Distribution Of Genetic Variation Research Articles

Multilocus sequence analysis and identification of mating-type idiomorphs distribution in Magnaporthe oryzae population of Karnataka state of India.

To investigate the genetic diversity, population structure and mating-type distribution among the eco-distinct isolates of Magnaporthe oryzae from Karnataka, India. A set of 38 isolates of M. oryzae associated with leaf blast disease of rice were collected from different rice ecosystems of Karnataka, India, and analysed for their diversity at actin, β-tubulin, calmodulin, translation elongation factor 1-α (TEF-1-α), and internal transcribed spacer (ITS) genes/region. The isolates were grouped into two clusters based on the multilocus sequence diversity, the majority being in cluster-IA (n=37), and only one isolate formed cluster-IB. Population structure was analysed using 123 SNP data to understand the genetic relationship. Based on K=2 and ancestry threshold of >70%, blast strains were classified into two subgroups (SG1 and SG2) whereas, based on K=4 and ancestry threshold of >70%, blast strains were classified into four subgroups (SG1, SG2, SG3 and SG4). We have identified 13 haplotype groups where haplotype group 2 was predominant (n=20) in the population. The Tajima's and Fu's Fs neutrality tests exhibited many rare alleles. Further, the mating-type analysis was also performed using MAT1 gene-specific primers to find the potentiality of sexual reproduction in different ecosystems. The majority of the isolates (54.5%) had MAT1-2 idiomorph, whereas 45.5% of the isolates possessed MAT1-1 idiomorph. The present study found the genetically homogenous population of M. oryzae by multilocus sequence analysis. Both mating types, MAT1-1 and MAT1-2, were found within the M. oryzae population of Karnataka. The study on the population structure and sexual mating behaviour of M. oryzae is important in developing region-specific blast-resistant rice cultivars. This is the first report of MAT1 idiomorphs distribution in the M. oryzae population in any Southern state of India.

Insight into the Enterovirus A71: A review.

Enterovirus A71 is a major causative pathogen of hand, foot and mouth disease. It has become a global public health threat, and is especially important for infants and young children in the Asian-Pacific countries. The enterovirus A71 is a non-enveloped virus of the Picornaviridae family having a single-stranded positive-sense RNA genome of about 7.4kb which encodes the structural and nonstructural proteins. Currently there are no US FDA-approved vaccines or antiviral therapy available against enterovirus A71 infection. Although enterovirus A71 vaccines have been licenced in China, clinically approved vaccines for widespread vaccination programs are lacking. Substantial progress has recently been achieved on understanding the structure and function of enterovirus A71 proteins together with information on the viral genetic diversity and geographic distribution. The present review is intended to provide an overview on our current understanding of the molecular biology and epidemiology of enterovirus A71 which will aid the development of vaccines, therapeutics and other control strategies so as to bolster the preparedness for future enterovirus A71 outbreaks.

Captive‐bred ancestry affects spatial patterns of genetic diversity and differentiation in brown trout (Salmo trutta) populations

AbstractIntraspecific genetic diversity is heterogeneously distributed in natural landscapes and often forms repeatable spatial patterns. For instance, in rivers, genetic diversity increases towards downstream areas, whereas genetic differentiation increases in isolated upstream areas. Nonetheless, these patterns can be modified by human‐induced perturbations, and documenting the extent to which human activities alter these natural patterns is important for conservation. Among the human pressures that affect freshwater biodiversity, stocking natural populations with captive‐bred strains is a common practice worldwide that can strongly alter the genetic integrity of wild populations.The main objectives of this study were to document the spatial distribution of captive‐bred ancestry in brown trout (Salmo trutta) populations from four French basins having been stocked according to different practices, and to quantify for each basin the effect of captive‐bred ancestry on the spatial distribution of genetic diversity and differentiation. The four basins were sampled along their upstream–downstream gradient, and a total of 1,686 individuals were genotyped at 192 single nucleotide polymorphism loci.For all basins, individuals with a strong assignment to the captive strain were mostly found in upper reaches, although the average proportion of captive‐bred ancestry varied strikingly among rivers (from 1.9 to 58.7%). Although spatial patterns of genetic differentiation were not affected by introgression and showed an expected increase with increasing distances from the river mouth in all basins, there was evidence that the classical pattern of downstream increase in genetic diversity was reversed when considering highly introgressed populations.These findings demonstrate that the stocking of captive‐bred strains can strongly modify natural spatial patterns of diversity, even when stocking occurred many generations ago and has now ended. The study illustrates the major impacts of humans on intraspecific biodiversity patterns, and emphasizes the importance of conservation plans that take into account this artificial distribution of genetic diversity.

Global and regional circulation trends of norovirus genotypes and recombinants, 1995-2019: A comprehensive review of sequences from public databases.

Human noroviruses are the leading global cause of viral gastroenteritis. Attempts at developing effective vaccines and treatments against norovirus disease have been stymied by the extreme genetic diversity and rapid geographic distribution of these viruses. The emergence and replacement of predominantly circulating norovirus genotypes has primarily been attributed to mutations on the VP1 capsid protein leading to genetic drift, and more recently to recombination events between the ORF1/ORF2 junction. However, large‐scale research into the historical and geographic distribution of recombinant norovirus strains has been limited in the literature. We performed a comprehensive historical analysis on 30,810 human norovirus sequences submitted to public databases between the years 1995 and 2019. During this time, 37 capsid genotypes and 56 polymerase types were detected across 90 different countries, and 97 unique recombinant genomes were also identified. GII.4, both capsid and polymerase, was the predominately circulating type worldwide for the majority of this time span, save for a brief swell of GII.17 and GII.2 capsid genotypes and a near‐total eclipse by GII.P16, GII.P21 and GII.P31 beginning in 2013. Interestingly, an analysis of 4067 recombinants found that 50.2% (N = 2039) of all recorded sequences belonged to three recently emerged recombinant strains: GII.2[P16], GII.4[P31], and GII.4[P16]. This analysis should provide an important historical foundation for future studies that evaluate the emergence and distribution of noroviruses, as well as the design of cross‐protective vaccines.

RAD-Seq and Ecological Niche Reveal Genetic Diversity, Phylogeny, and Geographic Distribution of Kadsura interior and Its Closely Related Species.

Most plants of Kadsura have economic value and medicinal application. Among them, K. interior and its closely related species have been demonstrated to have definite efficacy. However, the taxonomy and phylogenetic relationship of Kadsura in terms of morphology and commonly used gene regions remain controversial, which adversely affects its rational application. In this study, a total of 107 individuals of K. interior, K. heteroclita, K. longipedunculata, K. oblongifolia, and K. coccinea were studied from the perspectives of genetic diversity, phylogeny, and ecology via single nucleotide polymorphisms (SNPs) developed through restriction site-associated DNA sequencing (RAD-seq). Based on these SNPs, the genetic diversity, phylogenetic reconstruction, and population genetic structure were analyzed. Subsequently, divergence time estimation and differentiation scenario simulation were performed. Meanwhile, according to the species distribution records and bioclimatic variables, the Last Glacial Maximum and current potential distributions of five species were constructed, and the main ecological factors affecting the distribution of different species were extracted. The FST calculated showed that there was a moderate degree of differentiation among K. heteroclita, K. longipedunculata, and K. oblongifolia, and there was a high degree of genetic differentiation between K. interior and the above species. The phylogenetic tree indicated that each of the species was monophyletic. The results of population genetic structure and divergence scenario simulation and D-statistics showed that there were admixture and gene flow among K. heteroclita, K. longipedunculata, and K. oblongifolia. The results of ecological niche modeling indicated that the distribution areas and the bioclimatic variables affecting the distribution of K. interior and its related species were different. This study explored the differences in the genetic divergence and geographical distribution patterns of K. interior and its related species, clarifying the uniqueness of K. interior compared to its relatives and providing a reference for their rational application in the future.

Determinants of Genetic Structure in a Highly Heterogeneous Landscape in Southwest China.

Intra-specific genetic diversity is a fundamental component of biodiversity, and is key to species adaptation and persistence. However, significant knowledge gaps still exist in our understanding of the patterns of genetic diversity and their key determinants. Most previous investigations mainly utilized single-species and/or a limited number of explanatory variables; so here we mapped the patterns of plastid genetic diversity within 15 plant species, and explored the key determinants shaping these patterns using a wide range of variables. Population-level cpDNA sequence data for 15 plant species from the Longitudinal Range Gorge Region (LRGR), southwest China, were retrieved from literature and used to estimate haplotype diversity (HD) and population pairwise genetic differentiation (FST) indices. Genetic diversity and divergence landscape surfaces were then generated based on the HD and FST, respectively, to clarify the patterns of genetic structure in the region. Subsequently, we analyzed the relationships between plastid genetic diversity and 16 explanatory variables (classified as anthropogenic, climatic, and topographic). We found that the highest genetic diversity occurred in the Yulong Mountain region, with a significant proportion (~74.81%) of the high diversity land area being located outside of protected areas. The highest genetic divergence was observed approximately along the 25°N latitudinal line, with notable peaks in the western and eastern edges of the LRGR. Genetic diversity (HD) was weakly but significantly positively correlated with both Latitude (lat) and Annual Mean Wet Day Frequency (wet), yet significantly negatively correlated with all of Longitude (long), Annual Mean Cloud Cover Percent (cld), Annual Mean Anthropogenic Flux (ahf), and Human Footprint Index (hfp). A combination of climatic, topographic, and anthropogenic factors explained a significant proportion (78%) of genetic variation, with topographic factors (lat and long) being the best predictors. Our analysis identified areas of high genetic diversity (genetic diversity “hotspots”) and divergence in the region, and these should be prioritized for conservation. This study contributes to a better understanding of the features that shape the distribution of plastid genetic diversity in the LRGR and thus would inform conservation management efforts in this species-rich, but vulnerable region.

Genomic Epidemiology of Early SARS-CoV-2 Transmission Dynamics, Gujarat, India.

Limited genomic sampling in many high-incidence countries has impeded studies of severe respiratory syndrome coronavirus 2 (SARS-CoV-2) genomic epidemiology. Consequently, critical questions remain about the generation and global distribution of virus genetic diversity. We investigated SARS-CoV-2 transmission dynamics in Gujarat, India, during the state’s first epidemic wave to shed light on spread of the virus in one of the regions hardest hit by the pandemic. By integrating case data and 434 whole-genome sequences sampled across 20 districts, we reconstructed the epidemic dynamics and spatial spread of SARS-CoV-2 in Gujarat. Our findings indicate global and regional connectivity and population density were major drivers of the Gujarat outbreak. We detected >100 virus lineage introductions, most of which appear to be associated with international travel. Within Gujarat, virus dissemination occurred predominantly from densely populated regions to geographically proximate locations that had low population density, suggesting that urban centers contributed disproportionately to virus spread.

Chromosome size affects sequence divergence between species through the interplay of recombination and selection.

The structure of the genome shapes the distribution of genetic diversity and sequence divergence. To investigate how the relationship between chromosome size and recombination rate affects sequence divergence between species, we combined empirical analyses and evolutionary simulations. We estimated pairwise sequence divergence among 15 species from three different mammalian clades—Peromyscus rodents, Mus mice, and great apes—from chromosome‐level genome assemblies. We found a strong significant negative correlation between chromosome size and sequence divergence in all species comparisons within the Peromyscus and great apes clades but not the Mus clade, suggesting that the dramatic chromosomal rearrangements among Mus species may have masked the ancestral genomic landscape of divergence in many comparisons. Our evolutionary simulations showed that the main factor determining differences in divergence among chromosomes of different sizes is the interplay of recombination rate and selection, with greater variation in larger populations than in smaller ones. In ancestral populations, shorter chromosomes harbor greater nucleotide diversity. As ancestral populations diverge, diversity present at the onset of the split contributes to greater sequence divergence in shorter chromosomes among daughter species. The combination of empirical data and evolutionary simulations revealed that chromosomal rearrangements, demography, and divergence times may also affect the relationship between chromosome size and divergence, thus deepening our understanding of the role of genome structure in the evolution of species divergence.

Variation in intraspecific demography drives localised concordance but species-wide discordance in response to past climatic change

BackgroundUnderstanding how species biology may facilitate resilience to climate change remains a critical factor in detecting and protecting species at risk of extinction. Many studies have focused on the role of particular ecological traits in driving species responses, but less so on demographic history and levels of standing genetic variation. Additionally, spatial variation in the interaction of demographic and adaptive factors may further complicate prediction of species responses to environmental change. We used environmental and genomic datasets to reconstruct the phylogeographic histories of two ecologically similar and largely co-distributed freshwater fishes, the southern (Nannoperca australis) and Yarra (N. obscura) pygmy perches, to assess the degree of concordance in their responses to Plio-Pleistocene climatic changes. We described contemporary genetic diversity, phylogenetic histories, demographic histories, and historical species distributions across both species, and statistically evaluated the degree of concordance in co-occurring populations.ResultsMarked differences in contemporary genetic diversity, historical distribution changes and historical migration were observed across the species, with a distinct lack of genetic diversity and historical range expansion suggested for N. obscura. Although several co-occurring populations within a shared climatic refugium demonstrated concordant demographic histories, idiosyncratic population size changes were found at the range edges of the more spatially restricted species. Discordant responses between species were associated with low standing genetic variation in peripheral populations. This might have hindered adaptive potential, as documented in recent demographic declines and population extinctions for the two species.ConclusionOur results highlight both the role of spatial scale in the degree of concordance in species responses to climate change, and the importance of standing genetic variation in facilitating range shifts. Even when ecological traits are similar between species, long-term genetic diversity and historical population demography may lead to discordant responses to ongoing and future climate change.

Molecular Identification and Ecology of Portuguese Wild-Caught Phlebotomine Sandfly Specimens

Phlebotomine sandflies are important vectors of Leishmania spp. and phleboviruses causing disease in animals and humans. Morphological identification of phlebotomine sandflies to the species level is challenging, requiring microscopical examination of the genitalia, which is demanding and time consuming. Molecular sandfly species identification can be a practical solution to save resources since it enables further molecular studies capable of generating data, such as biting preferences by blood meal analysis. In this study, resorting to a sandfly dataset collected between 2014 and 2018 across Portuguese territory under active mosquito surveillance and sandfly specific surveys, we used molecular methods to explore the genetic diversity and spatial distribution, further exploring ecological co-variants of four sandfly species—Phlebotomus ariasi, P. perniciosus, P. sergenti, and Sergentomyia minuta—all of which are of public health importance. Sandflies were collected from Spring to Autumn (May–November) following local temperature patterns. P. perniciosus was the most widespread detected species, with a nationwide distribution. All studied species clustered together with known samples from the Iberian Peninsula. Further monitoring studies of sandfly species diversity, distribution, and seasonality are essential for surveillance and control of sandfly-borne pathogens both nationally and globally.

Evidence for multiple refugia and hotspots of genetic diversity for Westralunio carteri, a threatened freshwater mussel in south‐western Australia

Abstract Intraspecific genetic diversity provides the evolutionary potential to adapt to changing environments and ‘hotspots’ of high intraspecific diversity are recognized as key targets for conservation. In south‐western Australia, intraspecific genetic diversity for mesic taxa is not uniformly distributed. Many species comprise highly divergent lineages with unique haplotypes resulting from contraction to refugia during historical arid cycles. Sampling strategies in studies of the region’s unique and ancient freshwater fauna have often focused on broad distributional range, making it difficult to determine boundaries between lineages and the location of genetic hotspots. This study explored the spatial distribution of intraspecific genetic diversity in the threatened freshwater mussel, Westralunio carteri. Mitochondrial DNA sequences for 164 specimens, sampled from all basins within the distribution of the species, were used to describe lineage boundaries and the location of hotspots, and to reconstruct historical demographics. There was strong evidence for three subregions of genetic diversity based on the largely non‐overlapping distributions of three evolutionarily significant units. Spatial and demographic analyses suggest that these evolutionarily significant units persisted through past arid cycles in separate refugia. The majority of haplotypes were unique to a single location, indicating limited connectivity among populations in recent times. Hotspots were identified throughout the region. Most notably, a significant hotspot in the south‐western corner probably arose through the overlap of lineages in historical refugia. Conservation assessments often focus on the species as a whole, even though sublineages, hotspots and the threats faced are not evenly distributed across the species range. This paper highlights that effective conservation of spatially structured taxa requires targeted management of multiple genetic units. Given the importance of formal taxonomic description for conservation listings, further investigation of the potential for species delimitation within W. carteri is required.

Population structure analysis to explore genetic diversity and geographical distribution characteristics of cultivated-type tea plant in Guizhou Plateau

BackgroundTea plants originated in southwestern China. Guizhou Plateau is an original center of tea plants, and is rich in germplasm resources. However, the genetic diversity, population structure and distribution characteristics of cultivated-type tea plants in the region are unknown. In this study, we explored the genetic diversity and geographical distribution of cultivated-type tea accessions in Guizhou Plateau.ResultsWe used 112,072 high-quality genotyping-by-sequencing to analyze the genetic diversity, principal components, phylogeny, population structure, and linkage disequilibrium, and develop a core collection of 253 cultivated-type tea plant accessions from Guizhou Plateau. The results showed Genetic diversity of the cultivated-type tea accessions of the Pearl River Basin was significantly higher than that of the cultivated-type tea accessions of the Yangtze River Basin. Three inferred pure groups (CG-1, CG-2 and CG-3) and one inferred admixture group (CG-4), were identified by a population structure analysis, and verified by principal component and phylogenetic analyses. The highest genetic distance and differentiation coefficients were determined for CG-2 vs CG-3. The lower genetic distance and differentiation coefficients were determined for CG-4 vs CG-2 and CG-4 vs CG-3, respectively. We developed a core set and a primary set. The primary and core sets contained 77.0 and 33.6% of all individuals in the initial set, respectively. The primary set may serve as the primary population in genome-wide association studies, while the core collection may serve as the core population in multiple treatment setting studies.ConclusionsThe present study demonstrated the genetic diversity and geographical distribution characteristics of cultivated-type tea plants in Guizhou Plateau. Significant differences in genetic diversity and evolutionary direction were detected between the ancient landraces of the Pearl River Basin and the those of the Yangtze River Basin. Major rivers and ancient hubs were largely responsible for the genetic exchange between the Pearl River Basin and the Yangtze River Basin ancient landraces as well as the formation of the ancient hubs evolutionary group. Genetic diversity, population structure and core collection elucidated by this study will facilitate further genetic studies, germplasm protection, and breeding of tea plants.

Gene surfing of underdominant alleles promotes formation of hybrid zones.

The distribution of genetic diversity over geographical space has long been investigated in population genetics and serves as a useful tool to understand evolution and history of populations. Within some species or across regions of contact between two species, there are instances where there is no apparent ecological determinant of sharp changes in allele frequencies or divergence. To further understand these patterns of spatial genetic structure and potential species divergence, we model the establishment of clines that occur due to the surfing of underdominant alleles during range expansions. We provide analytical approximations for the fixation probability of underdominant alleles at expansion fronts and demonstrate that gene surfing can lead to clines in one-dimensional range expansions. We extend these results to multiple loci via a mixture of analytical theory and individual-based simulations. We study the interaction between the strength of selection against heterozygotes, migration rates, and local recombination rates on the formation of stable hybrid zones. Clines created by surfing at different loci can attract each other and align after expansion, if they are sufficiently close in space and in terms of recombination distance. Our findings suggest that range expansions can set the stage for parapatric speciation due to the alignment of multiple selective clines, even in the absence of ecologically divergent selection. This article is part of the theme issue 'Species' ranges in the face of changing environments (part I)'.

Phylogenomics and a revised tribal classification of subfamily Dipterocarpoideae (Dipterocarpaceae)

AbstractDipterocarpoideae, the largest subfamily in the Meranti family (Dipterocarpaceae) are an ecologically dominant group of trees throughout much of wet tropical Asia. Increasing anthropogenic pressures on this economically important tree family make it essential to resolve their complex evolutionary relationships and understand the distribution of genetic diversity throughout the family and distribution range. Dipterocarpaceae have been the focal group in a wide range of studies, owing to their economic value, importance in historical biogeography and key role in the evolution of the Asian tropical forest biome. Despite this, persistent taxonomic and evolutionary questions remain, ranging from questions on the geographic origin, sequence of dispersal and the identification of diagnostic characters to circumscribe proper evolutionary groups. Here we present a comprehensive phylogenomic hypothesis for Dipterocarpoideae, based on the analyses of plastome and nuclear cistron (NRC) data, and provide an in‐depth review on the validity of morphological characters underlying the new tribal classification proposed here for the subfamily. Phylogenomic relationships were inferred using maximum likelihood and Bayesian approaches. Estimates of origin and onset of diversification in major clades and lineages were reconstructed using plastome, nuclear and combined datasets. Results of the separate and combined genomic datasets partly corroborate elements of previous classification systems (with improved support at all levels for major clades) but provide strong support for revising the tribal classification of the subfamily into four main clades: Dipterocarpeae (Dipterocarpus), Dryobalanopseae (Dryobalanops), Shoreeae (Hopea, Neobalanocarpus, Parashorea, and all parts of a polyphyletic Shorea) and Vaterieae (including all other presently accepted Dipterocarpoideae genera). Multi‐fossil‐dated divergence time estimation suggests Vaterieae first originated in the Late Cretaceous, followed by Dipterocarpeae, with subsequent rise of the Dryobalanopseae and Shoreeae in the Eocene. Diversification of all tribes commenced before the Early Miocene. Our results provide strong support for the position of Neobalanocarpus heimii, Parashorea and (sub‐)sections of the genera Anisoptera, Hopea, Shorea and Vatica. Hypotheses on the origin of Neobalanocarpus heimii by intergeneric hybridisation between Anthoshorea (maternally inherited) and Hopea (paternally inherited) species were corroborated. Finally, our study provides support for future revisionary changes: (1) the elevation to generic rank of sections in Shorea; and (2) revising the infrageneric classification of Hopea as all (sub‐)sections were recovered as not monophyletic.

Genetic diversity and population structure analysis for Ampelopsis grossedentata using microsatellite markers

Ampelopsis grossedentata is an important national medicine in China. It is mainly used commonly by the Yao, Miao, Dong, and other ethnic minorities of China. The current literature, however, contains no study on the molecular genetics and taxonomy of A. grossedentata, which had led to potential problems in the conservation and utilization of this resource. Therefore, the present study was aimed to use simple sequence repeat (SSR) markers for assessing the levels and the distribution of genetic diversity in a sample set of 225 individuals from nine populations of A. grossedentata in China. The genetic differentiation among the nine populations was estimated at the level of 27 microsatellite loci. All loci were polymorphic in the nine populations analyzed. The average value of the Wright?s fixation index (Fis) was -0.1154, with the range of -0.4627 to 0.2399, at the population level. The average Fit value was -0.0119, with the range of -0.3523 to 0.3563, at the population level. The Fst value was 0.0928 on average, ranging from 0.0463 to 0.1567. The SSR analysis revealed high levels of genetic variations within the studied populations, while the genetic differentiation among the populations was low. This finding probably reflected the historical association among the different populations of A. grossedentata. It is possible that sexual reproduction in the natural breeding system of A. grossedentata increased the levels of genetic variation within the populations while it reduced the genetic differences among the populations. The genetic cluster analysis revealed that the basal clade comprised populations from South China and that the different populations of A. grossedentata were categorized into five branches, which had continuous southeastward and southwestward distributions. The genetic structure of the populations and the levels of genetic diversity of A. grossedentata observed in the present study could provide important insights into the current status and the protection value of this species.

Variability and Genetic Structure of the Montezuma Quail Cyrtonyx montezumae in the Northern Limit of its Distribution

A species’ geographic distribution of genetic variability is influenced by different factors including size of geographic distribution, dispersal capability, mating system, and migration. For instance, a low migration rate among populations may cause a decrease in genetic variation. Such is the case of the Montezuma quail (Cyrtonyx montezumae), a popular game bird with a limited flight capacity that prevents long-distance dispersal. In the northern limit of the species’ distribution in Arizona, New Mexico, and Texas in the United States, the species inhabits oak forests that are separated from one another by deserts. Consequently, Montezuma quail populations are distributed in patches or islands. Knowledge of the species’ genetic structure is likely to help inform habitat management decisions. The objective of this study was to determine patterns of genetic variation in populations of the Montezuma quail using 9 microsatellite DNA loci. We genotyped 119 individuals harvested from 4 populations: Arizona (AZ), western New Mexico (WNM), eastern New Mexico (ENM), and west Texas (WTX). Montezuma quail populations had low observed heterozygosity (Ho = 0.22 ± 0.04) and a low number of alleles per locus (A = 2.41 ± 0.27) compared to other quail species. A global population genetic differentiation index (RST) of 0.045 suggests a weak genetic structure. Max(RST) occurred among pairwise comparisons AZ-WTX, AZ-ENM, and WNM-WTX. A Bayesian allocation analysis indicates that individuals were separated into 3 groups (K = 3), placing the populations of Arizona and Texas in distinct groups apart from the 2 populations of New Mexico, which are in the same group. Despite this differentiation, the Bayesian allocation analysis suggests admixture among populations, which may be an indicator of migration between them, especially between the populations in New Mexico and Arizona. An isolation-by-distance analysis indicates that there is a strong correlation (R2 = 0.84) and suggestive evidence (P = 0.08) of non-independence between geographical and genetic distances, though Montezuma quail populations in the southwestern United States may not be isolated. Climate change projections indicate an increase in aridity conditions in this region, especially in temperate ecosystems where the species occurs. In this scenario, corridors between the populations may disappear, thus causing their complete isolation.

GENETIC DIVERSITY OF NATURAL AND RESTORED API-API PUTIH (AVICENNIA ALBA) POPULATIONS IN THE WEST COAST OF PENINSULAR MALAYSIA

A large tract of mangrove forest in Malaysia has been lost due to increased anthropogenic activities. Restorative practices of mangrove forest have been adopted nationwide to re-establish ecosystem services in combating coastal erosion. However, genetic considerations in local mangrove restoration practices are still far lacking despite the vast literature on their genetic diversity. To understand whether the restored mangroves can impact the genetic diversity distribution among natural populations, we used eight microsatellite markers to assess the genetic diversity of the Api-api putih (Avicennia alba) between the natural and restored populations along the west coast of Peninsular Malaysia. We found no difference in terms of genetic diversity between these populations. Two genetic clusters were detected among A. alba along the west coast based on Bayesian clustering and discriminant analysis of principal components (DAPC). The southwest monsoon current circulation that coincides the timing of seed dispersal of A. alba may explain such pattern of genetic differentiation. Despite the minimal genetic structure, our results suggest that seed sourcing from either population is viable for the local mangrove restoration programs in the future.

Distribution pattern and driving factors of genetic diversity of passerine birds in the Mountains of Southwest China

Genetic diversity is one of the three dimensions of biodiversity and fundamental to various life forms on the Earth. Understanding the distribution pattern of genetic diversity and its driving forces has been an important topic in ecology, biogeography and conservation biology since the last decade. We investigated the genetic diversity pattern of passerine birds in the Mountains of Southwest China, a global biodiversity hotspot with the highest species richness of birds in the entire Eurasia, and explored the influencing forces of environmental variables on genetic diversity. We compiled 1189 Cytochrome b sequences of 27 passerine species from 152 geographic sites, covering the range of Mountains of Southwest China and its adjoining areas. We generated genetic diversity distribution maps using a grid-cell method based on nucleotide diversity and haplotype diversity indices. We further analyzed the variation pattern of the two indices along latitudinal, longitudinal, and elevational gradients. The correlations between the two indices and environmental variables were also evaluated. The nucleotide diversity hotspots were mostly located in the southern Hengduan Mountains, while for haplotype diversity, three hotspots were detected: the southeast edge of the Qinghai-Tibetan Plateau, the southern Hengduan Mountains and the Qinling Mountains. There was no monotonic increasing or decreasing pattern in nucleotide diversity or haplotype diversity along latitudinal, longitudinal or elevational gradients except for altitudinal range. Correlation and model selection analyses detected multiple environmental variables in driving genetic diversity patterns, including temperature, precipitation, vegetation, human influence, longitude and altitude range. Similar to the pattern of species richness, the nucleotide diversity pattern of passerine birds in the Mountains of Southwest China presents a decreasing trend from southwest to northeast, while the haplotype diversity pattern is more likely decreased from west to east. Our results indicate that the distribution pattern of genetic diversity may be derived from the complex topography and diverse microclimates in the Mountains of Southwest China.

Population decline at distribution margins: Assessing extinction risk in the last glacial relictual but still functional metapopulation of a European butterfly

AbstractAimTo determine the interplay between climate and land use changes in driving population dynamics in a butterfly species, Coenonympha hero, at the southern limit of its distribution.LocationFrench Jura massif and Europe.MethodsWe analysed patterns of genetic diversity distribution at 817 loci in 136 butterflies from 31 sites using NGS to infer the genetic structure and population size changes over time, using two methods of demographic inference (SNP frequency spectrum analyses and coalescent ABC inferences). We then characterized the climate and land use descriptors of C. hero geographic distribution using species distribution modelling (SDM) and ordination method and compared demographic changes to changes in climatically suitable areas.ResultsCoenonympha hero persists in the Jura massif as three core populations that share a common history of decline in two steps: an old decline and a more recent decline that resulted in population fragmentation, the southernmost sites being the most threatened (lowest genetic diversity). Climate change during the Würm glaciation is presumably the main factor explaining the first demographic decline. The second decline started 2000 years ago possibly under increased human pressure as suggested by recent extinctions in several sites nowadays characterized by urban and agricultural surfaces. Both climate and land use variables are important descriptors of C. hero distribution, as SDM predictions were improved by adding aridity index, altitude and land use to bioclimatic predictors. Its habitats include forests in north‐eastern Europe and grasslands in the Jura massif.Main conclusionsUsing SDM and genetic demographic inferences, we identified a persistent glacial refuge for the species in Europe. We show that although this relictual population has declined and fragmented under the combined effects of climate warming and anthropization, the metapopulation is still functional but requires particular conservation attention to maintain its connectivity, and to favour the local persistence of this highly endangered butterfly species.

Podocarpus in the palaeogeographically complex island of Hispaniola: A stepping‐stone colonization and conservation recommendations

AbstractAimHispaniola is the second largest island in the Caribbean and a hot spot of biodiversity. The island was formed by the fusion of a northern and southern palaeo‐islands during the mid‐Miocene (15 Ma). The historical split of Hispaniola together with repeated marine incursions during the Pleistocene is known to have influenced lineage divergence and genetic structure in a few birds and mammals, but the effect on vascular plants is less understood. The conifer genus Podocarpus has two species, P.hispaniolensis and P.buchii, that are endemic to the mountains of Hispaniola and are IUCN endangered. The former occurs in the mountains of the north, and the latter in the south, with a region of sympatry in the Cordillera Central. Here, we evaluate the historical split of the two palaeo‐islands and repeated marine incursions as dispersal barriers to the geographical distribution of genetic diversity, genetic structure, divergence patterns and the historical demography of the two species.LocationHispaniola island, Caribbean.MethodsUsing genotyping‐by‐sequencing in 47 Podocarpus samples, we identified two sets of single nucleotide polymorphisms for our analyses (74,260 and 22,657 SNPs). We conducted a phylogenetic and an approximate Bayesian computation analysis to test evolutionary hypotheses of sympatric and allopatric speciation and stepping‐stone colonization.ResultsPodocarpus showed a population genetic structure that corresponds to the geographic distribution of the species. Podocarpus on Hispaniola fit a stepping‐stone colonization model with bottlenecks at each mountain colonization event and speciation in Cordillera Central.Main conclusionsThe historical events in question did not seem to have influenced the genetic structure, diversity or demography of Podocarpus; instead, the current geographic barriers imposed by lowland xeric valleys did. The clear divergence between species together with the elevated within‐population genetic diversity and significant genetic structure calls for a multi‐population in situ conservation of each species.