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A special issue of Forests (ISSN 1999-4907). This special issue belongs to the section "Genetics and Molecular Biology".

Deadline for manuscript submissions: closed (31 January 2023) | Viewed by 23718

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Prof. Dr. Rusea Go

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Guest Editor

Department of Biology, Faculty of Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
Interests: plant taxonomy and conservation (Orchidaceae, pteridophytes, seaweeds, Lamiaceae, Fagaceae, Moraceae); ethnobotany (including medicinal plants and indigenous knowledge); phytoremediation; forest ecology and management; environmental impact assessment

Dr. Christina Seok Yien Yong

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Guest Editor

Department of Biology, Faculty of Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
Interests: plant molecular genetics

Special Issue Information

Dear Colleagues,

The rapid extinction of species is associated with the destruction of populations by anthropogenic disturbances and the unviability of populations in small forests. Species richness and abundance are decreasing steadily because of deforestation, forest fire, as well as illegal collection and trade, resulting in high rates of species loss, population depletion, and genetic erosion. As shown by studies of tropical and subtropical forests on forest fragmentation and clear-felling effects on plant communities, factors including microclimate, host plant characteristics, distance, and habitat quality could explain floristic impoverishment in tropical forests. Additionally, knowledge of the pollination ecology, levels, and distribution of genetic variation is essential to understand the population dynamics, adaptation, and evolution, and is efficient for devising strategies for the conservation of endangered species. However, these baseline studies are currently lacking for most rainforests and ecosystems. Tropical rainforests comprise undisturbed forest differing in tree composition, stature, and microclimate regimes. Disturbance regimes encompass a wide range of temporal and spatial scales of frequency and magnitude. Understanding the degree of genetic variability within populations and identifying levels of genetic differentiation among populations in these distinctive forest ecosystems are desirable aims in the field of biodiversity.

This Special Issue of Forests aims to collect recent results from field experimental observations and laboratory studies at various sites around the world, as well as related meta-analysis and modeling studies which improve the understanding of diversity, ecology, distribution, and biotic and abiotic associations in undisturbed and disturbed tropical forests.

We invite submissions for a Special Issue of Forests on the subject of “Genetic Diversity and Conservation of Forest Species”. Topics for submissions may include, but are not limited to:

Species diversity and conservation;
Genetic diversity and conservation;
Forest ecology and species adaptation;
Pollination ecology and strategy;
Endangered species conservation case study.

Prof. Dr. Rusea Go
Dr. Christina Seok Yien Yong
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Forests is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

species diversity
ecology
conservation biology
genetic
pollination
endemism
tropical forests
climate change
deforestation

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Published Papers (9 papers)

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Research

13 pages, 2146 KiB

Open AccessArticle

Elucidating SNP-Based Population Structure and Genetic Diversity of Bruguiera gymnorhiza (L.) Savigny in Thailand

by Panthita Ruang-areerate, Chutima Sonthirod, Duangjai Sangsrakru, Pitchaporn Waiyamitra, Chatree Maknual, Poonsri Wanthongchai, Pranom Chomriang, Wirulda Pootakham and Sithichoke Tangphatsornruang

Forests 2023, 14(4), 693; https://doi.org/10.3390/f14040693 - 28 Mar 2023

Cited by 2 | Viewed by 1927

Abstract

Bruguiera gymnorhiza (L.) Savigny is one of the most important and widespread mangrove species in the Indo-West Pacific region. Here, the population structure and genetic diversity of B. gymnorhiza along the coastlines of Thailand were examined. A total of 73 B. gymnorhiza accessions in 15 provinces were sequenced using RAD-seq to generate their SNPs. Based on the high-quality SNPs, the topology of the maximum likelihood phylogenetic tree clearly presented two genetically distinct groups corresponding to two geographic regions, the Gulf of Thailand and the Andaman Sea coasts. The results for the population structure provided by STRUCTURE and PCA also showed two main genetic clusters and their genetic admixture. A moderate genetic diversity was observed among the accessions, with average observed and expected heterozygosity values of 0.397 and 0.317, respectively. A high genetic differentiation (F_ST = 0.16, p < 0.001) between the two subpopulations was significantly found. An analysis of molecular variance revealed 83.95% of the genetic variation within populations and 16.05% of the genetic variation among populations. A high genetic variation within the populations and admixture may facilitate adaptation to local environments and climate changes. These results provide important information on the population genetic structure and genetic diversity of B. gymnorhiza in Thailand for further mangrove management. Full article

(This article belongs to the Special Issue Genetic Diversity and Conservation of Forest Species)

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30 pages, 5831 KiB

Open AccessArticle

Habitat Ecology, Structure Influence Diversity, and Host-Species Associations of Wild Orchids in Undisturbed and Disturbed Forests in Peninsular Malaysia

by Edward Entalai Besi, Muskhazli Mustafa, Christina Seok Yien Yong and Rusea Go

Forests 2023, 14(3), 544; https://doi.org/10.3390/f14030544 - 9 Mar 2023

Cited by 1 | Viewed by 3413

Abstract

As an attempt to examine the causes of forest disturbance and degradation of the orchid community, a comparative study on diversity and ecology in eight undisturbed and ten disturbed forests in Peninsular Malaysia was conducted that varied in areas, elevations, vegetation types, and disturbance regimes. Density and individual-based rarefaction curves were used to describe the abundance. Univariate and multivariate analyses were also performed to explore the associations of species abundance with biotic and abiotic factors. The study reported 239 orchid species belonging to 65 genera. Species richness, abundance, density, and diversity of orchids varied by locality. Higher density of orchids (2.433 plants/km²) occurred in the undisturbed forests than in the disturbed forests (0.228 plants/km²). As with the character of undisturbed forests, the temperature was between 27.8 ± 0.3 °C and 31.2 ± 0.2 °C, humid (77.1 ± 1.2%–89.6 ± 0.9%), and with low light intensity (23.8 ± 3.3 μmol m⁻²s⁻¹–171.7 ± 18.8 μmol m⁻²s⁻¹), thus supporting the high density of the plants. Disturbed forests had higher diversity (H = 4.934 and 1-D = 0.990) and abundance (183 species of 57 genera) but were determined to be highly influenced by the higher abundance of epiphytic orchids on the fallen trees and ease of accessibility in the logged forests. Terrestrial and mycoheterotroph orchids were much lower in density and abundance in the disturbed habitat indicating a gradual reduction in their niche availability following the disturbance. Additionally, the ecology data show that the microclimate conditions of the canopy-covered forest was influenced by proximity to the logged area which had eventually reduced the orchids’ habitat quality. Furthermore, the results show that the abundance of epiphytic orchid communities was associated with the host plant characteristics. Host types and bark texture preference were apparent for the epiphytic orchid species, with certain types and textures hosting more orchid species than others. Overall results show that extreme temperature, humidity, and light intensity caused by the canopy opening inflicted damages to the habitat conditions and bark textures of the host plants and limits recolonisation of the orchids in the disturbed forests. The species diversity and density patterns of orchids in undisturbed and disturbed forests revealed in this study provide a baseline for conservationists, policy makers, and forest authorities in expanding the understanding of the forest ecology and vegetation along the disturbance gradient, forest regeneration, and criteria for plant selection for forest restoration in Peninsular Malaysia. Full article

(This article belongs to the Special Issue Genetic Diversity and Conservation of Forest Species)

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14 pages, 3260 KiB

Open AccessArticle

Genetic Diversity and Population Structure Analysis in the Chinese Endemic Species Michelia crassipes Based on SSR Markers

by Yuguang Xiao, Xiaolong Jiang, Chengcheng Lu, Jun Liu, Shu Diao and Jingmin Jiang

Forests 2023, 14(3), 508; https://doi.org/10.3390/f14030508 - 4 Mar 2023

Cited by 8 | Viewed by 3245

Abstract

Michelia crassipes Y. W. Law (Magnoliaceae) is endemic to China and is the only species with purple flowers in the genus Michelia. It is commonly used as an important parent for flower color improvement and hybrid breeding. M. crassipes is recognized as an endangered plant. An urgent need exists to explore the genetic diversity of M. crassipes to efficiently select hybrid parents and develop efficient conservation strategies. In this study, a total of 128 samples were selected from seven natural populations of M. crassipes to explore their genetic diversity and structure. A total of 14 microsatellite (SSR) markers with high polymorphism and repeatability were developed, and 218 alleles were detected. This study mainly revealed three results: (1) The parameters of expected heterozygosity (He = 0.536) and mean Shannon’s information index (I = 1.121) revealed moderately high levels of genetic diversity for the M. crassipes natural population; (2) The genetic differentiation coefficient (Fst = 0.108) showed that there was a low level of genetic differentiation, and AMOVA indicated that genetic variation existed mainly within populations and that there was frequent gene exchange between populations; and (3) The population genetic structure analysis showed that seven natural populations originated from two ancestral groups, and the Mantel test revealed that genetic and geographical distances between populations were significantly correlated. Our study is the first to explore the genetic diversity and structure of the M. crassipes natural population, which provides an important reference for the collection, conservation and utilization of Michelia crassipes germplasm resources. Full article

(This article belongs to the Special Issue Genetic Diversity and Conservation of Forest Species)

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26 pages, 1900 KiB

Open AccessArticle

Potentially Toxic Metals in the Tropical Mangrove Non-Salt Secreting Rhizophora apiculata: A Field-Based Biomonitoring Study and Phytoremediation Potentials

by Chee Kong Yap and Khalid Awadh Al-Mutairi

Forests 2023, 14(2), 237; https://doi.org/10.3390/f14020237 - 27 Jan 2023

Cited by 6 | Viewed by 2062

Abstract

The present study evaluated the potentials of phytoremediation and the biomonitoring of potentially toxic metals (PTMs) (Zn, Ni, Fe, Pb, and Cu) in the mangrove leaves of Rhizophora apiculata from the tropical mangrove ecosystem in the Sepang Besar River and Lukut River, Peninsular Malaysia. Overall, the present studies concluded that (a) the levels of essential Fe, Cu, and Zn in lamina are significantly (p < 0.05) higher than in MP, (b) the levels of Pb and Ni in MP are significantly (p < 0.05) higher than in lamina, (c) the lamina has better potential as a phytoremediator of Cu, Zn, and Fe, while MP is a better potential phytoremediator of Pb and Ni, (d) lamina is a potential biomonitoring agent of potentially toxic metals based on better correlation coefficients with the surface sedimentary geochemical fractions, and (e) metal uptake in the mangrove leaves and comparative levels of metals is low with reported studies. Specifically, based on bioconcentration factors (BCF), their most obtained values were considered low (<1), suggesting that R. apiculata can be considered as a low-efficiency plant for the bioaccumulation of PTM. However, the present findings also suggested that R. apiculata may be classified as a potential phytoremediator for Zn, Cu, Pb, and Ni in the leaves, as indicated by higher metal accumulation in the MP, with BCF_EFLE values > 1.0; BCF_AR > 1.0 for Cu, Pb, and Ni. The mangrove leaves are potential biomonitors of PTMs since positive correlations of PTMs were found between the leaves and their habitat surface sediments. Having been identified as a potential phytoremediator and biomonitor of PTMs, the present study emphasized the possibility of establishing a framework for managing the coastal aquatic ecosystems along the mangrove ecosystems of Sepang and Lukut. Full article

(This article belongs to the Special Issue Genetic Diversity and Conservation of Forest Species)

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20 pages, 3712 KiB

Open AccessFeature PaperArticle

Molecular Phylogenetics of the Orchid Genus Spathoglottis (Orchidaceae: Collabieae) in Peninsular Malaysia and Borneo

by Farah Alia Nordin, Kartini Saibeh, Rusea Go, Khairul Nasirudin Abu Mangsor and Ahmad Sofiman Othman

Forests 2022, 13(12), 2079; https://doi.org/10.3390/f13122079 - 7 Dec 2022

Cited by 5 | Viewed by 2512

Abstract

Phylogenetic relationships of the orchid genus Spathoglottis (Orchidaceae: Collabieae) in Peninsular Malaysia and Borneo were inferred using the internal transcribed spacer of a nuclear ribosomal DNA (nrITS), a plastid gene maturaseK (matK) and the plastid region trnL-F. Eleven species and three infraspecific taxa of Spathoglottis were examined, with two outgroup species, were included in the phylogenetic analysis. The combined plastid and nuclear data revealed Spathoglottis as monophyletic. From the maximum likelihood, maximum parsimony and Bayesian analyses, Spathoglottis is divided into four major groups which are, (1) the Dwarf Purple Spathoglottis, (2) the Dwarf Yellow Spathoglottis, (3) the Large Purple Spathoglottis, and (4) the Large Yellow Spathoglottis. The split in the Dwarf and Large Spathoglottis groups might reflect an early differentiation of plant size, flower colours and flower size. Phylogeny reconstruction of the orchid genus Spathoglottis also exhibited strong support towards the taxonomic delimitation of the two mostly debated taxa in the genus, S. aurea and S. microchilina. Full article

(This article belongs to the Special Issue Genetic Diversity and Conservation of Forest Species)

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17 pages, 13260 KiB

Open AccessArticle

Plastome Characterization, Phylogenetic Relationships, and Regional Conservation Status of Ficus populifolia Vahl. (Moraceae), a Peripherally Isolated Plant Population in the Arabian Peninsula

by Samah A. Alharbi, Widad S. AL-Juhani and Enas J. Albokhari

Forests 2022, 13(12), 2063; https://doi.org/10.3390/f13122063 - 4 Dec 2022

Cited by 2 | Viewed by 1983

Abstract

The Ficus populifolia Vahl. in the Arabian Peninsula is threatened, peripheral, and geographically isolated from its main population in Africa. Here, the entire plastome of F. populifolia from the Arabian Peninsula was sequenced and analyzed to provide a baseline genetic resource for future research. The F. populifolia plastome has a classic quadripartite structure with a size of 160,610 bp, the large and small single copies of 88,729 and 20,097 bp, respectively, and each pair of inverted repeats are 25,892 bp. The genome includes 113 unique genes, 79 protein-coding genes, 30 tRNAs, and 4 rRNAs. The results reveal a total of 49 long repeats, including (30) palindromic, (14) forward, and (5) reverse repeats. Similarly, a total of 186 simple sequence repeats were identified, 83.8% of which were mononucleotides. The genomic comparison with four Ficus species indicated that the plastome of F. populifolia was highly conserved, with some hypervariable noncoding regions. The phylogenomic analysis of 28 species of Ficus, based on 78 coding genes, revealed that F. populifolia is closely related to the African species F. lyrata. The genomic data generated in this study provide valuable resources for future investigations on the population genetics, authentication, and genetic conservation of the wild Arabian population of F. populifolia. Full article

(This article belongs to the Special Issue Genetic Diversity and Conservation of Forest Species)

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18 pages, 4287 KiB

Open AccessArticle

Morpho-Physiological Strategies of Shorea leprosula Miq. and Shorea acuminata Dyer in Response to Light Intensity and Nutrient Amendments

by Abd Razak Siti Nurfaeiza, Wan Ahmad Wan Juliana, Khamis Shamsul and Md. Nor Shukor

Forests 2022, 13(11), 1768; https://doi.org/10.3390/f13111768 - 27 Oct 2022

Cited by 1 | Viewed by 2014

Abstract

Successfully restoring degraded forest areas depends on seedlings adapting their growth to suit harsh environments. Hence, the requirements for seedlings’ growth need to be addressed before replanting degraded sites. The present study determines the effect of abiotic factors viz. light irradiance (8%, 30%, and 100%), nutrient addition (no fertiliser (NF), NPK, and vermicompost) on the growth performance and photosynthetic capacity of two dipterocarp species seedlings, Shorea leprosula Miq. and Shorea acuminata Dyer. The morphological characteristics assessed for growth performance comprised plant height, stem diameter, leaf count, leaf area, relative chlorophyll concentration, biomass, and root-to-shoot ratio. Li-Cor 6400 and 6800 were used to measure the leaf gas exchange traits, including photosynthetic rate (A), transpiration rate (E), intercellular CO₂ concentration (Ci), stomatal conductance (g_sw), and water-use efficiency (WUE). Our results demonstrated that different levels of light intensity and nutrient amendment significantly impacted plant-growth performance. Plants grown in 30% irradiance showed better growth performance in terms of relative height growth rate (RHGR), mean number of leaves, and leaf areas 41%, 24%, and 32% higher than the control. The A value was also higher in 30% irradiance, but no significant differences were observed between each level of light irradiance. The addition of vermicompost gave better growth for RHGR, relative diameter growth rate (RDGR), mean number of leaves, biomass, and relative chlorophyll concentrations 47%, 40%, 131%, 19%, and 27% higher than the control, respectively. However, the results obtained for photosynthetic parameters were contrary to growth performance. The photosynthesis rate (A) was higher (14.8%) in NPK compared to the control, and the other photosynthetic parameters did not differ significantly despite different nutrient amendments. In terms of species, S. leprosula has better growth performance and photosynthetic characteristics than S. acuminata in different light irradiance and nutrient amendments, thereby rendering S. leprosula the preferred rehabilitation species. Generally, nutrient addition of either NPK or vermicompost and 30% light irradiance gave better morphological and physiological growth for both species. The outcome of this study could provide a better understanding on the forest rehabilitation strategy to reduce the seedling-mortality rate, particularly for climax tree species. Full article

(This article belongs to the Special Issue Genetic Diversity and Conservation of Forest Species)

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17 pages, 1184 KiB

Open AccessArticle

Conservation Genetics of the Rare and Endangered Tree Species, Camellia nitidissima (Theaceae), Inferred from Microsatellite DNA Data

by Zongyou Chen, Junfang Wang, Jianmin Tang, Zhengfeng Wang, Shengfeng Chai, Xingjin He and Xiao Wei

Forests 2022, 13(10), 1662; https://doi.org/10.3390/f13101662 - 10 Oct 2022

Cited by 1 | Viewed by 2228

Abstract

Camellia nitidissima Chi, is a rare and endangered plant that is narrowly distributed in South China and North Vietnam. In this study, seven polymorphic microsatellite markers were used to investigate the genetic diversity, recent population bottlenecks as well as population structure of twelve remnant populations of the plant. Our results indicated that, despite their severely fragmented natural range, C. nitidissima remnants maintained a moderate level of genetic variability, and only a bottlenecked population was detected by the clear evidences. No significant correlation was found between genetic diversity and population size. Significantly high genetic differences among populations were found, and the twelve populations could be classified into two distinct genetic groups. AMOVA indicated that 16.14% (16.73%, after one suspected artificial population was excluded) of the molecular variation was attributable to regional divergences (between Nanning and Fangcheng), and the majority of genetic variation existed within populations which were 69.24% (70.63%, after one suspected artificial population was excluded). For conservation management plans, the genetic resources of the two distinct groups are of equal importance for conservation, separate management unit for each of them should be considered. Given that all remnant populations are small and isolated, and many plants are illegally dug out for commercial purposes, management efforts in terms of habitat protection and legal protection, as well as transplantations and reintroductions, would be necessary for this species. Full article

(This article belongs to the Special Issue Genetic Diversity and Conservation of Forest Species)

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14 pages, 3039 KiB

Open AccessArticle

Genetic Diversity of Nanmu (Phoebe zhennan S. Lee. et F. N. Wei) Breeding Population and Extraction of Core Collection Using nSSR, cpSSR and Phenotypic Markers

by Yan Zhu, Wenna An, Jian Peng, Jinwu Li, Yunjie Gu, Bo Jiang, Lianghua Chen, Peng Zhu and Hanbo Yang

Forests 2022, 13(8), 1320; https://doi.org/10.3390/f13081320 - 18 Aug 2022

Cited by 10 | Viewed by 3252

Abstract

Genetic characterization is vital for tree germplasm utilization and conservation. Nanmu (Phoebe zhennan S. Lee. et F. N. Wei) is an extremely valuable tree species that can provide logs for many industrial products. This study aimed to assess the genetic diversity of a Nanmu breeding population using nine nSSR, five newly-developed cpSSR markers, and nine phenotypic traits, and extract a core collection. In general, the Na, Ne, and PIC for each nSSR/cpSSR were 2–37/2–3, 1.160–11.276/1.020–1.940, and 0.306–0.934/0.109–0.384, respectively. Fifteen chlorotype haplotypes were detected in 102 germplasms. The breeding population exhibited a relatively high level of genetic diversity for both nSSR (I = 1.768), cpSSR (I = 0.440, h = 0.286), and phenotypic traits (H′ = 1.98). Bayesian and cluster analysis clustered these germplasms into three groups. The germplasms revealed a high level of admixture between clusters, which indicated a relatively high level of gene exchange between germplasms. The F value (0.124) also showed a moderate genetic differentiation in the breeding population. A core collection consisting of 64 germplasms (62.7% of the whole germplasm) was extracted from phenotypic and molecular data, and the diversity parameters were not significantly different from those of the whole germplasm. Thereafter, a molecular identity was made up for each core germplasm. These results may contribute to germplasm management and conservation in the Nanmu breeding program, as well as genetics estimation and core collection extraction in other wood production rare species. Full article

(This article belongs to the Special Issue Genetic Diversity and Conservation of Forest Species)

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