitoring programmes based on citizen science over more than two decades in Catalonia (NE Spain). We summarize the historical progress of these programmes, [...] Read more.

The Biodiversity and Bioindicators research group (BiBIO), based at the Natural Sciences Museum of Granollers, has coordinated four long-term faunal monitoring programmes based on citizen science over more than two decades in Catalonia (NE Spain). We summarize the historical progress of these programmes, describing their main conservation outputs, the challenges overcome, and future directions. The Catalan Butterfly Monitoring Scheme (CBMS) consists of a network of nearly 200 recording sites where butterfly populations have been monitored through visual censuses along transects for nearly three decades. This programme provides accurate temporal and spatial changes in the abundance of butterflies and relates them to different environmental factors (e.g., habitat and weather conditions). The Bat Monitoring Programme has progressively evolved to include passive acoustic monitoring protocols, as well as bat box-, underground- and river-bat surveys, and community ecological indices have been developed to monitor bat responses at assemblage level to both landscape and climatic changes. The Monitoring of common small mammals in Spain (SEMICE), a common small mammal monitoring programme with almost 80 active live-trapping stations, provides information to estimate population trends and has underlined the relevance of small mammals as both prey (of several predators) and predators (of insect forest pests). The Dormouse Monitoring Programme represents the first monitoring programme in Europe using specific nest boxes for the edible dormouse, providing information about biological and demographic data of the species at the southern limit of its distribution range. The combination and complementarity of these monitoring programmes provide crucial data to land managers to improve the understanding of conservation needs and develop efficient protection laws. Full article

(This article belongs to the Special Issue Citizen Science for Biodiversity Conservation: Harnessing the Power of the Public to Address Wicked Conservation Problems)

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24 pages, 7323 KiB

Open AccessEditor’s ChoiceArticle

Taxonomy of the Cryptocephalus heraldicus Group (Coleoptera: Chrysomelidae, Cryptocephalinae) from China

by Wenyuan Duan, Fengyan Wang and Hongzhang Zhou

Diversity 2021, 13(9), 451; https://doi.org/10.3390/d13090451 - 20 Sep 2021

Cited by 2 | Viewed by 3407

Abstract

This is a study on the leaf beetle subgenus Cryptocephalus Geoffroy, 1762 from China, with the particular emphasis upon the species-group classification of the subgenus and the taxonomy of the Cryptocephalus heraldicus species group. A new key is compiled to all the species [...] Read more.

This is a study on the leaf beetle subgenus Cryptocephalus Geoffroy, 1762 from China, with the particular emphasis upon the species-group classification of the subgenus and the taxonomy of the Cryptocephalus heraldicus species group. A new key is compiled to all the species groups found in China. Four new species are described from China: Cryptocephalus (Cryptocephalus) biordopunctatus sp. nov. from Yunnan, C. hani sp. nov. from Shanxi, Hubei, Shaanxi and Gansu, C. incisodentatus sp. nov. from Sichuan and Yunnan, and C. nigroflavusiventerus sp. nov. from Yunnan. Three species are found for the first time in China: C. lacosus Pic, 1922, C. nigriceps Allard, 1891 and C. rajah Jacoby, 1908. The species C. nigrolimbatus Jacoby, 1890 is transferred from the subgenus Burlinius Lopatin to this subgenus and assigned to the Cryptocephalus heraldicus group. The species number of this group is now 30 in total according to our result of taxonomic review. A key to all the mainland China species of this species group is provided as well as high quality color images and line drawings of adult habitus, aedeagus, and other important structures. All the types of the new species are deposited in the collection of Institute of Zoology, Chinese Academy of Sciences (IZ-CAS). Full article

(This article belongs to the Special Issue Diversity and Evolution of Coleoptera)

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19 pages, 3285 KiB

Open AccessFeature PaperEditor’s ChoiceArticle

The Role of Small Lowland Patches of Exotic Forests as Refuges of Rare Endemic Azorean Arthropods

by Noelline Tsafack, Simone Fattorini, Mário Boieiro, François Rigal, Alejandra Ros-Prieto, Maria Teresa Ferreira and Paulo A. V. Borges

Diversity 2021, 13(9), 443; https://doi.org/10.3390/d13090443 - 16 Sep 2021

Cited by 16 | Viewed by 3506

Abstract

Islands have been disproportionately affected by the current biodiversity crisis. In island biotas, one of the most recurrent anthropic alterations is species introduction. Invasion of exotic species may represent a major threat for island biotas, because invasive species may change species composition and [...] Read more.

Islands have been disproportionately affected by the current biodiversity crisis. In island biotas, one of the most recurrent anthropic alterations is species introduction. Invasion of exotic species may represent a major threat for island biotas, because invasive species may change species composition and simplify community dynamics. We investigated diversity patterns of native and introduced species in native and exotic forests of Terceira Island (Azores, Portugal) by using diversity profiles based on Hill numbers. Use of diversity profiles allows for a complete characterization of the community diversity because they combine information on species richness, rarity, and dominance. We found that native forest remnants are crucial for the maintenance of endemic Azorean arthropod diversity. However, we also found that some lowland patches of exotic forests can sustain populations of rare endemic species. Our findings reinforce the importance of the few and small remnants of native forests, which are a pillar to the conservation of Azorean endemic arthropods. However, areas occupied by exotic forests, whether they are large and contiguous or small and isolated, close to native forests, or embedded in a matrix of agriculture activities, can also play a role in the conservation of native species, including endemics. Full article

(This article belongs to the Collection Evolution and Extinctions on Islands)

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20 pages, 852 KiB

Open AccessFeature PaperEditor’s ChoiceArticle

Harnessing the Power of Metabarcoding in the Ecological Interpretation of Plant-Pollinator DNA Data: Strategies and Consequences of Filtering Approaches

by Nicola Tommasi, Andrea Ferrari, Massimo Labra, Andrea Galimberti and Paolo Biella

Diversity 2021, 13(9), 437; https://doi.org/10.3390/d13090437 - 10 Sep 2021

Cited by 13 | Viewed by 4048

Abstract

Although DNA metabarcoding of pollen mixtures has been increasingly used in the field of pollination biology, methodological and interpretation issues arise due to its high sensitivity. Filtering or maintaining false positives, contaminants, and rare taxa or molecular features could lead to different ecological [...] Read more.

Although DNA metabarcoding of pollen mixtures has been increasingly used in the field of pollination biology, methodological and interpretation issues arise due to its high sensitivity. Filtering or maintaining false positives, contaminants, and rare taxa or molecular features could lead to different ecological results. Here, we reviewed how this choice has been addressed in 43 studies featuring pollen DNA metabarcoding, which highlighted a very high heterogeneity of filtering methods. We assessed how these strategies shaped pollen assemblage composition, species richness, and interaction networks. To do so, we compared four processing methods: unfiltering, filtering with a proportional 1% of sample reads, a fixed threshold of 100 reads, and the ROC approach (Receiver Operator Characteristic). The results indicated that filtering impacted species composition and reduced species richness, with ROC emerging as a conservative approach. Moreover, in contrast to unfiltered networks, filtering decreased network Connectance and Entropy, and it increased Modularity and Connectivity, indicating that using cut-off thresholds better describes interactions. Overall, unfiltering might compromise reliable ecological interpretations, unless a study targets rare species. We discuss the suitability of each filtering type, plead for justifying filtering strategies on biological or methodological bases and for developing shared approaches to make future studies more comparable. Full article

(This article belongs to the Special Issue Advances in HTS-Based Identification of Species and Ecological Interactions)

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12 pages, 2914 KiB

Open AccessFeature PaperEditor’s ChoiceReview

The Number and Distribution of Introduced and Naturalized Parrots

by Carlos E. Calzada Preston and Stephen Pruett-Jones

Diversity 2021, 13(9), 412; https://doi.org/10.3390/d13090412 - 29 Aug 2021

Cited by 28 | Viewed by 5162

Abstract

Parrots have been transported and traded by humans for at least the last 2000 years and this trade continues unabated today. This transport of species has involved the majority of recognized parrot species (300+ of 382 species). Inevitably, some alien species either escape [...] Read more.

Parrots have been transported and traded by humans for at least the last 2000 years and this trade continues unabated today. This transport of species has involved the majority of recognized parrot species (300+ of 382 species). Inevitably, some alien species either escape captivity or are released and may establish breeding populations in the novel area. With respect to parrots, established but alien populations are becoming common in many parts of the world. In this review, we attempt to estimate the total number of parrot species introduced into the wild in non-native areas and assess how many of these have self-sustaining breeding populations. Based the public databases GAVIA, eBird, and iNaturalist, 166 species of Psittaciformes have been introduced (seen in the wild) into 120 countries or territories outside of the native range. Of these, 60 species are naturalized, and an additional 11 species are breeding in at least one country outside of their native range (86 countries or territories total). The Rose-ringed Parakeet (Psittacula krameri) and Monk Parakeet (Myiopsitta monachus) are the most widely distributed and successful of the introduced parrots, being naturalized in 47 and 26 countries or territories, respectively. Far and away, the United States and its territories support the greatest number of naturalized parrots, with 28 different species found in either the continental US, or Hawaii or Puerto Rico. Naturalized species as well as urbanized native species of parrots are likely to continue increasing in numbers and geographical range, and detailed studies are needed to both confirm species richness in each area as well mitigate potential ecological impacts and conflicts with humans. Full article

(This article belongs to the Special Issue Ecology and Conservation of Parrots in Their Native and Non-Native Ranges)

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5 pages, 529 KiB

Open AccessEditor’s ChoiceBrief Report

Hitchhiking Exotic Clam: Dreissena polymorpha (Pallas, 1771) Transported via the Ornamental Plant Trade

by Jiří Patoka and Barbora Patoková

Diversity 2021, 13(9), 410; https://doi.org/10.3390/d13090410 - 27 Aug 2021

Cited by 11 | Viewed by 2269

Abstract

Ornamental aquaculture is one of the main sources of non-native species worldwide. Unintentionally transported “hitchhiking” organisms have been previously recorded; although most of these species are transported from tropical regions, here we report on the first accidental transport of the zebra mussel ( [...] Read more.

Ornamental aquaculture is one of the main sources of non-native species worldwide. Unintentionally transported “hitchhiking” organisms have been previously recorded; although most of these species are transported from tropical regions, here we report on the first accidental transport of the zebra mussel (Dreissena polymorpha) in a shipment of ornamental Aegagropila linnaei (Chlorophyta) from Russia to the Czech Republic. This invasive mussel is listed on the national blacklist of alien species in the Czech Republic and can be easily released in outdoor garden ponds together with A. linnaei. Since the Czech Republic is known to be a gateway for aquatic ornamental species from a European perspective, re-export to other European countries is also possible. Thus, the spread of D. polymorpha via this pathway cannot be excluded. This finding should be of importance to conservationists, traders, decision-makers and other stakeholders. Full article

(This article belongs to the Special Issue 2021 Feature Papers by Diversity’s Editorial Board Members)

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36 pages, 2556 KiB

Open AccessEditor’s ChoiceReview

Retinoic Acid Signaling in Vertebrate Hindbrain Segmentation: Evolution and Diversification

by Alice M. H. Bedois, Hugo J. Parker and Robb Krumlauf

Diversity 2021, 13(8), 398; https://doi.org/10.3390/d13080398 - 23 Aug 2021

Cited by 5 | Viewed by 5838

Abstract

In metazoans, Hox genes are key drivers of morphogenesis. In chordates, they play important roles in patterning the antero-posterior (A-P) axis. A crucial aspect of their role in axial patterning is their collinear expression, a process thought to be linked to their response [...] Read more.

In metazoans, Hox genes are key drivers of morphogenesis. In chordates, they play important roles in patterning the antero-posterior (A-P) axis. A crucial aspect of their role in axial patterning is their collinear expression, a process thought to be linked to their response to major signaling pathways such as retinoic acid (RA) signaling. The amplification of Hox genes following major events of genome evolution can contribute to morphological diversity. In vertebrates, RA acts as a key regulator of the gene regulatory network (GRN) underlying hindbrain segmentation, which includes Hox genes. This review investigates how the RA signaling machinery has evolved and diversified and discusses its connection to the hindbrain GRN in relation to diversity. Using non-chordate and chordate deuterostome models, we explore aspects of ancient programs of axial patterning in an attempt to retrace the evolution of the vertebrate hindbrain GRN. In addition, we investigate how the RA signaling machinery has evolved in vertebrates and highlight key examples of regulatory diversification that may have influenced the GRN for hindbrain segmentation. Finally, we describe the value of using lamprey as a model for the early-diverged jawless vertebrate group, to investigate the elaboration of A-P patterning mechanisms in the vertebrate lineage. Full article

(This article belongs to the Special Issue Evolution, Development, and Diversification of Vertebrates)

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27 pages, 17708 KiB

Open AccessEditor’s ChoiceArticle

Integrative Descriptions of Two New Tardigrade Species along with the New Record of Mesobiotus skorackii Kaczmarek et al., 2018 from Canada

by Pushpalata Kayastha, Milena Roszkowska, Monika Mioduchowska, Magdalena Gawlak and Łukasz Kaczmarek

Diversity 2021, 13(8), 394; https://doi.org/10.3390/d13080394 - 22 Aug 2021

Cited by 12 | Viewed by 4268

Abstract

Two new tardigrade species from a moss sample collected in Canada, one representing Macrobiotus hufelandi complex and the second one belonging to the genus Bryodelphax, are described. Integrative analysis was undertaken based on morphological and morphometric data (using both light and scanning [...] Read more.

Two new tardigrade species from a moss sample collected in Canada, one representing Macrobiotus hufelandi complex and the second one belonging to the genus Bryodelphax, are described. Integrative analysis was undertaken based on morphological and morphometric data (using both light and scanning electron microscopy (SEM)) combined with multilocus molecular analysis (nuclear sequences, i.e., 18S rRNA, 28S rRNA and ITS-2 as well as mitochondrial COI barcode sequences). Based on COI sequences, Macrobiotus birendrai sp. nov. is most similar to Mac. canaricus (p-distance 17%), whereas Bryodelphax mareki sp. nov. is most similar to Bry. parvulus (p-distance 16%). Both species differ also from their congeners in some morphological and morphometric characters of adults and/or details of egg chorion. Additionally, a large population of Mesobiotus skorackii was found in the sample and this is the first report of this species outside its terra typica in Kirghizia. The original description of this species was prepared based solely on the morphology and morphometry, therefore, here we provide updated data for this species enclosing morphometric and molecular data for the Canadian population. Full article

(This article belongs to the Special Issue Selected Papers from 1st International Electronic Conference on Biological Diversity, Ecology, and Evolution (BDEE 2021))

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24 pages, 7391 KiB

Open AccessEditor’s ChoiceArticle

The Towakkalak System, A Hotspot of Subterranean Biodiversity in Sulawesi, Indonesia

by Louis Deharveng, Cahyo Rahmadi, Yayuk Rahayuningsih Suhardjono and Anne Bedos

Diversity 2021, 13(8), 392; https://doi.org/10.3390/d13080392 - 20 Aug 2021

Cited by 11 | Viewed by 3238

Abstract

The Towakkalak System located in the Maros karst of South Sulawesi is currently the richest of Southeast Asia in obligate subterranean species. It comprises several caves and shafts that give access to the subterranean Towakkalak river as well as many unconnected fossil caves, [...] Read more.

The Towakkalak System located in the Maros karst of South Sulawesi is currently the richest of Southeast Asia in obligate subterranean species. It comprises several caves and shafts that give access to the subterranean Towakkalak river as well as many unconnected fossil caves, stream sinks, and springs located within its footprint. The total length of the caves linked to the active system is 24,319 m and comprises two of the longest caves of Indonesia, Gua Salukkan Kallang and Gua Tanette. Studies of its fauna began in 1985. There are 10 stygobionts and 26 troglobionts that are known from the system. The smaller adjacent system of Saripa has 6 stygobionts and 18 troglobionts, of which 1 and 3, respectively, are absent from Towakkalak. Like all tropical cave inventories, our dataset has limits due to identification uncertainties, gaps in habitat (waters, guano) and taxonomic coverage (micro-crustaceans, mites), sampling methods (pitfall trapping, Karaman–Chappuis), and problems of ecological assignment. A number of additional species are therefore expected to be found in the future. The Towakkalak and Saripa cave systems are included in the Bantimurung-Bulusaraung National Park and are under efficient protection, but parts of the Maros karst outside the park are under serious threat, mainly from quarrying. Full article

(This article belongs to the Special Issue Hotspots of Subterranean Biodiversity)

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15 pages, 2736 KiB

Open AccessEditor’s ChoiceReview

Why Is the Alpine Flora Comparatively Robust against Climatic Warming?

by Christian Körner and Erika Hiltbrunner

Diversity 2021, 13(8), 383; https://doi.org/10.3390/d13080383 - 16 Aug 2021

Cited by 70 | Viewed by 9748

Abstract

The alpine belt hosts the treeless vegetation above the high elevation climatic treeline. The way alpine plants manage to thrive in a climate that prevents tree growth is through small stature, apt seasonal development, and ‘managing’ the microclimate near the ground surface. Nested [...] Read more.

The alpine belt hosts the treeless vegetation above the high elevation climatic treeline. The way alpine plants manage to thrive in a climate that prevents tree growth is through small stature, apt seasonal development, and ‘managing’ the microclimate near the ground surface. Nested in a mosaic of micro-environmental conditions, these plants are in a unique position by a close-by neighborhood of strongly diverging microhabitats. The range of adjacent thermal niches that the alpine environment provides is exceeding the worst climate warming scenarios. The provided mountains are high and large enough, these are conditions that cause alpine plant species diversity to be robust against climatic change. However, the areal extent of certain habitat types will shrink as isotherms move upslope, with the potential areal loss by the advance of the treeline by far outranging the gain in new land by glacier retreat globally. Full article

(This article belongs to the Special Issue Diversity, Ecology and Conservation of Alpine Plants)

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22 pages, 4635 KiB

Open AccessEditor’s ChoiceArticle

Applying Population Viability Analysis to Inform Genetic Rescue That Preserves Locally Unique Genetic Variation in a Critically Endangered Mammal

by Joseph P. Zilko, Dan Harley, Alexandra Pavlova and Paul Sunnucks

Diversity 2021, 13(8), 382; https://doi.org/10.3390/d13080382 - 16 Aug 2021

Cited by 17 | Viewed by 4811

Abstract

Genetic rescue can reduce the extinction risk of inbred populations, but it has the poorly understood risk of ‘genetic swamping’—the replacement of the distinctive variation of the target population. We applied population viability analysis (PVA) to identify translocation rates into the inbred lowland [...] Read more.

Genetic rescue can reduce the extinction risk of inbred populations, but it has the poorly understood risk of ‘genetic swamping’—the replacement of the distinctive variation of the target population. We applied population viability analysis (PVA) to identify translocation rates into the inbred lowland population of Leadbeater’s possum from an outbred highland population that would alleviate inbreeding depression and rapidly reach a target population size (N) while maximising the retention of locally unique neutral genetic variation. Using genomic kinship coefficients to model inbreeding in Vortex, we simulated genetic rescue scenarios that included gene pool mixing with genetically diverse highland possums and increased the N from 35 to 110 within ten years. The PVA predicted that the last remaining population of lowland Leadbeater’s possum will be extinct within 23 years without genetic rescue, and that the carrying capacity at its current range is insufficient to enable recovery, even with genetic rescue. Supplementation rates that rapidly increased population size resulted in higher retention (as opposed to complete loss) of local alleles through alleviation of genetic drift but reduced the frequency of locally unique alleles. Ongoing gene flow and a higher N will facilitate natural selection. Accordingly, we recommend founding a new population of lowland possums in a high-quality habitat, where population growth and natural gene exchange with highland populations are possible. We also recommend ensuring gene flow into the population through natural dispersal and/or frequent translocations of highland individuals. Genetic rescue should be implemented within an adaptive management framework, with post-translocation monitoring data incorporated into the models to make updated predictions. Full article

(This article belongs to the Special Issue Conservation Genetics for Management of Threatened Plant and Animal Species)

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14 pages, 775 KiB

Open AccessEditor’s ChoiceArticle

Mires in Europe—Regional Diversity, Condition and Protection

by Franziska Tanneberger, Asbjørn Moen, Alexandra Barthelmes, Edward Lewis, Lera Miles, Andrey Sirin, Cosima Tegetmeyer and Hans Joosten

Diversity 2021, 13(8), 381; https://doi.org/10.3390/d13080381 - 16 Aug 2021

Cited by 43 | Viewed by 11237

Abstract

In spite of the worldwide largest proportional loss of mires, Europe is a continent with important mire diversity. This article analyses the condition and protection status of European mire ecosystems. The overview is based on the system of European mire regions, representing regional [...] Read more.

In spite of the worldwide largest proportional loss of mires, Europe is a continent with important mire diversity. This article analyses the condition and protection status of European mire ecosystems. The overview is based on the system of European mire regions, representing regional variety and ecosystem biodiversity. We combined peatland distribution data with land cover maps of the Copernicus Land Monitoring Service as well as with the World Database on Protected Areas to assess the extent of degraded peatlands and the proportion of peatlands located in protected areas in each European mire region. The total proportion of degraded peatlands in Europe is 25%; within the EU it is 50% (120,000 km²). The proportion of degradation clearly increases from north to south, as does the proportion of peatlands located within protected areas. In more than half of Europe’s mire regions, the target of at least 17% of the area located in protected areas is not met with respect to peatlands. Data quality is discussed and the lessons learned from Europe for peatland conservation are presented. Full article

(This article belongs to the Special Issue Ecology, Biogeography and Evolutionary Biology of Peatlands)

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17 pages, 327 KiB

Open AccessEditor’s ChoiceReview

Sunscreens’ UV Filters Risk for Coastal Marine Environment Biodiversity: A Review

by Samuele Caloni, Tiziana Durazzano, Giada Franci and Letizia Marsili

Diversity 2021, 13(8), 374; https://doi.org/10.3390/d13080374 - 12 Aug 2021

Cited by 15 | Viewed by 6111

Abstract

Considering the rapid growth of tourism in recent years and the acknowledgement that exposure to solar UV radiation may cause skin cancer, sunscreens have been widely used by beachgoers in recent decades. UV filters contained in sunscreens, however, were recently identified as emerging [...] Read more.

Considering the rapid growth of tourism in recent years and the acknowledgement that exposure to solar UV radiation may cause skin cancer, sunscreens have been widely used by beachgoers in recent decades. UV filters contained in sunscreens, however, were recently identified as emerging pollutants in coastal waters since they accumulate in the marine environment with different adverse effects. In fact, exposure to these components was proven to be toxic to most invertebrate and vertebrate marine species. Some UV filters are linked to the production of significant amounts of reactive oxygen species (ROS), such as hydrogen peroxide, and the release of inorganic micronutrients that may alter the status of coastal habitats. Bioaccumulation and biomagnification have not yet been fully addressed. This review highlights recent progress in research and provides a comprehensive overview of the toxicological and ecotoxicological effects of the most used UV filters both on the abiotic and biotic compartments in different types of coastal areas, to gain a better understanding of the impacts on coastal biodiversity. Full article

(This article belongs to the Special Issue 2021 Feature Papers by Diversity’s Editorial Board Members)

21 pages, 1265 KiB

Open AccessEditor’s ChoiceArticle

Mammoth Cave: A Hotspot of Subterranean Biodiversity in the United States

by Matthew L. Niemiller, Kurt Helf and Rickard S. Toomey

Diversity 2021, 13(8), 373; https://doi.org/10.3390/d13080373 - 12 Aug 2021

Cited by 8 | Viewed by 8916

Abstract

The Mammoth Cave System in the Interior Low Plateau karst region in central Kentucky, USA is a global hotspot of cave-limited biodiversity, particularly terrestrial species. We searched the literature, museum accessions, and database records to compile an updated list of troglobiotic and stygobiotic [...] Read more.

The Mammoth Cave System in the Interior Low Plateau karst region in central Kentucky, USA is a global hotspot of cave-limited biodiversity, particularly terrestrial species. We searched the literature, museum accessions, and database records to compile an updated list of troglobiotic and stygobiotic species for the Mammoth Cave System and compare our list with previously published checklists. Our list of cave-limited fauna totals 49 species, with 32 troglobionts and 17 stygobionts. Seven species are endemic to the Mammoth Cave System and other small caves in Mammoth Cave National Park. The Mammoth Cave System is the type locality for 33 cave-limited species. The exceptional diversity at Mammoth Cave is likely related to several factors, such as the high dispersal potential of cave fauna associated with expansive karst exposures, high surface productivity, and a long history of exploration and study. Nearly 80% of the cave-limited fauna is of conservation concern, many of which are at an elevated risk of extinction because of small ranges, few occurrences, and several potential threats. Full article

(This article belongs to the Special Issue Hotspots of Subterranean Biodiversity)

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31 pages, 2399 KiB

Open AccessEditor’s ChoiceArticle

The Arthropod Fauna of Oak (Quercus spp., Fagaceae) Canopies in Norway

by Karl H. Thunes, Geir E. E. Søli, Csaba Thuróczy, Arne Fjellberg, Stefan Olberg, Steffen Roth, Carl-C. Coulianos, R. Henry L. Disney, Josef Starý, G. (Bert) Vierbergen, Terje Jonassen, Johannes Anonby, Arne Köhler, Frank Menzel, Ryszard Szadziewski, Elisabeth Stur, Wolfgang Adaschkiewitz, Kjell M. Olsen, Torstein Kvamme, Anders Endrestøl, Sigitas Podenas, Sverre Kobro, Lars O. Hansen, Gunnar M. Kvifte, Jean-Paul Haenni and Louis Boumans Show full author list Hide full author list

Diversity 2021, 13(7), 332; https://doi.org/10.3390/d13070332 - 19 Jul 2021

Cited by 12 | Viewed by 5111

Abstract

(1) We document the invertebrate fauna collected from 24 oak canopies in east and west Norway as a contribution to the Norwegian Biodiversity Information Centre’s ‘The Norwegian Taxonomy Initiative’. (2) A snap-shot inventory of the canopies was recorded by means of emitting a [...] Read more.

(1) We document the invertebrate fauna collected from 24 oak canopies in east and west Norway as a contribution to the Norwegian Biodiversity Information Centre’s ‘The Norwegian Taxonomy Initiative’. (2) A snap-shot inventory of the canopies was recorded by means of emitting a mist of natural pyrethrum into the canopies at night using a petrol-driven fogger and collecting the specimens in butterfly nets spread on the ground under the canopy. (3) Almost the entire catch of more than 6800 specimens was identified to 722 species. Out of 92 species new to the Norwegian fauna, 21 were new to science and, additionally, 15 were new to the Nordic fauna. Diptera alone constituted nearly half of the species represented, with 61 new records (18 new species). Additionally, 24 Hymenoptera (one new species), six oribatid mites (two new species) and one Thysanoptera were new to the Norwegian fauna. (4) Our study emphasizes the importance of the oak tree as a habitat both for a specific fauna and occasional visitors, and it demonstrates that the canopy fogging technique is an efficient way to find the ‘hidden fauna’ of Norwegian forests. The low number of red listed species found reflects how poor the Norwegian insect fauna is still studied. Moreover, the implication of the IUCN red list criteria for newly described or newly observed species is discussed. Full article

(This article belongs to the Special Issue Arthropods Associated with Forest Soil and Wood)

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16 pages, 2401 KiB

Open AccessEditor’s ChoiceReview

Ethnolichenology—The Use of Lichens in the Himalayas and Southwestern Parts of China

by Mei-Xia Yang, Shiva Devkota, Li-Song Wang and Christoph Scheidegger

Diversity 2021, 13(7), 330; https://doi.org/10.3390/d13070330 - 18 Jul 2021

Cited by 27 | Viewed by 8197

Abstract

Lichens are used in traditional medicine, food and various other ethnic uses by cultures across the Himalayas and southwestern parts of China. Evidence-based knowledge from historical and modern literatures and investigation of ethnic uses from 1990 proved that lichen species used as medicine [...] Read more.

Lichens are used in traditional medicine, food and various other ethnic uses by cultures across the Himalayas and southwestern parts of China. Evidence-based knowledge from historical and modern literatures and investigation of ethnic uses from 1990 proved that lichen species used as medicine in the Himalayas and southwestern parts of China totaled to 142 species; furthermore, 42 species were utilized as food. Moreover, some lichens are popularly used for lichen produce in ethnic and modern life. An understanding and clarification of the use of lichens in the Himalayas and southeastern parts of China can therefore be important for understanding uses of lichens elsewhere and a reference for additional research of lichen uses in the future. Full article

(This article belongs to the Special Issue Diversity of Lichens—Morphology, Anatomy, Physiology, Secondary Chemistry, Distribution and Their Use: Recent Aspects of Evergreen Topics)

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11 pages, 1537 KiB

Open AccessEditor’s ChoiceOpinion

The Future of DNA Barcoding: Reflections from Early Career Researchers

by Danielle M. Grant, Ole Bjørn Brodnicke, Ann M. Evankow, André O. Ferreira, João T. Fontes, Aslak Kappel Hansen, Mads Reinholdt Jensen, Tuğba Ergül Kalaycı, Alexandra Leeper, Shalaka Kiran Patil, Sebastian Prati, Anna Reunamo, Aradhana J. Roberts, Rajesh Shigdel, Valentina Tyukosova, Mika Bendiksby, Rakel Blaalid, Filipe O. Costa, Peter M. Hollingsworth, Elisabeth Stur and Torbjørn Ekrem Show full author list Hide full author list

Diversity 2021, 13(7), 313; https://doi.org/10.3390/d13070313 - 9 Jul 2021

Cited by 33 | Viewed by 11324

Abstract

Over the last two decades, the use of DNA barcodes has transformed our ability to identify and assess life on our planet. Both strengths and weaknesses of the method have been exemplified through thousands of peer-reviewed scientific articles. Given the novel sequencing approaches, [...] Read more.

Over the last two decades, the use of DNA barcodes has transformed our ability to identify and assess life on our planet. Both strengths and weaknesses of the method have been exemplified through thousands of peer-reviewed scientific articles. Given the novel sequencing approaches, currently capable of generating millions of reads at low cost, we reflect on the questions: What will the future bring for DNA barcoding? Will identification of species using short, standardized fragments of DNA stand the test of time? We present reflected opinions of early career biodiversity researchers in the form of a SWOT analysis and discuss answers to these questions. Full article

(This article belongs to the Special Issue DNA Barcodes for Evolution and Biodiversity)

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21 pages, 20553 KiB

Open AccessEditor’s ChoiceArticle

Orchids of Mongolia: Taxonomy, Species Richness and Conservation Status

by Shukherdorj Baasanmunkh, Batlai Oyuntsetseg, Petr Efimov, Zagarjav Tsegmed, Sumiya Vandandorj, Khurelpurev Oyundelger, Magsar Urgamal, Altangerel Undruul, Khurelbaatar Khaliunaa, Tugsuu Namuulin and Hyeok Jae Choi

Diversity 2021, 13(7), 302; https://doi.org/10.3390/d13070302 - 2 Jul 2021

Cited by 20 | Viewed by 6216

Abstract

Orchidaceae is a diverse, globally important plant family with high conservation assessment and prioritization requirements. The checklist of Orchidaceae in Mongolia was updated based on herbarium materials, literature, and field observations. Mongolian orchids were revised as comprising 26 taxa belonging to 14 genera [...] Read more.

Orchidaceae is a diverse, globally important plant family with high conservation assessment and prioritization requirements. The checklist of Orchidaceae in Mongolia was updated based on herbarium materials, literature, and field observations. Mongolian orchids were revised as comprising 26 taxa belonging to 14 genera with major updates were conducted on Herminium and Epipactis. In particular, H. alaschanicum, previously noted in the Alashan Gobi region, was added to the flora of Mongolia based on literature and type specimens. Epipactis helleborine and E. palustris were excluded from the Mongolian flora owing to the absence of herbarium specimens and wild collection from Mongolia. Assessment of all orchid species at the national level resulted in 1, 4, 7, 11, and 2 species as critically endangered (CR), endangered (EN), vulnerable (VU), near threatened (NT), and data deficient (DD), respectively, according to IUCN criteria. Species richness and conservation gap analyses of 970 georeferenced orchid records based on 0.5° × 0.5° grid cells across 16 phytogeographical regions of Mongolia, showed that four phytogeographical regions, Khangai, Khuvgul, Khentii and Mongolian Dauria, have a high number of orchids. Regrettably, most orchid-rich locations in Mongolia are not fully within protected areas, highlighting the need for protection management updates. Based on herbarium collections, we prepared grid distribution maps of the 26 taxa using 40 × 40 km² grids. Photographs of 18 taxa taken during fieldwork were included, providing valuable information on species morphology and typical habitat. Full article

(This article belongs to the Special Issue Biodiversity and Conservation of Vascular Flora)

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21 pages, 4879 KiB

Open AccessEditor’s ChoiceArticle

Roadside Car Surveys: Methodological Constraints and Solutions for Estimating Parrot Abundances across the World

by José L. Tella, Pedro Romero-Vidal, Francisco V. Dénes, Fernando Hiraldo, Bernardo Toledo, Federica Rossetto, Guillermo Blanco, Dailos Hernández-Brito, Erica Pacífico, José A. Díaz-Luque, Abraham Rojas, Alan Bermúdez-Cavero, Álvaro Luna, Jomar M. Barbosa and Martina Carrete

Diversity 2021, 13(7), 300; https://doi.org/10.3390/d13070300 - 1 Jul 2021

Cited by 12 | Viewed by 4939

Abstract

Parrots stand out among birds because of their poor conservation status and the lack of available information on their population sizes and trends. Estimating parrot abundance is complicated by the high mobility, gregariousness, patchy distributions, and rarity of many species. Roadside car surveys [...] Read more.

Parrots stand out among birds because of their poor conservation status and the lack of available information on their population sizes and trends. Estimating parrot abundance is complicated by the high mobility, gregariousness, patchy distributions, and rarity of many species. Roadside car surveys can be useful to cover large areas and increase the probability of detecting spatially aggregated species or those occurring at very low densities. However, such surveys may be biased due to their inability to handle differences in detectability among species and habitats. We conducted 98 roadside surveys, covering > 57,000 km across 20 countries and the main world biomes, recording ca. 120,000 parrots from 137 species. We found that larger and more gregarious species are more easily visually detected and at greater distances, with variations among biomes. However, raw estimates of relative parrot abundances (individuals/km) were strongly correlated (r = 0.86–0.93) with parrot densities (individuals/km²) estimated through distance sampling (DS) models, showing that variability in abundances among species (>40 orders of magnitude) overcomes any potential detectability bias. While both methods provide similar results, DS cannot be used to study parrot communities or monitor the population trends of all parrot species as it requires a minimum of encounters that are not reached for most species (64% in our case), mainly the rarest and more threatened. However, DS may be the most suitable choice for some species-specific studies of common species. We summarize the strengths and weaknesses of both methods to guide researchers in choosing the best–fitting option for their particular research hypotheses, characteristics of the species studied, and logistical constraints. Full article

(This article belongs to the Special Issue Ecology and Conservation of Parrots in Their Native and Non-Native Ranges)

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15 pages, 933 KiB

Open AccessFeature PaperEditor’s ChoiceReview

Of Necks, Trunks and Tails: Axial Skeletal Diversity among Vertebrates

by Moisés Mallo

Diversity 2021, 13(7), 289; https://doi.org/10.3390/d13070289 - 24 Jun 2021

Cited by 8 | Viewed by 5445

Abstract

The axial skeleton of all vertebrates is composed of individual units known as vertebrae. Each vertebra has individual anatomical attributes, yet they can be classified in five different groups, namely cervical, thoracic, lumbar, sacral and caudal, according to shared characteristics and their association [...] Read more.

The axial skeleton of all vertebrates is composed of individual units known as vertebrae. Each vertebra has individual anatomical attributes, yet they can be classified in five different groups, namely cervical, thoracic, lumbar, sacral and caudal, according to shared characteristics and their association with specific body areas. Variations in vertebral number, size, morphological features and their distribution amongst the different regions of the vertebral column are a major source of the anatomical diversity observed among vertebrates. In this review I will discuss the impact of those variations on the anatomy of different vertebrate species and provide insights into the genetic origin of some remarkable morphological traits that often serve to classify phylogenetic branches or individual species, like the long trunks of snakes or the long necks of giraffes. Full article

(This article belongs to the Special Issue Evolution, Development, and Diversification of Vertebrates)

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15 pages, 2683 KiB

Open AccessEditor’s ChoiceArticle

Spatial Distribution Patterns of Appendicularians in the Drake Passage: Potential Indicators of Water Masses?

by Marcin Kalarus and Anna Panasiuk

Diversity 2021, 13(7), 286; https://doi.org/10.3390/d13070286 - 23 Jun 2021

Cited by 3 | Viewed by 2245

Abstract

Appendicularians are one of the most common animals found within zooplankton assemblages. They play a very important role as filter feeders but are, unfortunately, inconsistently reported in the Antarctic literature. The present paper attempts to describe the zonal diversity of appendicularians and the [...] Read more.

Appendicularians are one of the most common animals found within zooplankton assemblages. They play a very important role as filter feeders but are, unfortunately, inconsistently reported in the Antarctic literature. The present paper attempts to describe the zonal diversity of appendicularians and the main environmental factors influencing their communities in the Drake Passage. Samples were collected during Antarctic summer in 2009–2010. A total of eight species of larvaceans were identified. Fritillaria borealis was the species found in the highest numbers in almost the entire studied area, and was observed at all sampling stations. The distributions of other taxa were limited to specific hydrological zones and hydrological conditions. F. fraudax and Oikopleura gaussica were typical of the areas between the Polar Front and the Subantarctic Front zones, and their distributions were significantly correlated with temperature and salinity, likely making them good indicator species. The F. fusiformis distribution was strictly related to South American waters. In summary, temperature was the strongest environmental factor influencing the larvacean community structure in the Drake Passage, and we also found that testing environmental factors on larvaceans as a whole group did not give entirely reliable results. Full article

(This article belongs to the Section Marine Diversity)

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18 pages, 3101 KiB

Open AccessEditor’s ChoiceArticle

Postojna-Planina Cave System in Slovenia, a Hotspot of Subterranean Biodiversity and a Cradle of Speleobiology

by Maja Zagmajster, Slavko Polak and Cene Fišer

Diversity 2021, 13(6), 271; https://doi.org/10.3390/d13060271 - 15 Jun 2021

Cited by 20 | Viewed by 4426

Abstract

The Postojna-Planina Cave System (PPCS) in central Slovenia is a globally exceptional site of subterranean biodiversity, comprised of many interconnected caves with cumulative passage length exceeding 34 km. Two rivers sink into the caves of the PPCS, called the Pivka and Rak, and [...] Read more.

The Postojna-Planina Cave System (PPCS) in central Slovenia is a globally exceptional site of subterranean biodiversity, comprised of many interconnected caves with cumulative passage length exceeding 34 km. Two rivers sink into the caves of the PPCS, called the Pivka and Rak, and join underground into Unica River, which emerges to the surface. The studies of fauna of PPCS began in the 19th century with the first scientific descriptions of specialized cave animals in the world, making it “the cradle of speleobiology”. Currently, the species list of PPCS contains 116 troglobiotic animal species belonging to eight phyla, confirming its status as the richest in the world. Of these, 47 species have been scientifically described from the PPCS, and more than 10 await formal taxonomic descriptions. We expect that further sampling, detailed analyses of less studied taxa, and the use of molecular methods may reveal more species. To keep the cave animals’ checklist in PPCS up-to-date, we have supplemented the printed checklist with an online interface. As the revised checklist is a necessary first step for further activities, we discuss the importance of PPCS in terms of future research and conservation. Full article

(This article belongs to the Special Issue Hotspots of Subterranean Biodiversity)

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19 pages, 2629 KiB

Open AccessEditor’s ChoiceArticle

Diversity of Testate Amoebae as an Indicator of the Conservation Status of Peatlands in Southwest Europe

by Rafael Carballeira and Xabier Pontevedra-Pombal

Diversity 2021, 13(6), 269; https://doi.org/10.3390/d13060269 - 15 Jun 2021

Cited by 12 | Viewed by 3631

Abstract

Testate amoebae are one of the most studied groups of microorganisms in Sphagnum peatland ecosystems and, therefore, one of the most reliable bioindicators of their ecological status. Peatland ecosystems are supported by a delicate biogeochemical balance that leads to the formation of peat, [...] Read more.

Testate amoebae are one of the most studied groups of microorganisms in Sphagnum peatland ecosystems and, therefore, one of the most reliable bioindicators of their ecological status. Peatland ecosystems are supported by a delicate biogeochemical balance that leads to the formation of peat, one of the main sinks of C, as a result of soil–atmosphere interaction, but currently they are one of the most threatened wetland types at their southern distribution limit. In the European continent, where climatic conditions limit peat formation, they have endured significant anthropic pressure for centuries, and the risk of loss of biodiversity linked to these ecosystems is critical. In addition, peatlands are poorly known ecosystems in the Iberian Peninsula compared with other wetlands; therefore, we have studied the chemical parameters of water and the diversity patterns of testate amoebae in the western Iberian Peninsula to better understand the current status of these ecosystems. The analysis of testate amoeba communities showed an inverse relationship between the diversity and conservation status of these peatlands, both in relation to chemical parameters (i.e., pH, electrical conductivity, phosphates) and to the proportion of anthropized area, with a marked geographical pattern in the degree of anthropogenic disturbance. Full article

(This article belongs to the Special Issue Ecology, Biogeography and Evolutionary Biology of Peatlands)

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15 pages, 3556 KiB

Open AccessEditor’s ChoiceArticle

Mediterranean Red Macro Algae Mats as Habitat for High Abundances of Serpulid Polychaetes

by Felix I. Rossbach, Edoardo Casoli, Milan Beck and Christian Wild

Diversity 2021, 13(6), 265; https://doi.org/10.3390/d13060265 - 11 Jun 2021

Cited by 9 | Viewed by 3315

Abstract

The Mediterranean Sea harbors more than 17,000 eukaryotic marine species, with several ecosystems recognized as biodiversity hotspots, such as Posidonia oceanica meadows. Recent research indicates that benthic mats formed by the fleshy red alga Phyllophora crispa are also associated with high species richness. [...] Read more.

The Mediterranean Sea harbors more than 17,000 eukaryotic marine species, with several ecosystems recognized as biodiversity hotspots, such as Posidonia oceanica meadows. Recent research indicates that benthic mats formed by the fleshy red alga Phyllophora crispa are also associated with high species richness. Among key groups found in these mats are sessile polychaetes, which live as epiphytes on the red algae thalli. Knowledge of abundance, species richness, and spatial variation of polychaetes associated with these habitats is still scarce. We carried out a comparative assessment focusing on serpulid polychaetes within samples from P. crispa mats and neighboring P. oceanica meadows at six different sampling sites around Giglio Island (Tyrrhenian Sea, Italy). A total of 17 serpulid taxa were identified. The abundance of serpulids (5665 individuals m⁻² of P. crispa mat) were similar to neighboring P. oceanica meadows (2304 individuals m⁻² leaves and 5890 individuals m⁻² shoots). The number of serpulid taxa was significantly higher in P. crispa mats (average 6.63 ± 1.32 taxa) compared to P. oceanica beds (average 1.56 ± 0.63 and 1.84 ± 1.04 taxa in leaves and shoots, respectively). Within habitat type, there were no significant differences in species richness between sites. The most abundant species found was Josephella marenzelleri (61% of individuals), while Vermiliopsis spp. and Bathyvermilia sp. were exclusively found in P. crispa samples. Our results highlight that P. crispa mats host an exceptional diversity and that these habitats should be included in conservation strategies. Further research should focus on the significance of other important taxonomic groups within these mats and evaluate the distribution of P. crispa in different regions of the Mediterranean Sea. Full article

(This article belongs to the Special Issue Biodiversity Conservation in Mediterranean Sea)

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23 pages, 2109 KiB

Open AccessEditor’s ChoiceReview

Turbid Coral Reefs: Past, Present and Future—A Review

by Adi Zweifler (Zvifler), Michael O’Leary, Kyle Morgan and Nicola K. Browne

Diversity 2021, 13(6), 251; https://doi.org/10.3390/d13060251 - 7 Jun 2021

Cited by 54 | Viewed by 13881

Abstract

Increasing evidence suggests that coral reefs exposed to elevated turbidity may be more resilient to climate change impacts and serve as an important conservation hotspot. However, logistical difficulties in studying turbid environments have led to poor representation of these reef types within the [...] Read more.

Increasing evidence suggests that coral reefs exposed to elevated turbidity may be more resilient to climate change impacts and serve as an important conservation hotspot. However, logistical difficulties in studying turbid environments have led to poor representation of these reef types within the scientific literature, with studies using different methods and definitions to characterize turbid reefs. Here we review the geological origins and growth histories of turbid reefs from the Holocene (past), their current ecological and environmental states (present), and their potential responses and resilience to increasing local and global pressures (future). We classify turbid reefs using new descriptors based on their turbidity regime (persistent, fluctuating, transitional) and sources of sediment input (natural versus anthropogenic). Further, by comparing the composition, function and resilience of two of the most studied turbid reefs, Paluma Shoals Reef Complex, Australia (natural turbidity) and Singapore reefs (anthropogenic turbidity), we found them to be two distinct types of turbid reefs with different conservation status. As the geographic range of turbid reefs is expected to increase due to local and global stressors, improving our understanding of their responses to environmental change will be central to global coral reef conservation efforts. Full article

(This article belongs to the Special Issue Marginal Reef Systems: Resilience in A Rapidly Changing World)

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22 pages, 2600 KiB

Open AccessEditor’s ChoiceArticle

Seagrass and Oyster Reef Restoration in Living Shorelines: Effects of Habitat Configuration on Invertebrate Community Assembly

by Cassie M. Pinnell, Geana S. Ayala, Melissa V. Patten and Katharyn E. Boyer

Diversity 2021, 13(6), 246; https://doi.org/10.3390/d13060246 - 4 Jun 2021

Cited by 9 | Viewed by 4666

Abstract

Restoration projects provide a valuable opportunity to experimentally establish foundational habitats in different combinations to test relative effects on community assembly. We evaluated the development of macroinvertebrate communities in response to planting of eelgrass (Zostera marina) and construction of reefs intended [...] Read more.

Restoration projects provide a valuable opportunity to experimentally establish foundational habitats in different combinations to test relative effects on community assembly. We evaluated the development of macroinvertebrate communities in response to planting of eelgrass (Zostera marina) and construction of reefs intended to support the Olympia oyster (Ostrea lurida) in the San Francisco Estuary. Plots of each type, alone or interspersed, were established in 2012 in a pilot living shorelines project, and quarterly invertebrate monitoring was conducted for one year prior to restoration, and three years post-restoration using suction sampling and eelgrass shoot collection. Suction sampling revealed that within one year, oyster reefs supported unique invertebrate assemblages as compared to pre-restoration conditions and controls (unmanipulated mudflat). The eelgrass invertebrate assemblage also shifted, becoming intermediate between reefs and controls. Interspersing both types of habitat structure led eelgrass invertebrate communities to more closely resemble those of oyster reefs alone, though the eelgrass assemblage maintained some distinction (primarily by supporting gammarid and caprellid amphipods). Eelgrass shoot collection documented some additional taxa known to benefit eelgrass growth through consumption of epiphytic algae; however, even after three years, restored eelgrass did not establish an assemblage equivalent to natural beds, as the eelgrass sea hare (Phyllaplysia taylori) and eelgrass isopod (Pentidotea resecata) remained absent or very rare. We conclude that the restoration of two structurally complex habitat types within tens of meters maximized the variety of invertebrate assemblages supported, but that close interspersion dampened the separately contributed distinctiveness. In addition, management intervention may be needed to overcome the recruitment limitation of species with important roles in maintaining eelgrass habitat. Full article

(This article belongs to the Special Issue Biodiversity in Seagrass Ecosystems)

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18 pages, 2658 KiB

Open AccessEditor’s ChoiceArticle

Stygobiont Diversity in the San Marcos Artesian Well and Edwards Aquifer Groundwater Ecosystem, Texas, USA

by Benjamin T. Hutchins, J. Randy Gibson, Peter H. Diaz and Benjamin F. Schwartz

Diversity 2021, 13(6), 234; https://doi.org/10.3390/d13060234 - 26 May 2021

Cited by 15 | Viewed by 3813

Abstract

The Edwards Aquifer and related Edwards-Trinity Aquifer of Central Texas, USA, is a global hotspot of stygobiont biodiversity. We summarize 125 years of biological investigation at the San Marcos Artesian Well (SMAW), the best studied and most biodiverse groundwater site (55 stygobiont taxa: [...] Read more.

The Edwards Aquifer and related Edwards-Trinity Aquifer of Central Texas, USA, is a global hotspot of stygobiont biodiversity. We summarize 125 years of biological investigation at the San Marcos Artesian Well (SMAW), the best studied and most biodiverse groundwater site (55 stygobiont taxa: 39 described and 16 undescribed) within the Edwards Aquifer Groundwater Ecosystem. Cluster analysis and redundancy analysis (RDA) incorporating temporally derived, distance-based Moran’s Eigenvector Mapping (dbMem) illustrate temporal dynamics in community composition in 85 high-frequency samples from the SMAW. Although hydraulic variability related to precipitation and discharge partially explained changes in community composition at the SMAW, a large amount of temporal autocorrelation between samples remains unexplained. We summarize potential mechanisms by which hydraulic changes can affect community structure in deep, phreatic karst aquifers. We also compile information on 12 other Edwards and Edwards-Trinity Aquifer sites with 10 or more documented stygobionts and used distance-based RDA to assess the relative influences of distance and site type on three measures of β-diversity. Distance between sites was the most important predictor of total dissimilarity and replacement, although site type was also important. Species richness difference was not predicted by either distance or site type. Full article

(This article belongs to the Special Issue Hotspots of Subterranean Biodiversity)

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10 pages, 2435 KiB

Open AccessEditor’s ChoiceArticle

Multivariate Abundance Analysis of Multi-Host/Multi-Parasite Lungworms in a Sympatric Wild Ruminant Population

by Tessa Carrau, Carlos Martínez-Carrasco, María Magdalena Garijo, Francisco Alonso, Rocío Ruiz de Ybáñez and Paolo Tizzani

Diversity 2021, 13(6), 227; https://doi.org/10.3390/d13060227 - 23 May 2021

Cited by 3 | Viewed by 2467

Abstract

In the analysis of a multi-host/multi-parasite system and its associated risk factors, it is particularly interesting to understand the natural dynamics among pathogens, their hosts, and the environment in wildlife populations. This analysis is particularly feasible in a scenario where multiple overlapping host [...] Read more.

In the analysis of a multi-host/multi-parasite system and its associated risk factors, it is particularly interesting to understand the natural dynamics among pathogens, their hosts, and the environment in wildlife populations. This analysis is particularly feasible in a scenario where multiple overlapping host populations are present in high densities, along with a complex community of parasites. We aimed to describe and analyze the naturally occurring lungworm polyparasitism in a wild ruminant community in Southeast Spain. The respiratory tracts of 250 specimens belonging to four different species (red deer, mouflon, Iberian ibex, and fallow deer) were studied. Almost half (48.0%) of the animals were infected with bronchopulmonary nematodes. Seven different nematodes were identified of which two genera (Protostrongylus spp. and Dictyocaulus spp.) and three additional species (Cystocaulus ocreatus, Muellerius capillaris, and Neostrongylus linearis) were recorded in at least two ruminants, with the mouflon as the commonest host. Our study shows a significant effect of host species and sampling area, plus a marginal effect of age, on parasite multivariate abundance at the host population level. Mouflon and adults of all hosts appear to carry the highest parasite load on average. From a spatial perspective, the highest parasite abundance was detected at the central part of the park. Full article

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14 pages, 1660 KiB

Open AccessEditor’s ChoiceArticle

Unravelling the Symbiotic Microalgal Diversity in Buellia zoharyi (Lichenized Ascomycota) from the Iberian Peninsula and Balearic Islands Using DNA Metabarcoding

by Patricia Moya, Salvador Chiva, Arantzazu Molins, Isaac Garrido-Benavent and Eva Barreno

Diversity 2021, 13(6), 220; https://doi.org/10.3390/d13060220 - 21 May 2021

Cited by 10 | Viewed by 3200

Abstract

Buellia zoharyi is a crustose placodioid lichen, usually occurring on biocrusts of semiarid ecosystems in circum-Mediterranean/Macaronesian areas. In previous work, we found that this lichenized fungus was flexible in its phycobiont choice in the Canary Islands. Here we test whether geography and habitat [...] Read more.

Buellia zoharyi is a crustose placodioid lichen, usually occurring on biocrusts of semiarid ecosystems in circum-Mediterranean/Macaronesian areas. In previous work, we found that this lichenized fungus was flexible in its phycobiont choice in the Canary Islands. Here we test whether geography and habitat influence phycobiont diversity in populations of this lichen from the Iberian Peninsula and Balearic Islands using Sanger and high throughput sequencing (HTS). Additionally, three thallus section categories (central, middle and periphery) were analyzed to explore diversity of microalgal communities in each part. We found that B. zoharyi populations hosted at least three different Trebouxia spp., and this lichen can associate with distinct phycobiont strains in different habitats and geographic regions. This study also revealed that the Trebouxia composition of this lichen showed significant differences when comparing the Iberian Peninsula with the Balearics thalli. No support for differences in microalgal communities was found among thallus sections; however, several thalli showed different predominant Trebouxia spp. at each section. This result corroborate that thallus parts selected for DNA extraction in metabarcoding analyses are key to not bias the total phycobiont diversity detected. This study highlights that inclusion of HTS analysis is crucial to understand lichen symbiotic microalgal diversity. Full article

(This article belongs to the Special Issue Advances in HTS-Based Identification of Species and Ecological Interactions)

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17 pages, 15325 KiB

Open AccessEditor’s ChoiceArticle

Not the Cryptic Species: Diversity of Hipposideros gentilis (Chiroptera: Hipposideridae) in Indochina

by Alexander P. Yuzefovich, Ilya V. Artyushin and Sergei V. Kruskop

Diversity 2021, 13(5), 218; https://doi.org/10.3390/d13050218 - 19 May 2021

Cited by 8 | Viewed by 3276

Abstract

We present here the result of phylogenetic analysis for Vietnamese Hipposideros gentilis specimens using 7 nuclear genes and one mitochondrial gene. The complex distribution of divergent mitochondrial DNA lineages contradicts, at least in part, nuclear and morphological data. The most likely explanation [...] Read more.

We present here the result of phylogenetic analysis for Vietnamese Hipposideros gentilis specimens using 7 nuclear genes and one mitochondrial gene. The complex distribution of divergent mitochondrial DNA lineages contradicts, at least in part, nuclear and morphological data. The most likely explanation for this discordance is the historical hybridization between ancestral populations of H. gentilis and H. rotalis/H. khaokhouayensis. Our data supports the species status of H. gentilis, while only partially corroborating its previously proposed subspecies delimitation. We suggest the lowland forest populations from south Vietnam may correspond to their own subspecies. At the same time, the close phylogenetic relationship and morphological similarity of mountain forms from south and central Vietnam to the north Vietnamese populations make doubtful the subspecies status of H. gentilis sinensis. Full article

(This article belongs to the Special Issue Diversity Aspects in Bats: Genetics, Morphology, Community Structure)

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18 pages, 3625 KiB

Open AccessEditor’s ChoiceArticle

Burrowing Parrots Cyanoliseus patagonus as Long-Distance Seed Dispersers of Keystone Algarrobos, Genus Prosopis, in the Monte Desert

by Guillermo Blanco, Pedro Romero-Vidal, Martina Carrete, Daniel Chamorro, Carolina Bravo, Fernando Hiraldo and José L. Tella

Diversity 2021, 13(5), 204; https://doi.org/10.3390/d13050204 - 12 May 2021

Cited by 7 | Viewed by 4358

Abstract

Understanding of ecosystem structure and functioning requires detailed knowledge about plant–animal interactions, especially when keystone species are involved. The recent consideration of parrots as legitimate seed dispersers has widened the range of mechanisms influencing the life cycle of many plant species. We examined [...] Read more.

Understanding of ecosystem structure and functioning requires detailed knowledge about plant–animal interactions, especially when keystone species are involved. The recent consideration of parrots as legitimate seed dispersers has widened the range of mechanisms influencing the life cycle of many plant species. We examined the interactions between the burrowing parrot Cyanoliseus patagonus and two dominant algarrobo trees (Prosopis alba and Prosopis nigra) in the Monte Desert, Argentina. We recorded the abundance and foraging behaviour of parrots; quantified the handling, consumption, wasting, and dispersal of ripe and unripe pods; and tested the viability of soft and hard ripe seeds wasted and transported by parrots. We found a high abundance of burrowing parrots. They predated on soft seeds from unripe pods while exclusively feeding upon pulp wrapping hard seeds from ripe pods. Frequent pod wasting beneath the plant or transport at a distance invariably implied the dispersal of multiple seeds in each event. Moreover, soft seeds retained viability after desiccation outside the mother plant, suggesting effective seed dispersal after partial pod predation due to a predator satiation effect. In about half of the foraging flocks, at least one parrot departed in flight with pods in its beak, with 10–34% of the flock components moving pods at distances averaging 238 m (P. alba) and 418 m (P. nigra). A snapshot sampling of faeces from livestock and wild mammals suggested a low frequency of seed dispersal by endozoochory and secondary dispersal by ants and dung beetles. The nomadic movements and long flights of burrowing parrots between breeding and foraging sites can lead to the dispersal of huge amounts of seeds across large areas that are sequentially exploited. Further research should evaluate the role of the burrowing parrot as a functionally unique species in the structure of the Monte Desert woods and the genetic structure of algarrobo species. Full article

(This article belongs to the Special Issue Ecology and Conservation of Parrots in Their Native and Non-Native Ranges)

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14 pages, 4509 KiB

Open AccessEditor’s ChoiceArticle

Reusing Old and Producing New Data Is Useful for Species Delimitation in the Taxonomically Controversial Iberian Endemic Pair Petrocoptis montsicciana/P. pardoi (Caryophyllaceae)

by Neus Nualart, Sonia Herrando-Moraira, Eduardo Cires, Moisès Guardiola, Emilio Laguna, David Pérez-Prieto, Llorenç Sáez and Jordi López-Pujol

Diversity 2021, 13(5), 205; https://doi.org/10.3390/d13050205 - 12 May 2021

Cited by 2 | Viewed by 2719

Abstract

Petrocoptis montsicciana and P. pardoi are two Iberian endemic taxa of Caryophyllaceae family with an unclear taxonomic delimitation, being variously treated as independent species, subspecies or even synonyms. In the present study, allozyme raw data obtained in the early 2000s have been reused [...] Read more.

Petrocoptis montsicciana and P. pardoi are two Iberian endemic taxa of Caryophyllaceae family with an unclear taxonomic delimitation, being variously treated as independent species, subspecies or even synonyms. In the present study, allozyme raw data obtained in the early 2000s have been reused with improved tools to survey genetic structure, and complemented with modeling and niche comparative analyses to shed light on species delimitation. Genetic structure was investigated using four approaches: Bayesian clustering, Monmonier’s algorithm, Principal Coordinate Analysis (PCoA), and Analysis of Molecular Variance (AMOVA). Ecological niche differences have been assessed through Ecological Niche Modeling (ENM) using MaxEnt, and Principal Component Analysis using both occurrence records and background climate (PCA-env). Genetic analysis confirms the distinction between both taxa, and the scenario of a progenitor–derivative (P–D) is suggested. In agreement with genetic data, niche analysis shows clear differences between their climate regarding species occurrences and background spaces. Climate divergence could be explained, at least partially, by the abundance of rocks where species live although differences at the microclimate instead of the regional climate should be explored in future research. Given the genetic distinction between P. montsicciana and P. pardoi, both taxa should be regarded as separate ‘Management Units’ (MUs). Full article

(This article belongs to the Special Issue Conservation Genetics and Biogeography of Seed Plant Species)

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12 pages, 24161 KiB

Open AccessEditor’s ChoiceArticle

Diversity of Pod Shape in Pisum

by Thomas Henry Noel Ellis, Julie M. I. Hofer, Eleni Vikeli, Michael J. Ambrose, Paola Higuera-Poveda, Luzie U. Wingen and Noam Chayut

Diversity 2021, 13(5), 203; https://doi.org/10.3390/d13050203 - 12 May 2021

Cited by 6 | Viewed by 5009

Abstract

The seed-containing pod is the defining structure of plants in the legume family, yet pods exhibit a wide range of morphological variation. Within a species pod characters are likely to be correlated with reproductive strategy, and within cultivated forms will correspond to aspects [...] Read more.

The seed-containing pod is the defining structure of plants in the legume family, yet pods exhibit a wide range of morphological variation. Within a species pod characters are likely to be correlated with reproductive strategy, and within cultivated forms will correspond to aspects of yield determination and/or end use. Here variation in pod size, described as pod length: pod width ratio, has been analyzed in pea germplasm represented by 597 accessions. This pod size variation is discussed with respect to population structure and to known classical pod morphology mutants. Variability of the pod length: width ratio can be explained by allelic variation at two genetic loci that may correspond to organ-specific negative regulators of growth. Full article

(This article belongs to the Special Issue Legume Evolution and Diversity)

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16 pages, 1089 KiB

Open AccessEditor’s ChoiceArticle

Mining Sorghum Biodiversity—Potential of Dual-Purpose Hybrids for Bio-Economy

by Adnan Kanbar, Noemi Flubacher, Jiří Hermuth, Klára Kosová, Thomas Horn and Peter Nick

Diversity 2021, 13(5), 192; https://doi.org/10.3390/d13050192 - 29 Apr 2021

Cited by 7 | Viewed by 2960

Abstract

Sweet, grain, and dual-purpose sorghums differ in a number of important traits, including biomass production, total solutes in the stem juice, and sugar accumulation across the stem. Ten dual-purpose hybrids, two sweet genotypes, and two grain landraces of sorghums were characterized under temperate [...] Read more.

Sweet, grain, and dual-purpose sorghums differ in a number of important traits, including biomass production, total solutes in the stem juice, and sugar accumulation across the stem. Ten dual-purpose hybrids, two sweet genotypes, and two grain landraces of sorghums were characterized under temperate environmental conditions to determine their potential for bioethanol production. Five sorghum hybrids (Ganymed, Hannibal, Tarzan, Merlin, and Zerberus) performed better with respect to cane yield, juice yield, potential sugar, and ethanol yields compared to sweet and grain genotypes. While the sweet genotype KIT1 produced the highest sugar concentration in the stem, the lowest concentration was produced by the grain landrace Razinieh. The study showed that plant height, leaf number, leaf weight, cane yield, and juice yield were positively correlated with the sugar yield in fresh stalk. Sugar accumulation was higher in the central internodes of all genotypes. Clustering analysis showed that sweet genotypes are located more closely to dual-purpose hybrids than grain landraces. We discuss the results with respect to the potential of dual-purpose sorghum hybrids for bio-economy in Germany. Full article

(This article belongs to the Special Issue Feature Papers in Plant Diversity)

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15 pages, 28896 KiB

Open AccessFeature PaperEditor’s ChoiceArticle

Karstic Landscapes Are Foci of Species Diversity in the World’s Third-Largest Vertebrate Genus Cyrtodactylus Gray, 1827 (Reptilia: Squamata; Gekkonidae)

by Lee Grismer, Perry L. Wood, Nikolay A. Poyarkov, Minh D. Le, Suranjan Karunarathna, Siriwadee Chomdej, Chatmongkon Suwannapoom, Shuo Qi, Shuo Liu, Jing Che, Evan S. H. Quah, Fred Kraus, Paul M. Oliver, Awal Riyanto, Olivier S. G. Pauwels and Jesse L. Grismer

Diversity 2021, 13(5), 183; https://doi.org/10.3390/d13050183 - 28 Apr 2021

Cited by 51 | Viewed by 5132

Abstract

Karstic landscapes are immense reservoirs of biodiversity and range-restricted endemism. Nowhere is this more evident than in the world’s third-largest vertebrate genus Cyrtodactylus (Gekkonidae) which contains well over 300 species. A stochastic character mapping analysis of 10 different habitat preferences across a phylogeny [...] Read more.

Karstic landscapes are immense reservoirs of biodiversity and range-restricted endemism. Nowhere is this more evident than in the world’s third-largest vertebrate genus Cyrtodactylus (Gekkonidae) which contains well over 300 species. A stochastic character mapping analysis of 10 different habitat preferences across a phylogeny containing 344 described and undescribed species recovered a karst habitat preference occurring in 25.0% of the species, whereas that of the other eight specific habitat preferences occurred in only 0.2–11.0% of the species. The tenth category—general habitat preference—occurred in 38.7% of the species and was the ancestral habitat preference for Cyrtodactylus and the ultimate origin of all other habitat preferences. This study echoes the results of a previous study illustrating that karstic landscapes are generators of species diversity within Cyrtodactylus and not simply “imperiled arks of biodiversity” serving as refugia for relics. Unfortunately, the immense financial returns of mineral extraction to developing nations largely outweighs concerns for biodiversity conservation, leaving approximately 99% of karstic landscapes with no legal protection. This study continues to underscore the urgent need for their appropriate management and conservation. Additionally, this analysis supports the monophyly of the recently proposed 31 species groups and adds one additional species group. Full article

(This article belongs to the Special Issue Evolutionary Ecology of Lizards)

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9 pages, 250 KiB

Open AccessEditor’s ChoiceReview

Progress on Research Regarding Ecology and Biodiversity of Coastal Fisheries and Nektonic Species and Their Habitats within Coastal Landscapes

by Mark S. Peterson and Michael J. Andres

Diversity 2021, 13(4), 168; https://doi.org/10.3390/d13040168 - 15 Apr 2021

Cited by 4 | Viewed by 3184

Abstract

This paper aims to highlight the new research and significant advances in our understanding of links between coastal habitat quality/quantity/diversity and the diversity of fisheries species and other mobile aquatic species (hereafter nekton) that use them within coastal landscapes. This topic is quite [...] Read more.

This paper aims to highlight the new research and significant advances in our understanding of links between coastal habitat quality/quantity/diversity and the diversity of fisheries species and other mobile aquatic species (hereafter nekton) that use them within coastal landscapes. This topic is quite diverse owing to the myriad of habitat types found in coastal marine waters and the variety of life history strategies fisheries species and nekton use in these environments. Thus, we focus our review on five selective but relevant topics, habitat templates, essential fish habitat, habitat mosaics/habitat connectivity, transitory/ephemeral habitat, and the emerging/maturing approaches to the study of fish-habitat systems as a roadmap to its development. We have highlighted selected important contributions in the progress made on each topic to better identify and quantify landscape scale interactions between living biota and structured habitats set within a dynamic landscape. Full article

(This article belongs to the Special Issue Ecology and Biodiversity of Coastal Marine Fisheries Species and Their Habitats)

11 pages, 9770 KiB

Open AccessEditor’s ChoiceArticle

Differing Life-History Strategies of Two Mycoheterotrophic Orchid Species Associated with Leaf Litter- and Wood-Decaying Fungi

by Yuki Ogura-Tsujita, Kenshi Tetsuka, Shuichiro Tagane, Miho Kubota, Shuichiro Anan, Yumi Yamashita, Koichi Tone and Tomohisa Yukawa

Diversity 2021, 13(4), 161; https://doi.org/10.3390/d13040161 - 8 Apr 2021

Cited by 6 | Viewed by 3536

Abstract

Mycoheterotrophic orchids depend completely on mycorrhizal fungi for their supply of carbon. The life-history traits of mycoheterotrophic plants (MHPs) can differ according to the characteristics of the associated mycorrhizal fungi. We compared the life-history strategies of two mycoheterotrophic orchids associated with wood- and [...] Read more.

Mycoheterotrophic orchids depend completely on mycorrhizal fungi for their supply of carbon. The life-history traits of mycoheterotrophic plants (MHPs) can differ according to the characteristics of the associated mycorrhizal fungi. We compared the life-history strategies of two mycoheterotrophic orchids associated with wood- and leaf litter-decaying fungi over a maximum of six years of field monitoring. Seventy percent of the aboveground stems of Erythrorchis altissima, associated with wood-decaying fungi, disappeared from the host wood within two years after tagging, likely due to nutrient depletion. In contrast, Gastrodia confusa, associated with leaf litter-decaying fungi, occurred continuously (18 to 108 fruiting stalks) every year within a small-scale plot (12 × 45 m) for six years through seed and clonal propagation. Our results support the idea that mycoheterotrophic orchids associated with wood-decaying fungi disappear from their habitats due to nutrient depletion after their host wood has mostly decayed, while mycoheterotrophic orchids associated with leaf litter-decaying fungi can survive in small-scale habitats where substantial leaf fall regularly occurs to sustain the associated fungi. Our study provides basic information about a unique life-history strategy in MHPs associated with saprotrophic fungi and an understanding of the variation in life-history strategies among MHPs. Full article

(This article belongs to the Special Issue The Ecology and Diversity of Orchids)

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11 pages, 1874 KiB

Open AccessEditor’s ChoiceArticle

Habitat Partitioning and Overlap by Large Lacertid Lizards in Southern Europe

by Daniel Escoriza and Félix Amat

Diversity 2021, 13(4), 155; https://doi.org/10.3390/d13040155 - 4 Apr 2021

Cited by 8 | Viewed by 3449

Abstract

South-western Europe has a rich diversity of lacertid lizards. In this study, we evaluated the occupancy patterns and niche segregation of five species of lacertids, focusing on large-bodied species (i.e., adults having >75 mm snout-vent length) that occur in south-western Europe (Italian to [...] Read more.

South-western Europe has a rich diversity of lacertid lizards. In this study, we evaluated the occupancy patterns and niche segregation of five species of lacertids, focusing on large-bodied species (i.e., adults having >75 mm snout-vent length) that occur in south-western Europe (Italian to the Iberian Peninsula). We characterized the niches occupied by these species based on climate and vegetation cover properties. We expected some commonality among phylogenetically related species, but also patterns of habitat segregation mitigating competition between ecologically equivalent species. We used multivariate ordination and probabilistic methods to describe the occupancy patterns and evaluated niche evolution through phylogenetic analyses. Our results showed climate niche partitioning, but with a wide overlap in transitional zones, where segregation is maintained by species-specific responses to the vegetation cover. The analyses also showed that phylogenetically related species tend to share large parts of their habitat niches. The occurrence of independent evolutionary lineages contributed to the regional species richness favored by a long history of niche divergence. Full article

(This article belongs to the Special Issue Evolutionary Ecology of Lizards)

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