A recent local sweep at the PHYA locus in the Northern European Spiterstulen population of Arabidopsis lyrata

Northern and central European Arabidopsis lyrata ssp. petraea populations are locally adapted to prevailing climatic conditions through differences in timing of life history events. The timing of flowering and, in perennials, the timing of growth cessation influence fitness. Phytochrome A may have an important role in regulating these life history traits as it perceives changes in daylength. We asked whether PHYA has contributed to local adaptation to the northern conditions in A. l. petraea. To search for signals of directional selection at the PHYA locus, we resequenced PHYA and 9 short fragments around PHYA from a 57‐kb region from a German (Plech) and a Norwegian (Spiterstulen) population and compared patterns of differentiation and diversity to a set of 19 reference loci around the genome. First, we found that the populations were highly differentiated: there were three nonsynonymous fixed differences at the PHYA locus, which was in stark contrast with the total four fixed differences in the 19 reference loci. Compatible with a sweep hypothesis, variation was almost completely removed from the 9.4‐kb region around PHYA in the northern Spiterstulen population. The overall level of linkage disequilibrium (LD) was higher in Spiterstulen, but there was no LD across the PHYA locus in the population, which is also a known consequence of a selective sweep. The sweep has likely occurred after the last glacial maximum, which suggests that it has contributed to adaptation to the northern conditions.     

Parallel adaptation to climate above the 35th parallel

Independent or parallel evolution of similar traits is key to understanding the genetics and limitations of adaptation. Adaptation from the same genetic changes in different populations defines parallel evolution. Such genetic changes can derive from standing ancestral variation or de novo mutations and excludes instances of adaptive introgression. In this issue of Molecular Ecology, Walden et al.(2020) investigate the scale of parallel climate adaptation from standing genetic variation between two North American Arabidopsis lyrata lineages, each formed by a distinct evolutionary history during the last glacial cycle. By identifying adaptive variants correlated with three ecologically significant climatic gradients, they show that instead of the same genetic variants or even genes, parallel evolution is only observed at the level of biological processes. The evolution of independent adaptive variants to climate in two genetically close lineages is explained by their different post‐glacial demographic histories. Separate glacial refugia and strong population bottlenecks were probably sufficient to change the landscape of shared allele frequencies, hindering the possibility of parallel evolution.     

Dual influence of terrestrial and marine historical processes on the phylogeography of the Brazilian intertidal red alga Gracilaria caudata

In this study, we explored how past terrestrial and marine climate changes have interacted to shape the phylogeographic patterns of the intertidal red seaweed Gracilaria caudata, an economically important species exploited for agar production in the Brazilian north‐east. Seven sites were sampled along the north‐east tropical and south‐east sub‐tropical Brazilian coast. The genetic diversity and structure of G. caudata was inferred using a combination of mitochondrial (COI and cox2‐3), chloroplast (rbcL) and 15 nuclear microsatellite markers. A remarkable congruence between nuclear, mitochondrial and chloroplast data revealed clear separation between the north‐east (from 03° S to 08° S) and the south‐east (from 20° S to 23° S) coast of Brazil. These two clades differ in their demographic histories, with signatures of recent demographic expansions in the north‐east and divergent populations in the south‐east, suggesting the maintenance of several refugia during the last glacial maximum due to sea‐level rise and fall. The Bahia region (around 12° S) occupies an intermediate position between both clades. Microsatellites and mtDNA markers showed additional levels of genetic structure within each sampled site located south of Bahia. The separation between the two main groups in G. caudata is likely recent, probably occurring during the Quaternary glacial cycles. The genetic breaks are concordant with (i) those separating terrestrial refugia, (ii) major river outflows and (iii) frontiers between tropical and subtropical regions. Taken together with previously published eco‐physiological studies that showed differences in the physiological performance of the strains from distinct locations, these results suggest that the divergent clades in G. caudata correspond to distinct ecotypes in the process of incipient speciation and thus should be considered for the management policy of this commercially important species.     

Palaeodistribution modelling and genetic evidence highlight differential post‐glacial range shifts of a rain forest conifer distributed across a latitudinal gradient

Aim We examine the range expansion/contraction dynamics during the last glacial cycle of the late‐successional tropical rain forest conifer Podocarpus elatus using a combination of modelling and molecular marker analyses. Specifically, we test whether distributional changes predicted by environmental niche modelling are in agreement with (1) the glacial maximum contractions inferred from the southern fossil record, and (2) population genetic‐based estimates of range disjunctions and demographic dynamics. In addition, we test whether northern and southern ranges are likely to have experienced similar expansion/contraction dynamics. Location Eastern Australian tropical and subtropical rain forests. Methods Environmental niche modelling was completed for three time periods during the last glacial cycle and was interpreted in light of the known palynology. We collected 109 samples from 32 populations across the entire range of P. elatus. Six microsatellite loci and Bayesian coalescence analysis were used to infer population expansion/contraction dynamics, and five sequenced loci (one plastid and four nuclear) were used to quantify genetic structure/diversity. Results Environmental niche modelling suggested that the northern and southern ranges of P. elatus experienced different expansion/contraction dynamics. In the northern range, the habitat suitable for P. elatus persisted in a small refugial area during the Last Glacial Maximum (LGM, 21 ka) and then expanded during the post‐glacial period. Conversely, in the south suitable habitat was widespread during the LGM but subsequently contracted. These differential dynamics were supported by Bayesian analyses of the population genetic data (northern dispersal) and are consistent with the greater genetic diversity in the south compared with the north. A contact zone between the two genetically divergent groups (corresponding to the Macleay Overlap Zone) was supported by environmental niche modelling and molecular analyses. Main conclusions The climatic fluctuations of the Quaternary have differentially impacted the northern and southern ranges of a broadly distributed rain forest tree in Australia. Recurrent contraction/expansion cycles contributed to the genetic distinction between northern and southern distributions of P. elatus. By combining molecular and environmental niche modelling evidence, this unique study undermines the general assumption that broadly distributed species respond in a uniform way to climate change.     

The xeric side of the Brazilian Atlantic Forest: The forces shaping phylogeographic structure of cacti

In order to investigate biogeographic influences on xeric biota in the Brazilian Atlantic Forest (BAF), a biodiversity hotspot, we used a monophyletic group including three cactus taxa as a model to perform a phylogeographic study: Cereus fernambucensis subsp. fernambucensis, C. fernambucensis subsp. sericifer, and C. insularis. These cacti are allopatric and grow in xeric habitats along BAF, including isolated granite and gneiss rock outcrops (Inselbergs), sand dune vegetation (Restinga forest), and the rocky shore of an oceanic archipelago (islands of Fernando de Noronha). The nucleotide information from nuclear gene phytochrome C and plastid intergenic spacer trnS‐trnG was used to perform different approaches and statistical analyses, comprising population structure, demographic changes, phylogenetic relationships, and biogeographic reconstruction in both spatial and temporal scales. We recovered four allopatric population groups with highly supported branches in the phylogenetic tree with divergence initiated in the middle Pleistocene: southern distribution of C. fernambucensis subsp. fernambucensis, northern distribution of C. fernambucensis subsp. fernambucensis together with C. insularis, southern distribution of C. fernambucensis subsp. sericifer, and northern distribution of C. fernambucensis subsp. sericifer. Further, the results suggest that genetic diversity of population groups was strongly shaped by an initial colonization event from south to north followed by fragmentation. The phylogenetic pattern found for C. insularis is plausible with peripatric speciation in the archipelago of Fernando de Noronha. To explain the phylogeographic patterns, the putative effects of both climatic and sea level changes as well as neotectonic activity during the Pleistocene are discussed.     

Whole‐genome resequencing reveals the pleistocene temporal dynamics of Branchiostoma belcheri and Branchiostoma floridae populations

Global climatic fluctuations governed the ancestral demographic histories of species and contributed to place the current population status into a more extensive ecological and evolutionary context. Genetic variations will leave unambiguous signatures in the patterns of intraspecific genetic variation in extant species since the genome of each individual is an imperfect mosaic of the ancestral genomes. Here, we report the genome sequences of 20 Branchiostoma individuals by whole‐genome resequencing strategy. We detected over 140 million genomic variations for each Branchiostoma individual. In particular, we applied the pairwise sequentially Markovian coalescent (PSMC) method to estimate the trajectories of changes in the effective population size (N_e) of Branchiostoma population during the Pleistocene. We evaluated the threshold of sequencing depth for proper inference of demographic histories using PSMC was ≥25×. The PSMC results highlight the role of historical global climatic fluctuations in the long‐term population dynamics of Branchiostoma. The inferred ancestral N_e of the Branchiostoma belcheri populations from Zhanjiang and Xiamen (China) seawaters was different in amplitude before the first (mutation rate = 3 × 10^?9) or third glaciation (mutation rate = 9 × 10^?9) of the Pleistocene, indicating that the two populations most probably started to evolve in isolation in their respective seas after the first or third glaciation of the Pleistocene. A pronounced population bottleneck coinciding with the last glacial maximum was observed in all Branchiostoma individuals, followed by a population expansion occurred during the late Pleistocene. Species that have experienced long‐term declines may be especially vulnerable to recent anthropogenic activities. Recently, the industrial pollution and the exploitation of sea sand have destroyed the harmonious living environment of amphioxus species. In the future, we need to protect the habitat of Branchiostoma and make full use of these detected genetic variations to facilitate the functional study of Branchiostoma for adaptation to local environments.     

Temporal dynamics of linkage disequilibrium in two populations of bighorn sheep

Linkage disequilibrium (LD) is the nonrandom association of alleles at two markers. Patterns of LD have biological implications as well as practical ones when designing association studies or conservation programs aimed at identifying the genetic basis of fitness differences within and among populations. However, the temporal dynamics of LD in wild populations has received little empirical attention. In this study, we examined the overall extent of LD, the effect of sample size on the accuracy and precision of LD estimates, and the temporal dynamics of LD in two populations of bighorn sheep (Ovis canadensis) with different demographic histories. Using over 200 microsatellite loci, we assessed two metrics of multi‐allelic LD, D′, and χ^′2. We found that both populations exhibited high levels of LD, although the extent was much shorter in a native population than one that was founded via translocation, experienced a prolonged bottleneck post founding, followed by recent admixture. In addition, we observed significant variation in LD in relation to the sample size used, with small sample sizes leading to depressed estimates of the extent of LD but inflated estimates of background levels of LD. In contrast, there was not much variation in LD among yearly cross‐sections within either population once sample size was accounted for. Lack of pronounced interannual variability suggests that researchers may not have to worry about interannual variation when estimating LD in a population and can instead focus on obtaining the largest sample size possible.     

Waterscape genetics of the yellow perch ( Perca flavescens): patterns across large connected ecosystems and isolated relict populations

Comparisons of a species' genetic diversity and divergence patterns across large connected populations vs. isolated relict areas provide important data for understanding potential response to global warming, habitat alterations and other perturbations. Aquatic taxa offer ideal case studies for interpreting these patterns, because their dispersal and gene flow often are constrained through narrow connectivity channels that have changed over geological time and/or from contemporary anthropogenic perturbations. Our research objective is to better understand the interplay between historic influences and modern‐day factors (fishery exploitation, stocking supplementation and habitat loss) in shaping population genetic patterns of the yellow perch Perca flavescens (Percidae: Teleostei) across its native North American range. We employ a modified landscape genetics approach, analysing sequences from the entire mitochondrial DNA control region and 15 nuclear DNA microsatellite loci of 664 spawning adults from 24 populations. Results support that perch from primary glacial refugium areas (Missourian, Mississippian and Atlantic) founded contemporary northern populations. Genetic diversity today is highest in southern (never glaciated) populations and also is appreciable in northern areas that were founded from multiple refugia. Divergence is greater among isolated populations, both north and south; the southern Gulf Coast relict populations are the most divergent, reflecting their long history of isolation. Understanding the influence of past and current waterway connections on the genetic structure of yellow perch populations may help us to assess the roles of ongoing climate change and habitat disruptions towards conserving aquatic biodiversity.     

Genome‐wide analyses suggest parallel selection for universal traits may eclipse local environmental selection in a highly mobile carnivore

Ecological and environmental heterogeneity can produce genetic differentiation in highly mobile species. Accordingly, local adaptation may be expected across comparatively short distances in the presence of marked environmental gradients. Within the European continent, wolves (Canis lupus) exhibit distinct north–south population differentiation. We investigated more than 67‐K single nucleotide polymorphism (SNP) loci for signatures of local adaptation in 59 unrelated wolves from four previously identified population clusters (northcentral Europe n = 32, Carpathian Mountains n = 7, Dinaric‐Balkan n = 9, Ukrainian Steppe n = 11). Our analyses combined identification of outlier loci with findings from genome‐wide association study of individual genomic profiles and 12 environmental variables. We identified 353 candidate SNP loci. We examined the SNP position and neighboring megabase (1 Mb, one million bases) regions in the dog (C. lupus familiaris) genome for genes potentially under selection, including homologue genes in other vertebrates. These regions included functional genes for, for example, temperature regulation that may indicate local adaptation and genes controlling for functions universally important for wolves, including olfaction, hearing, vision, and cognitive functions. We also observed strong outliers not associated with any of the investigated variables, which could suggest selective pressures associated with other unmeasured environmental variables and/or demographic factors. These patterns are further supported by the examination of spatial distributions of the SNPs associated with universally important traits, which typically show marked differences in allele frequencies among population clusters. Accordingly, parallel selection for features important to all wolves may eclipse local environmental selection and implies long‐term separation among population clusters.     

Footprints of selection in wild populations of Bicyclus anynana along a latitudinal cline

One of the major questions in ecology and evolutionary biology is how variation in the genome enables species to adapt to divergent environments. Here, we study footprints of thermal selection in candidate genes in six wild populations of the afrotropical butterfly Bicyclus anynana sampled along a c. 3000 km latitudinal cline. We sequenced coding regions of 31 selected genes with known functions in metabolism, pigment production, development and heat shock responses. These include genes for which we expect a priori a role in thermal adaptation and, thus, varying selection pressures along a latitudinal cline, and genes we do not expect to vary clinally and can be used as controls. We identified amino acid substitution polymorphisms in 13 genes and tested these for clinal variation by correlation analysis of allele frequencies with latitude. In addition, we used two F_ST‐based outlier methods to identify loci with higher population differentiation than expected under neutral evolution, while accounting for potentially confounding effects of population structure and demographic history. Two metabolic enzymes of the glycolytic pathway, UGP and Treh, showed clinal variation. The same loci showed elevated population differentiation and were identified as significant outliers. We found no evidence of clines in the pigmentation genes, heat shock proteins and developmental genes. However, we identified outlier loci in more localized parts of the range in the pigmentation genes yellow and black. We discuss that the observed clinal variation and elevated population divergence in UGP and Treh may reflect adaptation to a geographic thermal gradient.     

Phylogeography of northern Dolly Varden Salvelinus malma malma based on analysis of mitochondrial DNA

The northern Dolly Varden, Salvelinus malma malma, is a typical representative of arctic fauna distributed in northeastern Asia and northwestern North America. Because its spawning habitats were affected by Pleistocene glacial advances over most of its natural range, S. m. malma is among the most interesting objects of phylogeographic and microevolutionary studies. We reconstructed the genealogy of mtDNA haplotypes from 27 Alaskan and Asian populations to study the influence of glacial and geological vicariance events on the contemporary population genetic structure, phylogeographic subdivision and distribution of the northern Dolly Varden. Analysis of restriction site states in three PCR‐amplified mtDNA regions (ND1/ND2, ND5/ND6, Cytb/D‐loop; 47% of the mitochondrial genome) resolved 75 haplotypes in 436 fish. Similar patterns of subspecific variation apparent from hierarchical diversity and nested clade analyses of mtDNA haplotypes identify weak spatial differentiation and low levels of divergence. Our results suggest that (1) demographic history has been influenced by historical range expansions and recent isolation by distance, (2) present populations from Asia and North America were colonized from one main Beringian Refugium, and (3) that this taxon's ancestral population probably experienced a bottleneck in the Beringian Refugium during the late Pleistocene (Wisconsin) glacial period.     

Selection for population‐specific adaptation shaped patterns of variation in the photoperiod pathway genes in Arabidopsis lyrata during post‐glacial colonization

Spatially varying selection can lead to population‐specific adaptation, which is often recognized at the phenotypic level; however, the genetic evidence is weaker in many groups of organisms. In plants, environmental shifts that occur due to colonization of a novel environment may require adaptive changes in the timing of growth and flowering, which are often governed by location‐specific environmental cues such as day length. We studied locally varying selection in 19 flowering time loci in nine populations of the perennial herb Arabidopsis lyrata, which has a wide but patchy distribution in temperate and boreal regions of the northern hemisphere. The populations differ in their recent population demographic and colonization histories and current environmental conditions, especially in the growing season length. We searched for population‐specific molecular signatures of directional selection by comparing a set of candidate flowering time loci with a genomic reference set within each population using multiple approaches and contrasted the patterns of different populations. The candidate loci possessed approximately 20% of the diversity of the reference loci. On average the flowering time loci had more rare alleles (a smaller Tajima's D) and an excess of highly differentiated sites relative to the reference, suggesting positive selection. The strongest signal of selection was detected in photoperiodic pathway loci in the colonizing populations of Northwestern Europe, whereas no evidence of positive selection was detected in the Central European populations. These findings emphasized the population‐specific nature of selection and suggested that photoperiodic adaptation was important during postglacial colonization of the species.     

Diversification in a biodiversity hot spot: landscape correlates of phylogeographic patterns in the African spotted reed frog

The Eastern Afromontane Biodiversity Hotspot is known for microendemism and exceptional population genetic structure. The region's landscape heterogeneity is thought to limit gene flow between fragmented populations and create opportunities for regional adaptation, but the processes involved are poorly understood. Using a combination of phylogeographic analyses and circuit theory, I investigate how characteristics of landscape heterogeneity including regional distributions of slope, rivers and streams, habitat and hydrological basins (drainages) impact genetic distance among populations of the endemic spotted reed frog (Hyperolius substriatus), identifying corridors of connectivity as well as barriers to dispersal. Results show that genetic distance among populations is most strongly correlated to regional and local hydrologic structure and the distribution of suitable habitat corridors, not isolation by distance. Contrary to expectations, phylogeographic structure is not coincident with the two montane systems, but instead corresponds to the split between the region's two major hydrological basins (Zambezi and East Central Coastal). This results in a paraphyletic relationship for the Malawian Highlands populations with respect to the Eastern Arc Mountains and implies that the northern Malawian Highlands are the diversity centre for H. substriatus. Although the Malawian Highlands collectively hold the greatest genetic diversity, individual populations have lower diversity than their Eastern Arc counterparts, with an overall pattern of decreasing population diversity from north to south. Through the study of intraspecific differentiation across a mosaic of ecosystem and geographic heterogeneity, we gain insight into the processes of diversification and a broader understanding of the role of landscape in evolution.     

Linkage disequilibrium network analysis (LDna) gives a global view of chromosomal inversions,local adaptation and geographic structure

Recent advances in sequencing allow population‐genomic data to be generated for virtually any species. However, approaches to analyse such data lag behind the ability to generate it, particularly in nonmodel species. Linkage disequilibrium (LD, the nonrandom association of alleles from different loci) is a highly sensitive indicator of many evolutionary phenomena including chromosomal inversions, local adaptation and geographical structure. Here, we present linkage disequilibrium network analysis (LDna), which accesses information on LD shared between multiple loci genomewide. In LD networks, vertices represent loci, and connections between vertices represent the LD between them. We analysed such networks in two test cases: a new restriction‐site‐associated DNA sequence (RAD‐seq) data set for Anopheles baimaii, a Southeast Asian malaria vector; and a well‐characterized single nucleotide polymorphism (SNP) data set from 21 three‐spined stickleback individuals. In each case, we readily identified five distinct LD network clusters (single‐outlier clusters, SOCs), each comprising many loci connected by high LD. In A. baimaii, further population‐genetic analyses supported the inference that each SOC corresponds to a large inversion, consistent with previous cytological studies. For sticklebacks, we inferred that each SOC was associated with a distinct evolutionary phenomenon: two chromosomal inversions, local adaptation, population‐demographic history and geographic structure. LDna is thus a useful exploratory tool, able to give a global overview of LD associated with diverse evolutionary phenomena and identify loci potentially involved. LDna does not require a linkage map or reference genome, so it is applicable to any population‐genomic data set, making it especially valuable for nonmodel species.     

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.

     

Variability and adaptability of Miscanthus species evaluated for energy crop domestication

A growing body of evidence indicates that second‐generation energy crops can play an important role in the development of renewable energy and the mitigation of climate change. However, dedicated energy crops have yet to be domesticated in order to fully realize their productive potential under unfavorable soil and climatic conditions. To explore the possibility of domesticating Miscanthus crops in northern China where marginal and degraded land is abundant, we conducted common garden experiments at multiple locations to evaluate variation and adaptation of three Miscanthus species that are likely to serve as the wild progenitors of the energy crops. A total of 93 populations of Miscanthus sinensis, Miscanthus sacchariflorus, and Miscanthus lutarioriparius were collected across their natural distributional ranges in China and grown in three locations that represent temperate grassland with cold winter, the semiarid Loess Plateau, and relatively warm and wet central China. Evaluated with growth traits such as plant height, tiller number, tiller diameter, and flowering time, the Miscanthus species showed high levels of genetic variation within and between species. There were significant site × population interactions for almost all traits of M. sacchariflorus and M. sinensis, but not M. lutarioriparius. The northern populations of M. sacchariflorus had the highest establishment rates at the most northern site owing to their strong cold tolerance. An endemic species in central China, M. lutarioriparius, produced not only the highest biomass of the three species but also higher biomass at the Loess Plateau than the southern site near its native habitats. These results demonstrated that the wild species harbored a high level of genetic variation underlying traits important for crop establishment and production at sites that are colder and drier than their native habitats. The natural variation and adaptive plasticity found in the Miscanthus species indicated that they could provide valuable resources for the development of second‐generation energy crops.     

Differential introgression from a sister species explains high FST outlier loci within a mussel species

Scanning genomes for loci with high levels of population differentiation has become a standard of population genetics. F_ST outlier loci are most often interpreted as signatures of local selection, but outliers might arise for many other reasons too often left unexplored. Here, we tried to identify further the history and genetic basis underlying strong differentiation at F_ST outlier loci in a marine mussel. A genome scan of genetic differentiation has been conducted between Atlantic and Mediterranean populations of Mytilus galloprovincialis. The differentiation was low overall (F_ST = 0.03), but seven loci (2%) were strong F_ST outliers. We then analysed DNA sequence polymorphism at two outlier loci. The genetic structure proved to be the consequence of differential introgression of alleles from the sister‐hybridizing species Mytilus edulis. Surprisingly, the Mediterranean population was the most introgressed at these two loci, although the contact zone between the two species is nowadays localized along the Atlantic coasts of France and the British Isles. A historical contact between M. edulis and Mediterranean M. galloprovincialis should have happened during glacial periods. It proved difficult to disentangle two hypotheses: (i) introgression was adaptive, implying edulis alleles have been favoured in Mediterranean populations, or (ii) the genetic architecture of the barrier to edulis gene flow is different between the two M. galloprovincialis backgrounds. Five of the seven outliers between M. galloprovincialis populations were also outliers between M. edulis and Atlantic M. galloprovincialis, which would support the latter hypothesis. Differential introgression across semi‐permeable barriers to gene flow is a neglected scenario to interpret outlying loci that may prove more widespread than anticipated.     

Comparative phylogeography and demographic history of two marsupials of the Atlantic Forest in eastern Brazil

The Atlantic Forest biodiversity hotspot in eastern South America has been the focus of several phylogeographic studies concerning relationships between populations and areas and how taxa respond to environmental changes. We infer and compare the demographic and biogeographic histories of two didelphid marsupial species, Gracilinanus microtarsus and Marmosops incanus, from the Atlantic Forest of eastern Brazil to determine how these species responded to environmental changes over time, using mitochondrial and nuclear DNA sequences. We found great intraspecific genetic divergence in both species and a strong geographic structure related to similar and spatially cohesive groups within each species. These groups are consistent with the same topographical barriers, such as mountains and river valleys. Intraspecific clades are very old, dating back to a period of tectonic activities in the Neogene (5.39–8.57 Mya). Changes in the environment over the last 7 million years lead to fairly concordant demographic changes in both marsupial species, including population expansion during the last glacial maximum (ca. 21,000 years ago) or last interglacial (ca. 120,000 years ago) or both. These results do not fit the Pleistocene refuge hypothesis as an explanation of the historical biogeography and diversification of both species in the Atlantic Forest, but are compatible with the Atlantis Forest hypothesis.     

Structural genomic variation leads to genetic differentiation in Lake Tanganyika's sardines

Identifying patterns in genetic structure and the genetic basis of ecological adaptation is a core goal of evolutionary biology and can inform the management and conservation of species that are vulnerable to population declines exacerbated by climate change. We used reduced‐representation genomic sequencing methods to gain a better understanding of genetic structure among and within populations of Lake Tanganyika's two sardine species, Limnothrissa miodon and Stolothrissa tanganicae. Samples of these ecologically and economically important species were collected across the length of Lake Tanganyika, as well as from nearby Lake Kivu, where L. miodon was introduced in 1959. Our results reveal differentiation within both S. tanganicae and L. miodon that is not explained by geography. Instead, this genetic differentiation is due to the presence of large sex‐specific regions in the genomes of both species, but involving different polymorphic sites in each species. Our results therefore indicate rapidly evolving XY sex determination in the two species. Additionally, we found evidence of a large chromosomal rearrangement in L. miodon, creating two homokaryotypes and one heterokaryotype. We found all karyotypes throughout Lake Tanganyika, but the frequencies vary along a north–south gradient and differ substantially in the introduced Lake Kivu population. We do not find evidence for significant isolation by distance, even over the hundreds of kilometres covered by our sampling, but we do find shallow population structure.     

Contrasting patterns of genome‐wide polymorphism in the native and invasive range of the marine mollusc Crepidula fornicata

Selection processes are believed to be an important evolutionary driver behind the successful establishment of nonindigenous species, for instance through adaptation for invasiveness (e.g. dispersal mechanisms and reproductive allocation). However, evidence supporting this assumption is still scarce. Genome scans have often identified loci with atypical patterns of genetic differentiation (i.e. outliers) indicative of selection processes. Using microsatellite‐ and AFLP‐based genome scans, we looked for evidence of selection following the introduction of the mollusc Crepidula fornicata. Native to the northwestern Atlantic, this gastropod has become an emblematic invader since its introduction during the 19th and 20th centuries in the northeastern Atlantic and northeastern Pacific. We examined 683 individuals from seven native and 15 introduced populations spanning the latitudinal introduction and native ranges of the species. Our results confirmed the previously documented high genetic diversity in native and introduced populations with little genetic structure between the two ranges, a pattern typical of marine invaders. Analysing 344 loci, no outliers were detected between the introduced and native populations or in the introduced range. The genomic sampling may have been insufficient to reveal selection especially if it acts on traits determined by a few genes. Eight outliers were, however, identified within the native range, underlining a genetic singularity congruent with a well‐known biogeographical break along the Florida. Our results call into question the relevance of AFLP genome scans in detecting adaptation on the timescale of biological invasions: genome scans often reveal long‐term adaptation involving numerous genes throughout the genome but seem less effective in detecting recent adaptation from pre‐existing variation on polygenic traits. This study advocates other methods to detect selection effects during biological invasions—for example on phenotypic traits, although genome scans may remain useful for elucidating introduction histories.