Higher genetic diversity in recolonized areas than in refugia of Alnus glutinosa triggered by continent-wide lineage admixture

Across two phylogeographic breaks: Quaternary evolutionary history of a mountain aspen (Populus rotundifolia) in the Hengduan Mountains

Biogeographical barriers to gene flow are central to plant phylogeography. In East Asia, plant distribution is greatly influenced by two phylogeographic breaks, the Mekong-Salween Divide and Tanaka-Kaiyong Line, however, few studies have investigated how these barriers affect the genetic diversity of species that are distributed across both. Here we used 14 microsatellite loci and four chloroplast DNA fragments to examine genetic diversity and distribution patterns of 49 populations of Populus rotundifolia, a species that spans both the Mekong-Salween Divide and the Tanaka-Kaiyong Line in southwestern China. Demographic and migration hypotheses were tested using coalescent-based approaches. Limited historical gene flow was observed between the western and eastern groups of P. rotundifolia, but substantial flow occurred across both the Mekong-Salween Divide and Tanaka-Kaiyong Line, manifesting in clear admixture and high genetic diversity in the central group. Wind-borne pollen and seeds may have facilitated the dispersal of P. rotundifolia following prevalent northwest winds in the spring. We also found that the Hengduan Mountains, where multiple genetic barriers were detected, acted on the whole as a barrier between the western and eastern groups of P. rotundifolia. Ecological niche modeling suggested that P. rotundifolia has undergone range expansion since the last glacial maximum, and demographic reconstruction indicated an earlier population expansion around 600 Ka. The phylogeographic pattern of P. rotundifolia reflects the interplay of biological traits, wind patterns, barriers, niche differentiation, and Quaternary climate history. This study emphasizes the need for multiple lines of evidence in understanding the Quaternary evolution of plants in topographically complex areas.

Evolution of the Sabulina verna group (Caryophyllaceae) in Europe: A deep split, followed by secondary contacts, multiple allopolyploidization and colonization of challenging substrates

One of the major goals of contemporary evolutionary biology is to elucidate the relative roles of allopatric and ecological differentiation and polyploidy in speciation. In this study, we address the taxonomically intricate Sabulina verna group, which has a disjunct Arctic-alpine postglacial range in Europe and occupies a broad range of ecological niches, including substrates toxic to plants. Using genome-wide ddRAD sequencing combined with morphometric analyses based on extensive sampling of 111 natural populations, we aimed to disentangle internal evolutionary relationships and examine their correspondence with the pronounced edaphic and ploidy diversity within the group. We identified two spatially distinct groups of diploids: a widespread Arctic-alpine group and a spatially restricted yet diverse Balkan group. Most tetraploids exhibited a considerably admixed ancestry derived from both these groups, suggesting their allopolyploid origin. Four genetic clusters in congruence with geography and mostly supported by morphological traits were recognized in the diploid Arctic-alpine group. Tetraploids are split into two distinct and geographically vicariant groups, indicating their repeated polytopic origin. Furthermore, our results also revealed at least five-fold parallel colonization of toxic substrates (serpentine and metalliferous), altogether demonstrating a complex interaction between geography, challenging substrates and polyploidy in the evolution of the group. Finally, we propose a new taxonomic treatment of this complex.

Can a Forest Tree Species Progeny Trial Serve as an Ex Situ Collection? A Case Study on Alnus glutinosa

Scientifically informed decisions for the long-term conservation of extant genetic diversity should combine in situ and ex situ conservation methods. The aim of the present study was to assess if a progeny plantation consisting of several open pollinated (OP) families and established for breeding purposes can also serve as an ex situ conservation plantation, using the case study of a Lithuanian progeny trial of Alnus glutinosa, a keystone species of riparian ecosystems that warrants priority conservation actions. We employed 17 nuclear microsatellite (Simple Sequence Repeat) markers and compared the genetic diversity and copy number of the captured alleles of 22 OP progeny families from this plantation, with 10 wild A. glutinosa populations, originating from the two provenance regions of the species in Lithuania. We conclude that the progeny plantation could be used as an ex situ plantation for the A. glutinosa populations from the first provenance region (represented by eight genetic conservation units (GCU)). Based on the present study's results, we can expect that the A. glutinosa progeny plantation harbors enough genetic diversity of wild A. glutinosa populations from the first provenance region. This progeny plantation can serve as a robust ex situ collection containing local alleles present in at least one wild population with at least 0.05 frequency with 25 replications.

Evolutionary history of Castanea sativa in the Caucasus driven by Middle and Late Pleistocene paleoenvironmental changes

Due to global climate cooling and aridification since the Paleogene, members of the Neogene flora were extirpated from the Northern Hemisphere or were confined to a few refugial areas. For some species, the final reduction/extinction came in the Pleistocene, but some others have survived climatic transformations up to the present. This has occurred in Castanea sativa, a species of high commercial value in Europe and a significant component of the Caucasian forests' biodiversity. In contrast to the European range, neither the historical biogeography nor the population genetic structure of the species in its isolated Caucasian range has been clarified. Here, based on a survey of 21 natural populations from the Caucasus and a single one from Europe, we provide a likely biogeographic reconstruction and genetic diversity details. By applying Bayesian inference, species distribution modelling and fossil pollen data, we estimated (i) the time of the Caucasian-European divergence during the Middle Pleistocene, (ii) the time of divergence among Caucasian lineages and (iii) outlined the glacial refugia for species. The climate changes related to the Early-Middle Pleistocene Transition are proposed as the major drivers of the intraspecific divergence and European-Caucasian disjunction for the species, while the impact of the last glacial cycle was of marginal importance.

Wind-dispersed seeds blur phylogeographic breaks: The complex evolutionary history of Populus lasiocarpa around the Sichuan Basin

The strength of phylogeographic breaks can vary among species in the same area despite being subject to the same geological and climate history due to differences in biological traits. Several important phylogeographic breaks exist around the Sichuan Basin in Southwest China but few studies have focused on wind-dispersed plants. Here, we investigated the phylogeographic patterns and the evolutionary history of Populus lasiocarpa, a wind-pollinated and wind-dispersed tree species with a circum-Sichuan Basin distribution in southwest China. We sequenced and analyzed three plastid DNA fragments (ptDNA) and eight nuclear microsatellites (nSSRs) of 265 individuals of P. lasiocarpa from 21 populations spanning the entire distribution range. Distribution patterns based on nSSR data revealed that there are three genetic groups in P. lasiocarpa. This is consistent with the three phylogeographic breaks (Sichuan Basin, the Kaiyong Line and the 105°E line), where the Sichuan basin acts as the main barrier to gene flow between western and eastern groups. However, the distribution pattern based on ptDNA haplotypes poorly matched the phylogeographic breaks, and wind-dispersed seeds may be one of the main contributing factors. Species distribution modelling suggested a larger potential distribution in the last glacial maximum with a severe bottleneck during the last interglacial. A DIYABC model also suggested a population contraction and expansion for both western and eastern lineages. These results indicate that biological traits are likely to affect the evolutionary history of plants, and that nuclear molecular markers, which experience higher levels of gene flow, might be better indicators of phylogeographic breaks.

Parallel genetic and phenotypic differentiation of Erigeron annuus invasion in China

INTRODUCTION

The factors that determine the growth and spread advantages of an alien plant during the invasion process remain open to debate. The genetic diversity and differentiation of an invasive plant population might be closely related to its growth adaptation and spread in the introduced range. However, little is known about whether phenotypic and genetic variation in invasive plant populations covary during the invasion process along invaded geographic distances.

METHODS

In a wild experiment, we examined the genetic variation in populations of the aggressively invasive species Erigeron annuus at different geographical distances from the first recorded point of introduction (FRPI) in China. We also measured growth traits in the wild and common garden experiments, and the coefficient of variation (CV) of populations in the common garden experiments.

RESULTS AND DISCUSSION

We found that E. annuus populations had better growth performance (i.e., height and biomass) and genetic diversity, and less trait variation, in the long-term introduced region (east) than in the short-term introduced region (west). Furthermore, population growth performance was significantly positively or negatively correlated with genetic diversity or genetic variation. Our results indicate that there was parallel genetic and phenotypic differentiation along the invaded geographic distance in response to adaptation and spread, and populations that entered introduced regions earlier had consistently high genetic diversity and high growth dominance. Growth and reproduction traits can be used as reliable predictors of the adaptation and genetic variation of invasive plants.

Threats, biodiversity drivers and restoration in temperate floodplain forests related to spatial scales

Floodplain forests offer a diversity of habitats and resources for a very wide range of plant and animal species. They also offer many benefits to humankind and are considered essential to the mitigation of the effects of climate change. Nevertheless, throughout the world they are suffering the most intense of anthropogenic pressures so are, of all ecosystems, among the most endangered. Here, we bring together and synthesise existing ecological understanding of the mechanisms underlying the high heterogeneity and diversity of temperate floodplain forests and of the pressures threatening their high biological value due to habitat homogenisation. Floodplain forests depend on the periodic disturbances under which they evolved, including fluvial dynamics, traditional management practices and the activities of herbivores. However, they have been heavily degraded by climate change, invasion of exotic species, river-flow regulation, landscape fragmentation, eutrophication and the cessation of traditional management. We can now observe two general trends in temperate floodplain forests: (1) Due to intensive landscape exploitation, they are now more open and thus prone to the spread of competitive species, including of invasive exotics and (2) Due to the cessation of traditional management, along with modified hydrological conditions, they are composed of species in the later successional stages (i.e., more shade-tolerant and mesic) while light-demanding species are quickly vanishing. Restoration practices have brought about contrasting results when restoration of floodplains to their natural states has been problematic. This is likely because of interplay between various natural and artificial processes not previously taken into proper consideration. We would like to draw attention to the fact that restoration projects or the preservation of existing floodplain forest ecosystems should combine the restoration of watercourses with the mitigation of other important threats acting at different scales of the landscape (spread of invasive species, eutrophication of watersheds and inappropriate forest management).

Genomic constitution and relationships of Ziziphus species collected from Malakand Division, Pakistan

Polyploidization has played a major role in plant evolution and can alter plant morphology, phenology, and ecology within only one or a few generations. Ziziphus species are economically as well as nutritionally important fruit-yielding trees. Identification of genotypes with unique traits or those with higher ploidy levels or a broader genetic base could lead to further improvements within the species. The current study has assessed the ploidy levels in the Ziziphus species (Ziziphus jujuba Mill. and Ziziphus nummularia (Burm. f. Wight & Arn) with phenotypic traits, flow cytometry, and chromosomal count as well as with SSRs markers. Morphological traits were inferred to be the most important drivers of trait variations among the investigated genotypes. The total sugar, total cAMPs, titratable acid, and chlorophyll (a, b, and total) were also significantly different in contrast with diploid plants, which showed that tetraploid Ziziphus had the potential to increase nutritional contents. Out of twenty (20), five (5) Z. jujuba genotypes (ZJL-9, ZJL-12, ZJL-17, ZJL-18, and ZJL-19) were found tetraploid 2n = 4x = 48, with genome size ranging from 965.9 to1238.8 Mb that was significantly higher than the tetraploid Z. jujuba Mill. variety Dongzao. Similarly, Z. nummularia ZNL-07 to ZNL-15 have found tetraploid 2n = 4x = 72 with genomic sizes ranging from 1152.2 to 1746.8 Mb respectively. Simple sequence repeats (SSRs) marker was applied to assess the genetic relationship within Ziziphus genotypes. To the best of our understanding, this is the first report on the identification of naturalized random tetraploids within the Pakistani Ziziphus species. This study provides important insights into the genomic architecture of Ziziphus species with implications for classification, conservation, and improvements of Ziziphus germplasm resources.

Novel Insights Into Refugia at the Southern Margin of the Distribution Range of the Endangered Species Ulmus laevis

Riparian ecosystems, in long-time developed regions, are among the most heavily impacted by human activities; therefore, the distribution of tree riparian species, such as Ulmus laevis, is highly affected. This phenomenon is particularly relevant at the margins of the natural habitat of the species, where populations are small and rare. In these cases, it is difficult to distinguish between relics or introductions, but it is relevant for the restoration of natural habitats and conservation strategies. The aim of this study was to study the phylogeography of the southern distribution of the species. We sequenced the entire chloroplast (cp) genomes of 54 individuals from five sampled populations across different European regions to highlight polymorphisms and analyze their distribution. Thirty-two haplotypes were identified. All the sampled populations showed private haplotypes that can be considered an indicator of long-term residency, given the low mutation rate of organellar DNA. The network of all haplotypes showed a star-like topology, and Serbian haplotypes were present in all branches. The Balkan population showed the highest level of nucleotide and genetic diversity. Low genetic differentiation between populations was observed but we found a significant differentiation among Serbia vs. other provenances. Our estimates of divergent time of U. laevis samples highlight the early split of above all Serbian individuals from other populations, emphasizing the reservoir role of white elm genetic diversity of Serbian population.

Holocene chloroplast genetic variation of shrubs (Alnus alnobetula, Betula nana, Salix sp.) at the siberian tundra-taiga ecotone inferred from modern chloroplast genome assembly and sedimentary ancient DNA analyses

Climate warming alters plant composition and population dynamics of arctic ecosystems. In particular, an increase in relative abundance and cover of deciduous shrub species (shrubification) has been recorded. We inferred genetic variation of common shrub species (Alnus alnobetula, Betula nana, Salix sp.) through time. Chloroplast genomes were assembled from modern plants (n = 15) from the Siberian forest-tundra ecotone. Sedimentary ancient DNA (sedaDNA; n = 4) was retrieved from a lake on the southern Taymyr Peninsula and analyzed by metagenomics shotgun sequencing and a hybridization capture approach. For A. alnobetula, analyses of modern DNA showed low intraspecies genetic variability and a clear geographical structure in haplotype distribution. In contrast, B. nana showed high intraspecies genetic diversity and weak geographical structure. Analyses of sedaDNA revealed a decreasing relative abundance of Alnus since 5,400 cal yr BP, whereas Betula and Salix increased. A comparison between genetic variations identified in modern DNA and sedaDNA showed that Alnus variants were maintained over the last 6,700 years in the Taymyr region. In accordance with modern individuals, the variants retrieved from Betula and Salix sedaDNA showed higher genetic diversity. The success of the hybridization capture in retrieving diverged sequences demonstrates the high potential for future studies of plant biodiversity as well as specific genetic variation on ancient DNA from lake sediments. Overall, our results suggest that shrubification has species-specific trajectories. The low genetic diversity in A. alnobetula suggests a local population recruitment and growth response of the already present communities, whereas the higher genetic variability and lack of geographical structure in B. nana may indicate a recruitment from different populations due to more efficient seed dispersal, increasing the genetic connectivity over long distances.

Analyses of Hybrid Viability across a Hybrid Zone between Two Alnus Species Using Microsatellites and cpDNA Markers

Diploid Alnus glutinosa s. str. and autotetraploid A. rohlenae form a narrow hybrid zone in a study area in southern Serbia, which results in triploid hybrid formation. The vast majority of previous studies have been focused on studies of maternal plants, but the offspring resulting from their crossing have not been much studied. Here, we use the variability of microsatellites and chloroplast DNA between these species and their putative hybrids to create an overall picture of the development of the hybrid zone and its predicted type. To elucidate the gene transfer within both species, the origins of individual ploidies and especially the role of triploid hybrids, a germination experiment was carried out linked with a flow cytometry study of the resulting seedlings. The tension zone model seems to offer the most adequate explanation of our observations, with selection against triploid hybrids and the spatial positioning of the hybrid zone. Despite selection against them, the triploid hybrids play an important role in the exchange of genes between the two species and therefore serve as a bridge for introgression. The presence of fertile triploids is essential for enriching the haplotype diversity between these species and for the development of new genetic lineages.

High genomic diversity in the bank vole at the northern apex of a range expansion: The role of multiple colonizations and end-glacial refugia

The history of repeated northern glacial cycling and southern climatic stability has long dominated explanations for how genetic diversity is distributed within temperate species in Eurasia and North America. However, growing evidence indicates the importance of cryptic refugia for northern colonization dynamics. An important geographic region to assess this is Fennoscandia, where recolonization at the end of the last glaciation was restricted to specific routes and temporal windows. We used genomic data to analyse genetic diversity and colonization history of the bank vole (Myodes glareolus) throughout Europe (>800 samples) with Fennoscandia as the northern apex. We inferred that bank voles colonized Fennoscandia multiple times by two different routes; with three separate colonizations via a southern land-bridge route deriving from a "Carpathian" glacial refugium and one via a north-eastern route from an "Eastern" glacial refugium near the Ural Mountains. Clustering of genome-wide SNPs revealed high diversity in Fennoscandia, with eight genomic clusters: three of Carpathian origin and five Eastern. Time estimates revealed that the first of the Carpathian colonizations occurred before the Younger Dryas (YD), meaning that the first colonists survived the YD in Fennoscandia. Results also indicated that introgression between bank and northern red-backed voles (Myodes rutilus) took place in Fennoscandia just after end-glacial colonization. Therefore, multiple colonizations from the same and different cryptic refugia, temporal and spatial separations and interspecific introgression have shaped bank vole genetic variability in Fennoscandia. Together, these processes drive high genetic diversity at the apex of the northern expansion in this emerging model species.

Genetic Analysis by nuSSR Markers of Silver Birch (Betula pendula Roth) Populations in Their Southern European Distribution Range

In the main distribution area the genetic pattern of silver birch is dominated by two haplotypes: haplotype A located in the western and north-western Europe, and haplotype C in eastern and southeastern Europe, characterized by high levels of neutral genetic variability within populations, and low differentiation among populations. Information about the amount and structure of genetic variation in the southern marginal areas, representing rear populations left during the expansion of this species from southern glacial refugia, are lacking. The general aim of the study was to investigate the existence of the climatic characteristics typical of the environmental niche of the species, jointly to genetic organization, variation and gene flow, in marginal populations on the Italian Apennines and Greek Southern Rhodope and compare them with populations of the southern part of the main distribution range on the Alps and Balkans. Genetic analysis was performed using nuclear microsatellites loci on 311 trees sampled from 14 populations. Environmental analysis was performed on the multivariate analysis of derived climatic variables. The allelic pattern was analyzed to assess genetic diversity, population diversity and differentiation, population structure and gene flow. The geographic and environmental peripherality did not always match, with some Apennine sites at higher elevation enveloped in the environmental niche. In the peripheral populations on the Apennines, we observed a lower genetic diversity and higher differentiation, with evident genetic barriers detected around these sites. These characteristics were not shown in the marginal Greek populations. Unexpectedly, the southern Italian marginal populations showed genetic links with the Greek and central area of the distribution range. The Greek populations also showed evident gene flow with the Alpine and Balkan areas. The disparity of results in these two marginal areas show that it is not the geographic peripherality or even the ecological marginality that may shape the genetic diversity and structure of marginal populations, but primarily their position as part of the continuous range or as disjunct populations. This outcome suggests different considerations on how to manage their gene pools and the role that these rear populations can play in maintaining the biodiversity of this species.

Phylogeography and paleodistribution models of a widespread birch (Betula platyphylla Suk.) across East Asia: Multiple refugia, multidirectional expansion, and heterogeneous genetic pattern

Widespread tree species cover large geographical areas and play important roles in various vegetation types. Understanding how these species responded to historical climatic changes is important for understanding community assembly mechanisms with evolutionary and conservation implications. However, the location of refugial areas and postglacial history of widespread trees in East Asia remain poorly known. We combined microsatellite data (63 populations, 1756 individuals) and ecological niche modeling to examine the range-wide population diversity, genetic structure, and historical demography of a pioneer tree species, Asian white birch (Betula platyphylla Suk.) across East Asia. We found a north-to-south trend of declining genetic diversity and five clusters, corresponding to geographical regions. Different clusters were inferred to have diverged through Pleistocene climatic oscillations and have different expansion routes, leading to genetic admixture in some populations. Ecological niche models indicated that the distribution of B. platyphylla during the last glacial maximum still had a large latitude span with slight shifts toward southeast, and northern populations had more variable distribution ranges than those in the south during later climatic oscillations. Our results reflect the relatively stable distribution through the last glacial-interglacial cycles and recent multidirectional expansion of B. platyphylla, providing new hypotheses for the response pattern of widespread tree species to climate change. The gradual genetic pattern from northeast to southwest and alternative distribution dynamics possibly resulted from environmental differences caused by latitude and topographic heterogeneity.

Habitat preference differentiates the Holocene range dynamics but not barrier effects on two sympatric, congeneric trees (Tristaniopsis, Myrtaceae)

Niche partitioning can lead to differences in the range dynamics of plant species through its impacts on habitat availability, dispersal, or selection for traits that affect colonization and persistence. We investigated whether niche partitioning into upland and riparian habitats differentiates the range dynamics of two closely related and sympatric eastern Australian trees: the mountain water gum (Tristaniopsis collina) and the water gum (T. laurina). Using genomic data from SNP genotyping of 480 samples, we assessed the impact of biogeographic barriers and tested for signals of range expansion. Circuit theory was used to model isolation-by-resistance across three palaeo-environment scenarios: the Last Glacial Maximum, the Holocene Climate Optimum and present-day (1950-2014). Both trees showed similar genetic structure across historically dry barriers, despite evidence of significant environmental niche differentiation and different post-glacial habitat shifts. Tristaniopsis collina exhibits the signature of serial founder effects consistent with recent or rapid range expansion, whilst T. laurina has genetic patterns consistent with long-term persistence in geographically isolated populations despite occupying a broader bioclimatic niche. We found the minor influence of isolation-by-resistance on both species, though other unknown factors appear to shape genetic variation. We postulate that specialized recruitment traits (adapted to flood-disturbance regimes) rather than habitat availability limited post-glacial range expansion in T. laurina. Our findings indicate that niche breadth does not always facilitate range expansion through colonization and migration across barriers, though it can promote long-term persistence in situ.

A spatial stream-network approach assists in managing the remnant genetic diversity of riparian forests

Quantifying the genetic diversity of riparian trees is essential to understand their chances to survive hydroclimatic alterations and to maintain their role as foundation species modulating fluvial ecosystem processes. However, the application of suitable models that account for the specific dendritic structure of hydrographic networks is still incipient in the literature. We investigate the roles of ecological and spatial factors in driving the genetic diversity of Salix salviifolia, an Iberian endemic riparian tree, across the species latitudinal range. We applied spatial stream-network models that aptly integrate dendritic features (topology, directionality) to quantify the impacts of multiple scale factors in determining genetic diversity. Based on the drift hypothesis, we expect that genetic diversity accumulates downstream in riparian ecosystems, but life history traits (e.g. dispersal patterns) and abiotic or anthropogenic factors (e.g. drought events or hydrological alteration) might alter expected patterns. Hydrological factors explained the downstream accumulation of genetic diversity at the intermediate scale that was likely mediated by hydrochory. The models also suggested upstream gene flow within basins that likely occurred through anemophilous and entomophilous pollen and seed dispersal. Higher thermicity and summer drought were related to higher population inbreeding and individual homozygosity, respectively, suggesting that increased aridity might disrupt the connectivity and mating patterns among and within riparian populations.

Genetic Diversity and Population Structure of Alnus cremastogyne as Revealed by Microsatellite Markers

Alnus cremastogyne Burk. is a nonleguminous, nitrogen-fixing tree species. It is also the most important endemic species of Alnus Mill. in China, possessing important ecological functions. This study investigated population genetic variation in A. cremastogyne using 175 trees sampled from 14 populations native to Sichuan Province with 25 simple sequence repeat (SSR) markers. Our analysis showed that A. cremastogyne has an average of 5.83 alleles, 3.37 effective alleles, an expected heterozygosity of 0.63, and an observed heterozygosity of 0.739, indicating a relatively high level of genetic diversity. The A. cremastogyne populations in Liangshan Prefecture (Meigu, Mianning) showed the highest level of genetic diversity, whereas the Yanting population had the lowest. Our analysis also showed that the average genetic differentiation of 14 A. cremastogyne populations was 0.021. Analysis of molecular variance (AMOVA) revealed that 97% of the variation existed within populations; only 3% was among populations. Unweighted pair-group method with arithmetic means (UPGMA) clustering and genetic structure analysis showed that the 14 A. cremastogyne populations could be clearly divided into three clusters: Liangshan Prefecture population, Ganzi Prefecture population, the other population in the mountain area around the Sichuan Basin and central Sichuan hill area, indicating some geographical distribution. Further analysis using the Mantel test showed that this geographical distribution was significantly correlated with elevation.

Patterns of diversity, endemism and specialization in the root symbiont communities of alder species on the island of Corsica

We investigated whether the diversity, endemicity and specificity of alder symbionts could be changed by isolation in a Mediterranean glacial refugium. We studied both ectomycorrhizal (EM) fungi and nitrogen-fixing actinobacteria associated with alders, and compared their communities in Corsica and on the European continent. Nodules and root tips were sampled on the three alder species present in Corsica and continental France and Italy. Phylogenies based on internal transcribed spacer (ITS) and a multilocus sequence analysis approach were used to characterize fungal and Frankia species, respectively. Patterns of diversity, endemism and specialization were compared between hosts and regions for each symbiont community. In Corsica, communities were not generally richer than on the mainland. The species richness per site depended mainly on host identity: Alnus glutinosa and Alnus cordata hosted richer Frankia and EM communities, respectively. Half of the Frankia species were endemic to Corsica against only 4% of EM species. Corsica is not a hotspot of diversity for all alder symbionts but sustains an increased frequency of poor-dispersers such as hypogeous fungi. Generalist EM fungi and host-dependent profusely sporulating (Sp+) Frankia were abundantly associated with Corsican A. cordata, a pattern related to a more thermophilic and xerophylic climate and to the co-occurrence with other host trees.

Climatic differentiation in polyploid apomictic Ranunculus auricomus complex in Europe

Background

Polyploidy and apomixis are important factors influencing plant distributions often resulting in range shifts, expansions and geographical parthenogenesis. We used the Ranunculus auricomus complex as a model to asses if the past and present distribution and climatic preferences were determined by these phenomena.

Results

Ecological differentiation among diploids and polyploids was tested by comparing the sets of climatic variables and distribution modelling using 191 novel ploidy estimations and 561 literature data. Significant differences in relative genome size on the diploid level were recorded between the “auricomus” and “cassubicus” groups and several new diploid occurrences were found in Slovenia and Hungary. The current distribution of diploids overlapped with the modelled paleodistribution (22 kyr BP), except Austria and the Carpathians, which are proposed to be colonized later on from refugia in the Balkans. Current and historical presence of diploids from the R. auricomus complex is suggested also for the foothills of the Caucasus. Based on comparisons of the climatic preferences polyploids from the R. auricomus complex occupy slightly drier and colder habitats than the diploids.

Conclusions

The change of reproductive mode and selection due to competition with the diploid ancestors may have facilitated the establishment of polyploids within the R. auricomus complex in environments slightly cooler and drier, than those tolerated by diploid ancestors. Much broader distribution of polyploid apomicts may have been achieved due to faster colonization mediated by uniparental reproductive system.

Electronic supplementary material

The online version of this article (10.1186/s12898-018-0172-1) contains supplementary material, which is available to authorized users.

Strong population bottleneck and repeated demographic expansions of Populus adenopoda (Salicaceae) in subtropical China

BACKGROUND AND AIMS

Glacial refugia and inter-/postglacial recolonization routes during the Quaternary of tree species in Europe and North America are well understood, but far less is known about those of tree species in subtropical eastern Asia. Thus, we have examined the phylogeographic history of Populus adenopoda (Salicaceae), one of the few poplars that naturally occur in this subtropical area.

METHODS

Genetic variations across the range of the species in subtropical China were surveyed using ten nuclear microsatellite loci and four chloroplast fragments (matK, trnG-psbK, psbK-psbI and ndhC-trnV). Coalescent-based analyses were used to test demographic and migration hypotheses. In addition, species distribution models (SDMs) were constructed to infer past, present and future potential distributions of the species.

KEY RESULTS

Thirteen chloroplast haplotypes were detected, and haplotype-rich populations were found in central and southern parts of the species' range. STRUCTURE analyses of nuclear microsatellite loci suggest obvious lineage admixture, especially in peripheral and northern populations. DIYABC analysis suggests that the species might have experienced two independent rounds of demographic expansions and a strong bottleneck in the late Quaternary. SDMs indicate that the species' range contracted during the Last Glacial Maximum (LGM), and contracted northward but expanded eastward during the Last Interglacial (LIG).

CONCLUSIONS

Chloroplast data and SDMs suggest that P. adenopoda might have survived in multiple glacial refugia in central and southern parts of its range during the LGM. Populations of the Yunnan-Guizhou Plateau in the southern part have high chloroplast DNA diversity, but may have contributed little to the postglacial recolonization of northern and eastern parts. The three major demographic events inferred by DIYABC coincide with the initiation of the LIG, start of the LGM and end of the LGM, respectively. The species may have experienced multiple rounds of range contraction during glacial periods and range expansion during interglacial periods. Our study corroborates the importance of combining multiple lines of evidence when reconstructing Quaternary population evolutionary histories.

When new human-modified habitats favour the expansion of an amphibian pioneer species: Evolutionary history of the natterjack toad (Bufo calamita) in a coal basin

Human activities affect microevolutionary dynamics by inducing environmental changes. In particular, land cover conversion and loss of native habitats decrease genetic diversity and jeopardize the adaptive ability of populations. Nonetheless, new anthropogenic habitats can also promote the successful establishment of emblematic pioneer species. We investigated this issue by examining the population genetic features and evolutionary history of the natterjack toad (Bufo [Epidalea] calamita) in northern France, where populations can be found in native coastal habitats and coalfield habitats shaped by European industrial history, along with an additional set of European populations located outside this focal area. We predicted contrasting patterns of genetic structure, with newly settled coalfield populations departing from migration-drift equilibrium. As expected, coalfield populations showed a mosaic of genetically divergent populations with short-range patterns of gene flow, and native coastal populations indicated an equilibrium state with an isolation-by-distance pattern suggestive of postglacial range expansion. However, coalfield populations exhibited (i) high levels of genetic diversity, (ii) no evidence of local inbreeding or reduced effective population size and (iii) multiple maternal mitochondrial lineages, a genetic footprint depicting independent colonization events. Furthermore, approximate Bayesian computations suggested several evolutionary trajectories from ancient isolation in glacial refugia during the Pleistocene, with biogeographical signatures of recent expansion probably confounded by human-mediated mixing of different lineages. From an evolutionary and conservation perspective, this study highlights the ecological value of industrial areas, provided that ongoing regional gene flow is ensured within the existing lineage boundaries.

Alder and the Golden Fleece: high diversity of Frankia and ectomycorrhizal fungi revealed from Alnus glutinosa subsp. barbata roots close to a Tertiary and glacial refugium

BACKGROUND

Recent climatic history has strongly impacted plant populations, but little is known about its effect on microbes. Alders, which host few and specific symbionts, have high genetic diversity in glacial refugia. Here, we tested the prediction that communities of root symbionts survived in refugia with their host populations. We expected to detect endemic symbionts and a higher species richness in refugia as compared to recolonized areas.

METHODS

We sampled ectomycorrhizal (EM) root tips and the nitrogen-fixing actinomycete Frankia communities in eight sites colonized by Alnus glutinosa subsp. barbata close to the Caucasus in Georgia. Three sites were located in the Colchis, one major Eurasian climatic refugia for Arcto-Tertiary flora and alders, and five sites were located in the recolonized zone. Endemic symbionts and plant ITS variants were detected by comparing sequences to published data from Europe and another Tertiary refugium, the Hyrcanian forest. Species richness and community structure were compared between sites from refugia and recolonized areas for each symbionts.

RESULTS

For both symbionts, most MOTUs present in Georgia had been found previously elsewhere in Europe. Three endemic Frankia strains were detected in the Colchis vs two in the recolonized zone, and the five endemic EM fungi were detected only in the recolonized zone. Frankia species richness was higher in the Colchis while the contrary was observed for EM fungi. Moreover, the genetic diversity of one alder specialist Alnicola xanthophylla was particularly high in the recolonized zone. The EM communities occurring in the Colchis and the Hyrcanian forests shared closely related endemic species.

DISCUSSION

The Colchis did not have the highest alpha diversity and more endemic species, suggesting that our hypothesis based on alder biogeography may not apply to alder's symbionts. Our study in the Caucasus brings new clues to understand symbioses biogeography and their survival in Tertiary and ice-age refugia, and reveals that isolated host populations could be of interest for symbiont diversity conservation.

Molecular markers provide evidence for a broad-fronted recolonisation of the widespread calcareous grassland species Sanguisorba minor from southern and cryptic northern refugia

Calcareous grasslands belong to the most species-rich and endangered habitats in Europe. However, little is known about the origin of the species typically occurring in these grasslands. In this study we analysed the glacial and post-glacial history of Sanguisorba minor, a typical plant species frequently occurring in calcareous grasslands. The study comprised 38 populations throughout the whole distribution range of the species across Europe. We used molecular markers (AFLP) and applied Bayesian cluster analysis as well as spatial principal components analysis (sPCA) to identify glacial refugia and post-glacial migration routes to Central Europe. Our study revealed significant differences in the level of genetic variation and the occurrence of rare fragments within populations of S. minor and a distinct separation of eastern and western lineages. The analyses uncovered traditional southern but also cryptic northern refugia and point towards a broad fronted post-glacial recolonisation. Based on these results we postulate that incomplete lineage sorting may have contributed to the detected pattern of genetic variation and that S. minor recolonised Central Europe post-glacially from Iberia and northern glacial refugia in France, Belgium or Germany. Our results highlight the importance of refugial areas for the conservation of intraspecific variation in calcareous grassland species.

Panmixia and dispersal from the Mediterranean Basin to Macaronesian Islands of a macrolichen species

The Mediterranean region, comprising the Mediterranean Basin and the Macaronesian Islands, represents a center of diversification for many organisms. The genetic structure and connectivity of mainland and island microbial populations has been poorly explored, in particular in the case of symbiotic fungi. Here we investigated genetic diversity and spatial structure of the obligate outcrossing lichen-forming fungus Parmelina carporrhizans in the Mediterranean region. Using eight microsatellite and mating-type markers we showed that fungal populations are highly diverse but lack spatial structure. This is likely due to high connectivity and long distance dispersal of fungal spores. Consistent with low levels of linkage disequilibrium and lack of clonality, we detected both mating-type idiomorphs in all populations. Furthermore we showed that the Macaronesian Islands are the result of colonization from the Mediterranean Basin. The unidirectional gene flow, though, seemed not to be sufficient to counterbalance the effects of drift, resulting in comparatively allelic poor peripheral populations. Our study is the first to shed light on the high connectivity and lack of population structure in natural populations of a strictly sexual lichen fungus. Our data further support the view of the Macaronesian Islands as the end of the colonization road for this symbiotic ascomycete.

Species Delimitation and Lineage Separation History of a Species Complex of Aspens in China

Species delimitation in tree species is notoriously challenging due to shared polymorphisms among species. An integrative survey that considers multiple operational criteria is a possible solution, and we aimed to test it in a species complex of aspens in China. Genetic [four chloroplast DNA (cpDNA) fragments and 14 nuclear microsatellite loci (nSSR)] and morphological variations were collected for 76 populations and 53 populations, respectively, covering the major geographic distribution of the Populus davidiana-rotundifolia complex. Bayesian clustering, analysis of molecular variance (AMOVA), Principle Coordinate Analysis (PCoA), ecological niche modeling (ENM), and gene flow (migrants per generation), were employed to detect and test genetic clustering, morphological and habitat differentiation, and gene flow between/among putative species. The nSSR data and ENM suggested that there are two separately evolving meta-population lineages that correspond to P. davidiana (pd) and P. rotundifolia (pr). Furthermore, several lines of evidence supported a subdivision of P. davidiana into Northeastern (NEC) and Central-North (CNC) groups, yet they are still functioning as one species. CpDNA data revealed that five haplotype clades formed a pattern of [pdNEC, ((pdCNC, pr), (pdCNC, pr))], but most haplotypes are species-specific. Meanwhile, PCA based on morphology suggested a closer relationship between the CNC group (P. davidiana) and P. rontundifolia. Discrepancy of nSSR and ENM vs. cpDNA and morphology could have reflected a complex lineage divergence and convergence history. P. davidiana and P. rotundifolia can be regarded as a recently diverged species pair that experienced parapatric speciation due to ecological differentiation in the face of gene flow. Our findings highlight the importance of integrative surveys at population level, as we have undertaken, is an important approach to detect the boundary of a group of species that have experienced complex evolutionary history.

Genetic Structure in the Northern Range Margins of Common Ash, Fraxinus excelsior L

During post glacial colonization, loss of genetic diversity due to leading edge effects may be attenuated in forest trees because of their prolonged juvenile phase, allowing many migrants to reach the colonizing front before populations become reproductive. The northern range margins of temperate tree taxa in Europe are particularly suitable to study the genetic processes that follow colonization because they have been little affected by northern refugia. Here we examined how post glacial range dynamics have shaped the genetic structure of common ash (Fraxinus excelsior L.) in its northern range compared to its central range in Europe. We used four chloroplast and six nuclear microsatellites to screen 42 populations (1099 trees), half of which corresponded to newly sampled populations in the northern range and half of which represented reference populations from the central range obtained from previously studies. We found that northern range populations of common ash have the same chloroplast haplotypes as south-eastern European populations, suggesting that colonization of the northern range took place along a single migration route, a result confirmed by the structure at the nuclear microsatellites. Along this route, diversity strongly decreased only in the northern range, concomitantly with increasing population differentiation and complex population substructures, a pattern consistent with a leading edge colonization model. Our study highlights that while diversity is maintained in the central range of common ash due to broad colonizing fronts and high levels of gene flow, it profoundly decreases in the northern range, where colonization was unidirectional and probably involved repeated founder events and population fluctuations. Currently, common ash is threatened by ash dieback, and our results on northern populations will be valuable for developing gene conservation strategies.

Recent similarity in distribution ranges does not mean a similar postglacial history: a phylogeographical study of the boreal tree species Alnus incana based on microsatellite and chloroplast DNA variation

We reconstructed the historical pattern of postglacial biogeographic range expansion of the boreal tree species Alnus incana in Europe. To assess population genetic structure and diversity, we performed a combined analysis of nuclear microsatellite loci and chloroplast DNA sequences (65 populations, 1004 individuals). Analysis of haplotype and microsatellite diversity revealed that southeastern refugial populations situated in the Carpathians and the Balkan Peninsula did not spread north and cannot be considered as important source populations for postglacial recolonization of Europe; populations in Eastern Europe did not establish Fennoscandian populations; populations in Fennoscandia and Eastern Europe have no unique genetic cluster, but represent a mix with a predominant cluster typical for Central Europe; and that colonization of Fennoscandia and Eastern Europe took place from Central Europe. Our findings highlight the importance of an effective refugium in Central Europe located outside classical southern refugia confirming the existence of northern refugia for boreal trees in Europe. The postglacial range expansion of A. incana did not follow the model established for Picea abies. Fennoscandian populations are not derived from Eastern European ones, but from Central European ones.