Nuclear vs. plastid data: complex Pleistocene history of a circumpolar key species

Phylogeography of Morella nana: The Wumeng Mountains as a natural geographical isolation boundary on the Yunnan-Guizhou Plateau

The Yunnan-Guizhou Plateau (YGP) is characterized by the distinctive isolated habitat of the limestone Karst Islands and features the Wumeng Mountains, which divide the YGP into the two Plateaus of Yunnan and Guizhou. This study aimed to assess the effects of geographic isolation and past climate fluctuation on the distribution of flora in the YGP. To achieve this, we carried out the phylogeographical pattern and genetic structure based on chloroplast and nuclear ribosomal DNA sequence in relation to past (Last Glacial Maximum) and present distributions based on ecological niche modeling for Morella nana, an important wild plant resource and endemic to the YGP once considered a vulnerable species. The results suggest that the genetic and chlorotype network structures of M. nana are divided into at least two groups: cpDNA chlorotype H2 (or dominant nrDNA haplotypes h1 and h2), distributed primarily to the east of the Wumeng Mountains, and cpDNA chlorotypes H1 and H3-H10 (or dominant nrDNA haplotype h2 and h3), distributed to the west of the Wumeng Mountains. A deep genetic split was noted within the two groups to reach 25 steps, especially for the cpDNA fragment variation. This east-west divergence reveals the existence of a natural geographical isolation boundary in the form of the Wumeng Mountains, and supports the existence of at least two glacial refuges during the Quaternary glacial period, along with two genetic diversity center, and at least two large geographic protection units for the important species of M. nana. This study indicates that the phylogeographical pattern of M. nana can be attributed to geographic/environmental isolation caused by the Wumeng Mountains and climate fluctuation during the last glacial maximum, and proposes an effective strategy to protecting this important plant resource.

Topography-driven microclimate gradients shape forest structure, diversity, and composition in a temperate refugial forest

Macroclimate drives vegetation distributions, but fine-scale topographic variation can generate microclimate refugia for plant persistence in unsuitable areas. However, we lack quantitative descriptions of topography-driven microclimatic variation and how it shapes forest structure, diversity, and composition. We hypothesized that topographic variation and the presence of the forest overstory cause spatiotemporal microclimate variation affecting tree performance, causing forest structure, diversity, and composition to vary with topography and microclimate, and topography and the overstory to buffer microclimate. In a 20.2-ha inventory plot in the North American Great Plains, we censused woody stems ≥1 cm in diameter and collected detailed topographic and microclimatic data. Across 59-m of elevation, microclimate covaried with topography to create a sharp desiccation gradient, and topography and the overstory buffered understory microclimate. The magnitude of microclimatic variation mirrored that of regional-scale variation: with increasing elevation, there was a decrease in soil moisture corresponding to the difference across ~2.1° of longitude along the east-to-west aridity gradient and an increase in air temperature corresponding to the difference across ~2.7° of latitude along the north-to-south gradient. More complex forest structure and higher diversity occurred in moister, less-exposed habitats, and species occupied distinct topographic niches. Our study demonstrates how topographic and microclimatic gradients structure forests in putative climate-change refugia, by revealing ecological processes enabling populations to be maintained during periods of unfavorable macroclimate.

Environmental DNA unveils deep phylogeographic structure of a freshwater fish

Phylogeography bears an important part in ecology and evolution. However, current phylogeographic studies are largely constrained by limited numbers of individual samples. Using an environmental DNA (eDNA) assay for phylogeographic analyses, this study provides detailed information regarding the history of Siberian stone loach Barbatula toni, a primary freshwater fish across the whole range of Hokkaido, Japan. Based on an eDNA metabarcoding on 293 river water samples, we detected eDNA from B. toni in 189 rivers. A total of 51 samples, representing the entire island, were then selected from the B. toni eDNA-positive sample set for the subsequent analyses. To elucidate the phylogeographic structure of B. toni, newly developed eDNA metabarcoding primers (Barba-cytb-F/R) were applied to these samples, specifically targeting their haplotypic variation in cytochrome b. After a bioinformatic processing to mitigate haplotypic false positives, a total of 50 eDNA haplotypes were identified. Two regionally restricted, genetically distinct lineages of the species were revealed as a result of phylogeographic analyses on the haplotypes and tissue-derived DNA from B. toni. According to a molecular clock analysis, they have been genetically isolated for at least 1.5 million years, suggesting their ancient origin and colonisation of Hokkaido, presumably in the glacial periods. These results demonstrate how freshwater fishes can alter their distributions over evolutionary timescales and how eDNA assay can deepen our understanding of phylogeography.

Genetic analyses reveal regional structure and demographic expansion of the predominant tea pest Empoasca onukii (Hemiptera: Cicadellidae) in China

BACKGROUND

The tea green leafhopper, Empoasca onukii Matsuda, is the most destructive insect pest of tea plantations in East Asia. Despite its economic importance and previous studies on this species, it remains unclear as to how this small-sized pest can have such wide range.

RESULTS

By sequencing three mitochondrial genes and 17 microsatellite loci, we revealed the regional structure and demographic expansion of 59 E. onukii populations in China. Bayesian analysis of population genetic structure (BAPS) on microsatellites identified four genetic groups with spatial discontinuities, while analysis on mitochondrial genes inferred five nested and differentiated clusters. Both the Mantel test and the generalized linear model indicated a significant pattern of isolation by geographic distance in E. onukii populations. Based on the approximate Bayesian computation approach, E. onukii was found to have originated from southwestern China and expanded northward and eastward. While MIGRATE-N and Bayesian stochastic search variable selection (BSSVS) procedure in BEAST confirmed the possible eastward and northward dispersal from Yunnan, they also detected more gene flow from the derived populations in central and southeastern China.

CONCLUSION

Our results suggest that the current distribution and structure of E. onukii is complicatedly influenced by human activities of cultivation, wide dissemination of tea in ancient China as well as recent transportation of tea seedlings for establishing new tea plantations. Insights into genetic differentiation and demographic expansion patterns from this study provide an important basis for the development of area-wide management of the E. onukii populations. © 2022 Society of Chemical Industry.

Tracking habitat or testing its suitability? Similar distributional patterns can hide very different histories of persistence versus nonequilibrium dynamics

The expansions and contractions of a species' range in response to temporal changes in selective filters leave genetic signatures that can inform a more accurate reconstruction of their evolutionary history across the landscape. After a long period of continental decline, Australian rainforests settled into localized patterns of contraction or expansion during the climatic fluctuations of the Quaternary. The environmental impacts of recurring glacial and interglacial periods also intensified the arrival of new lineages from the Sunda shelf, and it can be expected that immigrant versus locally persistent taxa responded to environmental challenges in quantifiably different manner. To investigate how such differences impact on species' distribution, we contrast landscape genomic patterns and changes in habitat availability between a species with a long continental history on Doryphora sassafras and a Sunda-derived species (Toona ciliata), across a distributional overlap. Extensive landscape-level homogeneity across chloroplast and nuclear genomes for the Sunda-derived T. ciliata, characterize the genetic signature of a very recent invasion and a rapid southern "exploratory" expansion that had not been previously recorded in the Australian flora (i.e., of Gondwanan origin or Sahul-derived). In contrast, D. sassafras is consistent with other Sahul-derived species characterized by strong geographical divergence and regional differentiation. Interestingly, our findings suggest that admixture between genetically divergent populations during expansion events might be a contributing factor to the successful colonization of novel habitats. Overall, this study identifies some of the mechanisms regulating the rearrangements in species distributions and assemblage composition that follow major environmental shifts, and reminds us how a species' current range might not necessarily define species' habitat preference, with the consequence that estimates of past or future range might not always be reliable.

Landscape genetics of the tropical willow Salix humboldtiana: influence of climate, salinity, and orography in an altitudinal gradient

PREMISE

Gene flow in riparian ecosystems is influenced by landscape features such as orography, climate, and salinity. The downstream increase in genetic diversity (DIGD) hypothesis states that the unidirectionality of the watercourse causes an accumulation of genetic diversity toward downstream populations, while upstream populations are more structured and less diverse, especially in water-dispersed organisms.

METHODS

We used chloroplast and nuclear microsatellites to characterize genetic diversity, structure, and gene flow patterns among populations of Salix humboldtiana across an elevation and salinity gradient on three rivers (Actopan, Antigua, and Blanco) in Mexico. We used optimization of resistance surface methods to determine whether genetic distances between populations are correlated with landscape features.

RESULTS

Positive F_IS values evidenced biparental inbreeding in some populations, particularly at higher elevations where lower niche availability constrains colonization and persistence. Four genetic groups were distinguished, corresponding to populations on the Actopan and Antigua rivers and upstream and downstream on the Blanco, but with high admixture between populations on the Actopan and Antigua rivers. Higher gene flow rates were found among proximate populations on the same river than among different rivers. Genetic diversity increased toward the river mouths, in support of the DIGD hypothesis, probably due to greater niche availability and larger population size. Differences among rivers in precipitation patterns and salinity, as well as geographic distance, were significant predictors of gene flow.

CONCLUSIONS

Our results depict that the DIGD and gene flow patterns in S. humboldtiana result from the complex interaction among physiography, climate, river salinity, and life-history traits of the species.

Genetic variation of the relict maple Acer miyabei: uncovering its history of disjunct occurrence and the role of mountain refugia in shaping genetic diversity

PREMISE

Relict species provide valuable insights into the origin and formation of extant vegetation. Here, we aimed to elucidate the genetic structure and diversity of a riparian relic, Acer miyabei, in Japan. Once widely distributed, it now occurs in three isolated regions. The most northern regional group is located at low elevation on Hokkaido Island, whereas the southernmost group in central Honshu Island is at high elevation in a mountainous landscape. This contrastive distribution enables us to examine the effects of climate oscillations on genetic diversity in relation to topographic variation.

METHODS

We collected 604 individuals of A. miyabei from 43 sites. Their genetic structure and diversity were analyzed using 12 microsatellite markers and cpDNA sequences.

RESULTS

According to structure analyses, ∆K was lowest at K = 2; the clustering essentially separated many of the individuals in the most northern regional group from the others. In contrast, the two southern groups were not clearly differentiated from each other, despite their geographic discontinuity. The proportion of private alleles was high in populations from the mountain terrain in the southern group although the number of extant populations is limited.

CONCLUSIONS

Genetic clustering of A. miyabei is not perfectly congruent with the current patterns of geographic distribution. We infer that disjunction of the two southern groups occurred more recently than that between these groups and the northern group. The mountainous landscape in the most southern region likely provided multiple refugia and contributed to the retention of distinctive genetic variation.

Divergence in the Aquilegia ecalcarata complex is correlated with geography and climate oscillations: Evidence from plastid genome data

Quaternary climate oscillations and geographical heterogeneity play important roles in determining species and genetic diversity distribution patterns, but how these factors affect the migration and differentiation of East Asian plants species at the population level remains poorly understood. The Aquilegia ecalcarata complex, a group that originated in the Late Tertiary and is widely distributed throughout East Asia, displays high genetic variation that is suitable for studying elaborate phylogeographic patterns and demographic history related to the impact of Quaternary climate and geography. We used plastid genome data from 322 individuals in 60 populations of the A. ecalcarata complex to thoroughly explore the impact of Quaternary climate oscillations and geography on the phylogeographic patterns and demographic history of the A. ecalcarata complex through a series of phylogenetic, divergence time estimation, and demographic history analyses. The dry, cold climate and frequent climate oscillations that occurred during the early Pleistocene and the Mid-Pleistocene transition led to the differentiation of the A. ecalcarata complex, which was isolated in various areas. Geographically, the A. ecalcarata complex can be divided into Eastern and Western Clades and five subclades, which conform to the divergence of the East Asian flora. Our results clearly show the impact of Quaternary climate and geography on evolutionary history at the population level. These findings promote the understanding of the relationship between plant genetic differentiation and climate and geographical factors of East Asia at the population level.

Ancient divergence of Indian and Tibetan wolves revealed by recombination-aware phylogenomics

The grey wolf (Canis lupus) expanded its range across Holarctic regions during the late Pleistocene. Consequently, most grey wolves share recent (<100,000 years ago) maternal origins corresponding to a widespread Holarctic clade. However, two deeply divergent (200,000-700,000 years ago) mitochondrial clades are restricted, respectively, to the Indian subcontinent and the Tibetan Plateau, where remaining wolves are endangered. No genome-wide analysis had previously included wolves corresponding to the mitochondrial Indian clade or attempted to parse gene flow and phylogeny. We sequenced four Indian and two Tibetan wolves and included 31 additional canid genomes to resolve the phylogenomic history of grey wolves. Genomic analyses revealed Indian and Tibetan wolves to be distinct from each other and from broadly distributed wolf populations corresponding to the mitochondrial Holarctic clade. Despite gene flow, which was reflected disproportionately in high-recombination regions of the genome, analyses revealed Indian and Tibetan wolves to be basal to Holarctic grey wolves, in agreement with the mitochondrial phylogeny. In contrast to mitochondrial DNA, however, genomic findings suggest the possibility that the Indian wolf could be basal to the Tibetan wolf, a discordance potentially reflecting selection on the mitochondrial genome. Together, these findings imply that southern regions of Asia have been important centers for grey wolf evolution and that Indian and Tibetan wolves represent evolutionary significant units (ESUs). Further study is needed to assess whether these ESUs warrant recognition as distinct species. This question is especially urgent regarding the Indian wolf, which represents one of the world's most endangered wolf populations.

The role of anthropogenic dispersal in shaping the distribution and genetic composition of a widespread North American tree species

Dispersal and colonization are among the most important ecological processes for species persistence as they allow species to track changing environmental conditions. During the last glacial maximum (LGM), many cold-intolerant Northern Hemisphere plants retreated to southern glacial refugia. During subsequent warming periods, these species expanded their ranges northward. Interestingly, some tree species with limited seed dispersal migrated considerable distances after the LGM ~19,000 years before present (YBP). It has been hypothesized that indigenous peoples may have dispersed valued species, in some cases beyond the southern limits of the Laurentide Ice Sheet. To investigate this question, we employed a molecular genetics approach on a widespread North American understory tree species whose fruit was valued by indigenous peoples. Twenty putative anthropogenic (near pre-Columbian habitations) and 62 wild populations of Asimina triloba (pawpaw), which produces the largest edible fruit of any North American tree, were genetically assayed with nine microsatellite loci. Putative anthropogenic populations were characterized by reduced genetic diversity and greater excess heterozygosity relative to wild populations. Anthropogenic populations in regions that were glaciated during the LGM had profiles consistent with founder effects and reduced gene flow, and shared rare alleles with wild populations hundreds of kilometers away (mean = 723 km). Some of the most compelling evidence for human-mediated dispersal is that putative anthropogenic and wild populations sharing rare alleles were separated by significantly greater distances (mean = 695 km) than wild populations sharing rare alleles (mean = 607 km; p = .014). Collectively, the genetic data suggest that long-distance dispersal played an important role in the distribution of pawpaw and is consistent with the hypothesized role of indigenous peoples.

Plant material selection, collection, preservation, and storage for nuclear DNA content estimation

In theory, any plant tissue providing intact nuclei in sufficient quantity is suitable for nuclear DNA content estimation using flow cytometry (FCM). While this certainly opens a wide variety of possible applications of FCM, especially when compared to classical karyological techniques restricted to tissues with active cell division, tissue selection and quality may directly affect the precision (and sometimes even reliability) of FCM measurements. It is usually convenient to first consider the goals of the study to either aim for the highest possible accuracy of estimates (e.g., for inferring genome size, detecting homoploid intraspecific genome size variation, aneuploidy, among others), or to decide that histograms of reasonable resolution provide sufficient information (e.g., ploidy level screening within a single model species). Here, a set of best practices guidelines for selecting the optimal plant tissue for FCM analysis, sampling of material, and material preservation and storage are provided. In addition, factors potentially compromising the quality of FCM estimates of nuclear DNA content and data interpretation are discussed.

Phylogeographic reconstructions can be biased by ancestral shared alleles: The case of the polymorphic lichen Bryoria fuscescens in Europe and North Africa

Large phylogeographic studies on lichens are scarce, and none involves a single species within which different lineages show fixed alternative dispersal strategies. We investigated Bryoria fuscescens (including B. capillaris) in Europe and western North Africa by phenotypically characterizing 1400 specimens from 64 populations and genotyping them with 14 microsatellites. We studied population structure and genetic diversity at the local and continental scales, discussed the post-glacial phylogeography, and compared dispersal capacities of phenotypes with and without soralia. Our main hypothesis is that the estimated phylogeography, migration routes, and dispersal capacities may be strongly biased by ancestral shared alleles. Scandinavia is genetically the richest area, followed by the Iberian Peninsula, the Carpathians, and the Alps. Three gene pools were detected: two partially linked to phenotypic characteristics, and the third one genetically related to the American sister species B. pseudofuscescens. The comparison of one gene pool producing soredia and one not, suggested both as panmictic, with similar levels of isolation by distance (IBD). The migration routes were estimated to span from north to south, in disagreement with the assessed glacial refugia. The presence of ancestral shared alleles in distant populations can explain the similar IBD levels found in both gene pools while producing a false signal of panmixia, and also biasing the phylogeographic reconstruction. The incomplete lineage sorting recorded for DNA sequence loci also supports this hypothesis. Consequently, the high diversity in Scandinavia may rather come from recent immigration into northern populations than from an in situ diversification. Similar patterns of ancestral shared polymorphism may bias the phylogeographical reconstruction of other lichen species.

Phylogeographic analysis of shrubby beardtongues reveals range expansions during the Last Glacial Maximum and implicates the Klamath Mountains as a hotspot for hybridization

Quaternary glacial cycles often altered species' geographic distributions, which in turn altered the geographic structure of species' genetic diversity. In many cases, glacial expansion forced species in temperate climates to contract their ranges and reside in small pockets of suitable habitat (refugia), where they were likely to interact closely with other species, setting the stage for potential gene exchange. These introgression events, in turn, would have degraded species boundaries, making the inference of phylogenetic relationships challenging. Using high-throughput sequence data, we employed a combination of species distribution models and hybridization tests to assess the effect of glaciation on the geographic distributions, phylogenetic relationships, and patterns of gene flow of five species of Penstemon subgenus Dasanthera, long-lived shrubby angiosperms distributed throughout the Pacific Northwest of North America. Surprisingly, we found that rather than reducing their ranges to small refugia, most Penstemon subgenus Dasanthera species experienced increased suitable habitat during the Last Glacial Maximum relative to the present day. We also found substantial evidence for gene exchange between species, with the bulk of introgression events occurring in or near the Klamath Mountains of southwestern Oregon and northwestern California. Subsequently, our phylogenetic inference reveals blurred taxonomic boundaries in the Klamath Mountains, where introgression is most prevalent. Our results question the classical paradigm of temperate species' responses to glaciation and highlight the importance of contextualizing phylogenetic inference with species' histories of introgression.

Multisource noninvasive genetics of brown bears (Ursus arctos) in Greece reveals a highly structured population and a new matrilineal contact zone in southern Europe

In human-dominated landscapes, connectivity is crucial for maintaining demographically stable mammalian populations. Here, we provide a comprehensive noninvasive genetic study for the brown bear population in the Hellenic Peninsula. We analyze its population structuring and connectivity, estimate its population size throughout its distribution, and describe its phylogeography in detail for the first time. Our results, based on 150 multilocus genotypes and on 244-bp sequences of the mtDNA control region, show the population is comprised by three highly differentiated genetic clusters, consistent with geographical populations of Pindos, Peristeri, and Rhodope. By detecting two male bears with Rhodopean ancestry in the western demes, we provide strong evidence for the ongoing genetic connectivity of the geographically fragmented eastern and western distributions, which suggests connectivity of the larger East Balkan and Pindos-Dinara populations. Total effective population size (N e) was estimated to be 199 individuals, and total combined population size (N C) was 499, with each cluster showing a relatively high level of genetic variability, suggesting that migration has been sufficient to counteract genetic erosion. The mtNDA results were congruent with the microsatellite data, and the three genetic clusters were matched predominantly with an equal number of mtDNA haplotypes that belong to the brown bear Western mitochondrial lineage (Clade 1), with two haplotypes being globally new and endemic. The detection of a fourth haplotype that belongs to the Eastern lineage (Clade 3a1) in three bears from the western distribution places the southernmost secondary contact zone between the Eastern and Western lineages in Greece and generates new hypotheses about postglacial maxima migration routes. This work indicates that the genetic composition and diversity of Europe's low-latitude fringe population are the outcome of ancient and historical events and highlight its importance for the connectivity and long-term persistence of the species in the Balkans.

Genetic data improves niche model discrimination and alters the direction and magnitude of climate change forecasts

Ecological niche models (ENMs) have classically operated under the simplifying assumptions that there are no barriers to gene flow, species are genetically homogeneous (i.e., no population-specific local adaptation), and all individuals share the same niche. Yet, these assumptions are violated for most broadly distributed species. Here, we incorporate genetic data from the widespread riparian tree species narrowleaf cottonwood (Populus angustifolia) to examine whether including intraspecific genetic variation can alter model performance and predictions of climate change impacts. We found that (1) P. angustifolia is differentiated into six genetic groups across its range from México to Canada and (2) different populations occupy distinct climate niches representing unique ecotypes. Comparing model discriminatory power, (3) all genetically informed ecological niche models (gENMs) outperformed the standard species-level ENM (3-14% increase in AUC; 1-23% increase in pROC). Furthermore, (4) gENMs predicted large differences among ecotypes in both the direction and magnitude of responses to climate change and (5) revealed evidence of niche divergence, particularly for the Eastern Rocky Mountain ecotype. (6) Models also predicted progressively increasing fragmentation and decreasing overlap between ecotypes. Contact zones are often hotspots of diversity that are critical for supporting species' capacity to respond to present and future climate change, thus predicted reductions in connectivity among ecotypes is of conservation concern. We further examined the generality of our findings by comparing our model developed for a higher elevation Rocky Mountain species with a related desert riparian cottonwood, P. fremontii. Together our results suggest that incorporating intraspecific genetic information can improve model performance by addressing this important source of variance. gENMs bring an evolutionary perspective to niche modeling and provide a truly "adaptive management" approach to support conservation genetic management of species facing global change.

Refugia within refugium of Geranium yesoense (Geraniaceae) in Japan were driven by recolonization into the southern interglacial refugium

Recent studies have found that geographical fragmentation and recurrent colonization result in complex genetic structures in refugial areas. This phenomenon, known as ‘refugia within refugium’, has been identified from many geographical locations. In Japan, the high-elevation mountains of central Honshu provided an interglacial refugium for alpine plants. Here we focused on the Geranium yesoense complex, which exhibits increased morphological variation in the refugial area, to determine whether this variation was shaped by recurrent colonization, range fragmentation or phenotypic changes independent of population history. We analysed single nucleotide polymorphism data and chloroplast genome sequences. Diversification in the G. yesoense species complex occurred in the mid-Pleistocene. The varieties are distinct entities and suggest the presence of a genetic cluster with highly disjunct distributions, occurring both in northern Japan and in southern refugial areas in central Honshu. Demographic analysis suggests that a single ancestral variety (var. nipponicum) evolved in the alpine region of central Honshu, and that subsequent migration from one of the two diverged northern varieties (var. pseudopratense) led to secondary contact with var. nipponicum during the last glacial period. Recolonization into refugial populations in central Honshu and hybridization between diverged populations have resulted in complex genetic structures among refugial populations.

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.

Genomic insights on the contribution of balancing selection and local adaptation to the long-term survival of a widespread living fossil tree, Cercidiphyllum japonicum

'Living fossils' are testimonies of long-term sustained ecological success, but how demographic history and natural selection contributed to their survival, resilience, and persistence in the face of Quaternary climate fluctuations remains unclear. To better understand the interplay between demographic history and selection in shaping genomic diversity and evolution of such organisms, we assembled the whole genome of Cercidiphyllum japonicum, a widespread East Asian Tertiary relict tree, and resequenced 99 individuals of C. japonicum and its sister species, Cercidiphyllum magnificum (Central Japan). We dated this speciation event to the mid-Miocene, and the intraspecific lineage divergence of C. japonicum (China vs Japan) to the Early Pliocene. Throughout climatic upheavals of the late Tertiary/Quaternary, population bottlenecks greatly reduced the genetic diversity of C. japonicum. However, this polymorphism loss was likely counteracted by, first, long-term balancing selection at multiple chromosomal and heterozygous gene regions, potentially reflecting overdominance, and, second, selective sweeps at stress response and growth-related genes likely involved in local adaptation. Our findings contribute to a better understanding of how living fossils have survived climatic upheaval and maintained an extensive geographic range; that is, both types of selection could be major factors contributing to the species' survival, resilience, and persistence.

High-throughput sequencing of 5S-IGS in oaks: Exploring intragenomic variation and algorithms to recognize target species in pure and mixed samples

Measuring biological diversity is a crucial but difficult undertaking, as exemplified in oaks where complex patterns of morphological, ecological, biogeographical and genetic differentiation collide with traditional taxonomy, which measures biodiversity in number of species (or higher taxa). In this pilot study, we generated high-throughput sequencing amplicon data of the intergenic spacer of the 5S nuclear ribosomal DNA cistron (5S-IGS) in oaks, using six mock samples that differ in geographical origin, species composition and pool complexity. The potential of the marker for automated genotaxonomy applications was assessed using a reference data set of 1,770 5S-IGS cloned sequences, covering the entire taxonomic breadth and distribution range of western Eurasian Quercus, and applying similarity (blast) and evolutionary approaches (maximum-likelihood trees and Evolutionary Placement Algorithm). Both methods performed equally well, allowing correct identification of species in sections Ilex and Cerris in the pure and mixed samples, and main lineages shared by species of sect. Quercus. Application of different cut-off thresholds revealed that medium- to high-abundance (>10 or 25) sequences suffice for a net species identification of samples containing one or a few individuals. Lower thresholds identify phylogenetic correspondence with all target species in highly mixed samples (analogous to environmental bulk samples) and include rare variants pointing towards reticulation, incomplete lineage sorting, pseudogenic 5S units and in situ (natural) contamination. Our pipeline is highly promising for future assessments of intraspecific and interpopulation diversity, and of the genetic resources of natural ecosystems, which are fundamental to empower fast and solid biodiversity conservation programmes worldwide.

Incorporating differences between genetic diversity of trees and herbaceous plants in conservation strategies

Reviews that summarize the genetic diversity of plant species in relation to their life history and ecological traits show that forest trees have more genetic diversity at population and species levels than annuals or herbaceous perennials. In addition, among-population genetic differentiation is significantly lower in trees than in most herbaceous perennials and annuals. Possible reasons for these differences between trees and herbaceous perennials and annuals have not been discussed critically. Several traits, such as high rates of outcrossing, long-distance pollen and seed dispersal, large effective population sizes (N_e ), arborescent stature, low population density, longevity, overlapping generations, and occurrence in late successional communities, may make trees less sensitive to genetic bottlenecks and more resistant to habitat fragmentation or climate change. We recommend that guidelines for genetic conservation strategies be designed differently for tree species versus other types of plant species. Because most tree species fit an LH scenario (low [L] genetic differentiation and high [H] genetic diversity), tree seeds could be sourced from a few populations distributed across the species' range. For the in situ conservation of trees, translocation is a viable option to increase N_e . In contrast, rare herbaceous understory species are frequently HL (high differentiation and low diversity) species. Under the HL scenario, seeds should be taken from many populations with high genetic diversity. In situ conservation efforts for herbaceous plants should focus on protecting habitats because the typically small populations of these species are vulnerable to the loss of genetic diversity. The robust allozyme genetic diversity databases could be used to develop conservation strategies for species lacking genetic information. As a case study of reforestation with several tree species in denuded areas on the Korean Peninsula, we recommend the selection of local genotypes as suitable sources to prevent adverse effects and to insure the successful restoration in the long term.

Rear-edge, low-diversity, and haplotypic uniformity in cold-adapted Bupleurum euphorbioides interglacial refugia populations

The high genetic diversity of rear-edge refugia populations is predicted to have resulted from species repeatedly migrating to low latitudes during glacial periods over the course of Quaternary climate change. However, several recent empirical studies of cold-tolerant plants revealed the opposite pattern. We investigated whether current habitats of the cold-adapted and range-restricted Bupleurum euphorbioides in the Baekdudaegan, South Korea, and North Korea could be interglacial refugia, and documented how their rear-edge populations differ genetically from those of typical temperate species. Phylogeographic analysis and ecological niche modeling (ENM) were used. The genetic structure was analyzed using microsatellite markers and chloroplast DNA sequences. The congener B. longiradiatum was included as a typical temperate plant species. Despite having almost identical life history traits, these congeneric species exhibited contrasting patterns of genetic diversity. ENM revealed an apparent maximum range contraction during the last interglacial. In contrast, its range expanded northward to the Russian Far East (Primorsky) during the Last Glacial Maximum. Thus, we hypothesize that B. euphorbioides retreated to its current refugia during interglacial periods. Unlike populations in the central region, the rear-edge populations were genetically impoverished and uniform, both within populations and in pooled regional populations. The rear-edge B. euphorbioides survived at least one past interglacial, contributing to the species' genetic diversity. We believe that such genetic variation in the cold-adapted B. euphorbioides gives the species the necessary adaptations to survive an upcoming favorable environment (the next glacial), unless there is artificial environmental change.

Ancient drainage networks mediated a large-scale genetic introgression in the East Asian freshwater snails

Biogeography and genetic variation of freshwater organisms are influenced not only by current freshwater connections but also by past drainage networks. The Seto Inland Sea is a shallow enclosed sea in Japan, but geological evidence showed that a large freshwater drainage had intermittently appeared in this area between the late Pliocene and Pleistocene. Here, we demonstrated that this paleodrainage greatly affected the genetic variation of the East Asian freshwater snails, Semisulcospira spp. We found that the mtDNA haplotypes originated in the Lake Biwa endemic Semisulcospira species at the upstream side of the paleodrainage were frequently observed in the riverine Semisulcospira species at its downstream side. The genome-wide DNA and morphological analyses consistently showed that there was no clear evidence of nuclear introgression between the Lake Biwa endemics and riverine species. These results suggest that the large paleodrainage had facilitated mitochondrial introgression and had broadly spread the introgressed mtDNA haplotypes to its downstream region around the Seto Inland Sea. Our study highlights the role of paleodrainages in shaping the genetic variation of freshwater organisms.

Unraveling the mystery of the glacier bear: Genetic population structure of black bears (Ursus americanus) within the range of a rare pelage type

Glacier bears are a rare grey color morph of American black bear (Ursus americanus) found only in northern Southeast Alaska and a small portion of western Canada. We examine contemporary genetic population structure of black bears within the geographic extent of glacier bears and explore how this structure relates to pelage color and landscape features of a recently glaciated and highly fragmented landscape. We used existing radiocollar data to quantify black bear home-range size within the geographic range of glacier bears. The mean home-range size of female black bears in the study area was 13 km2 (n = 11), whereas the home range of a single male was 86.9 km2. We genotyped 284 bears using 21 microsatellites extracted from noninvasively collected hair as well as tissue samples from harvested bears. We found ten populations of black bears in the study area, including several new populations not previously identified, divided largely by geographic features such as glaciers and marine fjords. Glacier bears were assigned to four populations found on the north and east side of Lynn Canal and the north and west side of Glacier Bay with a curious absence in the nonglaciated peninsula between. Lack of genetic relatedness and geographic continuity between black bear populations containing glacier bears suggest a possible unsampled population or an association with ice fields. Further investigation is needed to determine the genetic basis and the adaptive and evolutionary significance of the glacier bear color morph to help focus black bear conservation management to maximize and preserve genetic diversity.

Afro-alpine flagships revisited: Parallel adaptation, intermountain admixture and shallow genetic structuring in the giant senecios (Dendrosenecio)

Distantly related lineages of the enigmatic giant rosette plants of tropical alpine environments provide classical examples of convergent adaptation. For the giant senecios (Dendrosenecio), the endemic landmarks of the East African sky islands, it has also been suggested that parallel adaptation has been important for within-lineage differentiation. To test this hypothesis and to address potential gene flow and hybridization among the isolated sky islands, we organized field expeditions to all major mountains. We sampled all currently accepted species and all but one subspecies and genotyped 460 plants representing 109 populations. We tested whether genetic structuring corresponds to geography, as predicted by a parallel adaptation hypothesis, or to altitudinal belt and habitat rather than mountains, as predicted by a hypothesis of a single origin of adaptations. Bayesian and Neighbor-Net analyses showed that the main genetic structure is shallow and largely corresponds to geography, supporting a hypothesis of recent, rapid radiation via parallel altitude/habitat adaptation on different mountains. We also found evidence for intermountain admixture, suggesting several long-distance dispersals by wind across vast areas of unsuitable habitat. The combination of parallel adaptation, secondary contact, and hybridization may explain the complex patterns of morphological variation and the contradicting taxonomic treatments of these rare enigmatic giants, supporting the use of wide taxonomic concepts. Notably, the within-population genetic diversity was very low and calls for increased conservation efforts.

Are glacial refugia hotspots of speciation and cytonuclear discordances? Answers from the genomic phylogeography of Spanish common frogs

Subdivided Pleistocene glacial refugia, best known as "refugia within refugia", provided opportunities for diverging populations to evolve into incipient species and/or to hybridize and merge following range shifts tracking the climatic fluctuations, potentially promoting extensive cytonuclear discordances and "ghost" mtDNA lineages. Here, we tested which of these opposing evolutionary outcomes prevails in northern Iberian areas hosting multiple historical refugia of common frogs (Rana cf. temporaria), based on a genomic phylogeography approach (mtDNA barcoding and RAD-sequencing). We found evidence for both incipient speciation events and massive cytonuclear discordances. On the one hand, populations from northwestern Spain (Galicia and Asturias, assigned to the regional endemic R. parvipalmata), are deeply-diverged at mitochondrial and nuclear genomes (~4 My of independent evolution), and barely admix with northeastern populations (assigned to R. temporaria sensu stricto) across a narrow hybrid zone (~25 km) located in the Cantabrian Mountains, suggesting that they represent distinct species. On the other hand, the most divergent mtDNA clade, widespread in Cantabria and the Basque country, shares its nuclear genome with other R. temporaria s. s. lineages. Patterns of population expansions and isolation-by-distance among these populations are consistent with past mitochondrial capture and/or drift in generating and maintaining this ghost mitochondrial lineage. This remarkable case study emphasizes the complex evolutionary history that shaped the present genetic diversity of refugial populations, and stresses the need to revisit their phylogeography by genomic approaches, in order to make informed taxonomic inferences.

From refugia to contact: Pine processionary moth hybrid zone in a complex biogeographic setting

Contact zones occur at the crossroad between specific dispersal routes and are facilitated by biogeographic discontinuities. Here, we focused on two Lepidoptera sister species that come in contact near the Turkish Straits System (TSS). We aimed to infer their phylogeographic histories in the Eastern Mediterranean and finely analyze their co-occurrence and hybridization patterns in this biogeographic context. We used molecular mitochondrial and nuclear markers to study 224 individuals from 42 localities. We used discordances between markers and complementary assignment methods to identify and map hybrids and parental individuals. We confirmed the parapatric distribution of Thaumetopoea pityocampa (Lepidoptera: Notodontidae) in the west and Thaumetopoea wilkinsoni in the east and identified a narrow contact zone. We identified several glacial refugia of T. wilkinsoni in southern Turkey with a strong east-west differentiation in this species. Unexpectedly, T. pityocampa crossed the TSS and occur in northern Aegean Turkey and some eastern Greek islands. We found robust evidence of introgression between the two species in a restricted zone in northwestern Turkey, but we did not identify any F1 individuals. The identified hybrid zone was mostly bimodal. The distributions and genetic patterns of the studied species were strongly influenced both by the Quaternary climatic oscillations and the complex geological history of the Aegean region. T. pityocampa and T. wilkinsoni survived the last glacial maximum in disjoint refugia and met in western Turkey at the edge of the recolonization routes. Expanding population of T. wilkinsoni constrained T. pityocampa to the western Turkish shore. Additionally, we found evidence of recurrent introgression by T. wilkinsoni males in several T. pityocampa populations. Our results suggest that some prezygotic isolation mechanisms, such as differences in timing of the adult emergences, might be a driver of the isolation between the sister species.

Genomic data provide new insights on the demographic history and the extent of recent material transfers in Norway spruce

Primeval forests are today exceedingly rare in Europe, and transfer of forest reproductive material for afforestation and improvement has been very common, especially over the last two centuries. This can be a serious impediment when inferring past population movements in response to past climate changes such as the last glacial maximum (LGM), some 18,000 years ago. In the present study, we genotyped 1,672 individuals from three Picea species (P. abies, P. obovata, and P. omorika) at 400K SNPs using exome capture to infer the past demographic history of Norway spruce (P. abies) and estimate the amount of recent introduction used to establish the Norway spruce breeding program in southern Sweden. Most of these trees belong to P. abies and originate from the base populations of the Swedish breeding program. Others originate from populations across the natural ranges of the three species. Of the 1,499 individuals stemming from the breeding program, a large proportion corresponds to recent introductions from mainland Europe. The split of P. omorika occurred 23 million years ago (mya), while the divergence between P. obovata and P. abies began 17.6 mya. Demographic inferences retrieved the same main clusters within P. abies than previous studies, that is, a vast northern domain ranging from Norway to central Russia, where the species is progressively replaced by Siberian spruce (P. obovata) and two smaller domains, an Alpine domain and a Carpathian one, but also revealed further subdivision and gene flow among clusters. The three main domains divergence was ancient (15 mya), and all three went through a bottleneck corresponding to the LGM. Approximately 17% of P. abies Nordic domain migrated from P. obovata ~103K years ago, when both species had much larger effective population sizes. Our analysis of genomewide polymorphism data thus revealed the complex demographic history of Picea genus in Western Europe and highlighted the importance of material transfer in Swedish breeding program.

Selfing ability and drift load evolve with range expansion

Colonization at expanding range edges often involves few founders, reducing effective population size. This process can promote the evolution of self-fertilization, but implicating historical processes as drivers of trait evolution is often difficult and requires an explicit model of biogeographic history. In plants, contemporary limits to outcrossing are often invoked as evolutionary drivers of self-fertilization, but historical expansions may shape mating system diversity, with leading-edge populations evolving elevated selfing ability. In a widespread plant, Campanula americana, we identified a glacial refugium in the southern Appalachian Mountains from spatial patterns of genetic drift among 24 populations. Populations farther from this refugium have smaller effective sizes and fewer rare alleles. They also displayed elevated heterosis in among-population crosses, reflecting the accumulation of deleterious mutations during range expansion. Although populations with elevated heterosis had reduced segregating mutation load, the magnitude of inbreeding depression lacked geographic pattern. The ability to self-fertilize was strongly positively correlated with the distance from the refugium and mutation accumulation-a pattern that contrasts sharply with contemporary mate and pollinator limitation. In this and other species, diversity in sexual systems may reflect the legacy of evolution in small, colonizing populations, with little or no relation to the ecology of modern populations.

The presence of a cryptic barrier in the West Pacific Ocean suggests the effect of glacial climate changes on a widespread sea-dispersed plant, Vigna marina (Fabaceae)

Ocean currents are an important driver of evolution for sea-dispersed plants, enabling them to maintain reciprocal gene flow via sea-dispersed diaspores and obtain wide distribution ranges. Although geographic barriers are known to be the primary factors shaping present genetic structure of sea-dispersed plants, cryptic barriers which form clear genetic structure within oceanic regions are poorly understood. To test the presence of a cryptic barrier, we conducted a phylogeographic study together with past demographic inference for a widespread sea-dispersed plant, Vigna marina, using 308 individuals collected from the entire Indo-West Pacific (IWP) region. Chloroplast DNA variation showed strong genetic structure that separated populations into three groups: North Pacific (NP), South Pacific (SP) and Indian Ocean (IN) (F'CT among groups = 0.954-1.000). According to the Approximate Bayesian computation inference, splitting time between NP and SP was approximately 20,200 years (95%HPD, 4,530-95,400) before present. Moreover, a signal of recent population expansion was detected in the NP group. This study clearly showed the presence of a cryptic barrier in the West Pacific region of the distributional range of V. marina. The locations of the cryptic barrier observed in V. marina corresponded to the genetic breaks found in other plants, suggesting the presence of a common cryptic barrier for sea-dispersed plants. Demographic inference suggested that genetic structure related to this cryptic barrier has been present since the last glacial maximum and may reflect patterns of past population expansion from refugia.

Implications of existing local (mal)adaptations for ecological forecasting under environmental change

Standing genetic variation represents a genetic load on population fitness but can also support a rapid response to short-term environmental change, and the greatest potential source of such standing genetic variation typically exists among locally adapted populations living along an environmental gradient. Here, we develop a spatially explicit simulation model to quantify the contribution of existing genetic variation arising from migration-mutation-selection-drift balance to time to extinction under environmental change. Simulations reveal that local adaptation across a species range associated with an underlying environmental gradient could extend time to extinction by nearly threefold irrespective of the rate of environmental change. The potential for preadapted alleles to increase the rate of adaptation changes the relative importance of established extinction risk factors; in particular, it reduced the importance of the breadth of environmental tolerance and it increased the relative importance of fecundity. Although migration of preadapted alleles generally increased persistence time, it decreased it at rates of environmental change close to the critical rate of change by creating a population bottleneck, which ultimately limited the rate at which de novo mutations could arise. An analysis of the extinction dynamics further revealed that one consequence of gene flow is the potential to maximize population growth rate in at least part of the species range, which is likely to have consequences for forecasting the consequences of ecological interactions. Our study shows that predictions of persistence time change fundamentally when existing local adaptations are explicitly taken into account, underscoring the need to preserve and manage genetic diversity.

Late Pleistocene speciation of three closely related tree peonies endemic to the Qinling-Daba Mountains, a major glacial refugium in Central China

Determining the factors promoting speciation is a major task in ecological and evolutionary research and can be aided by phylogeographic analysis. The Qinling-Daba Mountains (QDM) located in central China form an important geographic barrier between southern subtropical and northern temperate regions, and exhibit complex topography, climatic, and ecological diversity. Surprisingly, few phylogeographic analyses and studies of plant speciation in this region have been conducted. To address this issue, we investigated the genetic divergence and evolutionary histories of three closely related tree peony species (Paeonia qiui, P. jishanensis, and P. rockii) endemic to the QDM. Forty populations of the three tree peony species were genotyped using 22 nuclear simple sequence repeat markers (nSSRs) and three chloroplast DNA sequences to assess genetic structure and phylogenetic relationships, supplemented by morphological characterization and ecological niche modeling (ENM). Morphological and molecular genetic analyses showed the three species to be clearly differentiated from each other. In addition, coalescent analyses using DIYABC conducted on nSSR variation indicated that the species diverged from each other in the late Pleistocene, while ecological niche modeling (ENM) suggested they occupied a larger area during the Last Glacial Maximum (LGM) than at present. The combined genetic evidence from nuclear and chloroplast DNA and the results of ENM indicate that each species persisted through the late Pleistocene in multiple refugia in the Qinling, Daba, and Taihang Mountains with divergence favored by restricted gene flow caused by geographic isolation, ecological divergence, and limited pollen and seed dispersal. Our study contributes to a growing understanding of the origin and population structure of tree peonies and provides insights into the high level of plant endemism present in the Qinling-Daba Mountains of Central China.

Comparative phylogeography of five widespread tree species: Insights into the history of western Amazonia

Various historical processes have been put forth as drivers of patterns in the spatial distribution of Amazonian trees and their population genetic variation. We tested whether five widespread tree species show congruent phylogeographic breaks and similar patterns of demographic expansion, which could be related to proposed Pleistocene refugia or the presence of geological arches in western Amazonia. We sampled Otoba parvifolia/glycycarpa (Myristicaceae), Clarisia biflora, Poulsenia armata, Ficus insipida (all Moraceae), and Jacaratia digitata (Caricaceae) across the western Amazon Basin. Plastid DNA (trnH-psbA; 674 individuals from 34 populations) and nuclear ribosomal internal transcribed spacers (ITS; 214 individuals from 30 populations) were sequenced to assess genetic diversity, genetic differentiation, population genetic structure, and demographic patterns. Overall genetic diversity for both markers varied among species, with higher values in populations of shade-tolerant species than in pioneer species. Spatial analysis of molecular variance (SAMOVA) identified three genetically differentiated groups for the plastid marker for each species, but the areas of genetic differentiation were not concordant among species. Fewer SAMOVA groups were found for ITS, with no detectable genetic differentiation among populations in pioneers. The lack of spatially congruent phylogeographic breaks across species suggests no common biogeographic history of these Amazonian tree species. The idiosyncratic phylogeographic patterns of species could be due instead to species-specific responses to geological and climatic changes. Population genetic patterns were similar among species with similar biological features, indicating that the ecological characteristics of species impact large-scale phylogeography.

Ecotypic divergences of the alpine herb Potentilla matsumurae adapted to fellfield-snowbed habitats across a series of mountain sky islands

PREMISE

Divergent selection due to environmental heterogeneity can lead to local adaptation. However, the ecological and evolutionary processes of local adaptation that occurs across multiple regions are often unknown. Our previous studies reported on the ecotypic divergence within a local area of variation of Potentilla matsumurae, an alpine herb adapted to the fellfield-snowbed environment. Here we investigated large-scale geographic patterns of ecotypic differentiation in this species to infer local adaptation and selective forces across multiple regions.

METHODS

We compiled information on the overall distributions of fellfield and snowbed habitats on the mountains in Japan across the distribution of the species. Next, we conducted common garden experiments to test the adaptive divergence of the fellfield-snowbed plants derived from multiple regions. Finally, we evaluated phylogeographic structures based on cpDNA and allozyme variations and inferred the evolutionary history of ecotype differentiation.

RESULTS

The mosaic distribution of the fellfield-snowbed ecotypes across isolated mountaintops constitutes indirect evidence for habitat-specific natural selection. The significant difference in survivorship between the ecotypes observed in a controlled snow environment provides more substantial evidence of local selection. Phylogeographic structures support the hypothesis that ecotypic divergence events from fellfield to snowbed populations occurred independently in at least two distinct regions.

CONCLUSIONS

Ecotypic divergence of P. matsumurae has occurred across a series of mountain sky islands. Local selection in snowy environments is a driving force that maintains the divergent ecotypes across multiple mountain regions and can contribute to the diversification of plants in heavy-snow regions.

Pleistocene climate change and phylogeographic structure of the Gymnocarpos przewalskii (Caryophyllaceae) in the northwest China: Evidence from plastid DNA, ITS sequences, and Microsatellite

Northwestern China has a wealth of endemic species, which has been hypothesized to be affected by the complex paleoclimatic and paleogeographic history during Quaternary. In this paper, we used Gymnocarpos przewalskii as a model to address the evolutionary history and current population genetic structure of species in northwestern China. We employed two chloroplast DNA fragments (rps16 and psbB-psbI), one nuclear DNA fragment (ITS), and simple sequence repeat (SSRs) to investigate the spatial genetic pattern of G. przewalskii. High genetic diversity (cpDNA: h S = 0.330, h T = 0.866; ITS: h S = 0.458, h T = 0.872) was identified in almost all populations, and most of the population have private haplotypes. Moreover, multimodal mismatch distributions were observed and estimates of Tajima's D and Fu's FS tests did not identify significantly departures from neutrality, indicating that recent expansion of G. przewalskii was rejected. Thus, we inferred that G. przewalskii survived generally in northwestern China during the Pleistocene. All data together support the genotypes of G. przewalskii into three groups, consistent with their respective geographical distributions in the western regions-Tarim Basin, the central regions-Hami Basin and Hexi Corridor, and the eastern regions-Alxa Desert and Wulate Prairie. Divergence among most lineages of G. przewalskii occurred in the Pleistocene, and the range of potential distributions is associated with glacial cycles. We concluded that climate oscillation during Pleistocene significantly affected the distribution of the species.

Phylogeography of Potamon ibericum (Brachyura: Potamidae) identifies Quaternary glacial refugia within the Caucasus biodiversity hot spot

Refugia are critical for the maintenance of biodiversity during the periods of Quaternary climatic oscillations. The long-term persistence of refugial populations in a large continuous refugium has resulted in a homogenous pattern of genetic structure among populations, while highly structured evolutionary lineages characterize the restriction of refugial populations to smaller subrefugia. These mechanisms have resulted in the identification of hot spots of biodiversity within putative glacial refugia. We studied phylogeography of Potamon ibericum (Brachyura: Potamidae) in the drainages of the western Caucasus biodiversity hot spot (i.e., Colchis and the Caucasus) to infer spatial genetic structure and potential refugia for a freshwater crab in this region. These areas have traditionally considered as a refugium due to the presence of Tertiary relict species. We integrated population genetic data and historical demographic analysis from cytochrome oxidase subunit I sequences and paleoclimatic data from species distribution modeling (SDM). The results revealed the lack of phylogeographic structure and provided evidence for demographic expansion. The SDM presented a rather homogenous and large refugium that extended from northeast Turkey to Colchis during the last glacial period. In contrast to these findings, previous phylogeographic study on P. ibericum of the eastern Caucasus biodiversity hot spot (i.e., Hyrcania) identified multiple independent refugia. By combining these results, we explain the significance of this important western Palearctic hot spot of biological diversity in shaping the geographic distribution of intraspecific genetic diversity in a freshwater taxon.

Genetic diversity and phylogeography of Daphnia similoides sinensis located in the middle and lower reaches of the Yangtze River

Geographical patterns, climate, and environmental change have important influences on the distribution and spread of aquatic organisms. However, the relationships between the geographical pattern and phylogenetics of Daphnia as well as environmental change are not well known. The genetic diversity and phylogeography of seven D. similoides sinensis populations located in the middle and lower reaches of the Yangtze River were investigated based on the combination of mitochondrial (COI gene) and nuclear (14 microsatellite primers) markers. Based on the mitochondrial gene markers, D. similoides sinensis from the middle and lower reaches of the Yangtze River had one ancestral haplotype and two evolutionary clades. In addition, D. similoides sinensis population deviated from neutral evolution, showing signs of a bottleneck effect followed by population expansion. Based on the microsatellite markers, the seven D. similoides sinensis populations formed three main groups. The dendrogram (NJ/ME) showed that D. similoides sinensis based on the mitochondrial genes marker were obviously clustered two main clades, whereas there were three clades based on the microsatellite markers. Our results suggested that the habitat fragmentation due to the barrier of the dams and sluices promoted the genetic differentiation and phylogeography of D. similoides sinensis populations in the middle and lower reaches of the Yangtze River.

Chloroplast DNA variation in a hyperdiverse tropical tree community

We investigate chloroplast DNA variation in a hyperdiverse community of tropical rainforest trees in French Guiana, focusing on patterns of intraspecific and interspecific variation. We test whether a species genetic diversity is higher when it has congeners in the community with which it can exchange genes and if shared haplotypes are more frequent in genetically diverse species, as expected in the presence of introgression.We sampled a total of 1,681 individual trees from 472 species corresponding to 198 genera and sequenced them at a noncoding chloroplast DNA fragment.Polymorphism was more frequent in species that have congeneric species in the study site than in those without congeners (30% vs. 12%). Moreover, more chloroplast haplotypes were shared with congeners in polymorphic species than in monomorphic ones (44% vs. 28%).Despite large heterogeneities caused by genus-specific behaviors in patterns of hybridization, these results suggest that the higher polymorphism in the presence of congeners is caused by local introgression rather than by incomplete lineage sorting. Our findings suggest that introgression has the potential to drive intraspecific genetic diversity in species-rich tropical forests.

Cross-continental phylogeography of two Holarctic Nymphalid butterflies, Boloria eunomia and Boloria selene

Pleistocene glaciations had significant effects on the distribution and evolution of species inhabiting the Holarctic region. Phylogeographic studies concerning the entire region are still rare. Here, we compared global phylogeographic patterns of one boreo-montane and one boreo-temperate butterflies with largely overlapping distribution ranges across the Northern Hemisphere, but with different levels of range fragmentation and food specialization. We reconstructed the global phylogeographic history of the boreo-montane specialist Boloria eunomia (n = 223) and of the boreo-temperate generalist Boloria selene (n = 106) based on mitochondrial and nuclear DNA markers, and with species distribution modelling (SDM). According to the genetic structures obtained, both species show a Siberian origin and considerable split among populations from Nearctic and Palaearctic regions. According to SDMs and molecular data, both butterflies could inhabit vast areas during the moderate glacials. In the case of B. selene, high haplotype diversity and low geographic structure suggest long-lasting interconnected gene flow among populations. A stronger geographic structuring between populations was identified in the specialist B. eunomia, presumably due to the less widespread, heterogeneously distributed food resources, associated with cooler and more humid climatic conditions. Populations of both species show opposite patterns across major parts of North America and in the case of B. eunomia also across Asia. Our data underline the relevance to cover entire distribution ranges to reconstruct the correct phylogeographic history of species.

No borders during the post-glacial assembly of European bryophytes

Climatic fluctuations during the Last Glacial Maximum (LGM) exerted a profound influence on biodiversity patterns, but their impact on bryophytes, the second most diverse group of land plants, has been poorly documented. Approximate Bayesian computations based on coalescent simulations showed that the post-glacial assembly of European bryophytes involves a complex history from multiple sources. The contribution of allochthonous migrants was 95-100% of expanding populations in about half of the 15 investigated species, which is consistent with the globally balanced genetic diversities and extremely low divergence observed among biogeographical regions. Such a substantial contribution of allochthonous migrants in the post-glacial assembly of Europe is unparalleled in other plants and animals. The limited role of northern micro-refugia, which was unexpected based on bryophyte life-history traits, and of southern refugia, is consistent with recent palaeontological evidence that LGM climates in Eurasia were much colder and drier than what palaeoclimatic models predict.

Molecular Phylogeography and Ecological Niche Modeling of Sibbaldia procumbens s.l. (Rosaceae)

The phylogeographical analysis and ecological niche modeling (ENM) of the widely distributed Northern Hemisphere Sibbaldia procumbens s.l. can help evaluate how tectonic motion and climate change helped shape the current distribution patterns of this species. Three chloroplast regions (the atpI-atpH and trnL-trnF intergenic spacers and the trnL intron) were obtained from 332 (156 from present study and 176 from the previous study) individuals of S. procumbens s.l. An unrooted haplotype network was constructed using the software NETWORK, while BEAST was used to estimate the divergence times among haplotypes. ENM was performed by MAXENT to explore the historical dynamic distribution of S. procumbens s.l. The haplotype distribution demonstrates significant phylogeographical structure (N_ST > G_ST; P < 0.01). The best partitioning of genetic diversity by SAMOVA produced three groups, while the time to the most recent common ancestor of all haplotypes was estimated to originate during the Miocene, with most of the haplotype diversity having occurred during the Quaternary. The MAXENT analysis showed S. procumbens s.l. had a wider distribution range during the last glacial maximum and a narrower distribution range during the last interglacial, with predictions into the future showing the distribution range of S. procumbens s.l. shrinking.

Phylogeography of a widespread eastern North American shrub, Viburnum lantanoides

PREMISE OF THE STUDY

There have been relatively few phylogeographic studies of eastern North American plants, especially of animal-dispersed shrubby species, and this leaves a significant gap in our understanding of how such species were affected by glacial events. Here, we analyzed the phylogeography of the widespread understory shrub Viburnum lantanoides.

METHODS

We generated RADseq data and paleoclimatic species distribution models (SDMs) to identify the locations of refugia where V. lantanoides may have survived the Last Glacial Maximum (LGM) and how its range expanded as glaciers receded.

KEY RESULTS

Genetic diversity falls off with increasing latitude and longitude, indicating that range expansion likely occurred via serial founder events from southern source populations. Samples from the southern Appalachians form a grade, while those from the north form a clade, suggesting that a single genetic lineage recolonized the north. SDMs indicate that V. lantanoides probably survived the LGM in refugia on the mid-Atlantic Coastal Plain and/or the interior Gulf Coastal Plain.

CONCLUSIONS

Our analyses indicate that V. lantanoides survived the LGM in refugia south of the glacier but north of the extensive refugium along the Gulf Coast. Following the LGM, a single population expanded northward along the Appalachian Mountains and eventually into eastern Canada. The patterns observed here suggest that range expansion occurred in a stepwise manner, similar to postglacial dynamics observed in a number of European plant species.

Postglacial colonization history reflects in the genetic structure of natural populations of Festuca rubra in Europe

We conducted a large-scale population genetic survey of genetic diversity of the host grass Festuca rubra s.l., which fitness can be highly dependent on its symbiotic fungus Epichloë festucae, to evaluate genetic variation and population structure across the European range. The 27 studied populations have previously been found to differ in frequencies of occurrence of the symbiotic fungus E. festucae and ploidy levels. As predicted, we found decreased genetic diversity in previously glaciated areas in comparison with nonglaciated regions and discovered three major maternal genetic groups: southern, northeastern, and northwestern Europe. Interestingly, host populations from Greenland were genetically similar to those from the Faroe Islands and Iceland, suggesting gene flow also between those areas. The level of variation among populations within regions is evidently highly dependent on the postglacial colonization history, in particular on the number of independent long-distance seed colonization events. Yet, also anthropogenic effects may have affected the population structure in F. rubra. We did not observe higher fungal infection rates in grass populations with lower levels of genetic variability. In fact, the fungal infection rates of E. festucae in relation to genetic variability of the host populations varied widely among geographical areas, which indicate differences in population histories due to colonization events and possible costs of systemic fungi in harsh environmental conditions. We found that the plants of different ploidy levels are genetically closely related within geographic areas indicating independent formation of polyploids in different maternal lineages.