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Special Issue "Advances in Molecular Ecology"

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Biochemistry, Molecular Biology and Biophysics".

Deadline for manuscript submissions: closed (30 April 2011)

Special Issue Editor

Guest Editor
Prof. Dr. Olivier François (Website)

Grenoble INP, TIMC-IMAG, Faculty of Medicine, F38706 La Tronche, France

Special Issue Information

Dear Colleagues,

Molecular ecology is a recent discipline concerned with the application of molecular and evolutionary biology to questions in ecology. Contributions in molecular ecology utilize DNA, gene expression data and quantitative traits for inference about ecological and evolutionary processes in the field.

The "Advances in Molecular Ecology" issue will consider studies of natural variation, demographic processes, molecular adaptation, population structure and phylogeography, environmental genomics, landscape genetics and biodiversity. Submission of theoretical studies using computer simulations and developing new analytical methods are also encouraged.

Prof. Dr. Olivier François
Guest Editor

Keywords

  • phylogenetics
  • population genomics
  • landscape genetics
  • conservation genetics
  • gene flow and hybridization
  • molecular adaptation
  • molecular markers
  • evolutionary responses to changes in environmental conditions

Published Papers (10 papers)

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Research

Jump to: Review, Other

Open AccessArticle Isolation of Bacteria with Antifungal Activity against the Phytopathogenic Fungi Stenocarpella maydis and Stenocarpella macrospora
Int. J. Mol. Sci. 2011, 12(9), 5522-5537; doi:10.3390/ijms12095522
Received: 21 July 2011 / Revised: 12 August 2011 / Accepted: 19 August 2011 / Published: 29 August 2011
Cited by 11 | PDF Full-text (2237 KB) | HTML Full-text | XML Full-text
Abstract
Stenocarpella maydis and Stenocarpella macrospora are the causal agents of ear rot in corn, which is one of the most destructive diseases in this crop worldwide. These fungi are important mycotoxin producers that cause different pathologies in farmed animals and represent an [...] Read more.
Stenocarpella maydis and Stenocarpella macrospora are the causal agents of ear rot in corn, which is one of the most destructive diseases in this crop worldwide. These fungi are important mycotoxin producers that cause different pathologies in farmed animals and represent an important risk for humans. In this work, 160 strains were isolated from soil of corn crops of which 10 showed antifungal activity against these phytopathogens, which, were identified as: Bacillus subtilis, Pseudomonas spp., Pseudomonas fluorescens, and Pantoea agglomerans by sequencing of 16S rRNA gene and the phylogenetic analysis. From cultures of each strain, extracellular filtrates were obtained and assayed to determine antifungal activity. The best filtrates were obtained in the stationary phase of B. subtilis cultures that were stable to the temperature and extreme pH values; in addition they did not show a cytotoxicity effect against brine shrimp and inhibited germination of conidia. The bacteria described in this work have the potential to be used in the control of white ear rot disease. Full article
(This article belongs to the Special Issue Advances in Molecular Ecology)
Open AccessArticle Genetic Characterization of Five Hatchery Populations of the Pacific Abalone (Haliotis discus hannai) Using Microsatellite Markers
Int. J. Mol. Sci. 2011, 12(8), 4836-4849; doi:10.3390/ijms12084836
Received: 22 April 2011 / Revised: 5 July 2011 / Accepted: 19 July 2011 / Published: 29 July 2011
Cited by 8 | PDF Full-text (293 KB) | HTML Full-text | XML Full-text
Abstract
The Pacific abalone, Haliotis discus hannai, is a popular food in Eastern Asia. Aquacultural production of this species has increased because of recent resource declines, the growing consumption, and ongoing government-operated stock release programs. Therefore, the genetic characterization of hatchery populations is necessary to maintain the genetic diversity of this species and to develop more effective aquaculture practices. We analyzed the genetic structures of five cultured populations in Korea using six microsatellite markers. The number of alleles per locus ranged from 15 to 64, with an average of 23.5. The mean observed and expected heterozygosities were 0.797 and 0.904, respectively. The inbreeding coefficient FIS ranged from 0.054 to 0.184 (mean FIS = 0.121 ± 0.056). The genetic differentiation across all populations was low but significant (overall FST = 0.009, P < 0.01). Pairwise multilocus FST tests, estimates of genetic distance, and phylogenetic and principal component analyses did not show a consistent relationship between geographic and genetic distances. These results could reflect extensive aquaculture, the exchange of breeds and eggs between hatcheries and/or genetic drift due to intensive breeding practices. Thus, for optimal resource management, the genetic variation of hatchery stocks should be monitored and inbreeding controlled within the abalone stocks that are being released every year. This genetic information will be useful for the management of both H. discus hannai fisheries and the aquaculture industry. Full article
(This article belongs to the Special Issue Advances in Molecular Ecology)
Open AccessArticle An Unstructured Phylogeographic Pattern with Extensive Gene Flow in an Endemic Bird of South China: Collared Finchbill (Spizixos semitorques)
Int. J. Mol. Sci. 2011, 12(6), 3635-3647; doi:10.3390/ijms12063635
Received: 30 March 2011 / Revised: 24 May 2011 / Accepted: 3 June 2011 / Published: 7 June 2011
Cited by 5 | PDF Full-text (598 KB) | HTML Full-text | XML Full-text
Abstract
Recent phylogeographical studies indicated that glacial oscillations played a key role on the phylogeographic pattern of extant species. As most studies have previously been carried out on heavily ice-covered regions, such as in European and North American regions, potential effects of climatic [...] Read more.
Recent phylogeographical studies indicated that glacial oscillations played a key role on the phylogeographic pattern of extant species. As most studies have previously been carried out on heavily ice-covered regions, such as in European and North American regions, potential effects of climatic oscillations on species that are distributed on ice-free regions are less known. To address this, we investigated the phylogeographic pattern of an avian species endemic to South China, which was not glaciated during the Pleistocene glaciations. By using 2142 bp mitochondrial DNA, we identified 89 haplotypes defined by 39 polymorphic sites. A combination of high haplotype diversity (0.786–1.00) and low nucleotide diversity (0.00132–0.00252) was detected among geographic populations. Explicit genetic divergence was observed between S. s. semitorques and S. s. cinereicapillus but not detected among geographic populations of S. s. semitorques. Divergence time of the two subspecies was dated back to 87 Kyr which is congruent with the interglacial MIS 5. A weak phylogeographic structure due to strong gene flow among geographic populations was identified in this species, suggesting complex topography of South China has not formed barriers for this species. Full article
(This article belongs to the Special Issue Advances in Molecular Ecology)
Open AccessArticle Comparison of Bayesian Clustering and Edge Detection Methods for Inferring Boundaries in Landscape Genetics
Int. J. Mol. Sci. 2011, 12(2), 865-889; doi:10.3390/ijms12020865
Received: 15 December 2010 / Revised: 18 January 2011 / Accepted: 19 January 2011 / Published: 25 January 2011
Cited by 47 | PDF Full-text (1290 KB) | HTML Full-text | XML Full-text
Abstract
Recently, techniques available for identifying clusters of individuals or boundaries between clusters using genetic data from natural populations have expanded rapidly. Consequently, there is a need to evaluate these different techniques. We used spatially-explicit simulation models to compare three spatial Bayesian clustering [...] Read more.
Recently, techniques available for identifying clusters of individuals or boundaries between clusters using genetic data from natural populations have expanded rapidly. Consequently, there is a need to evaluate these different techniques. We used spatially-explicit simulation models to compare three spatial Bayesian clustering programs and two edge detection methods. Spatially-structured populations were simulated where a continuous population was subdivided by barriers. We evaluated the ability of each method to correctly identify boundary locations while varying: (i) time after divergence, (ii) strength of isolation by distance, (iii) level of genetic diversity, and (iv) amount of gene flow across barriers. To further evaluate the methods’ effectiveness to detect genetic clusters in natural populations, we used previously published data on North American pumas and a European shrub. Our results show that with simulated and empirical data, the Bayesian spatial clustering algorithms outperformed direct edge detection methods. All methods incorrectly detected boundaries in the presence of strong patterns of isolation by distance. Based on this finding, we support the application of Bayesian spatial clustering algorithms for boundary detection in empirical datasets, with necessary tests for the influence of isolation by distance. Full article
(This article belongs to the Special Issue Advances in Molecular Ecology)
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Review

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Open AccessReview Major Histocompatibility Complex (MHC) Markers in Conservation Biology
Int. J. Mol. Sci. 2011, 12(8), 5168-5186; doi:10.3390/ijms12085168
Received: 11 May 2011 / Revised: 27 June 2011 / Accepted: 5 August 2011 / Published: 15 August 2011
Cited by 22 | PDF Full-text (226 KB) | HTML Full-text | XML Full-text
Abstract
Human impacts through habitat destruction, introduction of invasive species and climate change are increasing the number of species threatened with extinction. Decreases in population size simultaneously lead to reductions in genetic diversity, ultimately reducing the ability of populations to adapt to a [...] Read more.
Human impacts through habitat destruction, introduction of invasive species and climate change are increasing the number of species threatened with extinction. Decreases in population size simultaneously lead to reductions in genetic diversity, ultimately reducing the ability of populations to adapt to a changing environment. In this way, loss of genetic polymorphism is linked with extinction risk. Recent advances in sequencing technologies mean that obtaining measures of genetic diversity at functionally important genes is within reach for conservation programs. A key region of the genome that should be targeted for population genetic studies is the Major Histocompatibility Complex (MHC). MHC genes, found in all jawed vertebrates, are the most polymorphic genes in vertebrate genomes. They play key roles in immune function via immune-recognition and -surveillance and host-parasite interaction. Therefore, measuring levels of polymorphism at these genes can provide indirect measures of the immunological fitness of populations. The MHC has also been linked with mate-choice and pregnancy outcomes and has application for improving mating success in captive breeding programs. The recent discovery that genetic diversity at MHC genes may protect against the spread of contagious cancers provides an added impetus for managing and protecting MHC diversity in wild populations. Here we review the field and focus on the successful applications of MHC-typing for conservation management. We emphasize the importance of using MHC markers when planning and executing wildlife rescue and conservation programs but stress that this should not be done to the detriment of genome-wide diversity. Full article
(This article belongs to the Special Issue Advances in Molecular Ecology)
Open AccessReview Back to the Suture: The Distribution of Intraspecific Genetic Diversity in and Around Anatolia
Int. J. Mol. Sci. 2011, 12(6), 4080-4103; doi:10.3390/ijms12064080
Received: 25 April 2011 / Accepted: 10 June 2011 / Published: 20 June 2011
Cited by 32 | PDF Full-text (837 KB) | HTML Full-text | XML Full-text
Abstract
The effect of ice ages in speciation and diversification is well established in the literature. In Europe, the Iberian, the Italian and the Balkan peninsulas comprise the main glacial refugia, where the subsequent re-population of Europe started. Though not studied as extensively, [...] Read more.
The effect of ice ages in speciation and diversification is well established in the literature. In Europe, the Iberian, the Italian and the Balkan peninsulas comprise the main glacial refugia, where the subsequent re-population of Europe started. Though not studied as extensively, Anatolia has also been hinted to be a potential glacial refugium for Europe, and with its proximity to the Caucasus and the Middle East at the same time, has potential to exhibit high levels of intraspecific diversity. The more ubiquitous use and cheaper availability of molecular methods globally now makes it possible to better understand molecular ecology and evolution of the fauna and flora in the genetically understudied regions of the world, such as Anatolia. In this review, the molecular genetic studies undertaken in Anatolia in the last decade, for 29 species of plants and animals, are examined to determine general phylogeographic patterns. In this regard, two major patterns are observed and defined, showing genetic breaks within Anatolia and between Anatolia and the Balkans. A third pattern is also outlined, which suggests Anatolia may be a center of diversity for the surrounding regions. The patterns observed are discussed in terms of their relevance to the location of suture zones, postglacial expansion scenarios, the effect of geographic barriers to gene flow and divergence time estimates, in order to better understand the effect of the geological history of Anatolia on the evolutionary history of the inhabitant species. In view of the current state of knowledge delineated in the review, future research directions are suggested. Full article
(This article belongs to the Special Issue Advances in Molecular Ecology)
Open AccessReview Applications and Implications of Neutral versus Non-neutral Markers in Molecular Ecology
Int. J. Mol. Sci. 2011, 12(6), 3966-3988; doi:10.3390/ijms12063966
Received: 28 April 2011 / Revised: 6 June 2011 / Accepted: 7 June 2011 / Published: 14 June 2011
Cited by 46 | PDF Full-text (334 KB) | HTML Full-text | XML Full-text
Abstract
The field of molecular ecology has expanded enormously in the past two decades, largely because of the growing ease with which neutral molecular genetic data can be obtained from virtually any taxonomic group. However, there is also a growing awareness that neutral [...] Read more.
The field of molecular ecology has expanded enormously in the past two decades, largely because of the growing ease with which neutral molecular genetic data can be obtained from virtually any taxonomic group. However, there is also a growing awareness that neutral molecular data can provide only partial insight into parameters such as genetic diversity, local adaptation, evolutionary potential, effective population size, and taxonomic designations. Here we review some of the applications of neutral versus adaptive markers in molecular ecology, discuss some of the advantages that can be obtained by supplementing studies of molecular ecology with data from non-neutral molecular markers, and summarize new methods that are enabling researchers to generate data from genes that are under selection. Full article
(This article belongs to the Special Issue Advances in Molecular Ecology)
Open AccessReview Recent Advances in Plant Early Signaling in Response to Herbivory
Int. J. Mol. Sci. 2011, 12(6), 3723-3739; doi:10.3390/ijms12063723
Received: 18 April 2011 / Revised: 17 May 2011 / Accepted: 26 May 2011 / Published: 7 June 2011
Cited by 43 | PDF Full-text (279 KB) | HTML Full-text | XML Full-text
Abstract
Plants are frequently attacked by herbivores and pathogens and therefore have acquired constitutive and induced defenses during the course of their evolution. Here we review recent progress in the study of the early signal transduction pathways in host plants in response to [...] Read more.
Plants are frequently attacked by herbivores and pathogens and therefore have acquired constitutive and induced defenses during the course of their evolution. Here we review recent progress in the study of the early signal transduction pathways in host plants in response to herbivory. The sophisticated signaling network for plant defense responses is elicited and driven by both herbivore-induced factors (e.g., elicitors, effectors, and wounding) and plant signaling (e.g., phytohormone and plant volatiles) in response to arthropod factors. We describe significant findings, illuminating the scenario by providing broad insights into plant signaling involved in several arthropod-host interactions. Full article
(This article belongs to the Special Issue Advances in Molecular Ecology)

Other

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Open AccessShort Note Isolation and Characterization of 11 New Microsatellite Loci in Erigeron breviscapus (Asteraceae), an Important Chinese Traditional Herb
Int. J. Mol. Sci. 2011, 12(10), 7265-7270; doi:10.3390/ijms12107265
Received: 26 September 2011 / Revised: 13 October 2011 / Accepted: 18 October 2011 / Published: 24 October 2011
PDF Full-text (75 KB) | HTML Full-text | XML Full-text
Abstract
Erigeron breviscapus (Vant.) Hand.-Mazz. (Asteraceae) is a species endemic to southwestern China and an important traditional Chinese herb for cardiovascular and cerebral vessel diseases. Applying a modified biotin-streptavidin capture method, 11 microsatellite loci were discovered. Polymorphism of each locus was assessed in [...] Read more.
Erigeron breviscapus (Vant.) Hand.-Mazz. (Asteraceae) is a species endemic to southwestern China and an important traditional Chinese herb for cardiovascular and cerebral vessel diseases. Applying a modified biotin-streptavidin capture method, 11 microsatellite loci were discovered. Polymorphism of each locus was assessed in 24 individuals collected from five wild populations. The number of alleles per locus ranged from 2 to 7, with an average of 4.273. The observed (HO) and expected (HE) heterozygosities varied from 0.250 to 0.958 and from 0.337 to 0.786, respectively. Over half of these loci were successfully amplified in two congeneric species. The developed microsatellite markers will be useful for future population genetics and conservation studies, as well as accurate identification of different varieties. Full article
(This article belongs to the Special Issue Advances in Molecular Ecology)
Open AccessTechnical Note Novel Polymorphic Microsatellite Loci for the Korean Black Scraper (Thamnaconus modestus), and Their Application to the Genetic Characterization of Wild and Farmed Populations
Int. J. Mol. Sci. 2011, 12(6), 4104-4119; doi:10.3390/ijms12064104
Received: 11 April 2011 / Revised: 10 June 2011 / Accepted: 13 June 2011 / Published: 20 June 2011
Cited by 5 | PDF Full-text (824 KB) | HTML Full-text | XML Full-text
Abstract
In this study, we developed 20 polymorphic microsatellite markers for the Korean black scraper, Thamnaconus modestus (Günther, 1877), Monacanthidae, and used them to compare allelic variation between wild and hatchery populations in Korea. All loci were readily amplified and demonstrated allelic variability, with the number of alleles ranging from 5–35 in the wild population and 5–22 in the farmed population. The average observed and expected heterozygosities were estimated, respectively, as 0.74 and 0.80 in the hatchery samples and 0.78 and 0.81 in the wild ones. These results indicate lower genetic variability in the hatchery population than in the wild population and minor, but significant, genetic differentiation between the two populations (FST = 0.005, P < 0.01). Additionally, cross-amplification was tested in another monacanthid species, Stephanolepis cirrhifer; many loci were found that yielded useful information. The high degree of polymorphism exhibited by the 20 microsatellites will be useful in future aquaculture and population genetic studies for developing conservation and management plans. Full article
(This article belongs to the Special Issue Advances in Molecular Ecology)

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