Significant Genetic Structure Research Articles

Density-dependent fitness, not dispersal movements, drives temporal variation in spatial genetic structure in dark-eyed juncos (Junco hyemalis).

Some studies have found that dispersal rates and distances increase with density, indicating that density-dependent dispersal likely affects spatial genetic structure. In an 11-year mark-recapture study on a passerine, the dark-eyed junco, we tested whether density affected dispersal distance and/or fine-scale spatial genetic structure. Contrary to expectations, we found no effect of predispersal density on dispersal distance or the proportion of locally produced juveniles returning to the population from which they hatched. However, even though density did not affect dispersal distance or natal return rates, we found that density still did affect spatial genetic structure. We found significant positive spatial genetic structure at low densities of (postdispersal) adults but not at high densities. In years with high postdispersal (adult) densities that also had high predispersal (juvenile) densities in the previous year, we found negative spatial genetic structure, indicating high levels of dispersal. We found that density also affected fitness of recruits, and fitness of immigrants, potentially linking these population parameters with the spatial genetic structure detected. Immigrants and recruits rarely nested in low postdispersal density years. In contrast, in years with high postdispersal density, recruits were common and immigrants had equal success to local birds, so novel genotypes diluted the gene pool and effectively eliminated positive spatial genetic structure. In relation to fine-scale spatial genetic structure, fitness of immigrants and new recruits is poorly understood compared to dispersal movements, but we conclude that it can have implications for the spatial distribution of genotypes in populations.

Population genetic structure of Zeugodacus tau species complex in Thailand

AbstractThe tephritid fruit fly Zeugodacus tau is a serious agriculture pest, especially of cucurbits in Thailand, where it is classified as a complex species of nine siblings (Z. tau A, B, C, D, E, F, G, I and J). Based on single‐strand conformation polymorphism (SSCP) analysis, 33 distinct mitochondrial cytochrome c oxidase subunit I (mtCOI) haplotypes were found in three sibling species, Z. tau A, C and J, in Thailand. Genetic structure analysis of the population revealed relatively large genetic differences among these sibling species, reflecting a tendency toward speciation. The maximum likelihood tree and median‐joining network reconstructed from the mtCOI sequences of 33 haplotypes supported the separation of these three sibling species within the Z. tau complex. The three‐level hierarchical analysis of molecular variance based on geographical regions and the Mantel test for isolation‐by‐distance showed significant genetic structuring of the Z. tau complex in Thailand. However, the genetic differentiation among geographical groups was rather low, which may be reasonably explained by natural and human mediated dispersal, as well as host associated differentiation. The SSCP analysis on the population genetic structure of Z. tau species complex in the present study should benefit pest management.

Genetic differentiation and asymmetric gene flow among Carpathian brown bear (Ursus arctos) populations-Implications for conservation of transboundary populations.

The abundance and distribution of large carnivores in Europe have been historically reduced. Their recovery requires multilevel coordination, especially regarding transboundary populations. Here, we apply nuclear and mitochondrial genetic markers to test for admixture level and its impact on population genetic structure of contemporary brown bears (Ursus arctos) from the Eastern, Southern, and Western Carpathians. Carpathian Mountains (Europe). Nearly 400 noninvasive brown bear DNA samples from the Western (Poland) and Eastern Carpathians (Bieszczady Mountains in Poland, Slovakia, Ukraine) were collected. Together with DNA isolates from Slovakia and Romania, they were analyzed using the set of eight microsatellite loci and two mtDNA regions (control region and cytochrome b). A set of 113 individuals with complete genotypes was used to investigate genetic differentiation across national boundaries, genetic structuring within and between populations, and movement between populations. Transboundary brown bear subpopulations (Slovakia and Poland) did not show significant internal genetic structure, and thus were treated as cohesive units. All brown bears from the Western Carpathians carried mitochondrial haplotypes from the Eastern lineage, while the Western lineage prevailed in the brown bears from the Bieszczady Mountains. Despite similar levels of microsatellite variability, we documented significant differentiation among the studied populations for nuclear markers and mtDNA. We also detected male‐biased and asymmetrical movement into the Bieszczady Mountains population from the Western Carpathians. Our findings suggest initial colonization of the Western Carpathians by brown bears possessing mtDNA from the Eastern lineage. Genetic structuring among populations at microsatellite loci could be a result of human‐mediated alterations. Detected asymmetric gene flow suggests ongoing expansion from more abundant populations into the Bieszczady Mountains and thus supports a metapopulation model. The knowledge concerning this complex pattern can be implemented in a joint Carpathian brown bear management plan that should allow population mixing by dispersing males.

Genetic structure, origin, and connectivity between nesting and foraging areas of hawksbill turtles of the Yucatan Peninsula: A study for conservation and management

Abstract Anthropogenic activities have resulted in declines in many marine turtle populations. Their complex life cycle (e.g. female philopatry, hatchling migration, adult movements between breeding and foraging areas) makes it difficult to fully understand some of the biological implications of human impacts on their populations, but genetic tools can play a major role in understanding population dynamics and thus improve conservation and management strategies. Using the mitochondrial DNA control region, this study examines the composition, population structure, and connectivity between rookeries and foraging aggregations, in addition to their relationship with Atlantic rookeries and foraging areas of the hawksbill turtle in the Yucatan Peninsula. Haplotype composition of rookeries showed EiA22, EiA39, and EiA41 as endemic haplotypes and revealed a segregation between the Gulf of Mexico and the Yucatan and Quintana Roo rookeries, defining two management units. Foraging aggregations present 15 haplotypes, some common for Atlantic and others for Mexican rookeries. Considering the Gulf of Mexico versus the Mexican Caribbean, significant population genetic structure was revealed, inferring a differential recruitment of hawksbill turtles. Rookery‐centric mixed‐stock analysis reveals a high contribution of Mexican turtles to local foraging aggregations, principally in the Gulf of Mexico. Foraging‐ground‐centric mixed‐stock analysis showed that the Gulf of Mexico foraging aggregation is predominantly composed of individuals from local rookeries, whereas Mexican Caribbean foraging groups have a mixed composition with individuals from Barbados, Brazil, and Puerto Rico rookeries. The connectivity between rookeries and foraging aggregations suggests that the ocean currents and swimming behaviour influence the distribution of hawksbill turtles. Our results highlighted the importance in identifying management units in nesting and foraging areas to develop monitoring and management programmes at appropriate geographic scales. In addition, understanding turtle habitat connectivity will allow for prioritized conservation actions considering particular threats, emphasizing the need for both national and international collaboration for conservation of this endangered species.

The Sarracenia alata pitcher plant system and obligate arthropod inquilines should be considered an evolutionary community

AbstractAimThe Sarracenia alata pitcher plant and inquiline species comprise an ecological community. These inquilines span the continuum in their ecological association with the host pitcher plant, from species that contain little‐to‐no interaction with the plant to species that are completely dependent on the plant for their entire life cycle. We are interested in testing if degree of ecological dependence is positively correlated with a shared evolutionary history, and in identifying members of this community that display concordant phylogeographic structure.LocationSoutheastern United States.MethodsWe collected genome‐wide sequence data from a set of arthropods that are ecologically associated with the plant to estimate comparative phylogeographic patterns among the species. We estimated species tree distributions from biallelic unlinked SNP data and used phylogeographic concordance factors (PCFs) to test degree of phylogeographic concordance among community members. In addition, for each species we conducted an analysis of molecular variance and calculated FST values to identify population genetic structure across the landscape, and compared these traditional values to the tree‐based approach.ResultsObligate members of the pitcher plant community display concordant phylogeographic patterns, suggesting their ecological dependence has manifested itself into a shared evolutionary history. In contrast, two spider species do not contain significant population genetic structure or similar phylogeographic histories, highlighting their loose association with the host pitcher plant.Main conclusionThe S. alata pitcher plant system should be considered an evolutionary community, where multiple members sharing strong ecological interactions also display concordant phylogeographic structure. This work demonstrates that PCFs provide an important quantitative measure into assessing community structure and illustrates how simulations can be used to assess significance of shared patterns of phylogeographic structure across the landscape.

The effect of population density on gene flow between adult trees and the seedling bank in Abies alba Mill.

Populations of smaller effective sizes or subjected to strong environmental filtering have a higher risk of stochastic changes in their genetic properties. This study tested the hypothesis that reducing the density of parent trees combined with environmental filtering during the stage of regeneration establishment affects gene flow between the parent and offspring populations of Abies alba Mill. The genetic variation and spatial genetic structure of parent trees and seedlings were compared in the Western Carpathians (southern Poland) in 27 stands with varying adult tree and regeneration densities. The analysis comprised 1592 individuals and was based on five nuclear microsatellite markers. The proportion of stands with significant spatial genetic structure in the adult tree and seedling cohorts increased as the density of adult trees decreased. The genetic differentiation between adult trees and seedlings expressed by the fixation index FST was between 0.005 and 0.021 and increased as the density of adult trees decreased but was not correlated with the seedling abundance. At the within-stand level, the analysis revealed shifts in the average number of alleles per locus (between − 15% and + 28%), the observed heterozygosity (between − 25% and + 20%) and expected heterozygosity (between − 8% and + 11%) between the populations of adult trees and seedlings. It was concluded that in mixed stands with densities of A. alba trees about 50 adult individuals per ha, there may be some risk of reduced effective population size and disturbed vertical gene flow, but significant shifts in the level of genetic variation are less likely.

Study on genetic structure differences and adjustment strategies in different areas of China

Objective: To describe the genetic structure of populations in different areas of China, and explore the effects of different strategies to control the confounding factors of the genetic structure in cohort studies. Methods: By using the genome-wide association study (GWAS) on data of 4 500 samples from 10 areas of the China Kadoorie Biobank (CKB), we performed principal components analysis to extract the first and second principal components of the samples for the component two-dimensional diagram generation, and then compared them with the source of sample area to analyze the characteristics of genetic structure of the samples from different areas of China. Based on the CKB cohort data, a simulation data set with cluster sample characteristics such as genetic structure differences and extensive kinship was generated; and the effects of different analysis strategies including traditional analysis scheme and mixed linear model on the inflation factor (λ) were evaluated. Results: There were significant genetic structure differences in different areas of China. Distribution of the principal components of the population genetic structure was basically consistent with the geographical distribution of the project area. The first principal component corresponds to the latitude of different areas, and the second principal component corresponds to the longitude of different areas. The generated simulation data showed high false positive rate (λ=1.16), even if the principal components of the genetic structure was adjusted or the area specific subgroup analysis was performed, λ could not be effectively controlled (λ>1.05); while, by using a mixed linear model adjusting for the kinship matrix, λ was effectively controlled regardless of whether the genetic structure principal component was further adjusted (λ=0.99). Conclusions: There were large differences in genetic structure among populations in different areas of China. In molecular epidemiology studies, bias caused by population genetic structure needs to be carefully treated. For large cohort data with complex genetic structure and extensive kinship, it is necessary to use a mixed linear model for association analysis.

Persistence of remnant patches and genetic loss at the distribution periphery in island and mainland populations of the quokka

Understanding the spatial structure of populations is important in developing effective management options for threatened species, and for managing habitat connectivity for metapopulation function, and for demographic and genetic heterogeneity. We used genetic information to investigate the structure of populations of the quokka, Setonix brachyurus, in south-west Western Australia. We hypothesised that movement between known populations would be relatively rare and result in significant genetic structuring. Genetic analyses from 412 adult individuals at 14 nuclear markers (microsatellite) from 33 sampling locations identified structure, diversity and spatial separation of quokkas across their mainland distribution and on two islands. We identified nine inferred (K = 9) populations of quokka that would be otherwise difficult to define with standard ecological techniques. The highest genetic diversity was evident in a large central population of quokka in the southern forest area and genetic diversity was lower at the peripheries of the distribution. The Rottnest Island population contained 70% of the genetic diversity of the mainland populations but the genetic diversity of animals on Bald Island was markedly lower. Populations of quokka in the northern jarrah forest were the only ones to show evidence of recent or long-term population bottlenecking. Of particular interest was the recently identified population at the Muddy Lakes area (the only remaining locality on the Swan Coastal Plain), which was identified as being genetically associated with the southern forest population. Overall, spatial and population cluster analysis showed small insular populations in the northern jarrah forest area, but in the southern forests there appears to be a large panmictic population.

Phylogeographic study on a cryptic dojo loach species (Misgurnus sp. Type I) in Japan

Event Abstract Back to Event Phylogeographic study on a cryptic dojo loach species (Misgurnus sp. Type I) in Japan Ryuya Okada1*, Keigo Morita1, Taichiro Toyama2, Hiroshi Onozato3, Keisuke Takata4 and Tadao Kitagawa1 1 Faculty of Agriculture, Kindai University, Japan 2 Other, Japan 3 Other, Japan 4 Faculty of Science, Shinshu University, Japan Recent genetic study revealed that the Japanese population of the dojo loach (Cypriniformes: Cobitidae: Misgurnus anguillicaudatus species complex) included a cryptic species distributed in discontinuous restricted areas in certain parts of north-eastern Japan (Misgurnus sp. Type I, hereafter called as Type I loach), and a common dojo loach species widely distributed throughout the Japanese Archipelago (Misgurnus anguillicaudatus, hereafter called as Type II loach). Type I loach is considered a relic species of the ancestral dojo loach type and its phylogeographic information can provide crucial perspective on the formation of Japanese archipelago and its fauna. However, its original distribution range is ambiguous due to the recent artificially created species and existence of hybrid populations involving Type II loach. In this study, we conducted comprehensive sample collection throughout the possible species’ range. Furthermore, we performed genetic analysis using the cytochrome b (cyt b) gene sequence of mtDNA to reveal the phylogeographic pattern of Type I loach. Mitochondrial haplotypes originating from Type I loach were detected from 34 populations from an eastern part of Honshu Island and Hokkaido Island. In the phylogenetic tree, the haplotypes of the Type I loach formed two major clades, namely consisting of haplotypes from populations in eastern Honshu’s Pacific slope and those from other areas (averaged sequence divergence was about 9 %). This intimated long-term isolation of the populations between the regions. Furthermore, the eastern Pacific Honshu clade consisted of three subclades, corresponding well with their geographic proximity. Similarly, the other clade consisted of three subclades; however, two subclades were haplotype admixtures detected from geographically distant areas. Since some haplotypes were commonly detected ranging from northern Honshu to Hokkaido even across the major faunal boundary line between the Honshu and Hokkaido Island (Brakiston Line), we found that the current distribution patterns are strongly affected by artificial introductions. No significant geographical genetic structures in Hokkaido Island populations were observed, suggesting that their origin was artificial. The hybrid origin populations’ distribution pattern corresponded with the areas related to artificial introductions. Conclusively, artificial disturbances within natural distribution are likely contributors of hybrid population formation. Keywords: mitochondrial DNA, Relic, Native population, Introduced population, hybridization, Hokkaido Conference: XVI European Congress of Ichthyology, Lausanne, Switzerland, 2 Sep - 6 Sep, 2019. Presentation Type: Poster Topic: TAXONOMY, PHYLOGENY AND ZOOGEOGRAPHY Citation: Okada R, Morita K, Toyama T, Onozato H, Takata K and Kitagawa T (2019). Phylogeographic study on a cryptic dojo loach species (Misgurnus sp. Type I) in Japan. Front. Mar. Sci. Conference Abstract: XVI European Congress of Ichthyology. doi: 10.3389/conf.fmars.2019.07.00118 Copyright: The abstracts in this collection have not been subject to any Frontiers peer review or checks, and are not endorsed by Frontiers. They are made available through the Frontiers publishing platform as a service to conference organizers and presenters. The copyright in the individual abstracts is owned by the author of each abstract or his/her employer unless otherwise stated. Each abstract, as well as the collection of abstracts, are published under a Creative Commons CC-BY 4.0 (attribution) licence (https://creativecommons.org/licenses/by/4.0/) and may thus be reproduced, translated, adapted and be the subject of derivative works provided the authors and Frontiers are attributed. For Frontiers’ terms and conditions please see https://www.frontiersin.org/legal/terms-and-conditions. Received: 12 May 2019; Published Online: 14 Aug 2019. * Correspondence: Dr. Ryuya Okada, Faculty of Agriculture, Kindai University, Nara, Japan, cop1008bz@yahoo.co.jp Login Required This action requires you to be registered with Frontiers and logged in. To register or login click here. Abstract Info Abstract The Authors in Frontiers Ryuya Okada Keigo Morita Taichiro Toyama Hiroshi Onozato Keisuke Takata Tadao Kitagawa Google Ryuya Okada Keigo Morita Taichiro Toyama Hiroshi Onozato Keisuke Takata Tadao Kitagawa Google Scholar Ryuya Okada Keigo Morita Taichiro Toyama Hiroshi Onozato Keisuke Takata Tadao Kitagawa PubMed Ryuya Okada Keigo Morita Taichiro Toyama Hiroshi Onozato Keisuke Takata Tadao Kitagawa Related Article in Frontiers Google Scholar PubMed Abstract Close Back to top Javascript is disabled. Please enable Javascript in your browser settings in order to see all the content on this page.

Phylogeography and genetic connectivity of the marine macro-alga Sargassum ilicifolium (Phaeophyceae, Ochrophyta) in the northwestern Pacific1.

The evolutionary influences of historical and contemporary factors on the population connectivity and phylogeographic structure of a brown seaweed, Sargassum ilicifolium, were elucidated using the nuclear ITS2 and mitochondrial COI markers for the collections newly sampled within its distribution range in the northwestern Pacific (NWP). Significant genetic structure at variable levels was identified between populations (pairwise FST ) and among populations grouped by geographical proximity (ΦCT among regions). The adjacent groups of populations with moderate structure revealed from AMOVA appeared to have high genetic connectivity. However, a lack of genealogical concordance with the geographic distribution was uncovered for S.ilicifolium from the NWP. Such genetic homogeneity is interpreted as a result of the interaction between postglacial recolonization and dynamic oceanic current regimes in the region. Two separated glacial refugia, the South China Sea and the Okinawa Trough, in the marginal seas of east China were recognized based on the presence of endemic haplotypes and high haplotype diversity in the populations at southern China and northeast of Taiwan. Populations persisting in these refugia may have served as the source for recolonization in the NWP with the rise of sea level during the warmer interglacial periods. The role of oceanic currents in maintaining genetic connectivity of S.ilicifolium in the region was further corroborated by the coherence between the direction of oceanic currents and that of gene flow, especially along the eastern coast of Taiwan. This study underlines the interaction between historical postglacial recolonization and contemporary coastal hydrodynamics in contributing to population connectivity and distribution for this tropical seaweed in the NWP.

Noninvasive sampling reveals population genetic structure in the Royle's pika, Ochotona roylei, in the western Himalaya.

Understanding population genetic structure of climate‐sensitive herbivore species is important as it provides useful insights on how shifts in environmental conditions can alter their distribution and abundance. Herbivore responses to the environment can have a strong indirect cascading effect on community structure. This is particularly important for Royle's pika (Lagomorpha: Ochotona roylei), a herbivorous talus‐dwelling species in alpine ecosystem, which forms a major prey base for many carnivores in the Himalayan arc. In this study, we used seven polymorphic microsatellite loci to detect evidence for recent changes in genetic diversity and population structure in Royle's pika across five locations sampled between 8 and 160 km apart in the western Himalaya. Using four clustering approaches, we found the presence of significant contemporary genetic structure in Royle's pika populations. The detected genetic structure could be primarily attributed to the landscape features in alpine habitat (e.g., wide lowland valleys, rivers) that may act as semipermeable barriers to gene flow and distribution of food plants, which are key determinants in spatial distribution of herbivores. Pika showed low inbreeding coefficients (F IS) and a high level of pairwise relatedness for individuals within 1 km suggesting low dispersal abilities of talus‐dwelling pikas. We have found evidence of a recent population bottleneck, possibly due to effects of environmental disturbances (e.g., snow melting patterns or thermal stress). Our results reveal significant evidence of isolation by distance in genetic differentiation (F ST range = 0.04–0.19). This is the first population genetics study on Royle's pika, which helps to address evolutionary consequences of climate change which are expected to significantly affect the distribution and population dynamics in this talus‐dwelling species.

Genetic structure and diversity in Brazilian populations of Anastrepha obliqua (Diptera: Tephritidae).

Anastrepha obliqua (Macquart), the West Indian fruit fly, is one of the most economically important pest species in the Neotropical region. It infests an extensive range of host plants that include over 60 species. The geographic range of A. obliqua is from northern Mexico to southern Brazil and includes the Caribbean Islands. Previous molecular studies have revealed significant genetic structure among populations. We used sequences from a fragment of the mitochondrial protein-coding gene cytochrome c oxidase I to estimate structure and genetic diversity of A. obliqua populations from Brazil. We analyzed a total of 153 specimens from the Amazon Forest, Atlantic Forest, Cerrado, and Caatinga biomes. Our study revealed weak genetic structure among the A. obliqua Brazilian populations sampled. Collections from the Amazon Forest had similar haplotype diversity compared to previously reported estimates for collections from the Caribbean and both populations are also closely related to each other, thus challenging the hypothesis that A. obliqua originated in the Caribbean and then moved to other regions of the Americas. Therefore, further evidence is necessary to draw a definite conclusion about the putative center of origin for A. obliqua. Additionally, we suggest a putative historical migration from the west to the east for the A. obliqua Brazilian populations, which could explain the high genetic diversity for this fly in the Amazon Forest and low genetic diversity in the other Brazilian biomes.

Gene expression is implicated in the ability of pikas to occupy Himalayan elevational gradient.

Species are shifting their ranges due to climate change, many moving to cooler and higher locations. However, with elevation increase comes oxygen decline, potentially limiting a species’ ability to track its environment depending on what mechanisms it has available to compensate for hypoxic stress. Pikas (Family Ochotonidae), cold-specialist small mammal species, are already undergoing elevational range shifts. We collected RNA samples from one population of Ochotona roylei in the western Himalaya at three sites– 3,600, 4,000, and 5,000 meters–and found no evidence of significant population genetic structure nor positive selection among sites. However, out of over 10,000 expressed transcripts, 26 were significantly upregulated at the 5,000 m site and were significantly enriched for pathways consistent with physiological compensation for limited oxygen. These results suggest that differences in gene expression may play a key role in enabling hypoxia tolerance on this local scale, indicating elevational flexibility that may facilitate successful range shifts in response to climate change.

Genetic diversity is retained in a bottlenecked Cinereous Vulture population in Turkey

Vulture populations worldwide have suffered precipitous declines in recent decades. The Cinereous Vulture Aegypius monachus, a highly philopatric scavenger distributed across southern Europe and the central Asian plateau, is threatened in many parts of its range. Turkey holds the second largest population of this species in the Western Palaearctic, but there has been no research on its genetic structure and the possible implications of this structure for the future of the species. Here we report nuclear diversity and relatedness determined by short tandem repeat genotyping of 81 individuals from the four largest colonies. Our results demonstrated no significant genetic structuring, suggesting a single panmictic metapopulation connected by frequent dispersal. Furthermore, we show that the study population has retained moderate levels of genetic diversity, despite passing through a recent demographic bottleneck. We estimated the effective population size to be 112 individuals (95% confidence interval 74–201). Our results imply that the observed lack of increase in population size since the 1990s has not been caused by lowered fitness due to genetic inbreeding but rather by increased mortality via demographic processes. In the short term, we suggest that conservation efforts should treat the Turkish subpopulations as a single management unit and aim to increase population size through effective protection, especially during the breeding season.

Geography and Environment Shape Landscape Genetics of Mediterranean Alpine Species Silene ciliata Poiret. (Caryophyllaceae).

The study of the drivers that shape spatial genetic structure across heterogeneous landscapes is one of the main approaches used to understand population dynamics and responses in changing environments. While the Isolation-by-Distance model (IBD) assumes that genetic differentiation increases among populations with geographical distance, the Isolation-by-Resistance model (IBR) also considers geographical barriers and other landscape features that impede gene flow. On the other hand, the Isolation-by-Environment model (IBE) explains genetic differentiation through environmental differences between populations. Although spatial genetic studies have increased significantly in recent years, plants from alpine ecosystems are highly underrepresented, even though they are great suitable systems to disentangle the role of the different factors that structure genetic variation across environmental gradients. Here, we studied the spatial genetic structure of the Mediterranean alpine specialist Silene ciliata across its southernmost distribution limit. We sampled three populations across an altitudinal gradient from 1850 to 2400 m, and we replicated this sample over three mountain ranges aligned across an E-W axis in the central part of the Iberian Peninsula. We genotyped 20 individuals per population based on eight microsatellite markers and used different landscape genetic tools to infer the role of topographic and environmental factors in shaping observed patterns along the altitudinal gradient. We found a significant genetic structure among the studied Silene ciliata populations which was related to the orography and E-W configuration of the mountain ranges. IBD pattern arose as the main factor shaping population genetic differentiation. Geographical barriers between mountain ranges also affected the spatial genetic structure (IBR pattern). Although environmental variables had a significant effect on population genetic diversity parameters, no IBE pattern was found on genetic structure. Our study reveals that IBD was the driver that best explained the genetic structure, whereas environmental factors also played a role in determining genetic diversity values of this dominant plant of Mediterranean alpine environments.

Two speed invasion: assisted and intrinsic dispersal of common mynas over 150 years of colonization

AbstractAimDespite the common myna's widespread distribution, and the significant impact it has caused in parts of its non‐native range, there have been no comprehensive genomic studies of its invasion of any region. We aimed to characterize the common myna invasion of the Australian continent to understand its population genetic landscape, introduction history, dispersal characteristics, and the interconnectedness between different source populations and invasive fronts.LocationCommon mynas from 26 geographical locations spanning the Australian continent were utilized in this study.TaxonCommon myna (Acridotheres tristis).MethodsWe used a reduced genome representation method (DArTseq) to generate thousands of single nucleotide polymorphism markers in 462 common mynas. We then applied population genomic techniques to identify the common myna's population attributes such as gene flow, genetic diversity, and effective dispersal, all of which are critical for understanding geographical range expansion of pest species.ResultsWe found significant genetic structuring across the common myna's Australian distribution, indicating limited levels of effective dispersal amongst the populations founded from historic introductions in the 19th century. The historic introduction points were found to be genetically distinct, such that in the region on the invasion front where admixture did occur, myna populations exhibited higher genetic diversity than in the source populations. Significant isolation by distance was evident amongst populations derived from the same founding population, with genetic diversity decreasing moving away from the point of colonization, and in general, higher levels of gene flow from source to front than vice versa.Main conclusionsThis study indicates that despite a 150‐year colonization history of mynas in Australia, contemporary genetic structure still largely reflects human‐mediated dispersal. However, expanding populations are now connecting and the consequent increased genetic diversity may improve evolutionary potential. These results suggest that more management focus should be directed towards the invasion fronts, rather than the large, historic source populations.

Historical biogeography reveals new independent evolutionary lineages in the Pantosteus plebeius-nebuliferus species-group (Actinopterygii: Catostomidae)

BackgroundThe Pantosteus plebeius-nebuliferus species-group is a group of freshwater fishes distributed in endo- and exorheic drainage basins in the Mexican Sierra Madre Occidental mountain range system and central North Mexico. The geological history of this region is considered an important factor in explaining the evolutionary history of low vagility animals like freshwaters fishes. The aim of this study was to examine the phylogenetic relationships and describe the evolutionary history of the species-group. We hypothesized that the genetic structure and distribution of the main clades of Pantosteus plebeius-nebuliferus are associated with the geological history of Northern Mexico. To this end, we obtained DNA sequences of mitochondrial and nuclear genes and performed phylogenetic and phylogeographic analyses. Divergence time estimation and ancestral area reconstruction were also carried out to propose a biogeographical hypothesis, and species boundaries within the species-group were also tested.ResultsWe identified four clades within the Pantosteus plebeius-nebuliferus species-group in both markers. Divergence ranged from 5.9% to 9.2% for cytb and 0.1% to 0.9% for GHI. We observed significant genetic structure and no shared haplotypes between clades. We estimated that the clades diverged during the last 5.1 Myr, with a biogeographic scenario suggesting eight vicariant and four dispersal events through the historic range of the species-group. We found that the best species-delimitation model is when four species are assumed, which correspond to the main clades. We identified nine evolutionary significance units (ESUs), pertinent to the conservation of the group, each representing populations present in distinct drainage basins.ConclusionsThe evolutionary history of the Pantosteus plebeius-nebuliferus species-group is characterized by vicariant post-dispersal processes, linked to geological changes in the Sierra Madre Occidental and central Northern Mexico since the Pliocene. This is congruent with biogeographic patterns described for other co-distributed fish species. We propose a new phylogenetic hypothesis for the species-group, clarifying the taxonomy of this evolutionarily complex group. Our results suggest that the species-group consists of at least four clades with independent evolutionary histories, two of which may represent new undescribed species. Our identification of ESUs provides a basis upon which conservation measures can be developed for the species-group.

Genetic variation of the epigeic earthworm Lumbricus castaneus populations in urban soils of the Paris region (France) revealed using eight newly developed microsatellite markers

Urban soils are subject to intense environmental pressures, e.g. physical disturbance, surface transformation and pollution, which greatly impact the activity of soil organisms. The epigeic earthworm Lumbricus castaneus (Savigny, 1826) is known to be tolerant to trace elements contamination of soils and was found to be abundant in the urban context. In order to investigate how urban environmental stressors shape the population genetic variation of this species, we developed 8 microsatellite loci from a microsatellite-enriched genomic library. Polymorphism was explored in 6 populations (153 individuals) from the Paris region. The number of alleles per locus varied from 7 to 29. The average expected heterozygosity within populations ranged from 0.596 to 0.705. These new microsatellite markers revealed a significant genetic structure at fine spatial scale, highlighting that they could be particularly useful for genetic studies of populations in urban soils.

Genetic structure of the Canarian palm tree (Phoenix canariensis) at the island scale: does the 'island within islands' concept apply to species with high colonisation ability?

Oceanic islands are dynamic settings that often promote within-island patterns of strong population differentiation. Species with high colonisation abilities, however, are less likely to be affected by genetic barriers, but island size may impact on species genetic structure regardless of dispersal ability. The aim of the present study was to identify the patterns and factors responsible for the structure of genetic diversity at the island scale in Phoenix canariensis, a palm species with high dispersal potential. To this end, we conducted extensive population sampling on the three Canary Islands where the species is more abundant and assessed patterns of genetic variation at eight microsatellite loci, considering different within-island scales. Our analyses revealed significant genetic structure on each of the three islands analysed, but the patterns and level of structure differed greatly among islands. Thus, genetic differentiation fitted an isolation-by-distance pattern on islands with high population densities (La Gomera and Gran Canaria), but such a pattern was not found on Tenerife due to strong isolation between colonised areas. In addition, we found a positive correlation between population geographic isolation and fine-scale genetic structure. This study highlights that island size is not necessarily a factor causing strong population differentiation on large islands, whereas high colonisation ability does not always promote genetic connectivity among neighbouring populations. The spatial distribution of populations (i.e. landscape occupancy) can thus be a more important driver of plant genetic structure than other island, or species' life-history attributes.

Population Genetic Structure of an Endangered Endemic Primate (Leontopithecus chrysomelas) in a Highly Fragmented Atlantic Coastal Rain Forest

This study evaluated the genetic structure of wild populations of the endangered primate, Leontopithecus chrysomelas. We tested the assumption that populations of L. chrysomelas, given their larger population size and a higher degree of habitat continuity, would have higher genetic diversity and less genetic structuring than other lion tamarins. We used 11 microsatellites and 122 hair samples from different locations to assess their genetic diversity and genetic structure, and to make inferences about the isolation by distance. The overall expected heterozygosity (0.51 ± 0.03) and the average number of alleles (3.6 ± 0.2) were relatively low, as is the case in other endangered lion tamarins. Genetic clustering analyses indicated two main clusters, whereas the statistical analyses based on genotype similarities and F_st suggested further substructure. A Mantel test showed that only 34% of this genetic differentiation was explained by the linear distance. In addition to linear distance, structural differences in the landscape, physical barriers and behavioural factors may be causing significant genetic structuring. Overall, this study suggests that these populations have a relatively low genetic diversity and a relatively high population genetic structure, putting in question whether the presence of agroforest systems (known locally as cabruca) is enough to fully re-establish functional landscape connectivity.