Distance,elevation and environment as drivers of diversity and divergence in bumble bees across latitude and altitude

Identifying drivers of dispersal limitation and genetic differentiation is a key goal in biogeography. We examine patterns of population connectivity and genetic diversity using restriction site‐associated DNA sequencing (RADseq) in two bumble bee species, Bombus vosnesenskii and Bombus bifarius, across latitude and altitude in mountain ranges from California, Oregon and Washington, U.S.A. Bombus vosnesenskii, which occurs across a broader elevational range at most latitudes, exhibits little population structure while B. bifarius, which occupies a relatively narrow higher elevation niche across most latitudes, exhibits much stronger population differentiation, although gene flow in both species is best explained by isolation with environmental niche resistance. A relationship between elevational habitat breadth and genetic diversity is also apparent, with B. vosnesenskii exhibiting relatively consistent levels of genetic diversity across its range, while B. bifarius has reduced genetic diversity at low latitudes, where it is restricted to high‐elevation habitat. The results of this study highlight the importance of the intersect between elevational range and habitat suitability in influencing population connectivity and suggest that future climate warming will have a fragmenting effect even on populations that are presently well connected, as they track their thermal niches upward in montane systems.     

Genetic variation in flowering phenology and reproductive performance in a Mediterranean high‐mountain specialist,Armeria caespitosa (Plumbaginaceae)

Adaptive responses to past climate change may play an important role in the persistence of high‐mountain plants, which are vulnerable to global warming. Armeria caespitosa is a high‐mountain plant, endemic to the Iberian Central Range. Differences in abiotic environment along the elevational gradient impose two opposing stress gradients (i.e. water stress and duration of the growth season) on the species. Furthermore, the species is found in two interspersed, contrasting microhabitats (rocky outcrops and dry cryophilic grasslands) that have different effects on plants depending of the elevation. As a result of this, the species shows great among‐population variation in many reproductive and vegetative traits. We used a common garden approach to determine whether this phenotypic variation has a genetic basis or is the result of plastic responses shaped by heterogeneous environmental conditions. Plants from the high‐elevation edge and dry cryophilic grasslands flowered earlier and produced more viable fruits but were smaller. These results confirm that among‐population variation in flowering phenology and reproductive performance traits in A. caespitosa is partially genetically based. The results also show that the stronger selection response in favour of early‐flowering individuals in populations at the low‐elevation edge did not correspond with the greater proportion of early‐flowering individuals. Genetic variability associated with flowering onset may be relevant in coping with the impacts of ongoing global warming. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 176 , 384–395.     

Genetic diversity and gene flow within and between two different habitats of Primula merrilliana (Primulaceae), an endangered distylous forest herb in eastern China

Understanding whether and how different habitats shape population genetics is a fundamental question and a specific goal for evolutionary and conservation biology research. This study examined genetic diversity and gene flow within and between mountain and foothill habitats of Primula merrilliana, an endangered distylous forest herb in eastern China. Eleven population characteristics, including area, size and density variation, from the two habitats were also investigated. Mountain populations had significantly higher mean genetic diversity than foothill populations, which may be explained by stronger self‐incompatibility breeding system, more opportunity to use elevational shifts to track suitable sites under conditions of climate change and more heterogeneous environments in the former habitat, rather than by the differences of population size, gene flow and genetic drift intensity between them. Genetic analysis revealed that two distinct lineages, corresponding to the two habitats, diverged at China's ‘Last Glaciation’ (11 700–67 500 yr BP), suggesting this divergence was probably triggered by warmer climates during inter‐ (or post‐) glacial periods. Low unidirectional gene flow from mountain to foothill habitats, chiefly by seed dispersal, played a more important role in overall gene flow between habitats than within‐habitat gene flow. Within habitats, pollen contributes more substantially to gene flow than seed dispersal, especially in foothill habitats, possibly due to higher individual density and larger population sizes. These results have implications for the conservation in this and similar landscape areas and indicate the need to protect suitable habitats with wide elevational spans and sufficient size to permit ecological and elevational shifts in response to climatic changes. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179 , 172–189.     

No effect of elevation and fragmentation on genetic diversity and structure in Polylepis australis trees from central Argentina

Phenological differences in flowering arising along elevational gradients may be caused by either local adaptation or phenotypic plasticity. Local adaptation can lead to reproductive isolation of populations at different elevational zones and thus produce elevational genetic structuring, while phenotypic plasticity does not produce elevational genetic structuring. In this study, we examined the effects of elevation and fragmentation on genetic diversity and structure of Polylepis australis populations, where individuals exhibit phenological differences in flowering along an elevational gradient. We assessed the polymorphism of amplified fragment length polymorphism markers in adults and saplings from one conserved and one fragmented forest covering elevations from 1600 to 2600 m asl. Over 98% of variation was found within populations, and we found very low and similar genetic differentiation along elevational gradients for adults and saplings in both continuous and fragmented forests. In addition, there was no significant relationship between genetic diversity and elevation. Results indicated that phenological differences along elevational gradients are more likely caused by phenotypic plasticity than local adaptation, and fragmentation does not appear to have affected genetic diversity and differentiation in the studied populations. Results therefore imply that if necessary, seeds for reforestation purposes may be collected from different elevations to the seeding or planting sites.     

Speciation in a keystone plant genus is driven by elevation: a case study in New Guinean Ficus

Much of the world's insect and plant biodiversity is found in tropical and subtropical ‘hotspots’, which often include long elevational gradients. These gradients may function as ‘diversity pumps’ and contribute to both regional and local species richness. Climactic conditions on such gradients often change rapidly along short vertical distances and may result in local adaptation and high levels of population genetic structure in plants and insects. We investigated the population genetic structure of two species of Ficus (Moraceae) along a continuously forested elevational gradient in Papua New Guinea. This speciose plant genus is pollinated by tiny, species‐specific and highly coevolved chalcid wasps (Agaonidae) and represented by at least 73 species at our study gradient. We present results from two species of Ficus sampled from six elevations between 200 m and 2700 m a.s.l. (almost the entire elevational range of the genus) and 10 polymorphic microsatellite loci. These results show that strong barriers to gene flow exist between 1200 m and 1700 m a.s.l. Whereas lowland populations are panmictic across distances over 70 km, montane populations can be disjunct over 4 km, despite continuous forest cover. We suggest that the limited gene flow between populations of these two species of montane Ficus may be driven by environmental limitations on pollinator or seed dispersal in combination with local adaptation of Ficus populations. Such a mechanism may have wider implications for plant and pollinator speciation across long and continuously forested elevational gradients if generalist insect pollinators and vertebrate seed dispersers also form populations based on elevation.     

Phylogeography reveals latitudinal population structure in the common herb Plantago coronopus

The increase in gene diversity from high to low latitudes is a widely recognized biogeographical pattern, often shaped by differential effects of Late Quaternary climatic changes. Here, we evaluate the effects of Pleistocene climatic changes from northern Europe to North Africa and their implications on the population differentiation of the widespread, short‐lived herb Plantago coronopus. We used amplified fragment length polymorphism to investigate the population structure and phylogeography of P. coronopus in 273 individuals from 29 populations covering its complete latitudinal range. Although Bayesian clustering, principal coordinates analysis and a consensus UPGMA tree were not fully congruent, two well‐supported clades, associated with distinct latitudinal zones (northern Europe and the Mediterranean region), were revealed as a general pattern. Moreover, populations from the western Atlantic edge and, to a lesser extent, the central Mediterranean region exhibited signs of admixture, suggesting secondary contacts. The admixed populations in the western Atlantic and central Mediterranean are geographically intermediate between the northern and southern lineages. The northernmost lineage exhibited low genetic diversity, a clear sign of a recent colonization. In contrast, populations from the southernmost part of the range showed the highest level of genetic diversity, indicating possible refugia for the species during the Quaternary ice ages. Overall, our study allows spatial structure of the genetic variation of a widespread herb across its latitudinal range to be disentangled and provides insights into how past climatic history influences present genetic patterns. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179 , 618–634.     

Environmental gradients shape the genetic structure of two medicinal Salvia species in Jordan

• Environmental gradients, and particularly climatic variables, exert a strong influence on plant distribution and, potentially, population genetic diversity and differentiation. Differences in water availability can cause among‐population variation in ecological processes and can thus interrupt populations’ connectivity and isolate them environmentally. The present study examines the effect of environmental heterogeneity on plant populations due to environmental isolation unrelated to geographic distance.
• Using AFLP markers, we analyzed genetic diversity and differentiation among 12 Salvia spinosa populations and 13 Salvia syriaca populations from three phytogeographical regions (Mediterranean, Irano‐Turanian and Saharo‐Arabian) representing the extent of the species’ geographic range in Jordan. Differences in geographic location and climate were considered in the analyses.
• For both species, flowering phenology varied among populations and regions. Irano‐Turanian and Saharo‐Arabian populations had higher genetic diversity than Mediterranean populations, and genetic diversity increased significantly with increasing temperature. Genetic diversity in Salvia syriaca was affected by population size, while genetic diversity responded to drought in S. spinosa. For both species, high levels of genetic differentiation were found as well as two well‐supported phytogeographical groups of populations, with Mediterranean populations clustering in one group and the Irano‐Turanian and Saharo‐Arabian populations in another. Genetic distance was significantly correlated to environmental distance, but not to geographic distance.
• Our data indicate that populations from moist vs. arid environments are environmentally isolated, where environmental gradients affect their flowering phenology, limit gene flow and shape their genetic structure. We conclude that environmental heterogeneity may act as driver for the observed variation in genetic diversity.

     

Large‐scale longitudinal gradients of genetic diversity: a meta‐analysis across six phyla in the Mediterranean basin

Biodiversity is the diversity of life at all scales, from genes to ecosystems. Predicting its patterns of variation across the globe is a fundamental issue in ecology and evolution. Diversity within species, that is, genetic diversity, is of prime importance for understanding past and present evolutionary patterns, and highlighting areas where conservation might be a priority. Using published data on the genetic diversity of species whose populations occur in the Mediterranean basin, we calculated a coefficient of correlation between within‐population genetic diversity indices and longitude. Using a meta‐analysis framework, we estimated the role of biological, ecological, biogeographic, and marker type factors on the strength and magnitude of this correlation in six phylla. Overall, genetic diversity increases from west to east in the Mediterranean basin. This correlation is significant for both animals and plants, but is not uniformly expressed for all groups. It is stronger in the southern than in the northern Mediterranean, in true Mediterranean plants than in plants found at higher elevations, in trees than in other plants, and in bi‐parentally and paternally than in maternally inherited DNA makers. Overall, this correlation between genetic diversity and longitude, and its patterns across biological and ecological traits, suggests the role of two non‐mutually exclusive major processes that shaped the genetic diversity in the Mediterranean during and after the cold periods of the Pleistocene: east‐west recolonization during the Holocene and population size contraction under local Last Glacial Maximum climate in resident western and low elevation Mediterranean populations.     

Genetic diversity of the imperilled bath sponge Spongia officinalis Linnaeus, 1759 across the Mediterranean Sea: patterns of population differentiation and implications for taxonomy and conservation

The Mediterranean bath sponge Spongia officinalis is an iconic species with high socio‐economic value and precarious future owing to unregulated harvesting, mortality incidents and lack of established knowledge regarding its ecology. This study aims to assess genetic diversity and population structure of the species at different geographical scales throughout its distribution. For this purpose, 11 locations in the Eastern Mediterranean (Aegean Sea), Western Mediterranean (Provence coast) and the Strait of Gibraltar were sampled; specimens were analysed using partial mitochondrial cytochrome oxidase subunit I (COI) sequences, along with a set of eight microsatellite loci. According to our results (i) no genetic differentiation exists among the acknowledged Mediterranean morphotypes, and hence, S. officinalis can be viewed as a single, morphologically variable species; (ii) a notable divergence was recorded in the Gibraltar region, indicating the possible existence of a cryptic species; (iii) restriction to gene flow was evidenced between the Aegean Sea and Provence giving two well‐defined regional clusters, thus suggesting the existence of a phylogeographic break between the two systems; (iv) low levels of genetic structure, not correlated to geographical distance, were observed inside geographical sectors, implying mechanisms (natural or anthropogenic) that enhance dispersal and gene flow have promoted population connectivity; (v) the genetic diversity of S. officinalis is maintained high in most studied locations despite pressure from harvesting and the influence of devastating epidemics. These findings provide a basis towards the effective conservation and management of the species.     

Effects of population size and isolation on the genetic structure of the East African mountain white‐eye Zosterops poliogaster (Aves)

Habitat size, quality and isolation determine the genetic structure and diversity of populations and may influence their evolutionary potential and vulnerability to stochastic events. Small and isolated populations are subject to strong genetic drift and can lose much of their genetic diversity due to stochastic fixation and loss of alleles. The mountain white‐eye Zosterops poliogaster, a cloud forest bird species, is exclusively found in the high mountains of East Africa. We analysed 13 polymorphic microsatellites for 213 individuals of this species that were sampled at different points in time in three mountain massifs differing in habitat size, isolation and habitat degradation. We analysed the genetic differentiation among mountain populations and estimated the effective population sizes. Our results indicate three mountain‐specific genetic clusters. Time cohorts did not show genetic divergences, suggesting that populations are large enough to prevent strong drift effects. Effective population sizes were higher in larger and geographically interconnected habitat patches. Our findings underline the relevance of ecological barriers even for mobile species and show the importance of investigating different estimators of population size, including both approaches based on single and multiple time‐points of sampling, for the inference of the demographic status of a population. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 114 , 828–836.     

Elevation as a barrier: genetic structure for an Atlantic rain forest tree (Bathysa australis) in the Serra do Mar mountain range,SE Brazil

Distance and discrete geographic barriers play a role in isolating populations, as seed and pollen dispersal become limited. Nearby populations without any geographic barrier between them may also suffer from ecological isolation driven by habitat heterogeneity, which may promote divergence by local adaptation and drift. Likewise, elevation gradients may influence the genetic structure and diversity of populations, particularly those marginally distributed. Bathysa australis (Rubiaceae) is a widespread tree along the elevation gradient of the Serra do Mar, SE Brazil. This self‐compatible species is pollinated by bees and wasps and has autochoric seeds, suggesting restricted gene dispersal. We investigated the distribution of genetic diversity in six B. australis populations at two extreme sites along an elevation gradient: a lowland site (80–216 m) and an upland site (1010–1100 m.a.s.l.). Nine microsatellite loci were used to test for genetic structure and to verify differences in genetic diversity between sites. We found a marked genetic structure on a scale as small as 6 km (F_ST = 0.21), and two distinct clusters were identified, each corresponding to a site. Although B. australis is continuously distributed along the elevation gradient, we have not observed a gene flow between the extreme populations. This might be related to B. australis biological features and creates a potential scenario for adaptation to the different conditions imposed by the elevation gradient. We failed to find an isolation‐by‐distance pattern; although on the fine scale, all populations showed spatial autocorrelation until ~10‐20 m. Elevation difference was a relevant factor though, but we need further sampling effort to check its correlation with genetic distance. The lowland populations had a higher allelic richness and showed higher rare allele counts than the upland ones. The upland site may be more selective, eliminating rare alleles, as we did not find any evidence for bottleneck.     

Genetic diversity analysis and conservation implications for the Iberian threatened populations of the irano-turanian relict Krascheninnikovia ceratoides (Chenopodiaceae)

Krascheninnikovia ceratoides (L.) Gueldenst. (Chenopodiaceae) is an irano‐turanian steppe plant with a striking geographical vicariance between the western Mediterranean and the central Asian regions. Its westernmost populations are located in the north‐east part of the Iberian Peninsula, in the narrow middle Ebro and Alfambra valleys, where they are threatened and have been catalogued as ‘vulnerable’. Genetic diversity and structure was studied in 150 individuals from five populations of these two valleys using inter‐simple sequence repeats (ISSR). A total of 121 informative bands allowed the identification of 150 genotypes. Nei's genetic diversity found in all natural populations (h = 0.448) was higher than that of other geographical restricted species. Analysis of molecular variance and spatial correlations analyses showed a strong genetic differentiation among populations (35.88%) and among valleys (22.33%). The unweighted pair‐group method of arithmetical averages and Neighbour‐joining clusterings further demonstrated a substructure of two population cores within the Ebro valley. Our genetic data suggest that the high levels of genetic diversity and the strong genetic structure found among the northern Iberian populations and ranges of K. ceratoides might result from the summed effects of its tetraploidy, its outbreeding nature, and its success in colonizing newly altered areas. However, the ISSR data might also reflect the existence of an ancient wider distribution range of the plant in the Iberian Peninsula coupled with a more recent history of habitat fragmentation. Different management conservation guidelines are recommended for this plant after our genetic analysis: a microreserve of approximately 2 km² is proposed for the highly threatened population of Osera (Ebro valley), whereas seed collection strategies and occasional population reinforcements are suggested for the remaining populations. © 2007 The Linnean Society of London, Biological Journal of the Linnean Society, 2007, 92 , 419–429.     

Quaternary range dynamics of ecologically divergent species (Edraianthus serpyllifolius and E. tenuifolius,Campanulaceae) within the Balkan refugium

Aim We investigated Quaternary range dynamics of two closely related but ecologically divergent species (cold‐tolerant Edraianthus serpyllifolius and thermophilic Edraianthus tenuifolius) with overlapping distribution ranges endemic to the western Balkan Peninsula, an important yet understudied Pleistocene refugium. Our aims were: to test predictions of the ‘refugia‐within‐refugia’ model of strong genetic subdivisions due to population isolation in separate refugia; to explore whether two ecologically divergent species reacted differently to Pleistocene climatic fluctuations; and to test predictions of the displacement refugia model of stronger differentiation among populations in the thermophilic E. tenuifolius compared with the cold‐tolerant E. serpyllifolius. Location The western Balkan Peninsula. Methods We gathered amplified fragment‐length polymorphism (AFLP) data and plastid DNA sequences from two to five individuals from 10 populations of E. serpyllifolius and 22 populations of E. tenuifolius, spanning their entire respective distribution areas. AFLP data were analysed using a Bayesian clustering approach and a distance‐based network approach. Plastid sequences were used to depict relationships among haplotypes in a statistical parsimony network, and to obtain age estimates in a Bayesian framework. Results In E. serpyllifolius, both AFLP and plastid sequence data showed clear geographic structure. Western populations showed high AFLP diversity and a high number of rare fragments. In E. tenuifolius, both markers congruently identified a major phylogeographic split along the lower Neretva valley in central Dalmatia. The most distinct and earliest diverging chloroplast DNA (cpDNA) haplotypes were found further south in the south‐easternmost populations. North‐western populations, identified as a separate cluster by Bayesian clustering, were characterized by low genetic diversity and a low number of rare AFLP markers. Main conclusions Clear evidence for multiple Pleistocene refugia is found not only in the high‐elevation E. serpyllifolius, but also in the lowland E. tenuifolius, despite the lack of obvious dispersal barriers, in line with the refugia‐within‐refugia model. Genealogical relationships and genetic diversity patterns support the hypothesis that cold‐adapted E. serpyllifolius responded to climatic oscillations mostly by elevational range shifts, whereas thermophilic E. tenuifolius did so mainly by latitudinal range shifts, with different phases (and probably extents) of range expansion. In contrast to the displacement refugia hypothesis, the two elevationally differentiated species do not differ in their genetic diversity.     

Long‐term ‘islands’ in the landscape: low gene flow,effective population size and genetic divergence in the shrub Hakea oldfieldii (Proteaceae)

The genetic structure of disjunct populations is determined by founding genetic properties, demographic processes, gene flow, drift and local selection. We aim to identify the genetic consequences of natural population disjunction at regional and local scales in Hakea oldfieldii using nuclear and plastid markers to investigate long‐term effective population sizes and gene flow, and patterns of diversity and divergence, among populations. Regional divergence was significant as shown by a consistent pattern in principal coordinates, neighbor‐joining and Bayesian analyses, but divergence at the local level was also significant with localized distribution of plastid haplotypes and populations clustering separately in Bayesian analyses. Historical, recent and first‐generation gene flow was low, suggesting that recent habitat fragmentation has not reduced gene migration significantly. Genetic bottlenecks were detected in three populations. Long‐term effective population size was significantly correlated with the number of alleles/locus and observed heterozygosity, but not with census population size, suggesting that the loss of diversity is associated with long‐term changes rather than recent fragmentation. Inbreeding coefficients were significant in only three populations, suggesting that the loss of diversity is linked to drift and bottlenecks associated with demographic processes (local extinction by fires) rather than inbreeding. Historical disjunction as a result of specific ecological requirements, contraction of habitats following drying during the Pleistocene, low gene flow and changes in population size are likely to have been important forces driving divergence through isolation by distance and drift. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179 , 319–334.     

Genetic diversity and differentiation of populations of Anthyllis vulneraria along elevational and latitudinal gradients

The abundant centre model (ACM) predicts that the suitability of environmental conditions for a species decreases from the centre of its distribution toward its range periphery and, consequently, its populations will become scarcer, smaller and more isolated, resulting in lower genetic diversity and increased differentiation. However, little is known about whether genetic diversity shows similar patterns along elevational and latitudinal gradients with similar changes in important environmental conditions. Using microsatellite markers, we studied the genetic diversity and structure of 20 populations each of Anthyllis vulneraria along elevational gradients in the Alps from the valleys to the elevational limit (2500 m) and along a latitudinal gradient (2500 km) from Central Europe to the range margin in northern Scandinavia. Both types of gradients corresponded to an 11.5°C difference in mean annual temperature. Genetic diversity strongly declined and differentiation increased with latitude in line with the predictions of the ACM. However, as population size did not decline with latitude and genetic diversity was not related to population size in A. vulneraria, this pattern is not likely to be due to less favorable conditions in the North, but due to serial founder effects during the post‐glacial recolonization process. Genetic diversity was not related to elevation, but we found significant isolation by distance along both gradients, although the elevational gradient was shorter by orders of magnitude. Subarctic populations differed genetically from alpine populations indicating that the northern populations did not originate from high elevational Alpine ones. Our results support the notion that postglacial latitudinal colonization over large distances resulted in a larger loss of genetic diversity than elevational range shifts. The lack of genetic diversity in subarctic populations may threaten their long‐term persistence in the face of climate change, whereas alpine populations could benefit from gene flow from low‐elevation populations.     

A landscape genetics approach reveals ecological‐based differentiation in populations of holm oak (Quercus ilex L.) at the northern limit of its range

The holm oak plays a relevant role in the functioning of Mediterranean forests. In the area north of Garda Lake, Italian Prealps, holm oak populations are at the northernmost edge of their distribution. Being peripheral, these populations are of particular interest for ecological, evolutionary and conservation studies. Through an explicit individual‐based landscape genetics approach, we addressed the following questions: (1) are levels of genetic variation reduced in these marginal populations compared with central populations?; (2) despite the narrow geographical scale, do individual‐based analyses have some power to detect genetic differentiation?; (3) do environmental and/or climatic factors exert a role in shaping patterns of genetic variation and differentiation? Through a Bayesian method, we identified three clusters whose genetic variability can be considered to be of the same order as that recorded in central Quercus ilex populations. Although being geographically very close (< 20 km), the differentiation was statistically significant (P < 0.05) with global F _st and Φ _Pt values of 0.019 and 0.038, respectively. Geography and phylogeography could not be invoked to explain this differentiation. A redundancy discriminant analysis revealed that relevant eco‐pedological and climatic features, such as soil depth, aspect, elevation and humidity, were correlated with the observed pattern of differentiation. Toblino was ecologically separated from the other clusters, as it lies on deep soil with subhumid conditions. The differentiation of the Brione–Ranzo–Val Busa cluster appeared to be related to superficial soils and drier conditions, whereas the Nanzone–Padaro cluster was differentiated mainly according to its mid‐elevation. Coupling spatial and genetic information on a local scale proved to be effective to investigate the evolutionary and demographic history of peripheral populations. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ?? , ??–??.     

Source–sink dynamics structure a common montane mammal

Assessing the relative role of evolutionary processes on genetic diversity is critical for understanding species response to climatic change. However, many processes, independent of climate, can lead to the same genetic pattern. Because effective population size and gene flow are affected directly by abundance and dispersal, population ecology has the potential to profoundly influence patterns of genetic variation over microevolutionary timescales. Here, we use aDNA data and simulations to explore the influence of population ecology and Holocene climate change on genetic diversity of the Uinta ground squirrel (Spermophilus armatus). We examined phylochronology from three modern and two ancient populations spanning the climate transitions of the last 3000 years. Population genetic analyses based on summary statistics suggest that changes in genetic diversity and structure coincided with the Medieval Warm Period (MWP), c. 1000 years ago. Serial coalescent simulations allowed us to move beyond correlation with climate to statistically compare the likelihoods of alternative population histories given the observed data. The data best fit source–sink models that include large, mid‐elevation populations that exchange many migrants and small populations at the elevational extremes. While the MWP is likely to have reduced genetic diversity, our model‐testing approach revealed that MWP‐driven changes in genetic structure were not better supported for the range of models explored. Our results point to the importance of species ecology in understanding responses to climate, and showcase the use of ancient genetic data and simulation‐based inference for unraveling the relative roles of microevolutionary processes.     

Spatial Patterns of Haplotype Variation in the Epiphytic Bromeliad Catopsis nutans

Identifying factors governing the origin, distribution, and maintenance of Neotropical plant diversity is an enduring challenge. To explore the complex and dynamic historical processes that shaped contemporary genetic patterns for a Central American plant species, we investigated the spatial distribution of chloroplast haplotypes of a geographically and environmentally widespread epiphytic bromeliad with wind‐dispersed seeds, Catopsis nutans, in Costa Rica. We hypothesized that genetic discontinuities occur between northwestern and southwestern Pacific slope populations, resembling patterns reported for other plant taxa in the region. Using non‐coding chloroplast DNA from 469 individuals and 23 populations, we assessed the influences of geographic and environmental distance as well as historical climatic variation on the genetic structure of populations spanning >1200 m in elevation. Catopsis nutans revealed seven haplotypes with low within‐population diversity (mean haplotype richness = 1.2) and moderate genetic structure (F_ST = 0.699). Pairwise F_ST was significantly correlated with both geographic and environmental distance. The frequency of dominant haplotypes was significantly correlated with elevation. A cluster of nine Pacific lowland populations exhibited a distinct haplotype profile and contained five of the seven haplotypes, suggesting historical isolation and limited seed‐mediated gene flow with other populations. Paleodistribution models indicated lowland and upland habitats in this region were contiguous through past climatic oscillations. Based on our paleodistribution analysis and comparable prior phylogeographic studies, the genetic signature of recent climatic oscillations are likely superimposed upon the distribution of anciently divergent lineages. Our study highlights the unique phylogeographic history of a Neotropical plant species spanning an elevation gradient.     

High gene flow in two thrips‐pollinated South‐East Asian pioneer trees: genetic diversity and population structure of Macaranga hypoleuca and M. beccariana (Euphorbiaceae)

As a result of intensive exploitation, disturbed forests now dominate large areas of lowland tropical rainforest in South‐East Asia. The genus Macaranga comprises some of the most important pioneer tree species of the region, among them M. beccariana and M. hypoleuca, two closely related obligate ant‐plants pollinated by thrips. We used nuclear and plastid DNA markers to address questions of genetic diversity and population structure. Twelve plastid haplotypes were detected among 281 samples, three of which were shared between the two study species. Hybrids between the two species appear to be rare. Overall, genetic diversity in both species was moderate to high, with low levels of population differentiation, consistent with other tropical pioneer trees. Genetic structure was generally more pronounced in plastid than in nuclear data, indicating that gene flow via pollen may be more efficient than via seeds. Thrips apparently also serve as efficient pollinators over long distances, perhaps through a combination of passive dispersal by wind and active search for inflorescences in the target area. Our results indicate that M. beccariana and M. hypoleuca populations from recently disturbed habitats do not yet suffer from reduced genetic diversity or increased inbreeding. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 173 , 606–621.     

Spatial genetic structure in Beta vulgaris subsp. maritima and Beta macrocarpa reveals the effect of contrasting mating system,influence of marine currents,and footprints of postglacial recolonization routes

Understanding the factors that contribute to population genetic divergence across a species' range is a long‐standing goal in evolutionary biology and ecological genetics. We examined the relative importance of historical and ecological features in shaping the present‐day spatial patterns of genetic structure in two related plant species, Beta vulgaris subsp. maritima and Beta macrocarpa. Using nuclear and mitochondrial markers, we surveyed 93 populations from Brittany (France) to Morocco – the southern limit of their species' range distribution. Whereas B. macrocarpa showed a genotypic structure and a high level of genetic differentiation indicative of selfing, the population genetic structure of B. vulgaris subsp. maritima was consistent with an outcrossing mating system. We further showed (1) a strong geographic clustering in coastal B. vulgaris subsp. maritima populations that highlighted the influence of marine currents in shaping different lineages and (2) a peculiar genetic structure of inland B. vulgaris subsp. maritima populations that could indicate the admixture of distinct evolutionary lineages and recent expansions associated with anthropogenic disturbances. Spatial patterns of nuclear diversity and differentiation also supported a stepwise recolonization of Europe from Atlantic‐Mediterranean refugia after the last glacial period, with leading‐edge expansions. However, cytoplasmic diversity was not impacted by postglacial recolonization: stochastic long‐distance seed dispersal mediated by major oceanic currents may mitigate the common patterns of reduced cytoplasmic diversity observed for edge populations. Overall, the patterns we documented here challenge the general view of reduced genetic diversity at the edge of a species' range distribution and provide clues for understanding how life‐history and major geographic features interact to shape the distribution of genetic diversity.