High Levels Of Gene Flow Research Articles

High levels of genetic diversity and an absence of genetic structure among breeding populations of the endangered Rufous-backed Bunting in Inner Mongolia, China: implications for conservation

BackgroundThe Rufous-backed Bunting, Emberiza jankowskii, is an endangered species that is primarily distributed in Inner Mongolia, China. The main threats to the continued persistence of this species are habitat loss and degradation. However, the impact of population loss on genetic diversity remains unclear. To support future conservation and management efforts, we assessed the genetic diversity and population structure of E. jankowskii using mitochondrial DNA and microsatellites.MethodsBlood samples were collected from 7‒8-day-old nestlings in Inner Mongolia, China between May and August of 2012 and 2013. Mitochondrial DNA sequences and microsatellite markers were used to assess the genetic diversity, genetic structure and inbreeding of E. jankowskii. The results of genetic diversity and inbreeding were compared to other avian species.ResultsWe found an unexpectedly high level of genetic diversity in terms of mitochondrial DNA and microsatellite compared to other avian species. However, there were high levels of gene flow and minimal genetic structuring, among the fragmented breeding populations of E. jankowskii in Inner Mongolia. These findings suggest that E. jankowskii in Inner Mongolia is a metapopulation. Despite the high genetic diversity of E. jankowskii, local populations in each small patch remain at risk of extinction due to habitat loss. In addition, the E. jankowskii population has a high risk of inbreeding.ConclusionsTo minimize further loss of genetic diversity of this endangered species, we suggest that the E. jankowskii in Inner Mongolia should be considered as a protected species for management purposes. Conservation efforts should concentrate on E. jankowskii habitat management. This may be most effectively achieved by protecting the current breeding habitats and prohibiting over-grazing.

Evaluating the genetic diversity in two tropical leguminous trees, Dalbergia cochinchinensis and D. nigrescens, in lowland forests in Cambodia and Thailand using MIG-seq.

It is vital to measure the levels of genetic diversity and differentiation between populations in a species to understand the current genetic structure and evolution of the species. Here, MIG-seq (multiplexed inter-simple sequence repeat genotyping by sequencing) was employed to assess the genetic variation in two tropical leguminous tree species, Dalbergia cochinchinensis and D. nigrescens, in Cambodia and Thailand. Sequence data for 255-618 loci, each with an approximate length of 100 bp, were obtained, and the nucleotide diversity, Tajima's D and FST were computed. The estimates calculated from the data obtained by MIG-seq were compared to those obtained by Sanger sequencing of nine nuclear coding genes in D. cochinchinensis in our previous study. The nucleotide diversity at the MIG-seq loci was slightly higher than that at silent sites in the coding loci, whereas the FST values at the MIG-seq loci were generally lower than those at the coding loci, although the differences were not significant. Moreover, nucleotide diversities within populations of the two species were similar to each other, at approximately 0.005. Three and four population clusters were genetically recognized in D. cochinchinensis and D. nigrescens, respectively. Although the populations were differentiated from each other, the levels of differentiation among them, as measured by FST, were higher in D. cochinchinensis than in D. nigrescens. This indicates higher levels of gene flow between the populations in the latter species. We recommend using MIG-seq for quick surveys of genetic variation because it is cost-effective and results in smaller variance in the estimates of population genetic parameters.

Genetic variation within a species of parasitic nematode, Skrjabingylus chitwoodorum, in skunks.

Carnivores in the families Mustelidae and Mephitidae are essential hosts for the cranial roundworm genus Skrjabingylus. A high prevalence of Skrjabingylus chitwoodorum has been observed in the striped skunk, Mephitis mephitis. Genetic barcoding studies of other nematodes have successfully used the cytochrome oxidase I (COI) mitochondrial gene to analyze genetic variation and divergence. We tested the hypothesis that low population structuring occurs within S. chitwoodorum because M. mephitis is widespread across much of North America and has high levels of gene flow. We extracted DNA from 38 samples of Skrjabingylus removed from the sinuses of M. mephitis and one from the plains spotted skunk, Spilogale putorius interrupta, for amplification and sequencing of COI. Analysis of 492 base pairs confirmed all samples were S. chitwoodorum and showed low genetic divergence (1.0%) within Texas, but high haplotype diversity. Supporting our hypothesis, no obvious divergent lineages based on geographic location were recovered within the samples based on Maximum Likelihood analysis and median joining haplotype network analysis. In fact, samples of Skrjabingylus from New York and South Dakota showed little difference compared with samples from Texas.

Low genetic diversity and population differentiation in Thuja sutchuenensis Franch., an extremely endangered rediscovered conifer species in southwestern China

Thuja sutchuenensis Franch. is an extremely endangered conifer (Cupressaceae) species that is endemic to southwestern China. It was once considered extinct in the wild and was rediscovered after 100 years later in October 1999. Due to the habitat destruction from nature and humans, the population has decreased sharply and the distribution range is narrow. Thus there is an urgent need to evaluate genetic variation within this species in order to establish a feasible conservation strategy. In this study, we used six single-copy nuclear loci (4CL, LEAFY, NEEDLY, CC1147, GAPC and RABGGTB) to investigate the genetic diversity, population structure and dynamics of T. sutchuenensis based on a sampling of 109 individuals from 6 natural populations across the known extant geographical range. Our results indicated that the genetic diversity of T. sutchuenensis was relatively lower (πt = 0.00219, θwt = 0.00240) than that of other Cupressaceae species. Extensive gene flow (Nm ≥ 11.07) and low genetic differentiation among populations were detected. Extended Bayesian skyline plots revealed that the population size of T. sutchuenensis has remained constant through time. The low genetic diversity was believed to result primarily from genetic drift caused by habitat fragmentation and population dynamics caused by climate fluctuations. The low genetic differentiation among populations was largely attributed to high levels of gene flow and small geographic distribution. Based on the above analyses, we should first conserve all extant populations and their habitats to maintain its current genetic diversity. Besides these, artificial propagation efforts such as seed propagation, cuttage breeding or tissue culture methods should be made to rescue this rare and endangered tree species.

High genetic and chemical diversity of wild hop populations from Central Italy with signals of a genetic structure influenced by both sexual and asexual reproduction

In order to investigate the intraspecific diversity of wild Humulus lupulus (hop) in Central Italy, 12 populations were evaluated for their genetic polymorphism by means of 13 SSR loci together with six commercial cultivars as a reference. High levels of polymorphism were found across the populations, being 140 the number of multilocus genotypes over 159 samples analyzed. Moreover, the observed heterozygosity was higher than expected in most of the populations. High levels of gene flow were thus envisaged to occur within and among wild populations, and our sampling strategy allowed us to gain insights on the propagation modes of this species, i.e. clonal versus sexual propagation. Nevertheless, a genetic structure of populations with at least five genetically different clusters was disclosed. Private alleles were observed in both wild and cultivated hops. Chemical analysis of bittering and aromatic quality of female flowers from a subset of 8 wild populations revealed a high variability among plants, especially for essential oil components. Overall, the high variability of wild accessions here examined represent a valid source to be exploited in future breeding programs for new or improved hop cultivars development.

Evidence for Two Main Domestication Trajectories in Saccharomyces cerevisiae Linked to Distinct Bread-Making Processes

Production of leavened bread dates to the second millennium BCE. Since then, the art of bread making has developed, yet the evolution of bread-associated microbial species remains largely unknown. Nowadays, leavened bread is made either by using a pure commercial culture of the yeast Saccharomyces cerevisiae or by propagating a sourdough-a mix of flour and water spontaneously fermented by yeasts and bacteria. We studied the domestication of S.cerevisiae originating from industrial sources and artisanal sourdoughs and tested whether different bread-making processes led to population divergence. We found that S.cerevisiae bakery strains are polyphyletic with 67% of strains clustering into two main clades: most industrial strains were tetraploid and clustered with strains having diverse origins, including beer. By contrast, most sourdough strains were diploid and grouped in a second clade of strains having mosaic genomes and diverse origins, including fruits and natural environments. They harbored a higher copy number of genes involved in maltose utilization, and a high level of gene flow from multiple contributors was detected. Bakery strains displayed higher CO2 production than do strains from other domesticated lineages (such as beer and wine), revealing a specific phenotypic signature of domestication. Interestingly, industrial strains had a shorter fermentation onset than sourdough strains, which were better adapted to a sourdough-like environment, suggesting divergent selection by industrial and artisanal processes. Our results reveal that the domestication of bakery yeast has been accompanied by dispersion, hybridization, and divergent selection through industrial and artisanal processes.

Variation in shell morphology of the European pond turtle,Emys orbicularis, in fragmented central European populations

AbstractThe European pond turtle (Emys orbicularis) is a widely distributed freshwater species inhabiting much of Europe, but it is often in population decrease or is locally extinct. In this study, we sampled five central European populations, of which four were autochthonous and one was introduced outside the native range. Moreover, two of the native populations were relatively isolated and at the periphery of the species, range. Using the frequency of shell anomalies, a geometric morphometric framework and an analysis of fluctuating asymmetry, we aimed to determine the degree of morphological differentiation among different populations. Significantly, a smaller number of individuals with a malformed shell or scutes occurred in the native core range population, which potentially has a high level of gene flow (Hungary). Although neither canonical variate analysis nor the morphological disparity analysis showed distinct differences between populations, we found significantly higher shell asymmetry in the two marginal populations (Austria and Slovakia) compared with the core range populations. Our results might thus support the central–marginal hypothesis and indicate potential genetically based conservation problems owing to demographic bottlenecks and/or isolation in marginal populations.

Anthropogenic and natural barriers affect genetic connectivity in an Alpine butterfly.

Dispersal is a key biological process serving several functions including connectivity among populations. Habitat fragmentation caused by natural or anthropogenic structures may hamper dispersal, thereby disrupting genetic connectivity. Investigating factors affecting dispersal and gene flow is important in the current era of anthropogenic global change, as dispersal comprises a vital part of a species' resilience to environmental change. Using finescale landscape genomics, we investigated gene flow and genetic structure of the Sooty Copper butterfly (Lycaena tityrus) in the Alpine Ötz valley system in Austria. We found surprisingly high levels of gene flow in L. tityrus across the region. Nevertheless, ravines, forests, and roads had effects on genetic structure, while rivers did not. The latter is surprising as roads and rivers have a similar width and run largely in parallel in our study area, pointing towards a higher impact of anthropogenic compared with natural linear structures. Additionally, we detected eleven loci potentially under thermal selection, including ones related to membranes, metabolism, and immune function. This study demonstrates the usefulness of molecular approaches in obtaining estimates of dispersal and population processes in the wild. Our results suggest that, despite high gene flow in the Alpine valley system investigated, L. tityrus nevertheless seems to be vulnerable to anthropogenically-driven habitat fragmentation. With anthropogenic rather than natural linear structures affecting gene flow, this may have important consequences for the persistence of species such as the butterfly studied here in altered landscapes.

Low Genetic Variability in Bemisia tabaci MEAM1 Populations within Farmscapes of Georgia, USA.

Simple SummarySweetpotato whitefly, Bemisia tabaci Gennadius, is a serious pest of many agricultural crops worldwide. Numerous studies have examined the genetic structure of whitefly populations separated by geographical barriers; however, very few have assessed the population structure of B. tabaci at a farmscape level. A farmscape in this study is defined as heterogenous habitat with crop and non-crop areas spanning approximately 8 square kilometers. To assess the roles of farmscapes as drivers of B. tabaci genetic variation, thirty-five populations of the sweetpotato whitefly were collected from crop and non-crop plant species from fifteen farmscapes. Using mitochondrial COI gene sequences (mtCOI) and six nuclear microsatellite markers, the genetic diversity and genetic differentiation among collected B. tabaci MEAM1 populations were examined. Haplotype analysis using mtCOI sequences revealed the presence of a single B. tabaci MEAM1 haplotype across farmscapes of Georgia. Results from microsatellite markers further showed no significant genetic structuring among populations that corresponded to plant species or farmscapes from which they were collected. Annual whitefly population explosions and subsequent dispersal might have facilitated the persistence of a single panmictic B. tabaci population over all sampled farmscapes in this region. Bemisia tabaci is a whitefly species complex comprising important phloem feeding insect pests and plant virus vectors of many agricultural crops. Middle East–Asia Minor 1 (MEAM1) and Mediterranean (MED) are the two most invasive members of the B. tabaci species complex worldwide. The diversity of agroecosystems invaded by B. tabaci could potentially influence their population structure, but this has not been assessed at a farmscape level. A farmscape in this study is defined as heterogenous habitat with crop and non-crop areas spanning ~8 square kilometers. In this study, mitochondrial COI gene (mtCOI) sequences and six microsatellite markers were used to examine the population structure of B. tabaci MEAM1 colonizing different plant species at a farmscape level in Georgia, United States. Thirty-five populations of adult whiteflies on row and vegetable crops and weeds across major agricultural regions of Georgia were collected from fifteen farmscapes. Based on morphological features and mtCOI sequences, five species/cryptic species of whiteflies (B. tabaci MEAM1, B. tabaci MED, Dialeurodes citri, Trialeurodes abutiloneus, T. vaporariorum) were found. Analysis of 102 mtCOI sequences revealed the presence of a single B. tabaci MEAM1 haplotype across farmscapes in Georgia. Population genetics analyses (AMOVA, PCA and STRUCTURE) of B. tabaci MEAM1 (microsatellite data) revealed only minimal genetic differences among collected populations within and among farmscapes. Overall, our results suggest that there is a high level of gene flow among B. tabaci MEAM1 populations among farmscapes in Georgia. Frequent whitefly population explosions driven by a single or a few major whitefly-suitable hosts planted on a wide spatial scale may be the key factor behind the persistence of a single panmictic population over Georgia’s farmscapes. These population structuring effects are useful for delineating the spatial scale at which whiteflies must be managed and predicting the speed at which alleles associated with insecticide resistance might spread.

High connectivity and migration potentiate the invasion of Limnoperna fortunei (Mollusca: Mytilidae) in South America

Even after almost 30 years of Limnoperna fortunei introduction into South America, it is still unclear how the source and propagules are connected. Here, we present genetic evidence of population connectivity and gene flow of L. fortunei propagules from Asia into South America, proposing the main invasion routes into South America. To achieve that we expanded the sampling effort to cover all occurrence points of L. fortunei in South America. We sequenced the mtDNA COI gene and genotyped eight microsatellite loci (ML), and we evaluated the genetic source of the recently introduced population in Sobradinho hydroelectric power plant reservoir in Northeast Brazil. Our results revealed that China is the main genetic source of propagules for the Sobradinho population. We also found COI haplotypes and ML genotypes unique to South American populations, demonstrating a bridgehead effect likely caused by local mutation, adaptation, and admixture patterns that are maintained by high levels of gene flow among them. However, two genetic barriers were also detected. We concluded that L. fortunei is a well-established invader and is still rapidly expanding in Brazil, and the Amazon hydrographic basin is under an alarming threat of invasion.

Ecological and evolutionary responses of an arctic plant to variation in microclimate and soil

The arctic and alpine regions are predicted to experience some of the highest rates of climate change, and the arctic vegetation is expected to be especially sensitive to such changes. Understanding the ecological and evolutionary responses of arctic plant species to changes in climate is therefore a key objective. Geothermal areas, where natural temperature gradients occur over small spatial scales, and without many of the confounding environmental factors present in latitudinal and other gradient studies, provide a natural experimental setting in which to examine the response of arctic–alpine plants to increasing temperatures. To test the ecological and evolutionary response of the circumpolar alpine bistort Persicaria vivipara to temperature, we collected plant material and soil from areas with low, intermediate and high soil temperatures and grew them at three different temperatures in a three‐factorial growth chamber experiment. At higher experimental soil temperatures, sprouting was earlier and plants had more leaves. Sprouting was earlier in soil originating from intermediate temperature and plants had more leaves when grown in soil originating from low temperatures. We did not find evidence of local adaptation or genetic variation in reaction norms among plants originating from areas with low, intermediate and high soil temperature. Our findings suggest that the alpine bistort has a strong plastic response to warming, but that differences in soil temperature have not resulted in genetic differentiation. The lack of an observed evolutionary response may, for example, be due to the absence of temperature‐mediated selection on P. vivipara, the low rate of sexual recombination, or high levels of gene flow balancing differences in selection. When placed within the context of other studies, we conclude that arctic–alpine plant species often show strong plastic responses to spring warming, while evidence of evolutionary responses varies among species.

Analysis of genetic diversity and population structure in endangered Populus wulianensis based on 18 newly developed EST-SSR markers

Populus wulianensis is an endangered tree species endemic to Shandong Province, China. Genetic diversity assessments represent the basis and a prerequisite for protecting endangered species. In our study, a total of 116 individuals of P. wulianensis from 4 extant populations (3 wild populations and 1 artificial population that covered the entire geographic distribution of the species) were analyzed using 18 expressed sequence tag-simple sequence repeat (EST-SSR) markers to assess their genetic diversity and population structure. The 18 EST-SSR markers had high levels of polymorphisms (PIC = 0.698), and 202 alleles were amplified. The present study revealed high genetic diversity at the population level (Na = 4.847, NR = 3.000, HS = 0.624, HE = 0.611, I = 1.114, and PPL = 98.6%) and the species level (HT = 0.741). Private alleles were detected in all four populations (including the artificial population JYS). Negative inbreeding coefficients (FIS<0) indicated that the populations of P. wulianensis produced too many heterozygotes due to outbreeding and that there might be a risk of outbreeding depression. The AMOVA results showed that 19.05% and 80.95% of the total variation occurred among and within populations, respectively. Obvious genetic differentiation between populations (FST = 0.191) and a high level of gene flow (Nm = 2.566) were detected, indicating that gene flow is not the main cause of genetic differentiation among populations. The results of UPGMA cluster analysis, PCoA and structure analysis (ΔK = 4) showed that the 4 populations were clustered into four groups and suggested that the natural population ZHS gave rise to the artificial population JYS. The genetic bottleneck analysis results suggested that three populations (ZHS, JXS and JYS) recently experienced bottleneck events. These genetic results are of great significance for scientifically formulating conservation strategies for endangered P. wulianensis.

Genetic diversity of ten Moroccan populations of Tetraclinis articulata as revealed by Inter Simple Sequence Repeat (ISSR) markers

Tetraclinis articulata (Vahl) Masters is one of Morocco's most important forest species. It is also found occasionally in Malta and Spain, showing significant adaptability to different bio-climatic conditions. However, the species is being affected by anthropogenic fragmentation, logging and neglect from authorities, which could lead to the irretrievable loss of this resource. In this study, the genetic diversity and genetic structure of ten Moroccan populations of T. articulata were assessed. Fifteen Inter-Simple Sequence Repeat (ISSR) markers were used. These generated 271 polymorphic fragments with an average of 18.06 per primer and showed 79.59% of polymorphism. The 129 individuals revealed a high level of genetic diversity (Hs = 0.221; Ht = 0.254) and 85% of genetic variation within populations. However, the genetic differentiation level was low (Gst = 0.13), which is consistent with the lack of correlation between genetic and geographic distances revealed by the Mantel test, resulting in a high level of gene flow (Nm = 3.294). Based on PCoA and neighbour-joining methods, the ten populations clustered under the effect of continental and marine climates. Compared with other conifers, the current genetic diversity and the pattern of T. articulata population structure indicate an important gene pool requiring efficient conservation strategies.

Genetic population structure of the monogenean parasite Gyrodactylus thymalli and its host European grayling (Thymallus thymallus) in a large Norwegian lake

Understanding how populations are structured in space and time is a central question in evolutionary biology. Parasites and their hosts are assumed to evolve together, however, detailed understanding of mechanisms leading to genetic structuring of parasites and their hosts are lacking. As a parasite depends on its host, studying the genetic structure of both parasite and host can reveal important insights into these mechanisms. Here, genetic structure of the monogenean parasite Gyrodactylus thymalli and its host the European grayling (Thymallus thymallus) was investigated in 10 tributaries draining into the large Lake Mjøsa in Norway. The population genetic structure of spawning grayling was studied using microsatellite genotyping, while G. thymalli was studied by sequencing a mitochondrial DNA gene (dehydrogenase subunit 5). Two main genetic clusters were revealed in grayling, one cluster comprising grayling from the largest spawning population, while the remaining tributaries formed the second cluster. For both taxa, some genetic differentiation was observed among tributaries, but there was no clear isolation-by-distance signature. The structuring was stronger for the host than for the parasite. These results imply that moderate to high levels of gene flow occur among the sub-populations of both taxa. The high parasite exchange among tributaries could result from a lack of strong homing behavior in grayling as well as interactions among individual fish outside of the spawning season, leading to frequent mixing of both host and parasite.

Genome wide analysis reveals genetic divergence between Goldsinny wrasse populations

BackgroundMarine fish populations are often characterized by high levels of gene flow and correspondingly low genetic divergence. This presents a challenge to define management units. Goldsinny wrasse (Ctenolabrus rupestris) is a heavily exploited species due to its importance as a cleaner-fish in commercial salmonid aquaculture. However, at the present, the population genetic structure of this species is still largely unresolved. Here, full-genome sequencing was used to produce the first genomic reference for this species, to study population-genomic divergence among four geographically distinct populations, and, to identify informative SNP markers for future studies.ResultsAfter construction of a de novo assembly, the genome was estimated to be highly polymorphic and of ~600Mbp in size. 33,235 SNPs were thereafter selected to assess genomic diversity and differentiation among four populations collected from Scandinavia, Scotland, and Spain. Global FST among these populations was 0.015–0.092. Approximately 4% of the investigated loci were identified as putative global outliers, and ~ 1% within Scandinavia. SNPs showing large divergence (FST > 0.15) were picked as candidate diagnostic markers for population assignment. One hundred seventy-three of the most diagnostic SNPs between the two Scandinavian populations were validated by genotyping 47 individuals from each end of the species’ Scandinavian distribution range. Sixty-nine of these SNPs were significantly (p < 0.05) differentiated (mean FST_173_loci = 0.065, FST_69_loci = 0.140). Using these validated SNPs, individuals were assigned with high probability (≥ 94%) to their populations of origin.ConclusionsGoldsinny wrasse displays a highly polymorphic genome, and substantial population genomic structure. Diversifying selection likely affects population structuring globally and within Scandinavia. The diagnostic loci identified now provide a promising and cost-efficient tool to investigate goldsinny wrasse populations further.

Genetic signature of hybridization between Chinese spot-billed ducks and domesticated ducks.

In this study, we analyzed 93 whole genomes from Chinese spot-billed ducks (CSB), meat-type ducks (MET), and egg and dual purpose-type ducks (EDT) to characterize the genetic material flowing between the CSB and modern ducks. Using a frequency of shared identical-by-descent method, approximately 10.9Mb introgression segments containing 140 genes were identified showing the signatures of introgression between CSB and EDT. Meanwhile, nearly 10.6M introgression regions containing 149 genes were identified between CSB and MET. Based on the haplotypes tree of each segment, we found that the introgression between CSB and domesticatedducks was asymmetric with a high level of gene flow from domestic to CSB and a low level of migration in the opposite direction. Moreover, we identified several genes that were introgressions from CSB and showed the signature of positive selection, which may contribute to the breeding of modern ducks. Our results provide new insight into the evolution and breeding history of domestic ducks and may be useful for the future management of wild and domestic duck populations.

Genetic structure of recently fragmented suburban populations of European stag beetle.

Habitat loss and fragmentation due to urbanization can negatively affect metapopulation persistence when gene flow among populations is reduced and population sizes decrease. Inference of patterns and processes of population connectivity derived from spatial genetic analysis has proven invaluable for conservation and management. However, a more complete account of population dynamics may be obtained by combining spatial and temporal sampling. We, therefore, performed a genetic study on European stag beetle (Lucanus cervus L.) populations in a suburban context using samples collected in three locations and during the period 2002–2016. The sampling area has seen recent landscape changes which resulted in population declines. Through the use of a suite of F ST, clustering analysis, individual assignment, and relatedness analysis, we assessed fine scale spatiotemporal genetic variation within and among habitat patches using 283 individuals successfully genotyped at 17 microsatellites. Our findings suggested the three locations to hold demographically independent populations, at least over time scales of relevance to conservation, though with higher levels of gene flow in the past. Contrary to expectation from tagging studies, dispersal appeared to be mainly female‐biased. Although the life cycle of stag beetle suggests its generations to be discrete, no clear temporal structure was identified, which could be attributed to the varying duration of larval development. Since population bottlenecks were detected and estimates of effective number of breeders were low, conservation actions are eminent which should include the establishment of suitable dead wood for oviposition on both local and regional scales to increase (re)colonization success and connectivity among current populations.

The Genetic Structure of Nilaparvata lugens (Stal.) in Java Populations

The brown planthopper Nilaparvata lugens (Stal.) causes hopperburn in the rice field. The wing macropterous adults of this insect have capability for long distance flight. We aimed to analyze the genetic structure of six N. lugens populations in Java inferred from the combined COI-COII mitochondrial and ten loci of microsatellites markers. This study found low levels of nucleotides and high levels of haplotype diversity of the planthopper. The demographic test might indicate the genetic bottleneck history of N. lugens population in Java. The genetic diversity analyzed by using microsatellite markers also showed high levels of heterozygosity (Ho&gt;He) that indicated an isolated-breaking effect in the six populations in Java. Moreover, we found a homogenous genetic structure of N. lugens based on pairwise fixation indices (Fst) analyzes that appears to be maintained by high levels of gene flow and showed no correlation between genetic and geographical distance. Importantly, these studies also support accurate information of widely distributed and genetically intermixed among N. lugens across Asia populations. Thus, our results support the theory of long-distance migration among N. lugenspopulations. The genetic structure information of N. lugens in Java could support regional management, such as the new controlling strategies based on forecasting systems.

Divergence, gene flow, and the origin of leapfrog geographic distributions: The history of colour pattern variation in Phyllobates poison-dart frogs.

The geographic distribution of phenotypic variation among closely related populations is a valuable source of information about the evolutionary processes that generate and maintain biodiversity. Leapfrog distributions, in which phenotypically similar populations are disjunctly distributed and separated by one or more phenotypically distinct populations, represent geographic replicates for the existence of a phenotype, and are therefore especially informative. These geographic patterns have mostly been studied from phylogenetic perspectives to understand how common ancestry and divergent evolution drive their formation. Other processes, such as gene flow between populations, have not received as much attention. Here, we investigate the roles of divergence and gene flow between populations in the origin and maintenance of a leapfrog distribution in Phyllobates poison frogs. We found evidence for high levels of gene flow between neighbouring populations but not over long distances, indicating that gene flow between populations exhibiting the central phenotype may have a homogenizing effect that maintains their similarity, and that introgression between 'leapfroging' taxa has not played a prominent role as a driver of phenotypic diversity in Phyllobates. Although phylogenetic analyses suggest that the leapfrog distribution was formed through independent evolution of the peripheral (i.e. leapfrogging) populations, the elevated levels of gene flow between geographically close populations poise alternative scenarios, such as the history of phenotypic change becoming decoupled from genome-averaged patterns of divergence, which we cannot rule out. These results highlight the importance of incorporating gene flow between populations into the study of geographic variation in phenotypes, both as a driver of phenotypic diversity and as a confounding factor of phylogeographic inferences.

Population genetic structure and gene flow of rare and endangered Tetraena mongolica Maxim. revealed by reduced representation sequencing

BackgroundStudying population genetic structure and gene flow of plant populations and their influencing factors is of particular significance in the field of conservation biology, especially important for species such as rare and endangered plants. Tetraena mongolica Maxim. (TM), belongs to Zygophyllaceae family, a rare and endangered plant with narrow distribution. However, for the last decade, due to excessive logging, urban expansion, industrial and tourism development, habitat fragmentation and loss of natural habitats have become major threats to the population of endangered plants.ResultsIn this study, genetic diversity, population genetic structure and gene flow of TM populations were evaluated by reduced representation sequencing technology, and a total of more than 133.45 GB high-quality clean reads and 38,097 high-quality SNPs were generated. Analysis based on multiple methods, we found that the existing TM populations have moderate levels of genetic diversity, and very low genetic differentiation as well as high levels of gene flow between populations. Population structure and principal coordinates analysis showed that 8 TM populations can be divided into two groups. The Mantel test detected no significant correlation between geographical distances and genetic distance for the whole sampling. Moreover, the migration model indicated that the gene flow is more of a north to south migration pattern in history.ConclusionsThis study demonstrates that the present genetic structure is mainly due to habitat fragmentation caused by urban sprawl, industrial development and coal mining. Our recommendation with respect to conservation management is that, all 8 populations should be preserved as a whole population, rather than just those in the core area of TM nature reserve. In particular, the populations near the edge of TM distribution in cities and industrial areas deserve our special protection.