Significant Population Genetic Structure Research Articles

Genetic variability and population structure of two sympatric cownose rays Rhinoptera (Myliobatiformes, Rhinopteridae) in the Western Atlantic Ocean

Cownose rays Rhinoptera bonasus and R. brasiliensis, are species distributed along the coastal waters from eastern United States, Gulf of Mexico to Brazil. This study represents the most extensive evaluation to date of the genetic diversity and population genetic structure of R. bonasus across its distribution, and it is the first to investigate the population genetics of R. brasiliensis. We analyzed sequences of COI and Cytb genes for Rhinoptera bonasus (COI: 230, Cytb: 108) and R. brasiliensis (COI: 181, Cytb: 105) to investigate the genetic diversity and their relationship with environmental variables, genetic structure, as well as demographic parameters. We found that benthic temperature and current velocity were the most important environmental variables in genetic diversity. The global population structure reveals the presence of significant population genetic structure in both species. Bayesian clusters in BAPS were consistent with the segregation pattern observed for haplotype networks based on COI and Cytb markers for both species, which may respond to philopatry and temperature. These results will further improve management and conservation efforts for theses species of ecological and economic importance.

Spatial genetic structure of Ficus superba (Moraceae) in mainland and insular Singapore

Monoecious Ficus L. (Moraceae) species have putatively effective long-distance pollen dispersal and low population densities. The lack of spatially defined populations and the assumption of high gene flow led to the dearth of work on the Spatial Genetic Structure (SGS) of monoecious species. Furthermore, as only forest or inland species were studied, the effects of landscape heterogeneity and discontinuous habitats have been overlooked. To address this, Ficus superba (Miq.) Miq., a monoecious spatially aggregated coastal and insular species from Singapore, was studied to ascertain if population homogenisation could result from pollen flow even when the assumptions of spatial and landscape homogeneity were violated. Individuals were genotyped using dominant Amplified Fragment Length Polymorphism (AFLP) markers. Bayesian clustering software and Principal Component Analysis (PCA) were used to test for population genetic structure. SGS analyses and Mantel’s Tests were performed to test for the presence of significant fine-scale SGS and Isolation By Distance (IBD). Significant population genetic structure and SGS were found, with one mainland population more differentiated from the remaining insular and mainland populations. It is hypothesised that the spatial aggregation and landscape heterogeneity significantly distort gene flow through aggregated seed dispersal and greater impedance to pollen flow over land than sea. This calls into question the supposed dichotomy in gene flow characteristics of monoecious versus dioecious figs attributed to pollinator behaviour.

Large scale genetic landscape and population structure of Ethiopian sesame (Sesamum indicum L.) germplasm revealed through molecular marker analysis

Sesame (Sesamum indicum L.) plays a crucial role in Ethiopian agriculture, serving both subsistence and commercial purposes. However, our understanding of the extensive genetic diversity and population structure of Ethiopian sesame remains limited. To address this knowledge gap, we genotyped 368 Ethiopian sesame germplasms, categorizing into four distinct breeding groups: Accessions, landraces, improved varieties, and wild types, using a comprehensive set of 28 polymorphic markers, including 23 simple sequence repeat (SSR) and five Insertion-Deletion (InDel) markers. These markers ensured robust genomic representation, with at least two markers per linkage group. Our results unveiled substantial genetic diversity, identifying a total of 535 alleles across all accessions. On average, each locus displayed 8.83 alleles, with observed and expected heterozygosity values of 0.30 and 0.36, respectively. Gene Diversity and Polymorphic Information Content (PIC) were recorded at 0.37 and 0.35. The percentage of polymorphic loci varied significantly among breeding groups, ranging from 8.00% to 82.40%, indicating high diversity in accessions (82.4%), moderate diversity in improved varieties (31.20%) and landraces (29.60%), and limited diversity in wild types (8.00). Analysis of Molecular Variance (AMOVA) results emphasized significant genetic differentiation among populations, with substantial diversity (P ​< ​0.001) within each population. Approximately 8% of the entire genetic diversity could be attributed to distinctions among populations, while the larger proportion of genetic diversity (92%) resided within each individual sesame population, showcasing heightened diversity within each group. Our study's findings received support from both Bayesian clustering and Neighbor-joining (NJ) analysis, reaffirming the credibility of our genetic structure insights. Notably, Population structure analysis at its highest Δk value (k ​= ​2) revealed the existence of two primary genetic clusters, further subdivided into four sub-populations at k ​= ​4. Similarly, NJ analysis identified two prominent clusters, each displaying additional sub-clustering. In conclusion, our research provides a comprehensive understanding of genetic groups, subpopulations, and overall diversity within Ethiopian sesame populations. These findings underscore the significant genetic diversity and population structure within Ethiopian sesame germplasm collections. This genetic richness holds promise for breeding and conservation efforts, highlighting the importance of preserving genetic diversity to ensure adaptation to changing environments and meet the needs of farmers and consumers.

Out to sea: ocean currents and patterns of asymmetric gene flow in an intertidal fish species.

Passive dispersal via wind or ocean currents can drive asymmetric gene flow, which influences patterns of genetic variation and the capacity of populations to evolve in response to environmental change. The mangrove rivulus fish (Kryptolebias marmoratus), hereafter "rivulus," is an intertidal fish species restricted to the highly fragmented New World mangrove forests of Central America, the Caribbean, the Bahamas, and Florida. Mangrove patches are biological islands with dramatic differences in both abiotic and biotic conditions compared to adjacent habitat. Over 1,000 individual rivulus across 17 populations throughout its range were genotyped at 32 highly polymorphic microsatellites. Range-wide population genetic structure was evaluated with five complementary approaches that found eight distinct population clusters. However, an analysis of molecular variance indicated significant population genetic structure among regions, populations within regions, sampling locations within populations, and individuals within sampling locations, indicating that rivulus has both broad- and fine-scale genetic differentiation. Integrating range-wide genetic data with biophysical modeling based on 10years of ocean current data showed that ocean currents and the distance between populations over water drive gene flow patterns on broad scales. Directional migration estimates suggested some significant asymmetries in gene flow that also were mediated by ocean currents and distance. Specifically, populations in the center of the range (Florida Keys) were identified as sinks that received migrants (and alleles) from other populations but failed to export individuals. These populations thus harbor genetic variation, perhaps even from extirpated populations across the range, but ocean currents and complex arrangements of landmasses might prevent the distribution of that genetic variation elsewhere. Hence, the inherent asymmetry of ocean currents shown to impact both genetic differentiation and directional migration rates may be responsible for the complex distribution of genetic variation across the range and observed patterns of metapopulation structure.

Genomic epidemiology of Mycobacterium bovis infection in sympatric badger and cattle populations in Northern Ireland.

Bovine tuberculosis (bTB) is a costly, epidemiologically complex, multi-host, endemic disease. Lack of understanding of transmission dynamics may undermine eradication efforts. Pathogen whole-genome sequencing improves epidemiological inferences, providing a means to determine the relative importance of inter- and intra-species host transmission for disease persistence. We sequenced an exceptional data set of 619 Mycobacterium bovis isolates from badgers and cattle in a 100 km2 bTB 'hotspot' in Northern Ireland. Historical molecular subtyping data permitted the targeting of an endemic pathogen lineage, whose long-term persistence provided a unique opportunity to study disease transmission dynamics in unparalleled detail. Additionally, to assess whether badger population genetic structure was associated with the spatial distribution of pathogen genetic diversity, we microsatellite genotyped hair samples from 769 badgers trapped in this area. Birth death models and TransPhylo analyses indicated that cattle were likely driving the local epidemic, with transmission from cattle to badgers being more common than badger to cattle. Furthermore, the presence of significant badger population genetic structure in the landscape was not associated with the spatial distribution of M. bovis genetic diversity, suggesting that badger-to-badger transmission is not playing a major role in transmission dynamics. Our data were consistent with badgers playing a smaller role in transmission of M. bovis infection in this study site, compared to cattle. We hypothesize, however, that this minor role may still be important for persistence. Comparison to other areas suggests that M. bovis transmission dynamics are likely to be context dependent, with the role of wildlife being difficult to generalize.

Molecular identification and phylogeography of Gonipterus spp. (Coleoptera: Curculionidae) in Brazil

AbstractThe identification of the Gonipterus scutellatus complex species, known as the eucalyptus snout beetle, remained confusing for several years worldwide. Currently, the species Gonipterus platensis and Gonipterus pulverulentus are cited as present in Brazil. However, precise Gonipterus species identification, geographic distribution and economic importance in Brazil are unknown. Thus, our objectives were (i) to confirm the identification of Gonipterus species from different localities in Brazil using the sequencing of COI gene fragment, (ii) design a specific multiplex PCR marker for rapid molecular identification of Gonipterus species present in Brazil and (iii) apply a phylogeographic approach to assess the genetic diversity, demographic parameters and genetic structure of G. platensis population in Brazil. We confirmed the presence of G. platensis and G. pulverulentus in Brazilian territory. The species show different distribution, where G. platensis is widely distributed and G. pulverulentus is restricted to the south region. Gonipterus platensis populations are in spatial expansion, probably associated with the growth of Eucalyptus‐cultivated areas in Brazilian territory. Significant regional genetic population structure reinforces that the long dispersion processes of G. platensis within Brazilian territory is mediated by human activities. Thus, quarantine practices must be maintained and implemented to prevent new domestic and international introductions of Gonipterus specimens in Eucalyptus fields in Brazil.

Genetic Diversity and Population Structure of the Giant Mottled Eel, Anguilla marmorata Quoy &amp; Gaimard, 1824 in Central Vietnam

The giant mottled eel, Anguilla marmorata, is at high risk of extinction due to overfishing of glass eels and elvers to provide stock for eel farming. In Vietnam, information on the genetic diversity and population structure of this species, which is necessary for resource management, is limited. In order to address this paucity of information, sequencing of the entire mitochondrial control region (mtDNA) was carried out for 176 individuals collected from central Vietnam. The sequences were investigated using various genetic, phylogenetic and population analyses. A total of 165 distinct haplotypes were identified. The percentage of variation within and among populations was 99.26% and 0.74%, respectively. The fixation index was low (0.007) and not significant (p = 0.096). Therefore, panmixia and a lack of significant population genetic structuring seem likely for A. marmorata in central Vietnam. Most sampled eels were genetically similar to eels found in North Pacific populations (Japan, Taiwan and the Philippines), except for one sample from Quang Tri and two samples from Binh Dinh, which had high values of genetic identity (97% to 99%) with South Pacific populations (Tahiti, Fiji, New Caledonia and Papua New Guinea). Taken together, we suggest that A. marmorata from the North and South Pacific populations co-exist in central Vietnam.

Population structure, phylogeography and demographic history of Tenualosa ilisha populations in the Indian Ocean region inferred from mitochondrial DNA sequence variation

Understanding evolutionary processes reshaping the genetic structure in the context of environmental changes is an important component of sustainable management for the fisheries resources. In this study, we analyzed mitochondrial control region sequence to reveal population structure, phylogeography and demographic history of six populations of hilsa shad (Tenualosa ilisha) in the Indian Ocean regions (Andaman Sea, Bay of Bengal, Arabian Sea and Persian Gulf). High haplotype diversity was found in all of the populations of T. ilisha. The Analysis of Molecular Variance and FST comparisons revealed high level of genetic variation and divergence between populations of the Bay of Bengal and Arabian Sea. Four cryptic genetic barriers were found for the studied populations of T. ilisha, and the highest degree of population divergence was found between the Western Indian Ocean (Arabian Sea and Persian Gulf) and Eastern Indian Ocean (Andaman Sea and Bay of Bengal) regions based on the Voronoï tessellation of BARRIER analysis. The gene flow analysis detected almost no migration between Eastern and Western part of the Indian Ocean regions. Besides, one-way migration was found from Pakistan of Arabian Sea to Kuwait population of Persian Gulf. Demographic history of population expansion and long stable population varied for different populations of hilsa shad. Distinct cryptic genetic barriers, limited gene flows and complex evolutionary process resulted in a significant population genetic and phylogeographic structure, and intricate demographic histories of T. ilisha populations. Further, the study provided valuable insights for conserving and managing of this fishery resource in its broad geographical coverage.

Population genomic dynamics of mesopelagic lanternfishes Diaphus dumerilii, Lepidophanes guentheri, and Ceratoscopelus warmingii (Family: Myctophidae) in the Gulf of Mexico

Assessing the impacts of the Deepwater Horizon oil spill (DWHOS) on deep-sea fish assemblages of the Gulf of Mexico (GOM) has been hindered by an absence of baseline (pre-spill) data concerning the population genetic dynamics of these fishes. The lanternfishes (Myctophidae) are a speciose, yet understudied, taxonomic group, that comprise a significant portion of the global deep-sea biomass, making them integral members of meso- and bathy-pelagic food webs. Herein, we used a genomic approach (double digest restriction site associated DNA sequencing) to investigate the temporal genetic dynamics of three species of lanternfishes within the northern GOM in the region of the oil spill: Ceratoscopelus warmingii (N = 65, SNP = 1804), Diaphus dumerilii (N = 42, SNP = 2577), and Lepidophanes guentheri (N = 44, SNP = 3462). Fishes were sampled in 2011, and then again in 2015, and 2016, and genotyped using single nucleotide polymorphisms (SNP) markers. An additional 22 C. warmingii samples collected in 2014 from the western North Atlantic were used to assess genetic connectivity between these two regions. Overall, all three species were characterized by low levels of genetic diversity and high inbreeding coefficients, and within two of the three species (C. warmingii and L. guentheri), little (if any) evidence of population genetic structure was found within northern GOM waters. Conversely, significant intra-GOM genetic population structure was found for D. dumerilii, highlighting the need for a more robust population genetic survey of these fishes within the GOM to understand how populations of these fishes may respond to future environmental perturbations. In addition, significant genetic population structure was also found between sub-populations of C. warmingii from the northern GOM and western North Atlantic; with evidence of a mixture of two genetic populations co-occurring within the western North Atlantic. Given the potential for future environmental perturbations caused by expanding oil and gas extraction and climate change on GOM mesopelagic communities, rigorous population genetic assessments are required to understand the population dynamics of fishes and to safeguard the genetic diversity and resilience of this functionally important group of deep-sea fishes.

Micro-endemic species of snails and amphipods show population genetic structure across very small geographic ranges.

Understanding variation in population genetic structure, even across small distances and for species with extremely limited ranges, is critical for conservation planning and the development of effective management strategies for imperiled species. Organisms that occupy the same geographic extent can maintain different population structures, ranging from highly diverged to panmictic. Such differences can result from differences in biological characteristics such as dispersal ability or demographic history. We used microsatellite loci to evaluate population genetic structure and variation of four desert spring invertebrates having high to low dispersal ability: the lung snail Physa acuta, two species of gilled snails (Juturnia kosteri and Pyrgulopsis roswellensis; family Hydrobiidae) and the amphipod Gammarus desperatus. The study location represents entire species ranges for the micro-endemic hydrobiids and G. desperatus, while P. acuta is ubiquitous throughout much of North America. We found little evidence of significant population genetic structure for P. acuta and J. kosteri, but much more for P. roswellensis and G. desperatus. Our results demonstrate differences in habitat preference and/or dispersal ability between the species. This information provides insight into how gene flow shapes varying population genetic structure between species across small spatial scales (<100 km2). Most importantly, our results suggest that conservation agencies should not consider these micro-endemic species to be composed of single populations, but rather, that management plans for such species should account for population genetic variation across the species' ranges.

Population genetic structure and dispersal of Pinus occidentalis in the Dominican Republic by chloroplastic SSR, with implications for its conservation, management, and reforestation

Pinus occidentalis Swartz is the dominant species of forest ecosystems in the Dominican Republic, located between 200 and 3000 m above sea level, with extensive and overexploited natural populations. However, over the years, various restoration plans have been performed, which could affect the genetic structure of P. occidentalis. Despite being the species with the highest occurrence in the Dominican forests, there is no existing information on the genetic structure and molecular characterization among natural populations with limited information on both phenological and productive characterization. In this study, the genetic structure, diversity, and gene flow of the five P. occidentalis natural populations of the Dominican Republic were determined using microsatellite markers. A total of 145 individuals were genotyped with eight polymorphic chloroplastic microsatellites, producing an average of 41 haplotypes with high genetic diversity across populations (HE = 0.90). Significant population genetic structure was found between populations (FST = 0.123). These results reflect the impact of reforestation programs on natural populations and diluting the natural genetic signature. Analysis of population genetic data are, therefore, crucial for the breeding and conservation programs of P. occidentalis in the country.

Genetic variation in sea otters (Enhydra lutris) from the North Pacific with relevance to the threatened Southwest Alaska Distinct Population Segment

AbstractFor the sea otter (Enhydra lutris), genetic population structure is an area of research that has not received significant attention, especially in Southwest Alaska where that distinct population segment has been listed as threatened since 2005 pursuant to the U.S. Endangered Species Act. In this study, 501 samples from 14 locations from Prince William Sound, Alaska to the Commander Islands in Russia were analyzed for variation at 13 microsatellite loci. Our results indicate a high degree of genetic divergence among the 14 locations (FST = 0.120) with gene flow conforming to the isolation by distance (IBD) model (r2 = 0.491, p &lt; .05). The 14 sampling locations formed six geographic associations in clustering and ordination analyses that likely correspond to remnant population lineages: (1) Southcentral Alaska, (2) Kodiak and North Alaska Peninsula, (3) South Alaska Peninsula and Bristol Bay, (4) Eastern Aleutian, (5) Western Aleutian, and (6) the Commander Islands. Except for South Alaska Peninsula and Bristol Bay, these clusters closely agree with previously defined stock and management unit boundaries. Our results reveal significant genetic population structure and are generally congruent with current management strategies for the threatened Southwest Alaska distinct population segment.

Contemporary adaptive evolution in fragmenting river landscapes: evidence from the native waterflea Ceriodaphnia cornuta

Abstract The hypothesis that adaptive evolution in cities can occur on both contemporary and microgeographic scales was tested by investigating morphological, genetic and life history traits of waterflea Ceriodaphnia cornuta in an urbanized river. After the partial isolation from the Yingtao River by urban construction 16 years ago, the population of C. cornuta in the Shangyi Pond showed a different pattern of genotypic composition. Nuclear microsatellite markers revealed significant population genetic structure of C. cornuta among the Shangyi Pond, the Yingtao River and the Dianshan Lake in the upstream area. Migration analyses demonstrated little gene flow among different waters. In a common garden experiment, the changes in multivariate reaction norms provided evidence of local adaptation to dietary cyanobacteria in the river and lake populations. The results indicated that fragmenting river landscapes with urbanization resulted in the significant genetic differentiation and subsequent adaptive evolution in zooplankton populations on a short temporal and geographical scale.

DNA barcode identification of Conopomorpha cramerella (Snellen, 1904) (Lepidoptera: Gracillariidae) and other moths affecting cacao in Papua New Guinea

AbstractEconomically important cacao (Theobroma cacao Linnaeus 1753) plantations in South East Asia and Papua New Guinea (PNG) are significantly affected by the cocoa pod borer (CPB) moth. Species identity of the pest is attributed to Conopomorpha cramerella (Snellen 1904), a gracillariid moth endemic to Australasian and Oriental tropic regions that has evolved a host preference for introduced cacao. Suspected presence of cryptic CPB biotypes is largely unsupported by earlier genetic work but remains a concern to organisations developing species‐specific lure and/or control tools for managing this pest. We report the use of DNA barcoding to investigate population and species genetic diversity of CPB infecting cacao plantations in PNG at the eastern periphery of the pest's distribution. DNA barcodes from 94.4% of 179 moths from three disjunct PNG provinces (East Sepik, Bougainville and East New Britain) matched to reported C. cramerella sequence accessions. Genetic diversity among C. cramerella in PNG was limited to four closely related haplotypes, two of which were common in PNG and have previously been reported in the Malay Archipelago at different frequencies. We found evidence of significant population genetic structure between mainland and eastern offshore PNG provinces marked by a reduction of genetic diversity at the offshore provinces. We suggest C. cramerella populations in these offshore island provinces likely arose recently from a genetically depauperate cohort of founders from western sources. Ten moths were genetically unmatched to C. cramerella. Of these, six incidentally captured and degraded adults had novel unmatched DNA barcodes. Four larvae infesting cacao pods were genetically matched to Thaumatotibia zophophanes (Turner 1946) (Lepidoptera: Tortricidae) and an undefined Conopomorpha species distantly related to C. cramerella. The extent to which these two additional moth species affect the cacao industry in PNG (and potentially elsewhere) remains unknown. However, their low representation here (&lt;2.3% of samples) indicates they may be of lesser prominence than the widespread C. cramerella. Nevertheless, organisations designing and/or implementing CPB controls tailored specifically for C. cramerella will need to ensure empirical evidence of control efficiency is monitored with respect to species identity of the captured pests.

Rivers, not refugia, drove diversification in arboreal, sub-Saharan African snakes.

The relative roles of rivers versus refugia in shaping the high levels of species diversity in tropical rainforests have been widely debated for decades. Only recently has it become possible to take an integrative approach to test predictions derived from these hypotheses using genomic sequencing and paleo‐species distribution modeling. Herein, we tested the predictions of the classic river, refuge, and river‐refuge hypotheses on diversification in the arboreal sub‐Saharan African snake genus Toxicodryas. We used dated phylogeographic inferences, population clustering analyses, demographic model selection, and paleo‐distribution modeling to conduct a phylogenomic and historical demographic analysis of this genus. Our results revealed significant population genetic structure within both Toxicodryas species, corresponding geographically to river barriers and divergence times from the mid‐Miocene to Pliocene. Our demographic analyses supported the interpretation that rivers are indications of strong barriers to gene flow among populations since their divergence. Additionally, we found no support for a major contraction of suitable habitat during the last glacial maximum, allowing us to reject both the refuge and river‐refuge hypotheses in favor of the river‐barrier hypothesis. Based on conservative interpretations of our species delimitation analyses with the Sanger and ddRAD data sets, two new cryptic species are identified from east‐central Africa. This study highlights the complexity of diversification dynamics in the African tropics and the advantages of integrative approaches to studying speciation in tropical regions.

Comprehensive evidence for subspecies designations in Cook’s Petrel Pterodroma cookii with implications for conservation management

SummaryCook’s Petrel Pterodroma cookii is an endemic New Zealand seabird that has experienced a large range decline since the arrival of humans and now only breeds on two offshore islands (Te Hauturu-o-Toi/Little Barrier Island and Whenua Hou/Codfish Island) at the extreme ends of its former distribution. Morphological, behavioural, and mitochondrial cytochrome oxidase 1 (CO1) sequence data led a previous study to recognise the two extant populations as distinct conservation management units. Here, we further examine the genetic relationship between the extant populations using two nuclear introns (β-fibint7 and PAX). Using one mitochondrial locus (CO1), we also investigate the past distribution of a single nucleotide polymorphism (SNP) that differentiates the modern populations using bone and museum skins sourced from within its former range across New Zealand’s North and South Islands. We found significant population genetic structure between the two extant Cook’s Petrel populations for one of the two nuclear introns (β-fibint7). The mitochondrial DNA CO1 analysis indicated that the SNP variant found in the Codfish Island population was formerly widely distributed across both the North and South Islands, whereas the Little Barrier Island variant was detected only in North Island samples. We argue that these combined data support the recognition of the extant populations as different subspecies. Previous names for these taxa exist, thus Cook’s Petrel from Little Barrier Island becomes Pterodroma cookii cookii and Cook’s Petrel from Codfish Island becomes P. c. orientalis. Furthermore, we suggest that both genetic and non-genetic data should be taken into consideration when planning future mainland translocations. Namely, any translocations on the South Island should be sourced from Codfish Island and future translocations on the North Island should continue to be sourced from Little Barrier Island only.

Insights from Chloroplast DNA into the Progenitor-Derivative Relationship Between Campanula punctata and C. takesimana (Campanulaceae) in Korea

Of the nearly 40 endemics present on Ulleung Island, Campanula takesimana Nakai represents an anagenetically derived lineage of a continental progenitor, C. punctata Lam. Other than its low morphological divergence, little is known about the genetic diversity and population structure of the species pair or the geographical origin of C. takesimana. We sampled a total of 240 accessions in 22 populations, including one Dokdo Island population, of the two species, sequenced four noncoding chloroplast regions (rps16-trnK, trnQ-rps16, psbD-trnT, and psbM-trnD; 4482 bp), and assessed the genetic consequences of anagenetic speciation. Based on chloroplast DNA, we found substantially lower genetic diversity statistics for C. takesimana compared to its progenitor, significant population genetic structuring in insular derivative species, and significant molecular divergence between C. punctata and C. takesimana. Mutually exclusive haplotypes were found in the two species, and the haplotype network suggested that Ulleung Island haplotypes were derived from the Dokdo Island haplotype, which was originally derived from a C. punctata population in Bonghwa-gun, Gyeongsangbuk-do Province. This study pinpoints a very narrow geographical source area and suggests the potentially important role of Dokdo Island as an initial stepping stone for Ulleung Island endemics.

Unearthing the genetic divergence and gene flow of the earthworm Amynthas_YN2017 sp. (Oligochaeta: Megascolecidae) populations based on restriction site-associated DNA sequencing

Despite the ecological function of earthworms being of undeniable importance, little is known about their population genetic diversity, dispersal, and gene flow patterns. Here, we applied 769,957 single-nucleotide polymorphisms (SNPs) gathered by restriction site-associated DNA sequencing (RAD-seq) to unearth the genetic variability of populations of the earthworm Amynthas_YN2017 sp. collected from Western Yunnan, China. The neighbor-joining (NJ) tree method revealed that 30 individuals strongly clustered into three lineages (G2, G3, and G5 lineages) that coincided with the geographic distribution proximity of the sampling locations. There was a low level of genetic differentiation among these lineages with an average genetic differentiation (FST) value ranging from 0.080 to 0.135. Clustering analysis demonstrated a clear population genetic structure with a low level of admixture. There was only one migration edge in the population from the G3 lineage to the G2 lineage. Therefore, we presume that a reduction in gene flow caused by geographic isolation influences the population genetic differentiation of Amynthas_YN2017 sp. Additionally, the presence of river (Nujiang River) as geographical barrier is likely to have limited the gene flow. Overall, the large number of SNPs gathered by RAD-seq reveals a significant population genetic structure over a restricted geographic scale, highlighting that the RAD-seq approach could be used to explore the population phylogenetic relationships and population genetic diversity of earthworms.

Restricted connectivity and population genetic fragility in a globally endangered Hammerhead Shark

Vagile, large-bodied marine organisms frequently have wide range dispersion but also dependence on coastal habitats for part of their life history. These characteristics may induce complex population genetic structure patterns, with resulting implications for the management of exploited populations. The scalloped hammerhead, Sphyrna lewini, is a cosmopolitan, migratory shark in tropical and warm temperate waters, inhabiting coastal bays during parturition and juvenile development, and the open ocean as adults. Here, we investigated the genetic connectivity and diversity of S. lewini in the western Atlantic using large sample coverage (N = 308), and data from whole mitochondrial control region (mtCR) sequences and ten nuclear microsatellite markers We detected significant population genetic structure with both mtCR and microsatellites markers (mtCR: ΦST = 0.60; p < 0.001; microsatellites: Dest 0.0794, p = 0.001, FST = 0.046, p < 0.05), and isolation by distance (mtCR r = 0.363, p = 0.009; microsatellites markers r = 0.638, p = 0.007). Migration and gene flow patterns were asymmetric and female reproductive philopatry is postulated to explain population subdivisions. The notable population differentiation at microsatellites markers indicates low-levels of male-mediated gene flow in the western Atlantic. The overall effective population size was estimated as 299 (215–412 CI), and there was no evidence of strong or recent bottleneck effects. Findings of at least three management units, moderate genetic diversity, and low effective population size in the context of current overfishing calls for intensive management aimed at short and long-term conservation for this endangered species in the western Atlantic Ocean.

The first genetic assessment of wild and farmed ball pythons (Reptilia, Serpentes, Pythonidae) in southern Togo

The ball python (Python regius) is the world’s most commonly traded python species for the “exotic” pet industry. The majority of these live snakes are produced via a number of python farms in West Africa that have been in operation since the 1960s and involved with “ranching” operations since the 1990s. However, to date no thorough taxonomic review or genetic studies have been conducted within its range, despite the fact that the evaluation of a species’ genetic variability is generally considered mandatory for effective management. We used mtDNA sequence data and eight polymorphic microsatellite markers to assess the underlying population genetic structure and to test the potential of the nuclear markers to assign farm individuals to wild reference populations in southern Togo. Despite the relatively large distances between sample locations, no significant genetic population structure was found, either in mtDNA sequence data or in the microsatellite data. Instead, our data indicate considerable gene flow among the locations. The absence of a distinct population subdivision may have resulted from an anthropogenic driven admixture of populations associated with commercial wildlife trade activity in recent decades. Given the ongoing largely unregulated nature of the commercial ranching of ball pythons in West Africa, should a wild release component continue, as a first measure we recommend that the Management Authorities should develop an action plan with specific release protocols for python farms to minimise any potential negative conservation impacts resulting from admixture (genetic pollution) between farmed and wild individuals.