Chloroplast diversity in Vouacapoua americana (Caesalpiniaceae), a neotropical forest tree

The chloroplast genome has been widely used to describe genetic diversity in plant species. Its maternal inheritance in numerous angiosperm species and low mutation rate are suitable characters when inferring historical events such as possible recolonization routes. Here we have studied chloroplast DNA variation using PCR-RFLP (polymerase chain reaction-restriction fragment length polymorphism) with seven pairs of primers and four restriction enzymes in 14 populations of Vouacapoua americana (Caesalpiniaceae) a neotropical tree sampled throughout French Guiana. Population diversity (Hs), total gene diversity (Ht) and differentiation among populations (GST) were estimated using Nei's method as 0.09, 0.87 and 0.89, respectively. This is consistent with the limited gene flow associated with synzoochory in this species. The genetic structure observed in the north of French Guiana suggests that historical events such as contractions and recent recolonizations have had a large impact on the distribution of genetic diversity in this species.     

青藏高原东北部及其邻近地区无苞香蒲的谱系地理学

第四纪冰期气候的反复变化对青藏高原及邻近地区植物的种群地理分布及种群遗传结构产生了巨大的影响。本研究对青藏高原东北部及其邻近地区无苞香蒲(Typha laxmannii)的15个种群148个个体的叶绿体rpl32-trnL间隔区和核基因(植物螯合肽合成酶, PS)进行测序, 共发现2个叶绿体单倍型和8个核基因单倍型。所有的单倍型被共享, 高原种群没有特有的单倍型。邻近地区种群的叶绿体遗传多样性和核基因遗传多样性分别是高原种群的4倍和2倍。高原种群的遗传分化水平明显高于邻近地区种群, 其中高原种群的遗传分化主要存在于东部种群与西部种群之间。研究结果表明, 冰期后从多个避难所回迁至高原台面和由此产生的奠基者效应造成了无苞香蒲在青藏高原东北及邻近地区目前的遗传多样性和基因谱系地理分布格局。     

Gene flow, historical population dynamics and genetic diversity within French Guianan populations of a rainforest tree species, Vouacapoua americana

Both gene flow and historical events influence the genetic diversity of natural populations. One way to understand their respective impact is to analyze population genetic structure at large spatial scales. We studied the distribution of genetic diversity of 17 populations of Vouacapoua americana (Caesalpiniaceae) in French Guiana, using nine microsatellite loci. Low genetic diversity was observed within populations, with a mean allelic richness and gene diversity of 4.1 and 0.506, respectively, which could be due to low effective population size and/or past bottlenecks. Using the regression between Fst/(1-Fst), estimated between pairs of populations, and the logarithm of the geographical distance, the spatial genetic structure can partly be explained by isolation-by-distance and limited gene flow among populations. This result is in agreement with the species' biology, including seed and pollen dispersal by rodents and insects, respectively. In contrast, no clear genetic signal of historical events was found when examining genetic differentiation among populations in relation to biogeographical hypotheses or by testing for bottlenecks within populations. Our conclusion is that nuclear spatial genetic structure of V. americana, at the geographic scale of French Guiana, is better explained by gene flow rather than by historical events.     

Rapid recovery of genetic diversity of dogwhelk (Nucella lapillus L.) populations after local extinction and recolonization contradicts predictions from life-history characteristics

The dogwhelk Nucella lapillus is a predatory marine gastropod populating North Atlantic rocky shores. As with many other gastropod species, N. lapillus was affected by tributyltin (TBT) pollution during the 1970s and 1980s, when local populations became extinct. After a partial ban on TBT in the United Kingdom in 1987, vacant sites have been recolonized. N. lapillus lacks a planktonic larval stage and is therefore expected to have limited dispersal ability. Relatively fast recolonization of some sites, however, contradicts this assumption. We compared levels of genetic diversity and genetic structuring between recolonized sites and sites that showed continuous population at three localities across the British Isles. No significant genetic effects of extinction/recolonization events were observed in SW Scotland and NE England. In SW England we observed a decrease in genetic diversity and an increase in genetic structure in recolonized populations. This last result could be an artefact, however, due to the superposition of other local factors influencing the genetic structuring of dogwhelk populations. We conclude that recolonization of vacant sites was accomplished by a relatively high number of individuals originating from several source populations (the 'migrant-pool' model of recolonization), implying that movements are more widespread than expected on the basis of development mode alone. Comparison with published data on genetic structure of marine organisms with contrasted larval dispersal supports this hypothesis. Our results also stress the importance of local factors (geographical or ecological) in determining genetic structure of dogwhelk populations.     

Phylogenomic approaches reveal how climate shapes patterns of genetic diversity in an African rain forest tree species

The world's second largest expanse of tropical rainforest is in Central Africa, and it harbours enormous species diversity. Population genetic studies have consistently revealed significant structure across Central African rainforest plants. In particular, previous studies have repeatedly demonstrated a north–south genetic discontinuity around the equatorial line, in a continuous expanse of rainforest where a climatic inversion is documented. Here, we took a phylogeographic approach by sequencing 351 nuclear markers in 112 individuals across the distribution of the African rainforest tree species Annickia affinis (Annonaceae). We showed for the first time that the north–south divide is the result of a single, major colonization event across the climatic inversion from an ancestral population located in Gabon. We suggested that differences in ecological niche of populations located on either side of this inversion may have contributed to this phylogenetic discontinuity. We found evidence for inland dispersal, predominantly in northern areas, and variable demographic histories among genetic clusters, indicating that populations responded differently to past climate change. We show how newly developed genomic tools can provide invaluable insights into our understanding of tropical rainforest evolutionary dynamics.     

Tropical rainforests that persisted: inferences from the Quaternary demographic history of eight tree species in the Guiana shield

How Quaternary climatic and geological disturbances influenced the composition of Neotropical forests is hotly debated. Rainfall and temperature changes during and/or immediately after the last glacial maximum (LGM) are thought to have strongly affected the geographical distribution and local abundance of tree species. The paucity of the fossil records in Neotropical forests prevents a direct reconstruction of such processes. To describe community‐level historical trends in forest composition, we turned therefore to inferential methods based on the reconstruction of past demographic changes. In particular, we modelled the history of rainforests in the eastern Guiana Shield over a timescale of several thousand generations, through the application of approximate Bayesian computation and maximum‐likelihood methods to diversity data at nuclear and chloroplast loci in eight species or subspecies of rainforest trees. Depending on the species and on the method applied, we detected population contraction, expansion or stability, with a general trend in favour of stability or expansion, with changes presumably having occurred during or after the LGM. These findings suggest that Guiana Shield rainforests have globally persisted, while expanding, through the Quaternary, but that different species have experienced different demographic events, with a trend towards the increase in frequency of light‐demanding, disturbance‐associated species.     

The complex biogeographic history of a widespread tropical tree species

Many tropical forest tree species have broad geographic ranges, and fossil records indicate that population disjunctions in some species were established millions of years ago. Here we relate biogeographic history to patterns of population differentiation, mutational and demographic processes in the widespread rainforest tree Symphonia globulifera using ribosomal (ITS) and chloroplast DNA sequences and nuclear microsatellite (nSSR) loci. Fossil records document sweepstakes dispersal origins of Neotropical S. globulifera populations from Africa during the Miocene. Despite historical long-distance gene flow, nSSR differentiation across 13 populations from Costa Rica, Panama, Ecuador (east and west of Andes) and French Guiana was pronounced (F(ST)= 0.14, R(ST)= 0.39, P < 0.001) and allele-size mutations contributed significantly (R(ST) > F(ST)) to the divergences between cis- and trans-Andean populations. Both DNA sequence and nSSR data reflect contrasting demographic histories in lower Mesoamerica and Amazonia. Amazon populations show weak phylogeographic structure and deviation from drift-mutation equilibrium indicating recent population expansion. In Mesoamerica, genetic drift was strong and contributed to marked differentiation among populations. The genetic structure of S. globulifera contains fingerprints of drift-dispersal processes and phylogeographic footprints of geological uplifts and sweepstakes dispersal.     

Evidence of low gene flow in a neotropical clustered tree species in two rainforest stands of French Guiana

The spatial genetic structure of the neotropical, clustered tree species Vouacapoua americana (Aublet) was studied in two natural forest stands (Paracou and Nouragues) in French Guiana. Using eight microsatellite loci, V. americana is characterized by a marked genetic structure at small spatial distances (under 30-60 m), in agreement with the limited seed dispersal by rodent species. Gene flow through pollen is also shown to be mainly restricted to less than 100 m. This result suggests that most pollination events (mediated through small insects) are probably limited to within-patches of individuals, which might explain the high genetic differentiation among patches (F(ST) = 0.11) separated by less than 2 km. We also assume that stronger genetic structure in Paracou is likely to be due to lower seed dispersal by rodents, large spatial distances separating patches, or a recent recolonization event.     

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.

     

Natural rewilding of the Great Basin: Genetic consequences of recolonization by black bears (Ursus americanus)

Aim

In the mid‐20th century, many populations of large‐bodied mammals experienced declines throughout North America. Fortunately, within the last several decades, some have begun to rebound and even recolonize extirpated portions of their native range, including black bears (Ursus americanus) in the montane areas of the western Great Basin. In this study, we examine genetic variation in source and recolonized areas to better understand the genetic consequences of recolonization.

Location

Western Great Basin, USA.

Methods

Using multiple loci, we characterized genetic variation among source and recently recolonized areas occupied by black bears, tested for population structure and applied approximate Bayesian computation to test competing hypotheses of demographic history. We assessed signals of gene flow using expectations of genetic consequences derived from alternative modes of recolonization (bottleneck, metapopulation, island model) and tested for significant signals of genetic bottlenecks in areas recently recolonized by black bears.

Results

As anticipated from field survey data and hypothesized expectations, genetic variation of western Great Basin black bears retain an overall signature of demographic decline followed by recent rebound. Furthermore, results reveal that bears in the recolonized range are minimally differentiated from the source area, but newly established subpopulations have lower effective population sizes and reduced allelic diversity. Nevertheless, recolonized areas fail to show a significant signal of a genetic bottleneck. Moreover, bears occupying recolonized areas experience asymmetric gene flow, yielding strong support for a model of genetic connectivity that is best described as a metapopulation.

Main Conclusion

This study presents one of the few empirical examples of genetic consequences of natural recolonization in large‐bodied mammals. Furthermore, these results have implications for understanding the complexities associated with the genetic consequences of recent and ongoing recolonization and highlight the need to develop management strategies uniquely tailored to support connectivity between source and recolonized areas.

     

Unique genetic variation at a species' rear edge is under threat from global climate change

Global climate change is having a significant effect on the distributions of a wide variety of species, causing both range shifts and population extinctions. To date, however, no consensus has emerged on how these processes will affect the range-wide genetic diversity of impacted species. It has been suggested that species that recolonized from low-latitude refugia might harbour high levels of genetic variation in rear-edge populations, and that loss of these populations could cause a disproportionately large reduction in overall genetic diversity in such taxa. In the present study, we have examined the distribution of genetic diversity across the range of the seaweed Chondrus crispus, a species that has exhibited a northward shift in its southern limit in Europe over the last 40 years. Analysis of 19 populations from both sides of the North Atlantic using mitochondrial single nucleotide polymorphisms (SNPs), sequence data from two single-copy nuclear regions and allelic variation at eight microsatellite loci revealed unique genetic variation for all marker classes in the rear-edge populations in Iberia, but not in the rear-edge populations in North America. Palaeodistribution modelling and statistical testing of alternative phylogeographic scenarios indicate that the unique genetic diversity in Iberian populations is a result not only of persistence in the region during the last glacial maximum, but also because this refugium did not contribute substantially to the recolonization of Europe after the retreat of the ice. Consequently, loss of these rear-edge populations as a result of ongoing climate change will have a major effect on the overall genetic diversity of the species, particularly in Europe, and this could compromise the adaptive potential of the species as a whole in the face of future global warming.     

Nuclear microsatellites reveal contrasting patterns of genetic structure between western and southeastern European populations of the common ash (Fraxinus excelsior L.)

To determine extant patterns of population genetic structure in common ash and gain insight into postglacial recolonization processes, we applied multilocus-based Bayesian approaches to data from 36 European populations genotyped at five nuclear microsatellite loci. We identified two contrasting patterns in terms of population genetic structure: (1) a large area from the British Isles to Lithuania throughout central Europe constituted effectively a single deme, whereas (2) strong genetic differentiation occurred over short distances in Sweden and southeastern Europe. Concomitant geographical variation was observed in estimates of allelic richness and genetic diversity, which were lowest in populations from southeastern Europe, that is, in regions close to putative ice age refuges, but high in western and central Europe, that is, in more recently recolonized areas. We suggest that in southeastern Europe, restricted postglacial gene flow caused by a rapid expansion of refuge populations in a mountainous topography is responsible for the observed strong genetic structure. In contrast, admixture of previously differentiated gene pools and high gene flow at the onset of postglacial recolonization of western and central Europe would have homogenized the genetic structure and raised the levels of genetic diversity above values in the refuges.     

Recent Demographic History and Present Fine-Scale Structure in the Northwest Atlantic Leatherback (Dermochelys coriacea) Turtle Population

The leatherback turtle Dermochelys coriacea is the most widely distributed sea turtle species in the world. It exhibits complex life traits: female homing and migration, migrations of juveniles and males that remain poorly known, and a strong climatic influence on resources, breeding success and sex-ratio. It is consequently challenging to understand population dynamics. Leatherbacks are critically endangered, yet the group from the Northwest Atlantic is currently considered to be under lower risk than other populations while hosting some of the largest rookeries. Here, we investigated the genetic diversity and the demographic history of contrasted rookeries from this group, namely two large nesting populations in French Guiana, and a smaller one in the French West Indies. We used 10 microsatellite loci, of which four are newly isolated, and mitochondrial DNA sequences of the control region and cytochrome b. Both mitochondrial and nuclear markers revealed that the Northwest Atlantic stock of leatherbacks derives from a single ancestral origin, but show current genetic structuration at the scale of nesting sites, with the maintenance of migrants amongst rookeries. Low nuclear genetic diversities are related to founder effects that followed consequent bottlenecks during the late Pleistocene/Holocene. Most probably in response to climatic oscillations, with a possible influence of early human hunting, female effective population sizes collapsed from 2 million to 200. Evidence of founder effects and high numbers of migrants make it possible to reconsider the population dynamics of the species, formerly considered as a metapopulation model: we propose a more relaxed island model, which we expect to be a key element in the currently observed recovering of populations. Although these Northwest Atlantic rookeries should be considered as a single evolutionary unit, we stress that local conservation efforts remain necessary since each nesting site hosts part of the genetic diversity and species history.     

Stronger spatial genetic structure in recolonized areas than in refugia in the European beech

Extant rear‐edge populations located in former glacial refugia remain understudied despite their high conservation value. These populations should have experienced strong genetic drift due to their small size and long isolation. Moreover, the prolonged action of isolation by distance in refugial areas should result in stronger regional spatial genetic structure (SGS) than in recolonized areas, but empirical tests of this prediction are scarce. To fill this gap, we first used a set of 16 microsatellite markers to investigate the genetic structure of European beech in France in 65 populations from three refugial areas and one control recolonized (nonrefugial) area. Then, using the same approach, we reanalysed published isozyme data from 375 populations distributed across the entire species range. We found stronger genetic differentiation among populations in refugia than in recolonized areas. However, contrary to expectations, regional SGS was lower within refugia than within recolonized areas. Published studies presenting similar analyses suggest that our results could have generality across different biogeographical settings and types of organisms. Strong and prolonged genetic drift in refugial areas could have erased the signature of range expansions that is still visible in recolonized areas. Our results therefore suggest that Pleistocene population isolation has played a key role in increasing the genetic complexity of extant rear‐edge populations.     

Spatial and temporal distribution of chloroplast DNA polymorphism in a tropical tree species

The level and the spatial organization of chloroplast DNA polymorphism were investigated in Dicorynia guianensis Hamshoff (Caesalpiniaceae) at different spatial and temporal scales. D. guianensis is a canopy tree of the rain forest that is distributed throughout the Guiana plateau in small aggregates. Twelve different haplotypes were identified using restriction analysis of polymerase chain reaction (PCR) amplified fragments of the chloroplast genome. When populations from different areas of French Guiana were compared, a clear geographical pattern of haplotype frequencies was identified along the Atlantic coast. This pattern is most likely the result of the restriction-expansion dynamics of the tropical forest during the Quaternary. At the local level, D. guianensis was characterized by a high level of within population diversity. Maintenance of within population diversity results from the dynamics of the aggregates; stochastic demography associated with the turnover of aggregates generates genetic differentiation among them. At the stand level, a strong spatial aggregation of haplotypes persisted from the adult to the seedling cohort indicating limited seed flow. There was also a strong difference in levels of diversity between the cohorts which suggested that recruitment over several years is needed in order to maintain genetic diversity during regeneration.     

Postglacial recolonization in a cold climate specialist in western Europe: patterns of genetic diversity in the adder (Vipera berus) support the central–marginal hypothesis

Understanding the impact of postglacial recolonization on genetic diversity is essential in explaining current patterns of genetic variation. The central–marginal hypothesis (CMH) predicts a reduction in genetic diversity from the core of the distribution to peripheral populations, as well as reduced connectivity between peripheral populations. While the CMH has received considerable empirical support, its broad applicability is still debated and alternative hypotheses predict different spatial patterns of genetic diversity. Using microsatellite markers, we analysed the genetic diversity of the adder (Vipera berus) in western Europe to reconstruct postglacial recolonization. Approximate Bayesian Computation (ABC) analyses suggested a postglacial recolonization from two routes: a western route from the Atlantic Coast up to Belgium and a central route from the Massif Central to the Alps. This cold‐adapted species likely used two isolated glacial refugia in southern France, in permafrost‐free areas during the last glacial maximum. Adder populations further from putative glacial refugia had lower genetic diversity and reduced connectivity; therefore, our results support the predictions of the CMH. Our study also illustrates the utility of highly variable nuclear markers, such as microsatellites, and ABC to test competing recolonization hypotheses.     

Congruent phylogeographical patterns of eight tree species in Atlantic Central Africa provide insights into the past dynamics of forest cover

Cycles of Quaternary climatic change are assumed to be major drivers of African rainforest dynamics and evolution. However, most hypotheses on past vegetation dynamics relied on palaeobotanical records, an approach lacking spatial resolution, and on current patterns of species diversity and endemism, an approach confounding history and environmental determinism. In this context, a comparative phylogeographical study of rainforest species represents a complementary approach because Pleistocene climatic fluctuations may have left interpretable signatures in the patterns of genetic diversity within species. Using 1274 plastid DNA sequences from eight tree species (Afrostyrax kamerunensis, A. lepidophyllus, Erythrophleum suaveolens, Greenwayodendron suaveolens, Milicia excelsa, Santiria trimera, Scorodophloeus zenkeri and Symphonia globulifera) sampled in 50 populations of Atlantic Central Africa (ACA), we averaged divergence across species to produce the first map of the region synthesizing genetic distinctiveness and standardized divergence within and among localities. Significant congruence in divergence was detected mostly among five of the eight species and was stronger in the northern ACA. This pattern is compatible with a scenario of past forest fragmentation and recolonization whereby forests from eastern Cameroon and northeastern Gabon would have been more affected by past climatic change than those of western Cameroon (where one or more refugia would have occurred). By contrast, southern ACA (Gabon) displayed low congruence among species that may reflect less drastic past forest fragmentation or a more complex history of vegetation changes. Finally, we also highlight the potential impact of current environmental barriers on spatial genetic structures.     

Genetic structure of the xerophilous bromeliad Pitcairnia geyskesii on inselbergs in French Guiana – a test of the forest refuge hypothesis

Inselbergs are isolated granitic rock outcrops that provide distinctive ecological conditions. In northern South America they rise above the surrounding rainforest. Among inselberg specialists, Pitcairnia geyskesii (Bromeliaceae) is restricted to these habitats in French Guiana. We studied populations from 12 inselbergs using 7 microsatellite loci to give a "reverse image" of the reduction-expansion of the rainforest in the context of the refuge hypothesis. Our analyses showed that populations are fragmented with dispersal occurring only over very short distances. Genetic diversity was higher in northern French Guiana, whereas specific alleles were observed in the south. The results point to the occurrence of a dry corridor in the north, as hypothesized by Tardy (1998) based on charcoal analyses, whereas de Granville's (1982) hypothesis of a unique past refuge is not confirmed. Moreover, our data suggests the importance of Oyapock River as a pathway for range expansion, arguing against the potential role of the Inini-Camopi Mountains as a physical barrier. Finally, in spite of a strongly argued scenario in favour of a north-to-south migration history, a clear genetic isolation of P. geyskesii populations living on inselbergs of the Mitaraka archipelago suggests a distinct ancestry of the most southern populations.