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We present an overview of the morphology, biogeography, and ecology of the fern genus Osmunda (i.e. without previously included taxa of Claytosmunda , Osmundastrum , and Plenasium), with a focus on the American O. spectabilis Willd. and Old World O. regalis L. While genetic data supports the separation of these taxa, commonly used morphologic characters to distinguish between O. regalis and O. spectabilis (maximum frond size; pinnae sessile vs. stalked; pinnules opposite vs. alternate; general pinnule proportions) are not infallible. We recorded morphometric differences among and between O. regalis and O. spectabilis and correlated these with spatio-environmental gradients. Our work provides an updated taxonomic overview with full synonymy and diagnostic key of Osmunda. We preliminarily recognize six informal subtaxa in O. regalis ('regalis', 'abyssinica', 'huegeliana', 'longifolia', 'transvaalensis', 'obtusifolia') and three in O. spectabilis ('spectabilis', 'palustris', 'piresii') that separate in a morphological traits-based principal component analysis. The morphotaxa appeared geographically structured and their distribution showed significant correlations with elevation, mean annual precipitation, annual mean temperature, and temperature seasonality. The taxonomic rank and validity of the proposed subtaxa has to be tested through a large-scale sampling, e.g. with comparative cp/nr genomic and cytogenetic analyses. Such future analyses may help to ascertain whether the observed morphologic peculiarities are conditioned solely by abiotic factors (which would allow addressing them as forms) or are manifested in the genome. [ABSTRACT FROM AUTHOR]

Background and Aims The timing of flowering onset is often correlated with latitude, indicative of climatic gradients. Flowering onset in temperate species commonly requires exposure to cold temperatures, known as vernalization. Hence, population differentiation of flowering onset with latitude might reflect adaptation to the local climatic conditions experienced by populations. Methods Within its western range, seeds from Linum bienne populations (the wild relative of cultivated Linum usitatissimum) were used to describe the latitudinal differentiation of flowering onset to determine its association with the local climate of the population. A vernalization experiment including different crop cultivars was used to determine how vernalization accelerates flowering onset, in addition to the vernalization sensitivity response among populations and cultivars. Additionally, genetic differentiation of L. bienne populations along the latitudinal range was scrutinized using microsatellite markers. Key Results Flowering onset varied with latitude of origin, with southern populations flowering earlier than their northern counterparts. Vernalization reduced the number of days to flowering onset, but vernalization sensitivity was greater in northern populations compared with southern ones. Conversely, vernalization delayed flowering onset in the crop, exhibiting less variation in sensitivity. In L. bienne , both flowering onset and vernalization sensitivity were better predicted by the local climate of the population than by latitude itself. Microsatellite data unveiled genetic differentiation of populations, forming two groups geographically partitioned along latitude. Conclusions The consistent finding of latitudinal variation across experiments suggests that both flowering onset and vernalization sensitivity in L. bienne populations are under genetic regulation and might depend on climatic cues at the place of origin. The association with climatic gradients along latitude suggests that the climate experienced locally drives population differentiation of the flowering onset and vernalization sensitivity patterns. The genetic population structure suggests that past population history could have influenced the flowering initiation patterns detected, which deserves further work. [ABSTRACT FROM AUTHOR]

The introduction of exotics is common in forestry, and majorly important species, like eucalypts, poplar, and Casuarina sp. occupy vast areas in the Indian subcontinent. Importantly, with the latest cost-effective sequencing techniques, genetic diversity research through molecular marker approaches on major exotics provides novel information for genetic improvement in economic traits with climatic adaptation. The study was carried out on Grevillea robusta to assess genetic relatedness and diversity among 228 genotypes belonging to five northwestern states in India. These genotypes were assayed using twelve simple sequence repeat (SSR) markers. A population structure analysis using structure software identified four major gene pool subgroups with clear-cut differences from each other. Principal coordinate analysis also supports the clustering patterns of the unweighted pair group method with arithmetic mean analysis. In the case of genetic diversity assessment, a total of seventy-three alleles were detected from twelve SSRs, with an average of 6.08 ± 0.71 per locus. Polymorphism information content ranged from 0.17 to 0.67 with a mean of 0.44 ± 0.045, indicating high levels of polymorphism across the genotypes. All the evaluated SSRs demonstrated moderate genetic diversity (observed heterozygosity = 0.31 ± 0.03; expected heterozygosity = 0.32 ± 0.03; and genetic differentiation = 0.295) among the sampled genotypes. These findings indicate significant genetic variability in the germplasm to warrant selection and have potential for a long-term tree improvement program of G. robusta in India. Study Implications: The study on population genetics of Grevillea robusta in exotic environments assessed probable gene pools, provenances, and genetic diversity in geographical distribution range of the species in the Indian scenario. The basic population genetic measures revealed the high diversity areas and probable seed zones of G. robusta in its exotic range. Importantly, the study will be helpful in the selection of candidate plus trees of G. robusta to further strengthen the genotype × environment interaction study for future breeding programs. Further, studying the genetic makeup for moderately diverse species offers valuable insights into evolutionary history, population dynamics, and ecological interactions, which may lead to conservation efforts and guidance for the management of trees such as G. robusta in their native and introduced regions. [ABSTRACT FROM AUTHOR]

Isolation by environment (IBE) is a population genomic pattern that arises when ecological barriers reduce gene flow between populations. Although current evidence suggests IBE is common in nature, few studies have evaluated the underlying mechanisms that generate IBE patterns. In this study, we evaluate five proposed mechanisms of IBE (natural selection against immigrants, sexual selection against immigrants, selection against hybrids, biased dispersal, and environment-based phenological differences) that may give rise to host-associated differentiation within a sympatric population of the redheaded pine sawfly, Neodiprion lecontei , a species for which IBE has previously been detected. We first characterize the three pine species used by N. lecontei at the site, finding morphological and chemical differences among the hosts that could generate divergent selection on sawfly host-use traits. Next, using morphometrics and ddRAD sequencing, we detect modest phenotypic and genetic differentiation among sawflies originating from different pines that is consistent with recent, in situ divergence. Finally, via a series of laboratory assays—including assessments of larval performance on different hosts, adult mate and host preferences, hybrid fitness, and adult eclosion timing—we find evidence that multiple mechanisms contribute to IBE in N. lecontei. Overall, our results suggest IBE can emerge quickly, possibly due to multiple mechanisms acting in concert to reduce migration between different environments. [ABSTRACT FROM AUTHOR]

Phenotypic differentiation among animal populations is common, yet few studies have simultaneously examined the adaptive and neutral mechanisms behind it. Such evolutionary processes become more relevant in species with complex behaviours that undergo global and local selective pressures throughout their geographical range. Here we measured and compared morphological and acoustic variation across the distribution range of a Neotropical gladiator tree frog that shows elaborate reproduction (territoriality, complex courtship and female choice). We then incorporated molecular and landscape data to examine the roles of sexual selection, genetic drift and acoustic adaptation to the environment in call differentiation, i.e. the acoustic adaptation hypothesis (AAH). We found that calls varied more than morphology among populations, but differences in calls or morphological traits were not explained by genetic differentiation. We found no evidence for the AAH, but a significant relationship in the opposite direction regarding call frequencies suggests an indirect role of sexual selection. Differentiation on call traits that are associated with individual discrimination and/or female attraction also corroborated an important role of sexual selection. We show that multitrait and multimechanism approaches can elucidate intricate processes leading to phenotypic variation among individuals and populations. We emphasize that studies of species with complex reproductive behaviours across their range may provide insights into different selective pressures leading to phenotypic differentiation. [ABSTRACT FROM AUTHOR]

Populations from different climates often show unique growth responses to temperature, reflecting temperature adaptation. Yet, whether populations from different climates differ in physiological temperature acclimation remains unclear. Here, we test whether populations from differing thermal environments exhibit different growth responses to temperature and differences in temperature acclimation of leaf respiration. We grew tropical and subtropical populations of two mangrove species (Avicennia germinans and Rhizophora mangle) under ambient and experimentally warmed conditions in a common garden at the species' northern range limit. We quantified growth and temperature responses of leaf respiration (R) at seven time points over ~10 months. Warming increased productivity of tropical populations more than subtropical populations, reflecting a higher temperature optimum for growth. In both species, R measured at 25 °C declined as seasonal temperatures increased, demonstrating thermal acclimation. Contrary to our expectations, acclimation of R was consistent across populations and temperature treatments. However, populations differed in adjusting the temperature sensitivity of R (Q 10) to seasonal temperatures. Following a freeze event, tropical Avicennia showed greater freeze damage than subtropical Avicennia , while both Rhizophora populations appeared equally susceptible. We found evidence of temperature adaptation at the whole-plant scale but little evidence for population differences in thermal acclimation of leaf physiology. Studies that examine potential costs and benefits of thermal acclimation in an evolutionary context may provide new insights into limits of thermal acclimation. [ABSTRACT FROM AUTHOR]

Background and aims Climate-change induced warmer spring temperatures advance tree leaf-out and result in earlier shading of the forest floor. Climate change also leads to more frequent droughts. Forest understorey herbs may respond to these environmental changes by varying traits at different hierarchical levels of organization. While trait mean variation at the inter-individual level in response to environmental changes is well-studied, little is known about how variation at the intra-individual level responds. Methods We sampled genets of the forest understorey herb Galium odoratum from 21 populations in three regions in Germany, varying in microclimatic conditions. The genets were transplanted into a common garden, where we applied shading and drought treatments. We measured plant height and leaf length and width, and calculated the coefficient of variation (CV) at different hierarchical levels: intra-population, intra-genet, intra-ramet and intra-shoot. Key results Variance partitioning showed that intra-shoot CV represented most of the total variation, followed by intra-ramet CV. We found significant variation in CV of plant height and leaf width among populations of origin, indicating that CV is at least partly genetically based. The soil temperature at populations' origins correlated negatively with CV in plant height, suggesting adaptation to local conditions. Furthermore, we observed that early shade led to increased intra-ramet CV in leaf length, while drought reduced intra-shoot CV in leaf width. Finally, intra-shoot leaf width mean and CV were independent under control conditions but correlated under drought. Conclusions Our experimental results reveal correlations of intra-individual variation with soil temperature, indicating that intra-individual variation can evolve and may be adaptive. Intra-individual variation responded plastically to drought and shading, suggesting functional changes to improve light capture and reduce evapotranspiration. In conclusion, intra-individual variation makes up the majority of total trait variation in this species and can play a key role in plant adaptation to climatic change. [ABSTRACT FROM AUTHOR]

The relationship between genetic differentiation and phenotypic plasticity can provide information on whether plasticity generally facilitates or hinders adaptation to environmental change. Here, we studied wing shape variation in a damselfly (Lestes sponsa) across a latitudinal gradient in Europe that differed in time constraints mediated by photoperiod and temperature. We reared damselflies from northern and southern populations in the laboratory using a reciprocal transplant experiment that simulated time‐constrained (i.e. northern) and unconstrained (southern) photoperiods and temperatures. After emergence, adult wing shape was analysed using geometric morphometrics. Wings from individuals in the northern and southern populations differed significantly in shape when animals were reared in their respective native environment. Comparing wing shape across environments, we found evidence for phenotypic plasticity in wing shape, and this response differed across populations (i.e. G × E interactions). This interaction was driven by a stronger plastic response by individuals from the northern population and differences in the direction of plastic wing shape changes among populations. The alignment between genetic and plastic responses depended on the specific combination of population and rearing environment. For example, there was an alignment between plasticity and genetic differentiation under time‐constrained, but not under non‐time‐constrained conditions for forewings. We thus find mixed support for the hypothesis that environmental plasticity and genetic population differentiation are aligned. Furthermore, although our laboratory treatments mimicked the natural climatic conditions at northern and southern latitudes, the effects of population differences on wing shape were two to four times stronger than plastic effects. We discuss our results in terms of time constraints and the possibility that natural and sexual selection is acting differently on fore‐ and hindwings. [ABSTRACT FROM AUTHOR]

Our main goal was to investigate the phylogeography of the butterfly Phengaris arion to reveal the evolutionary origin of its 'spring' and 'summer' forms. Molecular analyses based on highly variable microsatellites, together with Wolbachia screening, were carried out on 34 populations in Europe. We found three well-defined genetic lineages of different origins: the Apennine, the central and the eastern. The highly distinct Apennine lineage is limited by the Alps and evaluated as an Evolutionary Significant Unit (ESU). Therefore, the taxon name ligurica , described from the Ligurian coast (Italy), should not be applied to denote the 'summer form' of the Pannonian region. The central lineage is limited by the Carpathians and the most eastern ranges of the Alps, and lacks major range fluctuations related to glaciations, although there is evidence for extra-Mediterranean refugia in the Carpathian Basin. The eastern clade could have had refugia in central Asia. Our results exclude the potential allopatric origin of the 'spring' and 'summer' arion , and support the hypothesis that the existence of the two forms could be a result of local adaptation to the distinctive phenology of host plant flowering which is manifested in the genetic differences between them. Wolbachia infection has been ruled out as a driver of sympatric speciation in P. arion. [ABSTRACT FROM AUTHOR]

Understanding how historical and contemporary processes lead to genetic differentiation among populations is a fundamental goal of evolutionary and conservation biology. This study focuses on Galaxias maculatus , a widely distributed fish exhibiting diadromous and freshwater resident forms. We examine the genetic differentiation among resident populations from the Manso River System, a trans-Andean system which thus went through drainage reversal following the Last Glacial Maximum (LGM), and resident and diadromous populations from the connected Puelo River that drains into the Pacific Ocean. Single nucleotide polymorphic (SNP) markers revealed that resident populations from the Manso River System are genetically distinguishable from the diadromous and resident populations from the Puelo River. This suggests that G. maculatus from the Manso River System likely colonized the area from a glacial refugium east of the Andes and did not expand downstream during drainage reversal, whereas the populations from the Puelo River colonized the area from glacial refugia west of the Andes. The populations from the Manso River exhibited lower genetic diversity than the Puelo River populations. Galaxias maculatus resident populations in Patagonia are decreasing due to anthropogenic factors. The Manso River System resident populations are susceptible to these factors and may show further decreases in genetic diversity. [ABSTRACT FROM AUTHOR]

Recently diversified taxa commonly do not show complete reproductive isolation, and thus they represent an interesting model for studying the occurrence of hybridization and its influence on the integrity of species. In this study, we aim to elucidate the occurrence of hybridization and discuss species boundaries between three Aechmea spp. (Bromeliaceae) from southern Brazil. To achieve these aims, we used ten nuclear and six plastid microsatellite loci. We also investigated morphological and ecological differentiation and reproductive compatibility through interspecific cross-pollination experiments with these species. Molecular analyses confirmed the occurrence of hybridization between the three species, but interspecific gene flow was higher between A. comata and A. kertesziae than between A. comata and A. caudata. These Aechmea spp. showed morphological differentiation, and the results of the artificial interspecific crosses indicated that they can intercross. Aechmea caudata and A. kertesziae show distinct microhabitat preferences, whereas A. comata thrives in a microhabitat that is also inhabited by the other species. Despite the potential reproductive barriers being weak, especially those between A. comata and A. kertesziae , they may maintain the boundaries between these species and their integrity in sympatric populations. [ABSTRACT FROM AUTHOR]

High levels of genetic diversity are critical to the success of breeding programs. Russian honey bees are a selected stock that undergoes breeding in a closed block-based mating system. Given its established history, Russian stock has longitudinal measures of genetic integrity (i.e., genetically based stock identity) and diversity. Assessments using genetic stock identification (GSI) have shown that genetic diversity parameters were assessed across breeding blocks for three generations, spanning 6 yr (2014, 2017, and 2020), showing levels comparable to those when the stock was initially released in 2008. Allelic richness (mean number of alleles) and gene diversity levels were consistent over time and among blocks. Blocks were generally not differentiated from one another within each year. However, the 2020 population was distinct when compared with bees sampled in both 2014 and 2017. Genetic distance relationships supported differentiation of the 2020 population by distinct clustering. The patterns observed here are consistent with historical changes made to the breeding program to increase stringency of the selection criteria. [ABSTRACT FROM AUTHOR]

Important uncertainties persist regarding the genetic architecture of adaptive trait evolution in natural populations, including the number of genetic variants involved, whether they are drawn from standing genetic variation, and whether directional selection drives them to complete fixation. Here, we take advantage of a unique natural population of Drosophila melanogaster from the Ethiopian highlands, which has evolved larger body size than any other known population of this species. We apply a bulk segregant quantitative trait locus mapping approach to 4 unique crosses between highland Ethiopian and lowland Zambian populations for both thorax length and wing length. Results indicated a persistently variable genetic basis for these evolved traits (with largely distinct sets of quantitative trait loci for each cross), and at least a moderately polygenic architecture with relatively strong effects present. We complemented these mapping experiments with population genetic analyses of quantitative trait locus regions and gene ontology enrichment analysis, generating strong hypotheses for specific genes and functional processes that may have contributed to these adaptive trait changes. Finally, we find that the genetic architectures indicated by our quantitative trait locus mapping results for size traits mirror those from similar experiments on other recently evolved traits in this species. Collectively, these studies suggest a recurring pattern of polygenic adaptation in this species, in which causative variants do not approach fixation and moderately strong effect loci are present. [ABSTRACT FROM AUTHOR]

The crangonid shrimps Argis hozawai , A. lar and A. toyamaensis , co-distributed in the Sea of Japan, exhibit intriguing differences in geographical and bathymetric distributions and in reproductive biology. Argis hozawai (150–250 m depth) and A. lar (200–300 m) are broadly distributed in the north-western Pacific Ocean and spawn relatively large numbers of small eggs, whereas A. toyamaensis (250–2000 m) is distributed in the Sea of Japan and spawns a small number of large eggs. We examined the relationship between egg size and dispersal patterns in the deep sea by comparing genetic population structures using mitochondrial DNA sequence variation. We found little or no genetic divergence within the Sea of Japan for A. hozawai and A. lar , whereas there was a slight but significantly higher genetic differentiation in A. toyamaensis. This suggests that A. toyamaensis has lower dispersal ability than A. hozawai and A. lar , and therefore might maximize larval survival through larger size at hatching, with either direct or abbreviated larval development, to adapt to the deep-sea environment in the Sea of Japan. We also detected the effects of drastic environmental changes during the Pleistocene glacial periods on their demographic processes in the Sea of Japan. [ABSTRACT FROM AUTHOR]

Neogene orogenesis and climatic cycles strongly influenced inter- and intraspecific differentiation and variability of taxa. In this study, we focused on the southern margin of the western Palaearctic, known to be a geographically complex region. We performed mitochondrial DNA analyses of Buthus scorpions from the Moroccan Atlas Mountains, from the Hoggar Mountains in Algeria and from Tunisia, Iberia and Israel. Molecular species delimitation suggests the existence of ≥ 24 molecular operational taxonomic units. The data confirm complex differentiation patterns across the Atlas Mountains of Morocco, but structures in Iberia, Algeria and Tunisia have considerably lower complexity. This identifies the Atlas Mountain region as the most important differentiation centre of Buthus scorpions. Samples from the Hoggar Mountains (southern Algeria) cluster with those from the southernmost parts of Morocco in the middle and upper parts of the Draa Valley. This reinforces a recent connection of these regions. Samples from Israel are genetically similar to individuals from eastern Algeria and Tunisia. This suggests a widespread group across major parts of North Africa. Divergence time estimates indicate that differentiation in the genus began during the late Miocene, a period characterized by strong tectonic activities in this region. Further differentiation could be linked to subsequent climatic changes that have occurred since the end of the Miocene, with an increasing aridification of the Moroccan area. This also produced many microrefugia in the mountains of the area during the Pleistocene climatic fluctuations. [ABSTRACT FROM AUTHOR]

Habitat fragmentation strongly affects the genetic diversity of plant populations, and this has always attracted much research interest. Although numerous studies have investigated the effects of habitat fragmentation on the genetic diversity of plant populations, fewer studies have compared species with contrasting breeding systems while accounting for phylogenetic distance. Here, we compare the levels of genetic diversity and differentiation within and among subpopulations in metapopulations (at fine-scale level) of two closely related Zingiber species, selfing Zingiber corallinum and outcrossing Zingiber nudicarpum. Comparisons of the genetic structure of species from unrelated taxa may be confounded by the effects of correlated ecological traits or/and phylogeny. Thus, we possibly reveal the differences in genetic diversity and spatial distribution of genetic variation within metapopulations that relate to mating systems. Compared to outcrossing Z. nudicarpum , the subpopulation genetic diversity in selfing Z. corallinum was significantly lower, but the metapopulation genetic diversity was not different. Most genetic variation resided among subpopulations in selfing Z. corallinum metapopulations, while a significant portion of variation resided either within or among subpopulations in outcrossing Z. nudicarpum , depending on whether the degree of subpopulation isolation surpasses the dispersal ability of pollen and seed. A stronger spatial genetic structure appeared within subpopulations of selfing Z. corallinum potentially due to restricted pollen flow and seed dispersal. In contrast, a weaker genetic structure was apparent in subpopulations of outcrossing Z. nudicarpum most likely caused by extensive pollen movement. Our study shows that high genetic variation can be maintained within metapopulations of selfing Zingiber species, due to increased genetic differentiation intensified primarily by the stochastic force of genetic drift among subpopulations. Therefore, maintenance of natural variability among subpopulations in fragmented areas is key to conserve the full range of genetic diversity of selfing Zingiber species. For outcrossing Zingiber species, maintenance of large populations is an important factor to enhance genetic diversity. Compared to outcrossing Z. nudicarpum , the subpopulation genetic diversity in selfing Z. corallinum was significantly lower, but the metapopulation genetic diversity did not differ. Most genetic variation resided among subpopulations in selfing Z. corallinum metapopulations, while a significant portion of variation resided either within or among subpopulations in outcrossing Z. nudicarpum , depending on whether the degree of subpopulation isolation surpasses the dispersal ability of pollen and seed. Our study shows that selfing Z. corallinum could maintain high genetic diversity through differentiation intensified primarily by the stochastic force of genetic drift among subpopulations at fine-scale level, but not local adaptation. [ABSTRACT FROM AUTHOR]

Non‐native species experience novel selection pressures in introduced environments and may interbreed with native lineages. Species introductions therefore provide opportunities to investigate repeated patterns of adaptation and introgression across replicated contact zones. Here, we investigate genetic parallelism between multiple introduced populations of the invasive marine mussel, Mytilus galloprovincialis, in the absence (South Africa and California) and presence of hybridization with a native congener (Mytilus planulatus in Batemans Bay and Sydney Harbour, Australia). Repeatability in post‐introduction differentiation from native‐range populations varied between genetically distinct Atlantic and Mediterranean lineages, with Atlantic‐derived introductions displaying high differentiation (maxFST > 0.4) and parallelism at outlier loci. Identification of long noncoding RNA transcripts (lncRNA) additionally allowed us to clarify that parallel responses are largely limited to protein‐coding loci, with lncRNAs likely evolving under evolutionary constraints. Comparisons of independent hybrid zones revealed differential introgression most strongly in Batemans Bay, with an excess of M. galloprovincialis ancestry and resistance to introgression at loci differentiating parental lineages (M. planulatus and Atlantic M. galloprovincialis). Additionally, contigs putatively introgressed with divergent alleles from a closely related species, Mytilus edulis, showed stronger introgression asymmetries compared with genome‐wide trends and also diverged in parallel in both Atlantic‐derived introductions. These results suggest that divergent demographic histories experienced by introduced lineages, including pre‐introduction introgression, influence contemporary admixture dynamics. Our findings build on previous investigations reporting contributions of historical introgression to intrinsic reproductive architectures shared between marine lineages and illustrate that interspecific introgression history can shape differentiation between colonizing populations and their hybridization with native congeners. [ABSTRACT FROM AUTHOR]

Studies of colonization of new habitats that appear from rapidly changing environments are interesting and highly relevant to our understanding of divergence and speciation. Here, we analyse phenotypic and genetic variation involved in the successful establishment of a marine fish (sand goby, Pomatoschistus minutus) over a steep salinity drop from 35 PSU in the North Sea (NE Atlantic) to two PSU in the inner parts of the post‐glacial Baltic Sea. We first show that populations are adapted to local salinity in a key reproductive trait, the proportion of motile sperm. Thereafter, we show that genome variation at 22,190 single nucleotide polymorphisms (SNPs) shows strong differentiation among populations along the gradient. Sequences containing outlier SNPs and transcriptome sequences, mapped to a draft genome, reveal associations with genes with relevant functions for adaptation in this environment but without overall evidence of functional enrichment. The many contigs involved suggest polygenic differentiation. We trace the origin of this differentiation using demographic modelling and find the most likely scenario is that at least part of the genetic differentiation is older than the Baltic Sea and is a result of isolation of two lineages prior to the current contact over the North Sea–Baltic Sea transition zone. [ABSTRACT FROM AUTHOR]

Background and Aims Mikania micrantha , a climbing perennial weed of the family Asteraceae, is native to Latin America and is highly invasive in the tropical belt of Asia, Oceania and Australia. This study was framed to investigate the population structure of M. micrantha at a large spatial scale in Asia and to identify how introduction history, evolutionary forces and landscape features influenced the genetic pattern of the species in this region. Methods We assessed the genetic diversity and structure of 1052 individuals from 46 populations for 12 microsatellite loci. The spatial pattern of genetic variation was investigated by estimating the relationship between genetic distance and geographical, climatic and landscape resistances hypothesized to influence gene flow between populations. Key Results We found high genetic diversity of M. micrantha in this region, as compared with the genetic diversity parameters of other invasive species. Spatial and non-spatial clustering algorithms identified the presence of multiple genetic clusters and admixture between populations. Most of the populations showed heterozygote deficiency, primarily due to inbreeding, and the founder populations showed evidence of a genetic bottleneck. Persistent gene flow throughout the invasive range caused low genetic differentiation among populations and provided beneficial genetic variation to the marginal populations in a heterogeneous environment. Environmental suitability was found to buffer the detrimental effects of inbreeding at the leading edge of range expansion. Both linear and non-linear regression models demonstrated a weak relationship between genetic distance and geographical distance, as well as bioclimatic variables and environmental resistance surfaces. Conclusions These findings provide evidence that extensive gene flow and admixture between populations have influenced the current genetic pattern of M. micrantha in this region. High gene flow across the invaded landscape may facilitate adaptation, establishment and long-term persistence of the population, thereby indicating the range expansion ability of the species. [ABSTRACT FROM AUTHOR]

Evaluation of patterns of pollen dispersal, mating systems, population fitness, genetic diversity and differentiation in restoration and remnant plant populations can be useful in determining how well restoration activities have achieved their objectives. We used molecular tools to assess how well restoration objectives have been met for populations of Banksia media in the biodiversity hotspot of south-west Western Australia. We characterized patterns of pollen dispersal within, and pollen immigration into, two restoration populations. We compared mating system parameters, population fitness via seed weight, genetic diversity and genetic differentiation for restoration and associated reference remnant populations. Different patterns of pollen dispersal were revealed for two restoration sites that differed in floral display, spatial aggregation of founders and co-planted species. Proximity to remnant native vegetation was associated with enhanced immigration and more short-range pollen dispersal when other population variables were constant. Greater seed weights at remnant compared to restoration populations were not related to outcrossing rate. Equivalent mating system and genetic diversity parameters and low to moderate levels of genetic differentiation between restoration and remnant populations suggest pollinator services have been restored in genetically diverse restoration populations of local provenance B. media as early as four years from planting. [ABSTRACT FROM AUTHOR]

We know from human genetic studies that practically all aspects of biology are strongly influenced by the genetic background, as reflected in the advent of "personalized medicine." Yet, with few exceptions, this is not taken into account when using laboratory populations as animal model systems for research in these fields. Laboratory strains of zebrafish (Danio rerio) are widely used for research in vertebrate developmental biology, behavior, and physiology, for modeling diseases, and for testing pharmaceutic compounds in vivo. However, all of these strains are derived from artificial bottleneck events and therefore are likely to represent only a fraction of the genetic diversity present within the species. Here, we use restriction site-associated DNA sequencing to genetically characterize wild populations of zebrafish from India, Nepal, and Bangladesh, and to compare them to previously published data on four common laboratory strains. We measured nucleotide diversity, heterozygosity, and allele frequency spectra, and find that wild zebrafish are much more diverse than laboratory strains. Further, in wild zebrafish, there is a clear signal of GC-biased gene conversion that is missing in laboratory strains. We also find that zebrafish populations in Nepal and Bangladesh are most distinct from all other strains studied, making them an attractive subject for future studies of zebrafish population genetics and molecular ecology. Finally, isolates of the same strains kept in different laboratories show a pattern of ongoing differentiation into genetically distinct substrains. Together, our findings broaden the basis for future genetic, physiological, pharmaceutic, and evolutionary studies in Danio rerio. [ABSTRACT FROM AUTHOR]

Phenotypic plasticity is the primary mechanism of organismal resilience to abiotic and biotic stress, and genetic differentiation in plasticity can evolve if stresses differ among populations. Inducible defence is a common form of adaptive phenotypic plasticity, and long‐standing theory predicts that its evolution is shaped by costs of the defensive traits, costs of plasticity and a trade‐off in allocation to constitutive versus induced traits. We used a common garden to study the evolution of defence in two native populations of wild arugula Eruca sativa (Brassicaceae) from contrasting desert and Mediterranean habitats that differ in attack by caterpillars and aphids. We report genetic differentiation and additive genetic variance for phenology, growth and three defensive traits (toxic glucosinolates, anti‐nutritive protease inhibitors and physical trichome barriers) as well their inducibility in response to the plant hormone jasmonic acid. The two populations were strongly differentiated for plasticity in nearly all traits. There was little evidence for costs of defence or plasticity, but constitutive and induced traits showed a consistent additive genetic trade‐off within each population for the three defensive traits. We conclude that these populations have evolutionarily diverged in inducible defence and retain ample potential for the future evolution of phenotypic plasticity in defence. [ABSTRACT FROM AUTHOR]

Natural populations display a variety of spatial arrangements, each potentially with a distinctive impact on genetic diversity and genetic differentiation among subpopulations. Although the spatial arrangement of populations can lead to intricate migration networks, theoretical developments have focused mainly on a small subset of such networks, emphasizing the island-migration and stepping-stone models. In this study, we investigate all small network motifs: the set of all possible migration networks among populations subdivided into at most four subpopulations. For each motif, we use coalescent theory to derive expectations for three quantities that describe genetic variation: nucleotide diversity, F ST, and half-time to equilibrium diversity. We describe the impact of network properties on these quantities, finding that motifs with a high mean node degree have the largest nucleotide diversity and the longest time to equilibrium, whereas motifs with low density have the largest F ST. In addition, we show that the motifs whose pattern of variation is most strongly influenced by loss of a connection or a subpopulation are those that can be split easily into disconnected components. We illustrate our results using two example data sets—sky island birds of genus Sholicola and Indian tigers—identifying disturbance scenarios that produce the greatest reduction in genetic diversity; for tigers, we also compare the benefits of two assisted gene flow scenarios. Our results have consequences for understanding the effect of geography on genetic diversity, and they can assist in designing strategies to alter population migration networks toward maximizing genetic variation in the context of conservation of endangered species. [ABSTRACT FROM AUTHOR]

Small-bodied vertebrates sometimes evolve gigantism on islands, but there is a lack of consistent association with ecological factors or island characteristics. One possible reason is that, even if the ecological conditions are right, body size might fail to diverge on islands that were isolated recently or if there is gene flow between islands and the mainland. We studied body size, ventral colour polymorphism and genetic structure across nine islands and adjacent mainland populations of common wall lizards (Podarcis muralis) off the western coast of France. Population genetic data suggested that island populations might have maintained gene flow after their geographical isolation from the mainland. Island lizards were larger and heavier than mainland lizards on average, but the extent of gigantism varied substantially between islands. Island size and distance from the mainland were poor predictors of body size, but lizards from populations that were highly genetically differentiated from the mainland were larger than lizards from less differentiated populations. Colour morphs that were rare on the mainland tended to be more common on islands. We propose that genetic isolation or bottlenecks promote body size evolution in island lizards, which makes it challenging to identify ecological causes of island gigantism without complementary genetic information. [ABSTRACT FROM AUTHOR]

Although genetic and plastic responses are sometimes considered as unrelated processes, their phenotypic effects may often align because genetic adaptation is expected to mirror phenotypic plasticity if adaptive, but run counter to it when maladaptive. Because the magnitude and direction of this alignment has further consequences for both the tempo and mode of adaptation, they are relevant for predicting an organisms' reaction to environmental change. To better understand the interplay between phenotypic plasticity and genetic change in mediating adaptive phenotypic variation to climate variability, we here quantified genetic latitudinal variation and thermal plasticity in wing loading and wing shape in two closely related and widespread sepsid flies. Common garden rearing of 16 geographical populations reared across multiple temperatures revealed that wing loading decreases with latitude in both species. This pattern could be driven by selection for increased dispersal capacity in the cold. However, although allometry, sexual dimorphism, thermal plasticity and latitudinal differentiation in wing shape all show similar patterns in the two species, the relationship between the plastic and genetic responses differed between them. Although latitudinal differentiation (south to north) mirrored thermal plasticity (hot to cold) in Sepsis punctum, there was no relationship in Sepsis fulgens. While this suggests that thermal plasticity may have helped to mediate local adaptation in S. punctum, it also demonstrates that genetic wing shape differentiation and its relation to thermal plasticity may be complex and idiosyncratic, even among ecologically similar and closely related species. Hence, genetic responses can, but do not necessarily, align with phenotypic plasticity induced by changing environmental selection pressures. [ABSTRACT FROM AUTHOR]

To mine new favorable alleles for tomato breeding, we investigated the feasibility of utilizing Solanum pimpinellifolium as a diverse panel of genome-wide association study through the restriction siteassociated DNA sequencing technique. Previous attempts to conduct genome-wide association studies using S. pimpinellifolium were impeded by an inability to correct for population stratification and by lack of high-density markers to address the issue of rapid linkage disequilibrium decay. In the current study, a set of 24,330 SNPs was identified using 99 S. pimpinellifolium accessions from the Tomato Genetic Resource Center. Approximately 84% of PstI site-associated DNA sequencing regions were located in the euchromatic regions, resulting in the tagging of most SNPs on or near genes. Our genotypic data suggested that S. pimpinellifolium were divided into three single-ancestry subpopulations and four mixed-ancestry subpopulations. Additionally, our SNP genotypic data consistently confirmed the genetic differentiation, achieving a relatively reliable correction of population stratification. Previous studies utilized the 8K tomato SNP array, SolCAP, to investigate the genetic variation of S. pimpinellifolium and we performed a metaanalysis of these genotypes. The result suggested SolCAP array was less appropriate to profile the genetic differentiation of S. pimpinellifolium when more accessions were involved because the samples belonging to the same accession demonstrated different genome patterns. Moreover, as expected, rapid linkage disequilibrium decay was observed in S. pimpinellifolium, especially in euchromatic regions. Approximately two-thirds of the flanking SNP markers did not display linkage disequilibrium based on r2 = 0.1. However, the 18-Kb linkage disequilibrium decay indeed reveals the potential of single-gene resolution in GWAS when markers are saturated. [ABSTRACT FROM AUTHOR]

Background and Aims Phenotypic plasticity and genetic differentiation both play important roles in the establishment and spread of species after extra-range dispersal; however, the adaptive potential of plasticity and genetic divergence in successful invasions remains unclear. Methods We measured six anatomical traits associated with drought tolerance in contrasting water environments for individuals from the invasive and native range of the bunchgrass Brachypodium sylvaticum. To represent sources contributing to admixed genotypes in the invasive range accurately, we used unique alleles to determine probabilities of genetic contribution, and utilized these as weights in our analyses. The adaptive values of plasticity and genetic differentiation were assessed using regression. Key Results No plasticity was found in response to water availability for any of the measured traits. Bulliform cell area and three traits related to xylem morphology displayed genetic differentiation between invasive and native ranges, indicating a shift in the invasive range towards drought-tolerant phenotypes. Genetic divergence was not consistently in the direction indicated by selection, suggesting that responses are limited by trade-offs with other traits or physical constraints. Conclusions Our results indicate that invasive adaptation is the consequence of post-introduction selection leading to genetic differentiation. Selection, rather than plasticity, is driving B. sylvaticum success in its invaded range. [ABSTRACT FROM AUTHOR]

We investigated the genetic structure of seven populations of the narrow-clawed crayfish Pontastacus leptodactylus (Eschscholtz, 1823) from the Caspian Sea basin, Iran by partial sequencing of the control region (D-loop) of the mitochondrial DNA (mtDNA) and 10 microsatellites. Mitochondrial DNA sequences revealed significant haplotype diversity (0.811 ± 0.049) and nucleotide diversity (π) (0.0127 ± 0.0038) along the Astara region, Siah Darvishan and Chafrood rivers. Significant deviations from Hardy-Weinberg equilibrium within populations were detected for most populations in the screened microsatellite loci. The two types of markers were particularly informative in delineating population structure of P. leptodactylus. Analyses of molecular variance (AMOVA) showed significant genetic differentiation (P < 0.05) between populations for both microsatellite and mtDNA markers. At least three genetically distinct management units were observed using the two methods among the sampling sites investigated. Analyses of both genomes provided high resolution and confidence in characterizing the population structure of P. leptodactylus. The results are consistent with the findings from PCR-RFLP analysis and suggest considerable genetic diversity of the populations from the Caspian Sea basin. These results could give applicable information for the cultivation of stocks and also for future genetic improvement of this commercial species by a selective breeding program. [ABSTRACT FROM AUTHOR]

The South African (SAF) yellowfin tuna (Thunnus albacares) fishery represents a potential example of misalignment between management units and biological processes. The SAF fishery spans an operational stock with a boundary at 20°E, either side of which fish are considered part of Atlantic or Indian Ocean regional stocks. However, the actual recruitment of fish from Atlantic and Indian Ocean spawning populations into SAF waters is unknown. To address this knowledge gap, genomic analysis (11 101 SNPs) was performed on samples from Atlantic and Indian Ocean spawning sites, including SAF sites spanning the current stock boundary. Outlier loci conferred high discriminatory power to assignment tests and revealed that all SAF fish were assigned to the Indian Ocean population and that no Atlantic Ocean fish appeared in the SAF samples. Additionally, several Indian Ocean migrants were detected at the Atlantic spawning site demonstrating asymmetric dispersal and the occurrence of a mixed-stock fishery in Atlantic waters. This study highlights both the spatial inaccuracy of current stock designations and a misunderstanding of interactions between the underlying biological units, which must be addressed in light of local and global declines of the species. Specifically, the entire SAF fishery must be managed as part of the Indian Ocean stock. [ABSTRACT FROM AUTHOR]

Aims Seagrasses provide a variety of ecosystem goods and services, but they are subjected to frequently anthropogenic disturbances. In this study, we genotyped samples collected from Zostera japonica meadows with dramatic fluctuations in the area in order to understand the distribution of genetic variation within and among populations. Methods We collected samples from eight extant populations along coastal areas of southern China. Ten polymorphic microsatellites were adopted to genotype the samples. Parameters of genetic diversity and differentiation were calculated with general software. Important Findings High levels of genetic diversity were found in the studied populations, suggesting that the effective population size has not decreased significantly, which was supported by no signs of recent bottlenecks. High genetic diversity reflects an important role of sexual seedling recruitment in Z. japonica populations. We found a significant relationship between genetic differentiation and the shortest sea surface distance of populations, suggesting that ocean currents play a critical role in shaping the genetic structure of Z. japonica populations. STRUCTURE software analysis clustered the eight populations into two groups: western and eastern populations separated by the Qiongzhou Strait/Leizhou Peninsula, hinting that there was very limited gene flow through the narrow strait in this marine plant. Four populations had high contribution diversity and, thus, high priority for in situ conservation. [ABSTRACT FROM AUTHOR]

The advent of high throughput sequencing and genotyping technologies enables the comparison of patterns of polymorphisms at a very large number of markers. While the characterization of genetic structure from individual sequencing data remains expensive for many nonmodel species, it has been shown that sequencing pools of individual DNAs (Pool-seq) represents an attractive and cost-effective alternative. However, analyzing sequence read counts from a DNA pool instead of individual genotypes raises statistical challenges in deriving correct estimates of genetic differentiation. In this article, we provide a method-of-moments estimator of FST for Pool-seq data, based on an analysis-of-variance framework. We show, by means of simulations, that this new estimator is unbiased and outperforms previously proposed estimators. We evaluate the robustness of our estimator to model misspecification, such as sequencing errors and uneven contributions of individual DNAs to the pools. Finally, by reanalyzing published Pool-seq data of different ecotypes of the prickly sculpin Cottus asper, we show how the use of an unbiased FST estimator may question the interpretation of population structure inferred from previous analyses. [ABSTRACT FROM AUTHOR]

The mechanisms by which organisms adapt to variable environments are a fundamental question in evolutionary biology and are important to protect important species in response to a changing climate. An interesting candidate to study this question is the honey bee Apis cerana, a keystone pollinator with a wide distribution throughout a large variety of climates, that exhibits rapid dispersal. Here, we resequenced the genome of 180  A. cerana individuals from 18 populations throughout China. Using a population genomics approach, we observed considerable genetic variation in A. cerana. Patterns of genetic differentiation indicate high divergence at the subspecies level, and physical barriers rather than distance are the driving force for population divergence. Estimations of divergence time suggested that the main branches diverged between 300 and 500 Ka. Analyses of the population history revealed a substantial influence of the Earth’s climate on the effective population size of A. cerana, as increased population sizes were observed during warmer periods. Further analyses identified candidate genes under natural selection that are potentially related to honey bee cognition, temperature adaptation, and olfactory. Based on our results, A. cerana may have great potential in response to climate change. Our study provides fundamental knowledge of the evolution and adaptation of A. cerana. [ABSTRACT FROM AUTHOR]

• Background and Aims An altitudinal gradient of leaf wettability is often observed between and within species. To understand its functional significance, positional variation of leaf surfaces within plants should be taken into account. In rosette-forming plants, rosette leaves are near the ground and their adaxial surfaces are exposed, whereas cauline leaves are lifted from the ground throughout the reproductive season, and their abaxial surfaces are more exposed. Here, we investigated leaf wettability of cauline and rosette leaves of Arabidopsis halleri subsp. gemmifera growing in contrasting montane habitats along an altitudinal gradient at Mt Ibuki, Japan. • Methods We conducted field investigations and a growth chamber experiment to determine whether fieldobserved variation in leaf wettability was caused by genetic differentiation. We further performed gene expression analysis of a wax-related gene, i.e. AhgCER1, a homologue of A. thaliana ECERIFERUM1 (CER1) that may be involved in differentiation of leaf wettability. • Key Results We found cauline-leaf specific genetic differentiation in leaf wettability between contrasting montane habitats. Cauline leaves of semi-alpine plants, especially on abaxial surfaces, were non-wettable. Cauline leaves of low-altitudinal understorey plants were wettable, and rosette leaves were also wettable in both habitats. AhgCER1 expression corresponded to observed leaf wettability patterns. • Conclusions Low wettability of cauline leaves is hypothesized to keep exposed surfaces dry when they are wrapping flowering buds in early spring, and presumably protects flowering buds from frost damage. The genetic system that controls wax content, specifically for cauline leaves, should be involved in the observed genetic differentiation, and AhgCER1 control is a strong candidate for the underlying genetic mechanism. [ABSTRACT FROM AUTHOR]

• Background and Aims Some polyploid species show enhanced physiological tolerance to drought compared with their progenitors. However, very few studies have examined the consistency of physiological drought response between genetically differentiated natural polyploid populations, which is key to evaluation of the importance of adaptive evolution after polyploidization in those systems where drought exerts a selective pressure. • Methods A comparative functional approach was used to investigate differentiation of drought-tolerance-related traits in the Brachypodium species complex, a model system for grass polyploid adaptive speciation and functional genomics that comprises three closely related annual species: the two diploid parents, B. distachyon and B. stacei, and the allotetraploid derived from them, B. hybridum. Differentiation of drought-tolerance-related traits between ten genetically distinct B. hybridum populations and its ecological correlates was further analysed. • Key Results The functional drought response is overall well differentiated between Brachypodium species. Brachypodium hybridum allotetraploids showed a transgressive expression pattern in leaf phytohormone content in response to drought. In contrast, other B. hybridum physiological traits correlated to B. stacei ones. Particularly, proline and water content were the traits that best discriminated these species from B. distachyon under drought. • Conclusions After polyploid formation and/or colonization, B. hybridum populations have adaptively diverged physiologically and genetically in response to variations in aridity. [ABSTRACT FROM AUTHOR]

Though polyploidy is an important aspect of the evolutionary genetics of both plants and animals, the development of population genetic theory of polyploids has seriously lagged behind that of diploids. This is unfortunate since the analysis of polyploid genetic data -- and the interpretation of the results --requires even more scrutiny than with diploid data. This is because of several polyploidy-specific complications in segregation and genotyping such as tetrasomy, double reduction, and missing dosage information. Here, we review the theoretical and statistical aspects of the population genetics of polyploids. We discuss several widely used types of inferences, including genetic diversity, Hardy-Weinberg equilibrium, population differentiation, genetic distance, and detecting population structure. For each, we point out how the statistical approach, expected result, and interpretation differ between different ploidy levels. We also discuss for each type of inference what biases may arise from the polyploid-specific complications and how these biases can be overcome. From our overview, it is clear that the statistical toolbox that is available for the analysis of genetic data is flexible and still expanding. Modern sequencing techniques will soon be able to overcome some of the current limitations to the analysis of polyploid data, though the techniques are lagging behind those available for diploids. Furthermore, the availability of more data may aggravate the biases that can arise, and increase the risk of false inferences. Therefore, simulations such as we used throughout this review are an important tool to verify the results of analyses of polyploid genetic data. [ABSTRACT FROM AUTHOR]

The genetic structure of the populations of the sword prawn Parapenaeopsis hardwickii (Miers, 1878) in the Yellow Sea and East China Sea, an economically and ecologically important species in the Indo-West Pacific region, is described. Based on partial mtDNA COI gene, 27 COI haplotypes are recognized from 130 samples collected from seven locations. Nucleotide and haplotype diversities of the Yellow Sea and East China Sea populations were 0.00187 ± 0.00021 and 0.818 ± 0.049, and 0.00215 ± 0.00023 and 0.822 ± 0.042, respectively. AMOVA and pairwise FST reveal no significant genetic differentiation of the populations. Neither the Bayesian inference tree nor haplotype network reveals clades with geographic pattern, indicating high levels of gene flow between prawn populations of each sea. Mismatch distribution and neutrality tests suggest an historical population expansion of P. hardwickii, with Pleistocene glacial cycles likely having impacted this species' historical demography. This study provides background information for sustainable improvement and fisheries management of P. hardwickii in the Yellow Sea and East China Sea. [ABSTRACT FROM AUTHOR]

Gene flow between genetically differentiated populations can maintain variation in species interactions, especially when population structure is congruent between interacting species. However, large-scale empirical comparisons of the population structure of interacting species are rare, particularly in positive interspecific interactions (mutualisms). One agriculturally and ecologically important mutualism is the partnership between legume plants and rhizobia. Through characterizing and comparing the population genomic structure of the legume Medicago lupulina and two rhizobial species ( Ensifer medicae and E. meliloti), we explored the spatial scale of population differentiation between interacting partners in their introduced range in North America. We found high proportions of E. meliloti in southeastern populations and high proportions of E. medicae in northwestern populations. Medicago lupulina and the Ensifer genus showed similar patterns of spatial genetic structure (isolation by distance). However, we detected no evidence of isolation by distance or population structure within either species of bacteria. Genome-wide nucleotide diversity within each of the two Ensifer species was low, suggesting limited introduction of strains, founder events, or severe bottlenecks. Our results suggest that there is potential for geographically structured coevolution between M. lupulina and the Ensifer genus, but not between M. lupulina and either Ensifer species. [ABSTRACT FROM AUTHOR]

FST is one of the most widely used statistics in population genetics. Recent mathematical studies have identified constraints that challenge interpretations of FST as a measure with potential to range from 0 for genetically similar populations to 1 for divergent populations. We generalize results obtained for population pairs to arbitrarily many populations, characterizing the mathematical relationship between FST; the frequency M of the more frequent allele at a polymorphic biallelic marker, and the number of subpopulations K. We show that for fixed K, FST has a peculiar constraint as a function of M, with a maximum of 1 only if M = i/K, for integers i with [K/2]≤ i ≤ K - 1: For fixed M, as K grows large, the range of FST becomes the closed or half-open unit interval. For fixed K, however, some M < (K-1)/K always exists at which the upper bound on FST lies below 2√2-2 ≈ 0:8284: We use coalescent simulations to show that under weak migration, FST depends strongly on M when K is small, but not when K is large. Finally, examining data on human genetic variation, we use our results to explain the generally smaller FST values between pairs of continents relative to global FST values. We discuss implications for the interpretation and use of FST. [ABSTRACT FROM AUTHOR]

The last glacial period had a strong influence on the population genetic structure of boreal species in southern and central Europe. In addition, recent and current human impact on the boreal environment has led to habitat loss, which also has a large influence on population genetic structure of species. Here we present the spatial genetic structure of the boreal dragonfly Leucorrhinia dubia using ddRAD sequencing. We sampled individuals from nine locations in Europe, three in Asia (Russia and Japan) and one location of L. intermedia in Japan. Results showed three distinct genetic clusters in Europe. One genetic cluster consisted of individuals sampled from the locations in the Swiss Alps, a second consisted of individuals sampled in the United Kingdom, and a third cluster consisted of individuals from the rest of the seven sampled locations in Europe covering a latitudinal gradient from the French Pyrenees to the north of Finland. There was also a week support that the French Pyrenees and Austrian Alps samples differentiated from the cluster of the five samples from central and north Europe. We suggest that these clusters reflect historical recolonization patterns since the last glaciation. The L. dubia individuals sampled from locations in Asia formed one cluster referring to L. dubia orientalis separated from the individuals sampled in European and from the L. intermedia locality sampled. Our result suggests that aquatic insects in the fragmented boreal landscape in south central Europe and United Kingdom need conservation consideration. [ABSTRACT FROM AUTHOR]

* Background and Aims Olive is considered a native plant of the eastern side of the Mediterranean basin, from where it should have spread westward along the Mediterranean shores, while little is known about its diffusion in the eastern direction. * Methods Genetic diversity levels and population genetic structure of a wide set of olive ecotypes and varieties collected from several provinces of Iran, representing a high percentage of the entire olive resources present in the area, was screened with 49 chloroplast and ten nuclear simple sequence repeat markers, and coupled with archaeobotanical and historical data on Mediterranean olive varieties. Approximate Bayesian Computation was applied to define the demographic history of olives including Iranian germplasm, and species distribution modelling was performed to understand the impact of the Late Quaternary on olive distribution. * Key Results The results of the present study demonstrated that: (1) the climatic conditions of the last glacial maximum had an important role on the actual olive distribution, (2) all Iranian olive samples had the same maternal inheritance as Mediterranean cultivars, and (3) the nuclear gene flow from the Mediterranean basin to the Iranian plateau was almost absent, as well as the contribution of subspecies cuspidata to the diversity of Iranian olives. * Conclusions Based on this evidence, a new scenario for the origin and distribution of this important fruit crop has been traced. The evaluation of olive trees growing in the eastern part of the Levant highlighted a new perspective on the spread and distribution of olive, suggesting two routes of olive differentiation, one westward, spreading along the Mediterranean basin, and another moving towards the east and reaching the Iranian plateau before its domestication. [ABSTRACT FROM AUTHOR]

All examples of lake charr (Salvelinus namaycush) diversity occur within the largest, deepest lakes of North America (i.e. > 2000 km2). We report here Rush Lake (1.3 km2) as the first example of a small lake with two lake charr morphs (lean and huronicus). Morphology, diet, life history, and genetics were examined to demonstrate the existence of morphs and determine the potential influence of evolutionary processes that led to their formation or maintenance. Results showed that the huronicus morph, caught in deep-water, had a deeper body, smaller head and jaws, higher eye position, greater buoyancy, and deeper peduncle than the shallow-water lean morph. Huronicus grew slower to a smaller adult size, and had an older mean age than the lean morph. Genetic comparisons showed low genetic divergence between morphs, indicating incomplete reproductive isolation. Phenotypic plasticity and differences in habitat use between deep and shallow waters associated with variation in foraging opportunities seems to have been sufficient to maintain the two morphs, demonstrating their important roles in resource polymorphism. Rush Lake expands previous explanations for lake charr intraspecific diversity, from large to small lakes and from reproductive isolation to the presence of gene flow associated with strong ecological drivers. [ABSTRACT FROM AUTHOR]

Despite its population, geographic size, and emerging economic importance, disproportionately little genome-scale research exists into genetic factors that predispose Brazilians to disease, or the population genetics of risk. After identification of suitable proxy populations and careful analysis of tri-continental admixture in 1,538 North-Eastern Brazilians to estimate individual ancestry and ancestral allele frequencies, we computed 400,000 genome-wide locus-specific branch length (LSBL) Fst statistics of Brazilian Amerindian ancestry compared to European and African; and a similar set of differentiation statistics for their Amerindian component compared with the closest Asian 1000 Genomes population (surprisingly, Bengalis in Bangladesh). After ranking SNPs by these statistics, we identified the top 10 highly differentiated SNPs in five genome regions in the LSBL tests of Brazilian Amerindian ancestry compared to European and African; and the top 10 SNPs in eight regions comparing their Amerindian component to the closest Asian 1000 Genomes population. We found SNPs within or proximal to the genes CIITA (rs6498115), SMC6 (rs1834619), and KLHL29 (rs2288697) were most differentiated in the Amerindian-specific branch, while SNPs in the genes ADAMTS9 (rs7631391), DOCK2 (rs77594147), SLC28A1 (rs28649017), ARHGAP5 (rs7151991), and CIITA (rs45601437) were most highly differentiated in the Asian comparison. These genes are known to influence immune function, metabolic and anthropometry traits, and embryonic development. These analyses have identified candidate genes for selection within Amerindian ancestry, and by comparison of the two analyses, those for which the differentiation may have arisen during the migration from Asia to the Americas. [ABSTRACT FROM AUTHOR]

Background and Aims Anthosachne Steudel is a group of allopolyploid species that was derived from hexaploidization between the Asian StY genome Roegneria entity and the Australasia W genome Australopyrum species. Polyploidization and apomixis contribute to taxonomic complexity in Anthosachne. Here, a study is presented on the phylogeny and evolutionary history of Anthosachne australasica. The aims are to demonstrate the process of polyploidization events and to explore the differentiation patterns of the St genome following geographic isolation. Methods Chloroplast rbcL and trnH-psbA and nuclear Acc1 gene sequences of 60 Anthosachne taxa and nine Roegneria species were analysed with those of 33 diploid taxa representing 20 basic genomes in Triticeae. The phylogenetic relationships were reconstructed. A time-calibrated phylogeny was generated to estimate the evolutionary history of A. australasica. Nucleotide diversity patterns were used to assess the divergence within A. australasica and between Anthosachne and its putative progenitors. Key Results Three homoeologous copies of the Acc1 sequences from Anthosachne were grouped with the Acc1 sequences from Roegneria, Pseudoroegneria, Australopyrum, Dasypyrum and Peridictyon. The chloroplast sequences of Anthosachne were clustered with those from Roegneria and Pseudoroegneria. Divergence time for Anthosachne was dated to 4·66 million years ago (MYA). The level of nucleotide diversity in Australasian Anthosachne was higher than that in continental Roegneria. A low level of genetic differentiation within the A. australasica complex was found. Conclusions Anthosachne originated from historical hybridization between Australopyrum species and a Roegneria entity colonized from Asia to Australasia via South-east Asia during the late Miocene. The St lineage served as the maternal donor during the speciation of Anthosachne. A contrasting pattern of population genetic structure exists in the A. australasica complex. Greater diversity in island Anthosachne compared with continental Roegneria might be associated with mutation, polyploidization, apomixis and expansion. It is reasonable to consider that A. australasica var. scabra and A. australasica var. plurinervisa should be included in the A. australasica complex. [ABSTRACT FROM AUTHOR]

Varieties of the economically important ornamental species chrysanthemum have been bred to fit a number of market niches, but the genetic basis and evolutionary relationships among various cultivated types are poorly understood. Here, a DNA marker-based analysis of 199 chrysanthemum entries representing each of the five cultivated types is presented. Aset of >90,000 single nucleotide polymorphisms (SNPs) associated with a minor allele frequency of at least 5% was defined, and used to perform a phylogenetic analysis which corresponded well with the phenotypic classification. The analysis revealed that the small-flowered types, spray cut chrysanthemum (SCC) and potted and ground chrysanthemum (PGC), are more closely related to the wild progenitor species (WC) than are the large-flowered ones, disbud cut chrysanthemum (DCC) and traditional chrysanthemum (TC); and the PGC type was closest. Some 550 genetic regions appeared to have experienced selection in the separation of potted and ground-cover types from disbud cut types, and that between potted and ground-cover types from traditional types. A genome-wide association analysis revealed that seven SNPs lying within six genes were predictive of three important traits (ray floret type, cultivated type and flower shape), but no association with flower color was detected. The study has provided a number of novel insights into evolutionary relationships, the population structure and the genetic basis of some key ornamental traits. [ABSTRACT FROM AUTHOR]

Aims The two coexisting Leymus chinensis ecotypes exhibit remarkable divergences in adaptive strategies under drought and salinity in semi-humid meadows and semi-arid steppes. In order to detect the major genetic and environmental factors dominating the intraspecific phenotype variations and ecotype formation, the questions regarding the two distinct phenotypic forms (ecotypes) in L. chinensis were addressed: (i) did environments drive the L. chinensis ecotype formation? (ii) was there a molecular basis for the morphological divergence between the two ecotypes? (iii) which driving force dominated the intraspecies divergence, divergent natural selection, genetic drift or stabilizing selection?. Methods We applied a series experiments on demographical, morphological and physiological traits of two Leymus chinensis ecotypes with gray green (GG) and yellow green (YG) leaf color in nine wild sites along a longitudinal gradient from 114° to 124°E in northeast China. The environmental data including mean annual precipitation, mean annual temperature, elevation and soil properties were collected. We compared the differences of morphological, physiological and genetic differentiations between the two ecotypes. Important Findings The GG type exhibited stronger fitness than YG type from the population densities, morphological traits (e.g. shoot height, leaf area, leaf and seed weights et al.), leaf mass per area (LMA) and physiological traits [relative water content (RWC), proline, soluble sugar contents]. Most of above phenotypes (e.g. total shoot densities, spike length et al.) were significantly correlated with mean annual precipitation, mean annual temperature and soil water content (SWC), rarely a correlated with soil pH and soil nutrient. Transplanted populations showed convergence trend by their leaf chlorophyll contents and osmotic adjustments (proline and soluble sugar contents) in the greenhouse, but still exhibited their divergences between two ecotypes in the outdoor transplantation, suggesting that whether L. chinensis ecotype differentiated could be largely affected by the environmental conditions. Furthermore, by the comparison result of quantitative genetic variation (QST) values from phenotypes with theoretical neutral genetic differentiation (FST), differentiation in phenotypic traits greatly surpassed neutral predictions, implying that directional natural selection played a crucial role in L. chinensis ecotype differentiation. In addition, microsatellite analysis from Neighbor-joining tree and Bayesian assignment generated into two groups according to ecotypes, indicating molecular genetic differentiation also propelled the two ecotypes divergence. We conclude that L. chinensis population variations were driven by combing divergent natural selection (precipitation, temperature and SWCs) along the large-scale gradient and significantly intrinsic genetic differentiation. [ABSTRACT FROM AUTHOR]

We used data from 12 allozyme loci for two endemic Brassicaceae from Gran Canaria (the endangered narrow endemic Crambe tamadabensis and its more widespread congener C. pritzelii) to assess whether their genetic diversity patterns reflect their phylogenetic closeness and contrasting population sizes and distribution areas, and to derive conservation implications. Genetic diversity values are high for both species and slightly higher in C. tamadabensis, despite its narrow distribution in north-western Gran Canaria. At odds with the generally high interpopulation diversity levels reported in Canarian endemics, values of GST in C. tamadabensis and C. pritzelii are rather low (0.067 and 0.126, respectively). We construe that the higher genetic structure detected in C. pritzelii is mainly a result of unbalanced allele frequencies and low population sizes at the edges of its distribution. The overall high allozyme variation detected in C. tamadabensis and C. pritzelii is nevertheless compatible with an incipient but consistent genetic differentiation between the two species, modulated by recurrent bottlenecks caused by grazing and drift. Our data suggest that conservation efforts aimed at maintaining the existing genetic connectivity in each species and ex situ conservation of seeds are the best strategies to conserve their genetic diversity. [ABSTRACT FROM AUTHOR]

Body size, one of the most important quantitative traits under evolutionary scrutiny, varies considerably among species and among populations within species. Revealing the genetic basis underlying this variation is very important, particularly in humans where there is a close relationship with diseases and in domestic animals as the selective patterns are associated with improvements in production traits. The Debao pony is a horse breed with small body size that is unique to China; however, it is unknown whether the size-related candidate genes identified in Western breeds also account for the small body size of the Debao pony. Here, we compared individual horses from the Debao population with other two Chinese horse populations using single nucleotide polymorphisms (SNPs) identified with the Equine SNP 65 Bead Chip. The previously reported size-related candidate gene HMGA2 showed a significant signature for selection, consistent with its role observed inhuman populations. More interestingly, we found a candidate gene TBX3, which had not been observed in previous studies on horse body size that displayed the highest differentiation and most significant association, and thus likely is the dominating factor for the small stature of the Debao pony. Further comparison between the Debao pony and other breeds of horses from around the world demonstrated that TBX3 was selected independently in the Debao pony, suggesting that there were multiple origins of small stature in the horse. [ABSTRACT FROM AUTHOR]

Understanding the evolutionary processes driving the adaptive differentiation of populations is of broad interest in biology. Genome-wide nucleotide polymorphisms provide the basis for population genetic studies powered by advances in high-throughput sequencing technologies. These advances have led to an extension of genome projects to a variety of non-genetic model organisms, broadening our view on the evolution of gene families and taxonomic-restricted novelties. Here, we review the progress of genome projects in non-Drosophila arthropods, focusing on advances in the analysis of large-scale polymorphism data and functional genomics and examples of population genomic studies. [ABSTRACT FROM AUTHOR]

Local adaptation at range edges influences species' distributions and how they respond to environmental change. However, the factors that affect adaptation, including gene flow and local selection pressures, are likely to vary across different types of range edge. We performed a reciprocal transplant experiment to investigate local adaptation in populations of Plantago lanceolata and P. major from central locations in their European range and from their latitudinal and elevation range edges (in northern Scandinavia and Swiss Alps, respectively). We also characterized patterns of genetic diversity and differentiation in populations using molecular markers. Range-centre plants of P. major were adapted to conditions at the range centre, but performed similarly to range-edge plants when grown at the range edges. There was no evidence for local adaptation when comparing central and edge populations of P. lanceolata. However, plants of both species from high elevation were locally adapted when compared with plants from high latitude, although the reverse was not true. This asymmetry was associated with greater genetic diversity and less genetic differentiation over the elevation gradient than over the latitudinal gradient. Our results suggest that adaptation in some range-edge populations could increase their performance following climate change. However, responses are likely to differ along elevation and latitudinal gradients, with adaptation more likely at high-elevation. Furthermore, based upon these results, we suggest that gene flow is unlikely to constrain adaptation in range-edge populations of these species. [ABSTRACT FROM AUTHOR]

Cryptolaemus montrouzieri Mulsant (Coleoptera: Coccinellidae) is an effective biological control agent of Australian origin, which has been introduced worldwide to control mealybugs. Although successfully used for >100 yr, its introduction in a new area may cause environmental risks should the populations become invasive. In the present study, a population genetics method was used to make predictions of the invasive potential of C. montrouzieri. Our results showed a similar level of genetic diversity among all populations. No significant genetic differentiation between native and introduced populations was observed, while three populations from the native region were significantly divergent. The fact that genetic diversity was not reduced in introduced areas suggests that no bottleneck effect has occurred during introduction. To avoid rapid evolution of the introduced C. montrouzieri, the introduction records of each population should be clearly traced and introductions from multiple sources into the same area should be avoided. [ABSTRACT FROM AUTHOR]