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Special Issue "Genetic Diversity and Molecular Evolution"

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A special issue of Diversity (ISSN 1424-2818).

Deadline for manuscript submissions: closed (30 August 2014)

Special Issue Editor

Guest Editor
Dr. Genlou Sun (Website)

Biology Department, Saint Mary's University, Halifax, Nova Scotia, B3H 3C3, Canada
Interests: plant genetics; cytogenetics; systematics; molecular genetics; population genetics and biotechnology

Special Issue Information

Dear Colleagues,

Genetic diversity is fundamental to species survival, to the continued evolution of new species and adaptation to changing environments. The study of genetic diversity is important for conservation biologists because ecosystems possessing a high degree of genetic diversity are generally the healthiest, most stable, and most able to adapt to changing environmental conditions. The existence of genetic diversity is necessary for evolution to occur and it is genetic variation that natural selection acts on. The maintenance of biodiversity has practical application because having a large degree of genetic variation among economically valuable commodities (e.g. agricultural crops, livestock etc…) increases the resistance of these resources to pests and disease. 
Since the advent of various molecular techniques, these techniques have been widely used for characterizing genetic diversity, and studying molecular evolution, which have resulted in many new discoveries and upset many of our traditional views about the genetic diversity and evolution. Thus, it is a good time to summarize current status of genetic diversity and molecular evolution, and to discuss future perspective of this field.

Dr. Genlou Sun
Guest Editor

Submission

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. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as 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 refereed through a peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Diversity is an international peer-reviewed Open Access quarterly 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 800 CHF (Swiss Francs).

Keywords

  • genetic diversity and conservation
  • population genetics
  • nucleotides diversity and ecogenomics
  • molecular evolution and phylogeny

Published Papers (9 papers)

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Research

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Open AccessArticle Genotyping-By-Sequencing for Plant Genetic Diversity Analysis: A Lab Guide for SNP Genotyping
Diversity 2014, 6(4), 665-680; doi:10.3390/d6040665
Received: 25 August 2014 / Revised: 11 October 2014 / Accepted: 13 October 2014 / Published: 20 October 2014
Cited by 7 | PDF Full-text (2013 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Genotyping-by-sequencing (GBS) has recently emerged as a promising genomic approach for exploring plant genetic diversity on a genome-wide scale. However, many uncertainties and challenges remain in the application of GBS, particularly in non-model species. Here, we present a GBS protocol we developed [...] Read more.
Genotyping-by-sequencing (GBS) has recently emerged as a promising genomic approach for exploring plant genetic diversity on a genome-wide scale. However, many uncertainties and challenges remain in the application of GBS, particularly in non-model species. Here, we present a GBS protocol we developed and use for plant genetic diversity analysis. It uses two restriction enzymes to reduce genome complexity, applies Illumina multiplexing indexes for barcoding and has a custom bioinformatics pipeline for genotyping. This genetic diversity-focused GBS (gd-GBS) protocol can serve as an easy-to-follow lab guide to assist a researcher through every step of a GBS application with five main components: sample preparation, library assembly, sequencing, SNP calling and diversity analysis. Specifically, in this presentation, we provide a brief overview of the GBS approach, describe the gd-GBS procedures, illustrate it with an application to analyze genetic diversity in 20 flax (Linum usitatissimum L.) accessions and discuss related issues in GBS application. Following these lab bench procedures and using the custom bioinformatics pipeline, one could generate genome-wide SNP genotype data for a conventional genetic diversity analysis of a non-model plant species. Full article
(This article belongs to the Special Issue Genetic Diversity and Molecular Evolution)
Open AccessArticle Genetic Segregation and Genomic Hybridization Patterns Support an Allotetraploid Structure and Disomic Inheritance for Salix Species
Diversity 2014, 6(4), 633-651; doi:10.3390/d6040633
Received: 29 July 2014 / Revised: 16 September 2014 / Accepted: 22 September 2014 / Published: 29 September 2014
PDF Full-text (909 KB) | HTML Full-text | XML Full-text
Abstract
The Salix alba L. (white willow)—Salix fragilis L. (crack willow) complex includes closely related polyploid species, mainly tetraploid (2n = 4x = 76), which are dioecious and hence obligate allogamous. Because little is known about the genome constitution and [...] Read more.
The Salix alba L. (white willow)—Salix fragilis L. (crack willow) complex includes closely related polyploid species, mainly tetraploid (2n = 4x = 76), which are dioecious and hence obligate allogamous. Because little is known about the genome constitution and chromosome behavior of these pure willow trees, genetic analysis of their naturally occurring interspecific polyploid hybrids is still very difficult. A two-way pseudo-testcross strategy was exploited using single-dose AFLP markers in order to assess the main inheritance patterns of tetraploid biotypes (disomy vs. tetrasomy) in segregating populations stemmed from S. alba × S. fragilis crosses and reciprocals. In addition, a genomic in situ hybridization (GISH) technology was implemented in willow to shed some light on the genome structure of S. alba and S. fragilis species, and their hybrids (allopolyploidy vs. autopolyploidy). The frequency of S. alba-specific molecular markers was almost double compared to that of S. fragilis-specific ones, suggesting the phylogenetic hypothesis of S. fragilis as derivative species from S. alba-like progenitors. Cytogenetic observations at pro-metaphase revealed about half of the chromosome complements being less contracted than the remaining ones, supporting an allopolyploid origin of both S. alba and S. fragilis. Both genetic segregation and genomic hybridization data are consistent with an allotetraploid nature of the Salix species. In particular, the vast majority of the AFLP markers were inherited according to disomic patterns in S. alba × S. fragilis populations and reciprocals. Moreover, in all S. alba against S. fragilis hybridizations and reciprocals, GISH signals were observed only on the contracted chromosomes whereas the non-contracted chromosomes were never hybridized. In conclusion, half of the chromosomes of the pure species S. alba and S. fragilis are closely related and they could share a common diploid ancestor, while the rest of chromosomes are morphologically differentiated in either S. alba or S. fragilis and they should derive from distinct diploid ancestors. Full article
(This article belongs to the Special Issue Genetic Diversity and Molecular Evolution)
Open AccessArticle Novel Microsatellite Loci Variation and Population Genetics within Leafy Seadragons, Phycodurus eques
Diversity 2014, 6(1), 33-42; doi:10.3390/d6010033
Received: 2 October 2013 / Revised: 20 December 2013 / Accepted: 27 December 2013 / Published: 3 January 2014
PDF Full-text (285 KB) | HTML Full-text | XML Full-text
Abstract
Novel leafy seadragon (Phycodurus eques) microsatellite loci were developed via standard cloning techniques and tested for use in population genetics studies. Six out of a total of twelve microsatellites tested were usable for population analysis. Seadragon samples from Western Australia [...] Read more.
Novel leafy seadragon (Phycodurus eques) microsatellite loci were developed via standard cloning techniques and tested for use in population genetics studies. Six out of a total of twelve microsatellites tested were usable for population analysis. Seadragon samples from Western Australia (N = 6), Southern Australia (N = 11), and a captive group (N = 11) were analyzed. Here, we present leafy seadragon microsatellite primer sequences for all 12 loci and population genetics statistics for the six loci that amplified consistently and displayed adequate variability to estimate population parameters, such as diversity, population differences, and relatedness. Observed heterozygosities ranged from 0.225 to 0.926 and expected heterozygosities ranged from 0.278 to 0.650. Pairwise differences among populations (FST estimates) from samples collected off the southern coast of Western and South Australia, and captive animals ranged from a low of 0.188 between Southern Australia and captive animals, to a high of 0.212 between Western Australia and captive animals. Statistical assignment analyses suggested between one and three populations. Percent first order relatives among individuals was high and ranged from 40 within Western Australia to 55 within captive animals. These loci were tested on other species including weedy seadragons (Phyllopteryx taeniolatus), as well as assorted seahorses (Hippocampus reidi, H. erectus) and pipefish (Doryrhamphus dactyliophorus, D. pessuliferus, Corythoichthys intestinalis, Syngnathus leptorhynchus) with no success. Full article
(This article belongs to the Special Issue Genetic Diversity and Molecular Evolution)
Open AccessArticle Genetic Diversity and Population Structure of Two Freshwater Copepods (Copepoda: Diaptomidae), Neodiaptomus schmackeri (Poppe and Richard, 1892) and Mongolodiaptomus birulai (Rylov, 1922) from Taiwan
Diversity 2013, 5(4), 796-810; doi:10.3390/d5040796
Received: 22 September 2013 / Revised: 15 November 2013 / Accepted: 18 November 2013 / Published: 22 November 2013
Cited by 2 | PDF Full-text (1241 KB) | HTML Full-text | XML Full-text
Abstract
We used the mitochondria DNA COI (cytochrome c oxidase subunit I) sequence as a genetic marker to analyze the population genetic structure of two species of freshwater copepods, Neodiaptomus schmackeri (Poppe and Richard, 1892) and Mongolodiaptomus birulai (Rylov, 1922) from Taiwan. Four [...] Read more.
We used the mitochondria DNA COI (cytochrome c oxidase subunit I) sequence as a genetic marker to analyze the population genetic structure of two species of freshwater copepods, Neodiaptomus schmackeri (Poppe and Richard, 1892) and Mongolodiaptomus birulai (Rylov, 1922) from Taiwan. Four populations with 51 individuals of N. schmackeri and five populations with 65 individuals of M. birulai were included. We compared the nucleotide sequences of a 635-bp fragment of the COI gene of N. schmackeri and a 655-bp fragment of the COI gene of M. birulai, and eight and 14 unique haplotypes were recorded, respectively. Tseng-Wen reservoir and Wu-San-Tao reservoir are linked by a channel, and the gene flow between them was unrestricted (Fst = 0.058; Nm = 4.04; Fst, population differentiation parameter; Nm, the number of succesfull migrants per generation); the gene flow between all other populations of both species was restricted (Fst = 0.4–0.99; Nm = 0–0.37). Based on the COI gene diversification pattern, we suggest that most populations of N. schmackeri and M. birulai are isolated from each other. According to the neighbor-joining tree and the minimum spanning network (MSN), the species have similar metapopulation genetic structures. Genetic distance was not found to be correlated with geographical distance. The genetic diversification pattern was not shown to be comparable with geographical isolation owing to long-distance separation. The genetic structure of the present populations may result from serial extinction and redistribution of the populations formed in each reservoir relative to time. Human activity in the reservoirs with regards to water resource management and the fishery industry also exerts an effect on population redistribution. Full article
(This article belongs to the Special Issue Genetic Diversity and Molecular Evolution)
Open AccessArticle Upland Habitat Quality and Historic Landscape Composition Influence Genetic Variation of a Pond-Breeding Salamander
Diversity 2013, 5(4), 724-733; doi:10.3390/d5040724
Received: 29 July 2013 / Revised: 31 August 2013 / Accepted: 10 September 2013 / Published: 25 September 2013
Cited by 1 | PDF Full-text (735 KB) | HTML Full-text | XML Full-text
Abstract
Understanding the temporal and spatial scale at which habitat alteration impacts populations is important for conservation and management. Amphibians have declined more than other vertebrates, and pond-breeding species are particularly susceptible to habitat loss and fragmentation because they have terrestrial and aquatic [...] Read more.
Understanding the temporal and spatial scale at which habitat alteration impacts populations is important for conservation and management. Amphibians have declined more than other vertebrates, and pond-breeding species are particularly susceptible to habitat loss and fragmentation because they have terrestrial and aquatic life stages. One approach to management of pond-breeding species is protection of core upland habitat surrounding the breeding pond. We used genetic variation as an indicator of population status in a common amphibian species, spotted salamanders (Ambystoma maculatum), to determine how amount of suitable upland habitat relates to population status in the greater Charlotte, North Carolina, USA metropolitan area. We developed candidate models to evaluate the relative influence of historical and contemporary forested habitat availability on population genetic variation at two spatial scales of upland area (164 m and 2000 m) at four time intervals over the past seven decades (1938, 1978, 1993, 2005). We found that historical land cover best predicted contemporary allelic richness. Inbreeding coefficient and observed heterozygosity were not effectively predicted by forest cover at either spatial or temporal scales. Allelic richness was best predicted at the smaller spatial scale in the 1993 time interval. Predicting and understanding how future landscape configuration affects genetic variation of common and rare species is imperative for the conservation of amphibian and other wildlife populations. Full article
(This article belongs to the Special Issue Genetic Diversity and Molecular Evolution)
Open AccessArticle Genetic Diversity of Black Salamanders (Aneides flavipunctatus) across Watersheds in the Klamath Mountains
Diversity 2013, 5(3), 657-679; doi:10.3390/d5030657
Received: 31 May 2013 / Revised: 2 August 2013 / Accepted: 8 August 2013 / Published: 29 August 2013
Cited by 3 | PDF Full-text (8134 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Here we characterize the genetic structure of Black Salamanders (Aneides flavipunctatus) in the Klamath Mountains of northwestern California and southwestern Oregon using mitochondrial and nuclear DNA sequences. We hypothesized that the Sacramento, Smith, Klamath, and Rogue River watersheds would represent [...] Read more.
Here we characterize the genetic structure of Black Salamanders (Aneides flavipunctatus) in the Klamath Mountains of northwestern California and southwestern Oregon using mitochondrial and nuclear DNA sequences. We hypothesized that the Sacramento, Smith, Klamath, and Rogue River watersheds would represent distinct genetic populations based on prior ecological results, which suggest that Black Salamanders avoid high elevations such as the ridges that separate watersheds. Our mitochondrial results revealed two major lineages, one in the Sacramento River watershed, and another containing the Klamath, Smith, and Rogue River watersheds. Clustering analyses of our thirteen nuclear loci show the Sacramento watershed population to be genetically distinctive. Populations in the Klamath, Smith, and Rogue watersheds are also distinctive but not as differentiated and their boundaries do not correspond to watersheds. Our historical demographic analyses suggest that the Sacramento population has been isolated from the Klamath populations since the mid-Pleistocene, with negligible subsequent gene flow (2 Nm ≤ 0.1). The Smith and Rogue River watershed populations show genetic signals of recent population expansion. These results suggest that the Sacramento River and Klamath River watersheds served as Pleistocene refugia, and that the Rogue and Smith River watersheds were colonized more recently by northward range expansion from the Klamath. Full article
(This article belongs to the Special Issue Genetic Diversity and Molecular Evolution)
Open AccessArticle A Simple Sequence Repeat (SSR) Marker Comparison of a Large In- and Ex-situ Potato Landrace Cultivar Collection from Peru Reaffirms the Complementary Nature of both Conservation Strategies
Diversity 2013, 5(3), 505-521; doi:10.3390/d5030505
Received: 24 April 2013 / Revised: 19 June 2013 / Accepted: 21 June 2013 / Published: 10 July 2013
Cited by 2 | PDF Full-text (988 KB) | HTML Full-text | XML Full-text
Abstract
An enhanced understanding of the temporal dynamics of intraspecific diversity is anticipated to improve the adequacy of conservation priorities, methods and metrics. We report on the comparative genetic composition of ex- and in-situ landrace cultivar populations from a potato diversity hotspot in [...] Read more.
An enhanced understanding of the temporal dynamics of intraspecific diversity is anticipated to improve the adequacy of conservation priorities, methods and metrics. We report on the comparative genetic composition of ex- and in-situ landrace cultivar populations from a potato diversity hotspot in the Andes. A total of 989 landrace cultivars belonging to contemporary custodian-farmer in situ collections from central Peru were compared with 173 accessions from a spatially analogous, but temporally differential ex situ composite genotype reference (CGR) set using 15 nuclear microsatellite markers. A total of 173 alleles were detected, with 129 alleles (74.6%) being shared between both populations. Both populations contain exclusive allelic diversity with 32 and 12 unique alleles belonging to the ex- and in-situ population, respectively. The mean unbiased expected heterozygosity values of the ex- and in-situ population are very similar, 0.749 versus 0.727, with a slightly wider range and standard deviation encountered for the in situ population. Analysis of Molecular Variance shows that 98.8% of the total variation is found within both populations, while the fixation index (Fst = 0.01236) corroborates that the populations are not well differentiated. Surprisingly, only 41.0% of the ex situ population encounters a similar landrace cultivar in 23.4% of the in situ population at a non-stringent threshold similarity coefficient of 0.80. While the ex- and in-situ population under comparison show similarities and unique features at the allelic level, their landrace cultivar composition is surprisingly distinct. Results affirm that crop evolution is an ongoing phenomenon and that change in fixed geographies is occurring. Full article
(This article belongs to the Special Issue Genetic Diversity and Molecular Evolution)
Open AccessArticle Re-Evaluating Causal Modeling with Mantel Tests in Landscape Genetics
Diversity 2013, 5(1), 51-72; doi:10.3390/d5010051
Received: 30 November 2012 / Revised: 18 January 2013 / Accepted: 1 February 2013 / Published: 18 February 2013
Cited by 37 | PDF Full-text (1764 KB) | HTML Full-text | XML Full-text
Abstract
The predominant analytical approach to associate landscape patterns with gene flow processes is based on the association of cost distances with genetic distances between individuals. Mantel and partial Mantel tests have been the dominant statistical tools used to correlate cost distances and [...] Read more.
The predominant analytical approach to associate landscape patterns with gene flow processes is based on the association of cost distances with genetic distances between individuals. Mantel and partial Mantel tests have been the dominant statistical tools used to correlate cost distances and genetic distances in landscape genetics. However, the inherent high correlation among alternative resistance models results in a high risk of spurious correlations using simple Mantel tests. Several refinements, including causal modeling, have been developed to reduce the risk of affirming spurious correlations and to assist model selection. However, the evaluation of these approaches has been incomplete in several respects. To demonstrate the general reliability of the causal modeling approach with Mantel tests, it must be shown to be able to correctly identify a wide range of landscape resistance models as the correct drivers relative to alternative hypotheses. The objectives of this study were to (1) evaluate the effectiveness of the originally published causal modeling framework to support the correct model and reject alternative hypotheses of isolation by distance and isolation by barriers and to (2) evaluate the effectiveness of causal modeling involving direct competition of all hypotheses to support the correct model and reject all alternative landscape resistance models. We found that partial Mantel tests have very low Type II error rates, but elevated Type I error rates. This leads to frequent identification of support for spurious correlations between alternative resistance hypotheses and genetic distance, independent of the true resistance model. The frequency in which this occurs is directly related to the degree of correlation between true and alternative resistance models. We propose an improvement based on the relative support of the causal modeling diagnostic tests. Full article
(This article belongs to the Special Issue Genetic Diversity and Molecular Evolution)

Review

Jump to: Research

Open AccessReview Patterns of Evolutionary Speed: In Search of a Causal Mechanism
Diversity 2013, 5(4), 811-823; doi:10.3390/d5040811
Received: 25 October 2013 / Revised: 21 November 2013 / Accepted: 25 November 2013 / Published: 2 December 2013
Cited by 2 | PDF Full-text (440 KB) | HTML Full-text | XML Full-text
Abstract
The “integrated evolutionary speed hypothesis” proposes that the rate of genetic evolution influences all major biogeographical patterns of diversity including those associated with temperature, water availability, productivity, spatial heterogeneity and area. Consistent with this theory, rates of genetic evolution correspond with patterns [...] Read more.
The “integrated evolutionary speed hypothesis” proposes that the rate of genetic evolution influences all major biogeographical patterns of diversity including those associated with temperature, water availability, productivity, spatial heterogeneity and area. Consistent with this theory, rates of genetic evolution correspond with patterns of diversity and diversification. Here we review the mechanisms that have been proposed to explain these biogeographic patterns in rates of genetic evolution. Tests of several proposed mechanisms have produced equivocal results, whereas others such as those invoking annual metabolic activity, or a “Red Queen” effect, remain unexplored. However, rates of genetic evolution have been associated with both productivity mediated rates of germ cell division and active metabolic rates and these explanations therefore justify further empirical investigation. Full article
(This article belongs to the Special Issue Genetic Diversity and Molecular Evolution)
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