Geographic Patterns Of Genetic Variation Research Articles

CattleAssigner: A framework for accurate assignment of individuals to cattle lineages and populations using minimum informative markers

Assigning individual animals to their respective breeds, populations or lineages has immense significance in the evolutionary analyses of global cattle populations besides detecting the underlying genetic variation that may likely have facilitated the adaptation of these breeds to diverse environmental conditions. It is also important in discovering the geographic patterns of genetic variation in cattle populations as well as tracing the geographical origin of breeds, food products, and diseases. Given this, the present study was undertaken to elucidate the minimum number of informative single nucleotide polymorphism (SNP) markers, originally generated using medium-density BovineSNP50 BeadChip across 1823 individuals represnting 73 populations, to assign individual animals to the corresponding lineage/group (African or European or Indicine or admixed) and respective populations within that lineage/group using two well-known supervised machine learning (ML) algorithms namely Random Forest (RF) and Extreme Gradient Boosting (XGBoost). Each of the two ML models were trained with the most informative SNP panels (with sizes of 48, 96, and 192) that were elucidated using two statistical methods i.e., principal component analysis (PCA) and Wright's fixation index (FST), and two ML methods (RF with Gini, and RF with MDA). Three panels with the topmost discriminant SNPs (at 192, 96, and 48 densities) were created for each of the marker preselection approaches. These panels were evaluated, based on their performance vis-à-vis animals’ assignment to respective lineage, population group or population. The results showed that XGBoost achieved the best accuracy of 95% with 192-SNP panel (selected via RF with MDA), followed by RF (93% accuracy) with 192-SNP panel (selected via RF with either Gini or MDA), for animal to lineage assignment. Similarly, RF trained with 48-SNP panel (selected via RF with Gini algorithm) achieved the best accuracy of 97% for assigning animals to African lineage, while it achieved the best accuracy of 89% for assigning animals to admixed populations using 96-SNP panel (selected via PCA). On the other hand, XGBoost achieved the best accuracy of 88% for assigning animals to European breeds using 192-SNP panel (selected via FST method). Furthermore, the results with both RF and XGBoost achieved a poor performance of assigning animals of Indicine lineage to the correct group as the best accuracy for such assignment was 66%, achieved using RF with 192-SNP panel (selected via FST method). In conclusion, the study reports the applicability of statistical and ML approaches for identification of discriminatory SNPs, useful the assignment of individuals to corresponding lineages and to respective populations within lineages besides revealing the efficiency of XGBoost and RF-based ML models in performing such assignments. Both the ML models achieved better performance as compared to statistical ones in assigning the animals to specific lineages while they faired comparably similar to each other for the assignment of individuals to respective populations within respective lineages or population groups.

Testing for variation in photoperiodic plasticity in a butterfly: Inconsistent effects of circadian genes between geographic scales.

The genetic components of the circadian clock have been implicated as involved in photoperiodic regulation of winter diapause across various insect groups, thereby contributing to adaptation to adverse seasonal conditions. So far, the effects of within-population variation in these genes have not been well explored. Here, we present an experimental test of the effects of within-population variation at two circadian genes, timeless and period, on photoperiodic responses in the butterfly Pararge aegeria. While nonsynonymous candidate SNPs in both of these genes have previously shown to be associated with diapause induction on a between-population level, in the present experiment no such effect was found on a within-population level. In trying to reconcile these results, we examine sequence data, revealing considerable, previously unknown protein-level variation at both timeless and period across Scandinavian populations, including variants unique to the population studied here. Hence, we hypothesize that these variants may counteract the previously observed diapause-averting effect of the candidate SNPs, possibly explaining the difference in results between the experiments. Whatever the cause, these results highlight how the effects of candidate SNPs may sometimes vary across genetic backgrounds, which complicates evolutionary interpretations of geographic patterns of genetic variation.

Genetic structure of California's elk: a legacy of extirpations, reintroductions, population expansions, and admixture

AbstractCalifornia, USA, is home to 3 subspecies of North American elk (Cervus canadensis): Roosevelt (C. c. roosevelti), Rocky Mountain (C. c. nelsoni), and tule (C. c. nannodes). Effective management requires a baseline understanding of each subspecies' range, admixture zones, and geographic patterns of genetic diversity. To address these questions, we genotyped 1,271 individual elk from California (n = 1,204) and reference populations of Rocky Mountain and Roosevelt elk from Nevada (n = 32) and Oregon (n = 35), USA. Using 19 polymorphic microsatellite loci, we detected admixture between Roosevelt and Rocky Mountain elk at a contact zone in northern California, and between Roosevelt and tule elk in north‐coastal California and central‐coastal California. We identified a genetically distinct population of Roosevelt elk in northwestern California, likely reflecting the remnant population that survived a large demographic decline from overhunting during the 1800s. Tule elk exhibited lower levels of heterozygosity (0.44 ± 0.03 [SD]) and allelic richness (2.9 ± 0.2) than Rocky Mountain (0.58 ± 0.05, 4.9 ± 0.4, respectively) and Roosevelt (0.50 ± 0.06, 4.4 ± 0.6, respectively) elk. Among tule elk populations, heterozygosity varied, with the lowest heterozygosity (0.23 ± 0.05) corresponding to the oldest enclosed herd used over the past century as a source of translocations. Among tule elk populations, genetic structure revealed several cases of successful and unsuccessful reintroduction or augmentation attempts. Results provide an essential baseline for future monitoring and decisions about harvest management, translocations to preserve genetic diversity, and landscape‐level conservation planning to maintain, enhance, or obstruct connectivity of elk populations. Genome‐wide sequencing and analyses are needed to quantify inbreeding absolutely and assess genetic load and the age of admixture where subspecies currently exchange genes.

Taxonomy of West-Palaearctic Lampromeloe (Coleoptera: Meloidae) with the description of a new species

Widely distributed phoretic blister beetles usually display unstructured geographic patterns of genetic diversity within species, resulting from recurrent long-dispersal events across their range. To investigate the extent of this pattern in the phoretic genus Lampromeloe, and particularly in western Mediterranean and European populations of L. variegatus, we performed: (1) a phylogeographic analysis based on fragments of the mitochondrial genes COI and 16S, and (2) a morphological revision based on qualitative and morphometric traits. Two allopatric lineages were recovered within L. variegatus, one distributed across Europe and the other in North Africa. These lineages are readily distinguishable based on morphological traits. We conclude that these lineages constitute two diagnosable evolutionary units and, consequently, we describe the North African populations as a new species, Lampromeloe pantherinus sp. nov. The new species is closely related to L. variegatus, from which it differs mainly by the elytral macrosculpture and by the shape of male genitalia. The elytral macrosculpture of L. pantherinus is somewhat similar to that of L. cavensis, a species widely distributed in the lowlands of the Mediterranean Basin. However, these two non-sister species can be distinguished by the morphology and macrosculpture of the pronotum and by the shape of the male genitalia.

Genomic insights into differentiation and adaptation of Amorphophallus yunnanensis in the mountainous region of Southwest China.

The role of geographical isolation and environmental adaptation in driving the differentiation and radiation of species has been a hotspot in evolutionary biology. The extremely complicated and fragmented geography of the mountainous region of Southwest China provides an excellent system for investigating the process of species divergence in heterogeneous habitats. Amorphophallus yunnanensis is a species of extreme habitat preference that resides mainly in the mountainous region of Southwest China. Here, we used restriction site-associated DNA sequencing (RAD-seq) to characterize the geographic pattern of genetic variation among 19 populations of A. yunnanensis as well as the genomic basis of environmental adaptation. A pattern of low population genetic diversity and high level of genetic differentiation was observed. The genomic data revealed a clear east-west genetic differentiation, with two distinct genetic lineages corresponding to the Guizhou plateau and Yunnan plateau, respectively. However, we discovered demographic expansion of the Guizhou Plateau lineage and recent hybridization in populations at the contact region. Significant levels of isolation by distance along with isolation by environment were detected. Outlier tests and genome-environment association analyses identified 89 putatively adaptive loci that might play a role in environmental adaptation. Our results suggest that the genetic divergence of A. yunnanensis is attributed to geographical isolation together with divergent selection in the mountainous region of Southwest China.

Temperature is a cryptic factor shaping the geographical pattern of genetic variation in Ceratophyllum demersum across a subtropical freshwater lake

Macrophyte habitats exhibit remarkable heterogeneity, encompassing the spatial variation of abiotic and biotic components such as changes in water conditions and weather as well as anthropogenic stressors. Environmental factors are thought to be important drivers shaping the genetic and epigenetic variation of aquatic plants. However, the links among genetic diversity, epigenetic variation, and environmental variables remain largely unclear, especially for clonal aquatic plants. Here, we performed population genetic and epigenetic analyses in conjunction with habitat discrimination to elucidate the environmental factors driving intraspecies genetic and epigenetic variation in hornwort (Ceratophyllum demersum) in a subtropical lake. Environmental factors were highly correlated with the genetic and epigenetic variation of C. demersum, with temperature being a key driver of the genetic variation. Lower temperature was detected to be correlated with greater genetic and epigenetic variation. Genetic and epigenetic variation were positively driven by water temperature, but were negatively affected by ambient air temperature. These findings indicate that the genetic and epigenetic variation of this clonal aquatic herb is not related to the geographic feature but is instead driven by environmental conditions, and demonstrate the effects of temperature on local genetic and epigenetic variation in aquatic systems.

Molecular species delimitation reveals hidden endemism in Faxonius placidus (Hagen 1870) (Decapoda: Astacidea: Cambaridae) in southeastern USA

Abstract Molecular surveys are critical for understanding species boundaries and evolutionary relationships of North American crayfishes, as traditional morphological characters used for taxonomy frequently misrepresent crayfish diversity. The bigclaw crayfish, Faxonius placidus (Hagen, 1870), is currently described as a widely distributed crayfish that is common throughout the Cumberland, Tennessee, and Lower Ohio river drainages. The geographic distribution of F. placidus is based on identifications using traditional morphological characters including the first-form male gonopod, chelae, and rostrum. Within F. placidus, color pattern variation is specific to populations separated by hydrogeographic barriers. We used DNA barcoding data (mtDNA-COI) and genome-wide molecular markers (nuclear SNPs) to examine geographic patterns of genetic variation in F. placidus within the Cumberland and Tennessee river drainages. The federally endangered Nashville crayfish, F. shoupi (Hobbs, 1948), was included in our analyses, as previous phylogenetic reconstructions suggest F. placidus is paraphyletic with respect to F. shoupi. Phylogenetic reconstructions and molecular species delimitation identified four genetically distinct lineages within F. placidus that are paraphyletic with respect to F. shoupi. Our results add to numerous studies demonstrating the utility of robust molecular analyses for understanding the biodiversity of North American crayfishes.

Population bottleneck associated with but likely preceded the recent evolution of self-fertilization in a coastal dune plant.

Evolution of self-fertilization may be initiated by a historical population bottleneck, which should diagnostically reduce lineage-wide genetic variation. However, selfing can also strongly reduce genetic variation after it evolves. Distinguishing process from pattern is less problematic if mating system divergence is recent and geographically simple. Dramatically reduced diversity is associated with the transition from outcrossing to selfing in the Pacific coastal endemic Abronia umbellata that includes large-flowered, self-incompatible populations (var. umbellata) south of San Francisco Bay and small-flowered, autogamous populations (var. breviflora) to the north. Compared to umbellata, synonymous nucleotide diversity across 10 single-copy nuclear genes was reduced by 94% within individual populations and 90% across the whole selfing breviflora lineage, which contained no unique polymorphisms. The geographic pattern of genetic variation is consistent with a single origin of selfing that occurred recently (7-28 kya). These results are best explained by a historical bottleneck, but the two most northerly umbellata populations also contained little variation and clustered with selfing populations, suggesting that substantial diversity loss preceded the origin of selfing. A bottleneck may have set the stage for the eventual evolution of selfing by purging genetic load that prevents the spread of selfing.

Unveiling a hotspot of genetic diversity in southern Italy for the endangered Hermann’s tortoise Testudo hermanni

BackgroundHotspots of intraspecific genetic diversity represent invaluable resources for species to cope with environmental changes, and their identification is increasingly recognized as a major goal of conservation ecology research. However, even for iconic and endangered species, conservation strategies are often planned without thorough information on the geographic patterns of genetic variation. Here, we investigated the spatial patterns of genetic variation of the endangered Hermann’s tortoise Testudo hermanni in the Italian Peninsula by genotyping 174 individuals at 7 microsatellite loci, with the aim to contribute to planning effective conservation strategies.ResultsOrdination-based and Bayesian clustering analyses consistently identified three main genetic clusters, one spread in the central and northern part of the peninsula, and two restricted to southern Italy and Sicily, respectively. The highest levels of genetic diversity were found in populations of the southern cluster and, in particular, at the northern edges of its distribution (He > 0.6, Ar > 2.8 ), that correspond to areas of putative secondary contact and admixture between distinct lineages. Our results clearly identify a hotspot of genetic diversity for the Hermann’s tortoise in southern Italy.ConclusionWe inferred the evolutionary history and the spatial patterns of genetic variation of the Hermann’s tortoise in the Italian Peninsula. We identified three main genetic clusters along the peninsula and a hotspot of intraspecific diversity in southern Italy. Our results underline the urgent need for conservation actions to warrant the long-term persistence of viable tortoise populations in this area. Furthrmore, these data add further evidence to the role of southern Italy as a biodiversity hotspot for temperate fauna, claiming for higher consideration of this area in large scale conservation programs.

Ancient DNA analysis reveals temporal and geographical patterns of mitochondrial diversity in pre-Hispanic populations from Central Argentina.

The study of the ancient populations of Central Argentina has a crucial importance for our understanding of the evolutionary processes in the Southern Cone of South America, given its geographic position as a crossroads. Therefore, the aim of this study is to evaluate the temporal and geographical patterns of genetic variation among the groups that inhabited the current territory of Córdoba Province during the Middle and Late Holocene. We analyzed the mitochondrial haplogroups of 74 individuals and 46 Hypervariable Region I (HVR-I) sequences, both novel and previously reported, from archeological populations of the eastern Plains and western Sierras regions of the province of Córdoba. The HVR-I sequences were also compared with other ancient groups from Argentina and with present-day populations from Central Argentina by pairwise distance analysis and identification of shared haplotypes. Significant differences in haplogroup and haplotype distributions between the two geographical regions were found. Sierras showed genetic affinities with certain ancient populations of Northwestern Argentina, while Plains resembled its neighbors from Santiago del Estero Province and the Pampas region. We did not observe genetic differences among the pre 1200 and post 1200 yBP temporal subsets of individuals defined by the emergence of horticulture, considering both geographical samples jointly. The observed patterns of geographical heterogeneity could indicate the existence of biologically distinct populations inhabiting the mountainous region and the eastern plains of Córdoba Province in pre-Hispanic times. Maternal lineages analyses support a scenario of local evolution with great temporal depth in Central Argentina, with continuity until the present.

What DNA barcodes reveal: microhabitat preference, hunting strategy and dispersal ability drive genetic variation across Iberian spider species

ABSTRACT The current rate of species loss calls for immediate actions to preserve biodiversity and ecosystem functioning. Cataloguing species richness and composition, and revealing how diversity is geographically distributed are the first steps towards designing efficient conservation strategies. Here, we aim to determine diversity patterns and potential drivers of taxonomic and genetic diversity and population structure of Iberian spiders. We used a community level perspective, analysing more than 3000 DNA barcode sequences representing ~370 spider species dwelling in white‐oak forest habitats across the Spanish National Park network. By combining and comparing morphological and DNA barcode‐based species delimitation methods, we assessed their performance and identified putative factors behind cases of incongruence. Our findings uncovered potential overlooked diversity as suggested by the geographic patterns of genetic variation and put a red flag on those taxa that may be undergoing overlooked evolutionary or ecological processes. Spider functional traits associated with foraging strategy, microhabitat preference, ballooning ability and circadian activity explained the observed patterns of population structure across species but did not explain variation in genetic diversity. Overall, our study represents a major step forward in the understanding of large‐scale diversity patterns in Iberian spiders at the community level and provides relevant information to guide future conservation strategies of the so‐far largely overlooked invertebrate diversity.

Another Piece of the Puzzle: Echinococcus oligarthrus Recorded in Jaguarundis (Herpailurus yagouaroundi) in Southern Brazil.

Echinococcus oligarthrus is a tapeworm endemic to South America and widely distributed in the Amazon region. Its lifecycle is maintained by relationships between felids and their prey, mainly small sylvatic rodents, but humans can be infected occasionally. We report two female jaguarundis (Herpailurus yagouaroundi) harboring E. oligarthrus in southern Brazil. The felines were found road killed in periurban areas, and, during necropsy, the small intestine was examined. Visual inspection revealed helminths, which were submitted to microscopy and molecular examination. Morphologically, they were around 2.5 mm long, with four suckers and an armed scolex with two rows of hooks. Phylogenetic reconstruction using cytochrome c oxidase subunit I gene sequences placed samples from south Brazil in the same clade as all other E. oligarthrus samples, but as a sister group. Genetic distance gave similar results, resulting in a divergence of 0.087% between the samples described in this study and other samples. The geographic pattern of genetic diversity, as assessed by analysis of molecular variance, suggests that the divergency results from isolation by distance. This finding expands the geographic range of E. oligarthrus and brings new insights to help understand and prevent the zoonosis it causes.

Population dynamics linked to glacial cycles in Cercis chuniana F. P. Metcalf (Fabaceae) endemic to the montane regions of subtropical China.

The mountains of subtropical China are an excellent system for investigating the processes driving the geographical distribution of biodiversity and radiation of plant populations in response to Pleistocene climate fluctuations. How the major mountain ranges in subtropical China have affected the evolution of plant species in the subtropical evergreen broadleaved forest is an issue with long‐term concern. Here, we focused on Cercis chuniana, a woody species endemic to the southern mountain ranges in subtropical China, to elucidate its population dynamics. We used genotyping by sequencing (GBS) to investigate the spatial pattern of genetic variation among 11 populations. Geographical isolation was detected between the populations located in adjacent mountain ranges, thought to function as geographical barriers due to their complex physiography. Bayesian time estimation revealed that population divergence occurred in the middle Pleistocene, when populations in the Nanling Mts. separated from those to the east. The orientation and physiography of the mountain ranges of subtropical China appear to have contributed to the geographical pattern of genetic variation between the eastern and western populations of C. chuniana. Complex physiography plus long‐term stable ecological conditions across glacial cycles facilitated the demographic expansion in the Nanling Mts., from which contemporary migration began. The Nanling Mts. are thus considered as a suitable area for preserving population diversity and large population sizes of C. chuniana compared with other regions. As inferred by ecological niche modeling and coalescent simulations, secondary contact occurred during the warm Lushan–Tali Interglacial period, with intensified East Asia summer monsoon and continuous habitat available for occupation. Our data support the strong influence of both climatic history and topographic characteristics on the high regional phytodiversity of the subtropical evergreen broadleaved forest in subtropical China.

High-throughput sequencing-based microsatellite genotyping for polyploids to resolve allele dosage uncertainty and improve analyses of genetic diversity, structure and differentiation: A case study of the hexaploid Camellia oleifera.

Conventional microsatellite (simple sequence repeat, SSR) genotyping methods cannot accurately identify polyploid genotypes leading to allele dosage uncertainty, introducing biases in population genetic analysis. Here, a new SSR genotyping method was developed to directly infer accurate polyploid genotypes. The frequency distribution of SSR sequences was obtained based on deep-coverage high-throughput sequencing data. Corrections were performed accounting for the "stutter peak" and amplification efficiency of SSR sequences. Perl scripts and an online SSR genotyping tool "SSRSeq" were provided to process the sequencing data and output genotypes with corrected allele dosages. Hexaploid Camellia oleifera is the dominant woody oilseed crop in China. Understanding the geographical pattern of genetic variation in wild C. oleifera is essential for the conservation and utilization of genetic resources. Six wild C. oleifera populations were sampled across geographical ranges in subtropical evergreen broadleaf forests of China. Using 35 SSR markers, the high-throughput sequencing-based SSRSeq method was applied to obtain accurate hexaploid genotypes of wild C. oleifera. The results demonstrated that the new method could resolve allele dosage uncertainty and considerably improve genetic diversity, structure and differentiation analyses for polyploids. The genetic variation patterns of wild C. oleifera across geographical ranges agree with the "central-marginal hypothesis", stating that genetic diversity is high in the central population and declines from the central to the peripheral populations, and genetic differentiation increases from the centre to the periphery. This method and findings can facilitate the utilization of wild C. oleifera genetic resources for the breeding of cultivated C. oleifera.

Geographic patterns of genetic diversity and fertility restoration ability of Asian and African origin pearl millet populations

A set of 45 diverse Asian and African origin/bred populations of pearl millet were investigated multi-locationally for morphological traits including grain yield and assessed for their fertility restoration ability on three cytoplasmic male sterility (CMS) systems in two contrasting seasons. Significant genetic variation was found for all the yield linked traits. Multivariate analysis for grain yield and its component traits grouped these populations into five clusters. Most of the Asian origin populations grouped into single cluster (Cluster III) and separated from the rest of the African origin populations indicating the presence of correspondence between clustering pattern and geographical origin of the populations. Clusters dominated with Asian populations (As-As) had linkages with early flowering, short plant height, more number of tillers, small and thin panicles, small seeded and low grain yield compared to the clusters dominated by African populations (Af-Af) or African origin and Asian bred (Af-As) populations. Genetically related populations having common parentage were found grouped in same clusters. Fertility restoration/maintainer frequency of 45 populations on three diverse CMS systems revealed that overall fertility restoration frequency was highest for A1 (86%) followed by A4 (37%) and for A5 (7%) CMS system. Five populations were identified as potential sources for developing maintainer lines for all three CMS systems and eight populations were identified specifically for A4 and A5 CMS systems. A set of 11 and four populations were identified for restorer line development exclusively for A1 and A5 CMS system, respectively. Six populations were identified for the development of dual restorers for both A1 and A4 CMS system.

Geographic patterns of genetic diversity in North American trees: a continent-wide analysis

In the Northern Hemisphere, many species have been reported to have greater genetic diversity in southern populations than northern populations — ostensibly due to migration northward following the last glacial maximum. The generality of this pattern, while well-established for some taxa, remains unclear for North American trees. To address this issue, I collected published population genetics data for 73 North American tree species and tested whether genetic diversity was associated with latitude or longitude and whether geographic trends were associated with dispersal traits, range, or study characteristics. I found there were no general geographic patterns in genetic diversity and the strength of the geographic gradients was not associated with any species or study characteristics. The northern and western regions of North America tended to have more species with genetic diversity that declined with latitude, but most species had no significant trend. This work shows that North American trees have complex and individualistic patterns of genetic diversity that may negate explanation by any particular dispersal trait or range characteristic.

Phylogeographic history of Japanese macaques

AbstractAimUnderstanding patterns and processes of geographic genetic variation within and among closely related species is the essence of phylogeography. Japanese macaques, also called snow monkeys, have been extensively studied, particularly in the fields of sociobiology, ecology and experimental biology; however, our knowledge of their evolutionary history is relatively limited. In this study we aimed to elucidate the geographic patterns of genetic variation in Japanese macaques and the processes that underlie them.LocationJapan.TaxaJapanese macaque, Macaca fuscata; rhesus macaque, M. mulatta; Taiwanese macaque, M. cyclopis.MethodsDouble‐digest restriction site‐associated DNA (RAD) sequencing was used to identify genome‐wide single nucleotide variants. We used fineRADstructure, ADMIXTURE and principal component analyses to estimate the genetic population structure. Phylogenetic relationships were then inferred based on neighbour‐net, neighbour‐joining, maximum likelihood and SVDquartets algorithms. We assessed gene flow using demographic inference and ABBA‐BABA tests, and estimated past distributions during the Last Glacial Maximum (LGM) using ecological niche modelling.ResultsJapanese macaques show a sister group relationship with a clade comprising Chinese rhesus, Indian rhesus and Taiwanese macaques. Japanese macaques comprise major north‐eastern and south‐western clades, with a boundary located near central Japan, and gene flow between the north‐eastern and south‐western lineages was detected. Refugia during the LGM were estimated to be distributed in limited areas along the south coasts of the Japanese archipelago.Main conclusionsPhylogeographic variation of Japanese macaques is likely due mainly to northeast–southwest divergence, which resulted from withdrawal into refugia during the glacial period, and subsequent gene flow.

Life history and demographic evolution: Comparative population genetics in sandy beach crustaceans

Studies comparing the distribution of genetic diversity may help revealing connectivity patterns in marine populations, as they allow identifying factors behind genetic population structure and elucidating the relationship between the habitat and resident species. The macrofauna of sandy beaches constitutes an interesting study subject, since it includes species with contrasting life histories and dispersal strategies, with potential implications on connectivity. In this work, COI sequences of three peracaridan species with direct development (the talitrid amphipod Atlantorchestoidea brasiliensis and the cirolanid isopods Excirolana braziliensis and Excirolana armata), and one decapod with planktonic larvae (the hippid mole crab Emerita brasiliensis), were compared in order to evaluate the influence of dispersal and historical processes in the distribution of their genetic diversity in the Uruguayan coast, covering both marine and estuarine beaches located along the Rio de la Plata. The hypothesis that species with similar life histories show similar geographic patterns of genetic diversity did not completely explain the genetic variability observed in these species. The intertidal Emerita brasiliensis and the supralittoral Excirolana braziliensis presented high genetic homogeneity, with evidence of population expansion originated at similar times. This shared pattern of genetic variability could be explained by their tropical origin and recent colonization of the Uruguayan coast. The intertidal Excirolana armata and the supralittoral Atlantorchestoidea brasiliensis presented high variability, although differences between them could be associated with the beach zone they inhabit. The role of salinity affecting connectivity patterns was important in Excirolana armata and Atlantorchestoidea brasiliensis, which showed genetic differentiation between estuarine and oceanic beaches. Results reinforce the concept that the distribution of genetic variability not always reflects contemporary population structure and that it is important to consider the evolutionary history of the species when studying connectivity in sandy beach populations. Finally, the accelerated rates of warming in the region could favor a demographic explosion of Emerita brasiliensis and Excirolana braziliensis, species with tropical affinities, which is coherent with the documented demographic history of both species.

Genetic structure of a widespread alpine shrub Rhododendron aureum (Ericaceae) across East Asia.

The vast territory of East Asia, including southwestern Beringia, is considered to have been almost ice free during the Pleistocene. Cold-resistant flora may have persisted in this region expanding or contracting its range during the climate cooling. Only a few plant genera have been studied with a sampling area across their entire geographic range in East Asia; therefore, the understanding of the biogeographic history of alpine flora in this region remains limited. In the present study, genetic variation and population structure in 21 populations of the alpine shrub Rhododendron aureum across its range in East Asia were assessed using 18 microsatellite loci. Phylogenetic analyses revealed three main genetic groups: Siberia, Northeast, and North Pacific. According to the geographical pattern of genetic diversity, the North Pacific group includes populations from Kamchatka, south of Russian Far East, and territories close to central Japan. This group is the most diverse and likely diverged earlier than the Siberia and Northeast groups. Ecological niche modeling predicts range expansion of this species during the period of cooling and, together with demographic history, suggests that the divergence between the three main genetic groups predated the Last Glacial Maximum. Similar to other cold-resistant species such as Larix sibirica and Juniperus communis, the pattern of genetic diversity of R. aureum supports the survival of the species at high latitudes during the Pleistocene with limited contribution of the southern populations to expansion of the species range to the Northeast region and Siberia.

Hybridization, polyploidy and clonality influence geographic patterns of diversity and salt tolerance in the model halophyte seashore paspalum (Paspalum vaginatum).

In plant species, variation in levels of clonality, ploidy and interspecific hybridization can interact to influence geographic patterns of genetic diversity. These factors commonly vary in plants that specialize on saline habitats (halophytes) and may play a role in how they adapt to salinity variation across their range. One such halophyte is the turfgrass and emerging genomic model system seashore paspalum (Paspalum vaginatum Swartz). To investigate how clonal propagation, ploidy variation, and interspecific hybridization vary across ecotypes and local salinity levels in wild P.vaginatum, we employed genotyping-by-sequencing, cpDNA sequencing and flow cytometry in 218 accessions representing>170 wild collections from throughout the coastal southern United States plus USDA germplasm. We found that the two morphologically distinct ecotypes of P.vaginatum differ in their adaptive strategies. The fine-textured ecotype is diploid and appears to reproduce in the wild both sexually and by clonal propagation; in contrast, the coarse-textured ecotype consists largely of clonally-propagating triploid and diploid genotypes. The coarse-textured ecotype appears to be derived from hybridization between fine-textured P.vaginatum and an unidentified Paspalum species. These clonally propagating hybrid genotypes are more broadly distributed than clonal fine-textured genotypes and may represent a transition to a more generalist adaptive strategy. Additionally, the triploid genotypes vary in whether they carry one or two copies of the P.vaginatum subgenome, indicating multiple evolutionary origins. This variation in subgenome composition shows associations with local ocean salinity levels across the sampled populations and may play a role in local adaptation.