The homogenous genetic structure and inferred unique history of range shifts during the Pleistocene climatic oscillations of <Emphasis Type="Italic">Arcterica nana</Emphasis> (Maxim.) Makino (Ericaceae)

Previous phylogeographic studies of alpine plants in Japan have inferred that populations in central Honshu persisted during the Pleistocene climatic oscillations and suggested interglacial survival in high mountains. However, Arcterica nana (Maxim.) Makino (Ericaceae) exhibits a homogenous genetic structure throughout Japan and may therefore have a unique phylogeographic history. This inconsistency could have resulted from insufficient resolution of previously analyzed chloroplast DNA sequences. Therefore, we conducted a phylogeographic investigation based on amplified fragment length polymorphisms. Using 176 individuals from 21 populations, the relationships among individuals and populations were determined by principal coordinate analysis and a neighbor-joining tree, respectively. In addition, genetic differentiation was estimated using analysis of molecular variance and spatial autocorrelation analysis. These analyses demonstrate a homogenous structure throughout the entire Japanese range, supporting the previous cpDNA phylogeography. Although this genetic structure is inconsistent with those of other alpine plants, it is difficult to postulate that pre-existing genetic differentiation was swamped exclusively within A. nana. Therefore, this homogenous genetic structure may have been caused by the distinct history of populations of A. nana. Specifically, the southern-ward migration and the subsequent continuous populations enabled gene flow throughout the Japanese archipelago during the last glacial period. Thus, our data suggest that alpine plants in the Japanese archipelago did not always experience a shared distribution change following climatic oscillations.     

Phylogeography of Arcterica nana (Ericaceae) suggests another range expansion history of Japanese alpine plants

We conducted a phylogeographic study on the alpine plant Arcterica nana based on haplotypes of chloroplast DNA. Using a sequence of approximately 1,071 bp of intergenic spacers of chloroplast DNA (trnT-L, psbB–psbF), we detected 13 haplotypes among 193 individuals sampled from 22 populations. Two dominant haplotypes were distributed over the entire range of this species in Japan, and we found several local private haplotypes. An analysis of molecular variance (AMOVA) indicated no geographic structure within the haplotype distribution. In addition, the genetic distance was not related to its corresponding geographic distance (Mantel test: r=−0.049, P=0.66), indicating a homogeneous geographic structure throughout the entire distribution range in the Japanese archipelago. The most parsimonious explanation for this geographic structure is that A. nana spread across its extant distribution range in the Japanese archipelago through a recent range expansion event. However, this pattern is inconsistent with the previous phylogeography of Japanese alpine plants, which reveals that haplotypes in central Honshu are differentiated from those in more northern regions. Arcterica nana may have experienced a different history from other alpine plants, suggesting that the history of Japanese alpine flora may include at least two different geographic radiation patterns.     

Post-glacial range fragmentation is responsible for the current distribution of Potentilla matsumurae Th. Wolf (Rosaceae) in the Japanese archipelago

Aim We aimed to elucidate how the current geographic distribution of alpine plants in the Japanese archipelago was shaped during Quaternary climatic oscillations, using Potentilla matsumurae as a case study. According to previous phylogeographic studies, post‐glacial range fragmentation (vicariance scenario) and stepwise migration (dispersal scenario) are both possible. We thus aimed to assess which scenario is more probable for the distribution changes of alpine plants in the Japanese archipelago. Location The alpine zone in the Japanese archipelago. Methods Using amplified fragment length polymorphism we determined the genotype of 161 individuals of P. matsumurae from 22 populations. Relationships among individuals and populations were examined using principal coordinates analysis and a neighbour‐joining (NJ) tree, respectively. To examine the genetic population structure, we performed analysis of molecular variance (amova ) and structure analysis. Results Differentiation between central Honshu and northern Japan was not very strong based on the principal coordinates analysis among individuals, the NJ tree of populations (59% bootstrap support), or amova (12% of genetic variation). Moreover, structure analysis did not detect clear geographic differentiation across populations. Although the populations in central Honshu were structured geographically (Mantel test: r = 0.45, P < 0.005; NJ tree), those in northern Japan did not exhibit geographic structure regardless of geographic distance (Mantel test: r = 0.26, P = 0.03; NJ tree). Population relationships in the NJ tree did not always reflect the geographic location. Main conclusions The current geographic structure of P. matsumurae could not be explained by stepwise migration. This suggests that a single continuous distribution during the last glacial period was later fragmented, perhaps by recovering forest, during the post‐glacial period, resulting in the current distribution and phylogeographic structure of P. matsumurae. Our data support the vicariance scenario.     

Evolved variation in cold tolerance among populations of Eldana saccharina (Lepidoptera: Pyralidae) in South Africa

Among‐population variation in chill‐coma onset temperature (CT_min) is thought to reflect natural selection for local microclimatic conditions. However, few studies have investigated the evolutionary importance of cold tolerance limits in natural populations. Here, using a common‐environment approach, we show pronounced variation in CT_min (± 4 °C) across the geographic range of a nonoverwintering crop pest, Eldana saccharina. The outcomes of this study provide two notable results in the context of evolved chill‐coma variation: (1) CT_min differs significantly between geographic lines and is significantly positively correlated with local climates, and (2) there is a stable genetic architecture underlying CT_min trait variation, likely representing four key genes. Crosses between the most and least cold‐tolerant geographic lines confirmed a genetic component to CT_min trait variation. Slower developmental time in the most cold‐tolerant population suggests that local adaptation involves fitness costs; however, it confers fitness benefits in that environment. A significant reduction in phenotypic plasticity in the laboratory population suggests that plasticity of this trait is costly to maintain but also likely necessary for field survival. These results are significant for understanding field population adaption to novel environments, whereas further work is needed to dissect the underlying mechanism and gene(s) responsible.     

Geographic clines in wing morphology relate to colonization history in New World but not Old World populations of yellow dung flies

Geographic clines offer insights about putative targets and agents of natural selection as well as tempo and mode of adaptation. However, demographic processes can lead to clines that are indistinguishable from adaptive divergence. Using the widespread yellow dung fly Scathophaga stercoraria (Diptera: Scathophagidae), we examine quantitative genetic differentiation (Q_ST) of wing shape across North America, Europe, and Japan, and compare this differentiation with that of ten microsatellites (F_ST). Morphometric analyses of 28 populations reared at three temperatures revealed significant thermal plasticity, sexual dimorphism, and geographic differentiation in wing shape. In North America morphological differentiation followed the decline in microsatellite variability along the presumed route of recent colonization from the southeast to the northwest. Across Europe, where S. stercoraria presumably existed for much longer time and where no molecular pattern of isolation by distance was evident, clinal variation was less pronounced despite significant morphological differentiation (Q_ST>F_ST). Shape vector comparisons further indicate that thermal plasticity (hot‐to‐cold) does not mirror patterns of latitudinal divergence (south‐to‐north), as might have been expected under a scenario with temperature as the major agent of selection. Our findings illustrate the importance of detailed phylogeographic information when interpreting geographic clines of dispersal traits in an adaptive evolutionary framework.     

Local adaptation and ecological differentiation under selection,migration, and drift in Arabidopsis lyrata*

How the balance between selection, migration, and drift influences the evolution of local adaptation has been under intense theoretical scrutiny. Yet, empirical studies that relate estimates of local adaptation to quantification of gene flow and effective population sizes have been rare. Here, we conducted a reciprocal transplant trial, a common garden trial, and a whole‐genome‐based demography analysis to examine these effects among Arabidopsis lyrata populations from two altitudinal gradients in Norway. Demography simulations indicated that populations within the two gradients are connected by gene flow (0.1 < 4N_em < 11) and have small effective population sizes (N_e < 6000), suggesting that both migration and drift can counteract local selection. However, the three‐year field experiments showed evidence of local adaptation at the level of hierarchical multiyear fitness, attesting to the strength of differential selection. In the lowland habitat, local superiority was associated with greater fecundity, while viability accounted for fitness differences in the alpine habitat. We also demonstrate that flowering time differentiation has contributed to adaptive divergence between these locally adapted populations. Our results show that despite the estimated potential of gene flow and drift to hinder differentiation, selection among these A. lyrata populations has resulted in local adaptation.     

Molecular Evolution of Phytochromes in Cardamine nipponica (Brassicaceae) Suggests the Involvement of PHYE in Local Adaptation

Given that plants are sessile organisms, traits involved in adapting to local environments and/or in monitoring the surrounding environment, such as having photoreceptors, are significant targets of natural selection in plant evolution. To assess the intraspecific adaptive evolution of photoreceptors, we investigated sequence variations in four phytochrome genes (PHYA–C and PHYE) of Cardamine nipponica (Brassicaceae), an endemic Japanese alpine plant. The genealogies of haplotypes and genetic differentiations showed inconsistent patterns of evolution across phytochromes, suggesting that evolutionary forces were distinct in phytochromes of C. nipponica. An overall low level of nucleotide diversity in phytochrome genes suggests that the evolution of phytochromes is constrained by purifying selection within C. nipponica, which is consistent with previous findings on phytochromes. However, PHYE alone exhibited a non-neutral pattern of polymorphisms (Tajima''s D = 1.91, P < 0.05) and an accumulation of nonsynonymous substitutions between central and northern Japan. In particular, the PHY domain, which plays an important role in stabilizing the active form (Pfr) of phytochromes, harbored a specific nonsynonymous fixation between regions. Thus, our finding indicates that local adaptation is involved in the evolution of PHYE in C. nipponica and is the first to suggest the involvement of PHYE in local adaptation.GIVEN that plants are sessile organisms, adapting to the surrounding environment and monitoring environmental changes such as temperature, aridity, and day length are important not only for survival, but also for reproductive success. Thus, natural selection has likely played a significant role in selecting for such traits in the evolution of plants. In particular, various developmental responses are influenced by the light environment (known as photomorphogenesis); for example, germination, de-etiolation, shade avoidance, and flowering are regulated by light signals (Whitelam and Devlin 1997; Whitelam et al. 1998; Smith 2000; Mathews 2006). Thus, plants have obtained sophisticated systems, including photoreceptors, to monitor light signals such as intensity, direction, quality, and duration. In particular, phytochromes, which sense red and far-red light, are among the most studied photoreceptors and play a major role in developmental pathways as well as in evolutionary history.Phytochromes have two photoreversible conformations: an inactive red-light-absorbing form (Pr) and an active far-red-light-absorbing form (Pfr). Red light converts Pr to Pfr, while far-red light converts Pfr back to Pr. At least three phytochromes are widely known in angiosperms (PHYA–C; Mathews et al. 1995), and five have been identified in Arabidopsis thaliana (PHYA–E; Sharrock and Quail 1989; Clack et al. 1994). According to phylogenetic analyses, these gene families are clustered into two major groups, PHYA/C and PHYB/D/E (Alba et al. 2000), and the duplication of these two major clusters occurred prior to angiosperm radiation (Mathews et al. 1995). Further duplication resulted in PHYA and PHYC and PHYB/D and PHYE, although some groups, such as monocots and poplars, lack PHYE (Mathews and Sharrock 1996), and PHYD was duplicated from PHYB specifically in the Brassicaceae (Mathews and McBreen 2008). The evolutionary consequences following gene duplications have recently been reported. Positive selection was involved in the functional divergence following duplications in PHYA and PHYC and PHYB/D and PHYE, whereas purifying selection suppressed the divergence in each group (Yang and Nielsen 2002). Moreover, adaptive evolution was involved in the evolution of PHYA in early angiosperms (Mathews et al. 2003).Because light signals differ among habitats, such as forest understory, canopy, and open meadow, as well as among populations at high and low latitudes and altitudes, the functions of phytochromes should be both a target for natural selection and adapted to the local light environment. This hypothesis was recently supported by studies of A. thaliana, which showed that amino acid substitutions in PHYA, PHYB, and PHYC may be responsible for intraspecific phenotypic differences among accessions (Maloof et al. 2001; Balasubramanian et al. 2006; Filiault et al. 2008). In addition to the conclusions of the Arabidopsis studies, the importance of PHYB2 for local adaptation was also suggested in studies of Populus tremula (Ingvarsson et al. 2006, 2008). Thus, determining polymorphisms in phytochrome genes and their geographic distribution could demonstrate the importance of phytochromes for local adaptation.A previous phylogeographic study on Cardamine nipponica Franch. et Savat. (Brassicaceae), an endemic Japanese alpine plant, found a higher level of fixation of nonsynonymous substitutions among populations in a partial sequence of PHYE (Ikeda et al. 2008b), indicating the involvement of PHYE in local adaptation. In the Japanese archipelago, alpine flora are distributed on high mountaintops from central to northern Japan. Nearly half of the Japanese alpine flora species are also found in Arctic regions [such as Dryas octopetala (Rosaceae), Loiseleuria procumbens (Ericaceae), and Diapensia lapponica (Diapensiaceae)], indicating that Arctic plants significantly contributed to the Japanese alpine flora. According to recent phylogeographic investigations, most alpine plants show strong genetic differentiation between populations from central and northern Japan, suggesting a history of vicariance in the Japanese archipelago (Fujii et al. 1997, 1999; Senni et al. 2005; Fujii and Senni 2006; Ikeda et al. 2006, 2008a,b; Ikeda and Setoguchi 2007, 2009). Most importantly, the genetic structure of 10 nuclear genes in C. nipponica revealed that haplotypes of most loci were closely related in each region and diverged from those in the other region. Moreover, the isolation with migration model (Nielsen and Wakeley 2001; Hey and Nielsen 2004, 2007) demonstrated no migration between the two regions after the regions were split, suggesting that the divergence in functional genes occurred following the vicariance between regions (H. Ikeda, N. Fujii and H. Setoguchi, unpublished results). In a partial sequence of PHYE (∼700 of the 3700 bp), three nonsynonymous substitutions were fixed between central and northern Japan, whereas nine other loci showed few nonsynonymous substitutions between the two regions. Thus, local adaptation in PHYE may have occurred following the vicariance between central and northern Japan, while genetic drift following the vicariance happened to fix the nonsynonymous substitutions. Further investigations that evaluate evolutionary patterns along the functional domains of phytochromes, including determining the entire sequences of PHYE, may demonstrate the involvement of PHYE in local adaptation.In this study, to test the hypothesis that PHYE has been involved in local adaptation between central and northern Japan, we determined the entire sequences of PHYE from the entire distribution range of C. nipponica and examined polymorphisms and their geographic structures. Furthermore, to assess whether the signature of local adaptation was exclusively detected in PHYE or whether other phytochromes were also involved, we determined the entire sequences of PHYA–C and examined their polymorphisms.     

Genomewide scan for adaptive differentiation along altitudinal gradient in the Andrew's toad Bufo andrewsi

Recent studies of humans, dogs and rodents have started to discover the genetic underpinnings of high altitude adaptations, yet amphibians have received little attention in this respect. To identify possible signatures of adaptation to altitude, we performed a genome scan of 15 557 single nucleotide polymorphisms (SNPs) obtained with restriction site‐associated DNA sequencing of pooled samples from 11 populations of Andrew's toad (Bufo andrewsi) from the edge of the Tibetan Plateau, spanning an altitudinal gradient from 1690 to 2768 m.a.s.l. We discovered significant geographic differentiation among all sites, with an average F_ST = 0.023 across all SNPs. Apart from clear patterns of isolation by distance, we discovered numerous outlier SNPs showing strong associations with variation in altitude (1394 SNPs), average annual temperature (1859 SNPs) or both (1051 SNPs). Levels and patterns of genetic differentiation in these SNPs were consistent with the hypothesis that they have been subject to directional selection and reflect adaptation to altitudinal variation among the study sites. Genes with footprints of selection were significantly enriched in binding and metabolic processes. Several genes potentially related to high altitude adaptation were identified, although the identity and functional significance of most genomic targets of selection remain unknown. In general, the results provide genomic support for results of earlier common garden and low coverage genetic studies that have uncovered substantial adaptive differentiation along altitudinal and latitudinal gradients in amphibians.     

Molecular evolution of cryptochrome genes and the evolutionary manner of photoreceptor genes in <Emphasis Type="Italic">Cardamine nipponica</Emphasis> (Brassicaceae)

Various photoreceptors in plants are used to monitor important environmental light signals and regulate plant development. Despite their functional importance, recent studies have demonstrated that red/far-red absorbing phytochromes or blue/UV-A absorbing cryptochromes are involved in local adaptation within a species’ range. In the present study, to exemplify the intraspecific photoreceptor evolutionary pattern, the genetic structures of cryptochrome genes (CRY1 and CRY2) in Cardamine nipponica (Brassicaceae), of which PHYE, a gene coding one of the phytochromes, was found to be involved in local adaptation between central and northern Japanese populations. Although clear genetic differentiations between central and northern Japan were detected (CRY1: F _ST = 0.63, CRY2: F _ST = 0.53), overall nucleotide diversity was very low (CRY1: π _Total = 0.0014, CRY2: π _Total = 0.0013), and the polymorphism patterns were neutral (CRY1: Tajima’s D = 0.084, P = 0.32, CRY2: D = −0.014, P = 0.39). Therefore, the involvement of cryptochromes in the adaptation to local environments is difficult to postulate. Consequently, this study along with our previous findings suggest that intraspecific photoreceptor gene polymorphisms in C. nipponica were mostly suppressed by purifying selection due to their functional importance as photoreceptors, while some of the photoreceptors may play substantial roles in adaptation to local environments.     

The importance of environmental heterogeneity and spatial distance in generating phylogeographic structure in edaphic specialist and generalist tree species of Protium (Burseraceae) across the Amazon Basin

Aim Edaphic heterogeneity may be an important driver of population differentiation in the Amazon but remains to be investigated in trees. We compared the phylogeographic structure across the geographic distribution of two Protium (Burseraceae) species with different degrees of edaphic specialization: Protium alvarezianum, an edaphic specialist of white‐sand habitat islands; and Protium subserratum, an edaphic generalist found in white sand as well as in more widespread soil types. We predicted that in the edaphic specialist, geographic distance would structure populations more strongly than in the edaphic generalist, and that soil type would not structure populations in the edaphic generalist unless habitat acts as a barrier promoting population differentiation. Location Tropical rain forests of the Peruvian and Brazilian Amazon, Guyana and French Guiana. Methods We sequenced 1209–1211 bp of non‐coding nuclear ribosomal DNA (internal transcribed spacer and external transcribed spacer) and a neutral low‐copy nuclear gene (phytochrome C) from P. subserratum (n = 65, 10 populations) and P. alvarezianum (n = 19, three populations). We conducted a Bayesian phylogenetic analysis, constructed maximum parsimony haplotype networks and assessed population differentiation among groups (soil type or geographic locality) using analysis of molecular variance and spatial analysis of molecular variance. Results The edaphic specialist exhibited considerable genetic differentiation among geographically distant populations. The edaphic generalist showed significant genetic differentiation between the Guianan and Amazon Basin populations. Within Peru, soil type and not geographic distance explained most of the variation among populations. Non‐white‐sand populations in Peru exhibited lower haplotype/nucleotide diversity than white‐sand populations, were each other’s close relatives, and formed an unresolved clade derived from within the white‐sand populations. Main conclusions Geographic distance is a stronger driver of population differentiation in the edaphic specialist than in the generalist. However, this difference did not appear to be related to edaphic generalism per se as adjacent populations from both soil types in the edaphic generalist did not share many haplotypes. Populations of the edaphic generalist in white‐sand habitats exhibited high haplotype diversity and shared haplotypes with distant white‐sand habitat islands, indicating that they have either efficient long‐distance dispersal and/or larger ancestral effective population sizes and thus retain ancestral polymorphisms. These results highlight the importance of edaphic heterogeneity in promoting population differentiation in tropical trees.     

High degree of genetic differentiation in marine three‐spined sticklebacks (Gasterosteus aculeatus)

Populations of widespread marine organisms are typically characterized by a low degree of genetic differentiation in neutral genetic markers, but much less is known about differentiation in genes whose functional roles are associated with specific selection regimes. To uncover possible adaptive population divergence and heterogeneous genomic differentiation in marine three‐spined sticklebacks (Gasterosteus aculeatus), we used a candidate gene‐based genome‐scan approach to analyse variability in 138 microsatellite loci located within/close to (<6 kb) functionally important genes in samples collected from ten geographic locations. The degree of genetic differentiation in markers classified as neutral or under balancing selection—as determined with several outlier detection methods—was low (F_ST = 0.033 or 0.011, respectively), whereas average F_ST for directionally selected markers was significantly higher (F_ST = 0.097). Clustering analyses provided support for genomic and geographic heterogeneity in selection: six genetic clusters were identified based on allele frequency differences in the directionally selected loci, whereas four were identified with the neutral loci. Allelic variation in several loci exhibited significant associations with environmental variables, supporting the conjecture that temperature and salinity, but not optic conditions, are important drivers of adaptive divergence among populations. In general, these results suggest that in spite of the high degree of physical connectivity and gene flow as inferred from neutral marker genes, marine stickleback populations are strongly genetically structured in loci associated with functionally relevant genes.     

Critical thermal maxima of juvenile alligator gar (Atractosteus spatula,Lacépède, 1803) from three Mississippi‐drainage populations acclimated to three temperatures

Local adaptation may cause thermal tolerance to vary between nearby but distinct populations of a species. During the summer of 2013, alligator gar Atractosteus spatula spawned from broodstock collected from three populations within the Mississippi River drainage separated by a 5° latitudinal gradient were acclimated to three temperatures (25, 30, and 35°C). Ten fish from each population were acclimated at each temperature. CT_Max was determined at each temperature for each population, using five fish for each population‐acclimation temperature pairing. CT_Max for each population‐acclimation temperature pairing was compared using two‐factor anova . CT_Max increased significantly with acclimation temperature (F_2,40 = 600.5, P < 0.001) but population had no significant effect (F_2,40 = 1.882, P = 0.166). Temperature tolerance appears to be consistent across populations of alligator gar, with no evidence of local adaptation.     

Local selection modifies phenotypic divergence among Rana temporaria populations in the presence of gene flow

In ectotherms, variation in life history traits among populations is common and suggests local adaptation. However, geographic variation itself is not a proof for local adaptation, as genetic drift and gene flow may also shape patterns of quantitative variation. We studied local and regional variation in means and phenotypic plasticity of larval life history traits in the common frog Rana temporaria using six populations from central Sweden, breeding in either open‐canopy or partially closed‐canopy ponds. To separate local adaptation from genetic drift, we compared differentiation in quantitative genetic traits (Q_ST) obtained from a common garden experiment with differentiation in presumably neutral microsatellite markers (F_ST). We found that R. temporaria populations differ in means and plasticities of life history traits in different temperatures at local, and in F_ST at regional scale. Comparisons of differentiation in quantitative traits and in molecular markers suggested that natural selection was responsible for the divergence in growth and development rates as well as in temperature‐induced plasticity, indicating local adaptation. However, at low temperature, the role of genetic drift could not be separated from selection. Phenotypes were correlated with forest canopy closure, but not with geographical or genetic distance. These results indicate that local adaptation can evolve in the presence of ongoing gene flow among the populations, and that natural selection is strong in this system.     

Phylogeography of the mottled spinefoot Siganus fuscescens: Pleistocene divergence and limited genetic connectivity across the Philippine archipelago

Historical isolation during Pleistocene low sea level periods is thought to have contributed to divergence among marine basin populations across the Coral Triangle. In the Philippine archipelago, populations in the South China Sea, Sulu Sea–inland seas, and Philippine Sea‐Celebes Sea basins might have been partially isolated. Meanwhile, present‐day broadscale oceanographic circulation patterns suggest connectivity between these basins. To evaluate hypotheses regarding the influence of historical and contemporary factors on genetic structure, phylogeographic patterns based on mitochondrial control region sequences for a reef‐associated fish, Siganus fuscescens, were analysed. Three distinct lineages were recovered. One lineage was identified as the morphologically similar species Siganus canaliculatus, while two lineages are monophyletic with S. fuscescens. Clade divergence and demographic expansion in S. fuscescens occurred during the Pleistocene. A strong signal of latitudinal structure was detected (Φ_CT = 0.188), driven by marked differences in clade distribution: one clade is widely distributed (clade A), while a second clade (clade B) has a restricted northern distribution. Regional structure of clade A is consistent with the basin isolation hypothesis (Φ_CT = 0.040) and suggests isolation of the South China Sea (Φ_CT = 0.091). Fine‐scale structure was observed in the South China Sea and south Philippine Sea, while Sulu Sea and inland seas were unstructured. Genetic structure across multiple spatial scales (archipelagic, regional, and fine‐scale within basins) suggests the influence of vicariant barriers and contemporary limits to gene flow in S. fuscescens that may be influenced by oceanographic circulation, geographical distance between available habitats, and latitudinal temperature differences.     

Population genomics of the eastern cottonwood (Populus deltoides)

Despite its economic importance as a bioenergy crop and key role in riparian ecosystems, little is known about genetic diversity and adaptation of the eastern cottonwood (Populus deltoides). Here, we report the first population genomics study for this species, conducted on a sample of 425 unrelated individuals collected in 13 states of the southeastern United States. The trees were genotyped by targeted resequencing of 18,153 genes and 23,835 intergenic regions, followed by the identification of single nucleotide polymorphisms (SNPs). This natural P. deltoides population showed low levels of subpopulation differentiation (F_ST = 0.022–0.106), high genetic diversity (θ_W = 0.00100, π = 0.00170), a large effective population size (N_e ≈ 32,900), and low to moderate levels of linkage disequilibrium. Additionally, genomewide scans for selection (Tajima's D), subpopulation differentiation (X^TX), and environmental association analyses with eleven climate variables carried out with two different methods (LFMM and BAYENV2) identified genes putatively involved in local adaptation. Interestingly, many of these genes were also identified as adaptation candidates in another poplar species, Populus trichocarpa, indicating possible convergent evolution. This study constitutes the first assessment of genetic diversity and local adaptation in P. deltoides throughout the southern part of its range, information we expect to be of use to guide management and breeding strategies for this species in future, especially in the face of climate change.     

Limited connectivity and a phylogeographic break characterize populations of the pink anemonefish,Amphiprion perideraion,in the Indo‐Malay Archipelago: inferences from a mitochondrial and microsatellite loci

To enhance the understanding of larval dispersal in marine organisms, species with a sedentary adult stage and a pelagic larval phase of known duration constitute ideal candidates, because inferences can be made about the role of larval dispersal in population connectivity. Members of the immensely diverse marine fauna of the Indo‐Malay Archipelago are of particular importance in this respect, as biodiversity conservation is becoming a large concern in this region. In this study, the genetic population structure of the pink anemonefish, Amphiprion perideraion, is analyzed by applying 10 microsatellite loci as well as sequences of the mitochondrial control region to also allow for a direct comparison of marker‐derived results. Both marker systems detected a strong overall genetic structure (Φ_ST = 0.096, P < 0.0001; mean D_est = 0.17; F_ST = 0.015, P < 0.0001) and best supported regional groupings (Φ_CT = 0.199 P < 0.0001; F_CT = 0.018, P < 0.001) that suggested a differentiation of the Java Sea population from the rest of the archipelago. Differentiation of a New Guinea group was confirmed by both markers, but disagreed over the affinity of populations from west New Guinea. Mitochondrial data suggest higher connectivity among populations with fewer signals of regional substructure than microsatellite data. Considering the homogenizing effect of only a few migrants per generation on genetic differentiation between populations, marker‐specific results have important implications for conservation efforts concerning this and similar species.     

Selection on life‐history traits and genetic population divergence in rotifers

A combination of founder effects and local adaptation – the Monopolization hypothesis – has been proposed to reconcile the strong population differentiation of zooplankton dwelling in ponds and lakes and their high dispersal abilities. The role genetic drift plays in genetic differentiation of zooplankton is well documented, but the impact of natural selection has received less attention. Here, we compare differentiation in neutral genetic markers (F_ST) and in quantitative traits (Q_ST) in six natural populations of the rotifer Brachionus plicatilis to assess the importance of natural selection in explaining genetic differentiation of life‐history traits. Five life‐history traits were measured in four temperature × salinity combinations in common‐garden experiments. Population differentiation for neutral genetic markers – 11 microsatellite loci – was very high (F_ST = 0.482). Differentiation in life‐history traits was higher in traits related to sexual reproduction than in those related to asexual reproduction. Q_ST values for diapausing egg production (a trait related to sexual reproduction) were higher than their corresponding F_ST in some pairs of populations. Our results indicate the importance of divergent natural selection in these populations and suggest local adaptation to the unpredictability of B. plicatilis habitats.     

Ancient genome‐wide admixture extends beyond the current hybrid zone between Macaca fascicularis and M. mulatta

Macaca fascicularis and Macaca mulatta are two of the most commonly used laboratory macaques, yet their genetic differences at a genome‐wide level remain unclear. We analysed the multilocus DNA sequence data of 54 autosomal loci obtained from M. fascicularis samples from three different geographic origins and M. mulatta samples of Burmese origin. M. fascicularis shows high nucleotide diversity, four to five times higher than humans, and a strong geographic population structure between Indonesian‐Malaysian and Philippine macaques. The pattern of divergence and polymorphism between M. fascicularis and M. mulatta shows a footprint of genetic exchange not only within their current hybrid zone but also across a wider range for more than 1 million years. However, genetic admixture may not be a random event in the genome. Whereas randomly selected genic and intergenic regions have the same evolutionary dynamics between the species, some cytochrome oxidase P450 (CYP) genes (major chemical metabolizing genes and potential target genes for local adaptation) have a significantly larger species divergence than other genes. By surveying CYP3A5 gene sequences of more than a hundred macaques, we identified three nonsynonymous single nucleotide polymorphisms that were highly differentiated between the macaques. The mosaic pattern of species divergence in the genomes may be a consequence of genetic differentiation under ecological adaptation and may be a salient feature in the genomes of nascent species under parapatry.