Genomic islands of divergence in the Yellow Tang and the Brushtail Tang Surgeonfishes

The current ease of obtaining thousands of molecular markers challenges the notion that full phylogenetic concordance, as proposed by phylogenetic species concepts, is a requirement for defining species delimitations. Indeed, the presence of genomic islands of divergence, which may be the cause, or in some cases the consequence, of speciation, precludes concordance. Here, we explore this issue using thousands of RAD markers on two sister species of surgeonfishes (Teleostei: Acanthuridae), Zebrasoma flavescens and Z. scopas, and several populations within each species. Species are readily distinguished based on their colors (solid yellow and solid brown, respectively), yet populations and species are neither distinguishable using mitochondrial markers (cytochrome c oxidase 1), nor using 5193 SNPs (pairwise Φst = 0.034). In contrast, when using outlier loci, some of them presumably under selection, species delimitations, and strong population structure follow recognized taxonomic positions (pairwise Φst = 0.326). Species and population delimitation differences based on neutral and selected markers are likely due to local adaptation, thus being consistent with the idea that these genomic islands of divergence arose as a consequence of isolation. These findings, which are not unique, raise the question of a potentially important pathway of divergence based on local adaptation that is only evident when looking at thousands of loci.     

Adaptive divergence along environmental gradients in a climate‐change‐sensitive mammal

In the face of predicted climate change, a broader understanding of biotic responses to varying environments has become increasingly important within the context of biodiversity conservation. Local adaptation is one potential option, yet remarkably few studies have harnessed genomic tools to evaluate the efficacy of this response within natural populations. Here, we show evidence of selection driving divergence of a climate‐change‐sensitive mammal, the American pika (Ochotona princeps), distributed along elevation gradients at its northern range margin in the Coast Mountains of British Columbia (BC), Canada. We employed amplified‐fragment‐length‐polymorphism‐based genomic scans to conduct genomewide searches for candidate loci among populations inhabiting varying environments from sea level to 1500 m. Using several independent approaches to outlier locus detection, we identified 68 candidate loci putatively under selection (out of a total 1509 screened), 15 of which displayed significant associations with environmental variables including annual precipitation and maximum summer temperature. These candidate loci may represent important targets for predicting pika responses to climate change and informing novel approaches to wildlife conservation in a changing world.     

Environmental effects on molecular and phenotypic variation in populations of Eruca sativa across a steep climatic gradient

In Israel Eruca sativa has a geographically narrow distribution across a steep climatic gradient that ranges from mesic Mediterranean to hot desert environments. These conditions offer an opportunity to study the influence of the environment on intraspecific genetic variation. For this, we combined an analysis of neutral genetic markers with a phenotypic evaluation in common‐garden experiments, and environmental characterization of populations that included climatic and edaphic parameters, as well as geographic distribution. A Bayesian clustering of individuals from nine representative populations based on amplified fragment length polymorphism (AFLP) divided the populations into a southern and a northern geographic cluster, with one admixed population at the geographic border between them. Linear mixed models, with cluster added as a grouping factor, revealed no clear effects of environment or geography on genetic distances, but this may be due to a strong association of geography and environment with genetic clusters. However, environmental factors accounted for part of the phenotypic variation observed in the common‐garden experiments. In addition, candidate loci for selection were identified by association with environmental parameters and by two outlier methods. One locus, identified by all three methods, also showed an association with trichome density and herbivore damage, in net‐house and field experiments, respectively. Accordingly, we propose that because trichomes are directly linked to defense against both herbivores and excess radiation, they could potentially be related to adaptive variation in these populations. These results demonstrate the value of combining environmental and phenotypic data with a detailed genetic survey when studying adaptation in plant populations.     

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.     

Genetic divergence and isolation by thermal environment in geothermal populations of an aquatic invertebrate

Temperature is one of the most influential forces of natural selection impacting all biological levels. In the face of increasing global temperatures, studies over small geographic scales allowing investigations on the effects of gene flow are of great value for understanding thermal adaptation. Here, we investigated genetic population structure in the freshwater gastropod Radix balthica originating from contrasting thermal habitats in three areas of geothermal activity in Iceland. Snails from 32 sites were genotyped at 208 AFLP loci. Five AFLPs were identified as putatively under divergent selection in Lake Mývatn, a geothermal lake with an almost 20 °C difference in mean temperature across a distance of a few kilometres. In four of these loci, variation across all study populations was correlated with temperature. We found significant population structure in neutral markers both within and between the areas. Cluster analysis using neutral markers classified the sites mainly by geography, whereas analyses using markers under selection differentiated the sites based on temperature. Isolation by distance was stronger in the neutral than in the outlier loci. Pairwise differences based on outlier F_ST were significantly correlated with temperature at different spatial scales, even after correcting for geographic distance or neutral pairwise F_ST differences. In general, genetic variation decreased with increasing environmental temperature, possibly suggesting that natural selection had reduced the genetic diversity in the warm origin sites. Our results emphasize the influence of environmental temperature on the genetic structure of populations and suggest local thermal adaptation in these geothermal habitats.     

Potential adaptive divergence between subspecies and populations of snapdragon plants inferred from QST–FST comparisons

Phenotypic divergence among natural populations can be explained by natural selection or by neutral processes such as drift. Many examples in the literature compare putatively neutral (F_ST) and quantitative genetic (Q_ST) differentiation in multiple populations to assess their evolutionary signature and identify candidate traits involved with local adaptation. Investigating these signatures in closely related or recently diversified species has the potential to shed light on the divergence processes acting at the interspecific level. Here, we conducted this comparison in two subspecies of snapdragon plants (eight populations of Antirrhinum majus pseudomajus and five populations of A. m. striatum) in a common garden experiment. We also tested whether altitude was involved with population phenotypic divergence. Our results identified candidate phenological and morphological traits involved with local adaptation. Most of these traits were identified in one subspecies but not the other. Phenotypic divergence increased with altitude for a few biomass‐related traits, but only in A. m. striatum. These traits therefore potentially reflect A. m. striatum adaptation to altitude. Our findings imply that adaptive processes potentially differ at the scale of A. majus subspecies.     

Evidence for adaptive divergence of thermal responses among Bemisia tabaci populations from tropical Colombia following a recent invasion

There is an increasing evidence that populations of ectotherms can diverge genetically in response to different climatic conditions, both within their native range and (in the case of invasive species) in their new range. Here, we test for such divergence in invasive whitefly Bemisia tabaci populations in tropical Colombia, by considering heritable variation within and between populations in survival and fecundity under temperature stress, and by comparing population differences with patterns established from putatively neutral microsatellite markers. We detected significant differences among populations linked to mean temperature (for survival) and temperature variation (for fecundity) in local environments. A Q_ST ? F_ST analysis indicated that phenotypic divergence was often larger than neutral expectations (Q_ST > F_ST). Particularly, for survival after a sublethal heat shock, this divergence remained linked to the local mean temperature after controlling for neutral divergence. These findings point to rapid adaptation in invasive whitefly likely to contribute to its success as a pest species. Ongoing evolutionary divergence also provides challenges in predicting the likely impact of Bemisia in invaded regions.     

Rivers,refuges and population divergence of fire‐eye antbirds (Pyriglena) in the Amazon Basin

The identification of ecological and evolutionary mechanisms that might account for the elevated biotic diversity in tropical forests is a central theme in evolutionary biology. This issue is especially relevant in the Neotropical region, where biological diversity is the highest in the world, but where few studies have been conducted to test factors causing population differentiation and speciation. We used mtDNA sequence data to examine the genetic structure within white‐backed fire‐eye (Pyriglena leuconota) populations along the Tocantins River valley in the south‐eastern Amazon Basin, and we confront the predictions of the river and the Pleistocene refuge hypotheses with patterns of genetic variation observed in these populations. We also investigated whether these patterns reflect the recently detected shift in the course of the Tocantins River. We sampled a total of 32 individuals east of, and 52 individuals west of, the Tocantins River. Coalescent simulations and phylogeographical and population genetics analytical approaches revealed that mtDNA variation observed for fire‐eye populations provides little support for the hypothesis that populations were isolated in glacial forest refuges. Instead, our data strongly support a key prediction of the river hypothesis. Our study shows that the Tocantins River has probably been the historical barrier promoting population divergence in fire‐eye antbirds. Our results have important implications for a better understanding of the importance of large Amazonian rivers in vertebrate diversification in the Neotropics.     

A population genomic scan in Chorthippus grasshoppers unveils previously unknown phenotypic divergence

Understanding the genetics of speciation and the processes that drive it is a central goal of evolutionary biology. Grasshoppers of the Chorthippus species group differ strongly in calling song (and corresponding female preferences) but are exceedingly similar in other characteristics such as morphology. Here, we performed a population genomic scan on three Chorthippus species (Chorthippus biguttulus, C. mollis and C. brunneus) to gain insight into the genes and processes involved in divergence and speciation in this group. Using an RNA‐seq approach, we examined functional variation between the species by calling SNPs for each of the three species pairs and using F_ST‐based approaches to identify outliers. We found approximately 1% of SNPs in each comparison to be outliers. Between 37% and 40% of these outliers were nonsynonymous SNPs (as opposed to a global level of 17%) indicating that we recovered loci under selection. Among the outliers were several genes that may be involved in song production and hearing as well as genes involved in other traits such as food preferences and metabolism. Differences in food preferences between species were confirmed with a behavioural experiment. This indicates that multiple phenotypic differences implicating multiple evolutionary processes (sexual selection and natural selection) are present between the species.     

Using remote sensing to model tree species distribution in Peruvian lowland Amazonia

Species distribution models for Amazonian trees have mostly been produced at scales and resolutions that are too broad and coarse for practical use in either conservation or forestry. On the other hand, several studies have shown that elevation and the medium‐resolution remote sensing data available via Landsat imagery can be successfully used to detect differences in plant species composition in Amazonia. Therefore, it seems likely that the same data can also be used to predict geographical distributions of individual taxa. Here we use remotely sensed data and a maximum entropy algorithm (MaxEnt) to generate landscape‐scale distribution models at 30‐m‐resolution for five economically important timber tree genera (Apuleia, Amburana, Crepidospermum, Dipteryx, and Manilkara). Individual Landsat Thematic Mapper bands and normalized difference vegetation index yielded acceptable model performance, and the use of averaging filters (3 × 3 and 5 × 5 pixel low‐pass filters) improved model performance further. Including elevation as a predictor also improved model performance for all the genera. Our results suggest that it is possible to use Landsat bands and elevation as predictors for modeling the potential distribution of tree species in lowland Amazonia at a fine enough resolution to facilitate the practical management of forest resources.     

An invasive tree facilitates the persistence of native rodents on an over‐grazed floodplain in tropical Australia

In an ecosystem under simultaneous threat from multiple alien species, one invader may buffer the impact of another. Our surveys on a remote floodplain in the Kimberley region of north western Australia show that invasive chinee apple trees (Ziziphus mauritiana) provide critical refuge habitat for native rodents (pale field rats, Rattus tunneyi). Feral horses (Equus caballus) have trampled most of the remaining floodplain, but are excluded from the area around each chinee apple tree by thorny foliage. Although chinee apple trees constituted <10% of trees along our transects, they represented >50% of trees that harboured rat burrows. The mean number of burrows under each chinee apple tree was twice as high as under most other tree species, and we trapped more than seven times as many rats under chinee apple trees as under other types of trees. The extensive burrow systems under chinee apple trees contained female as well as male rats, whereas we only captured males around the smaller burrow systems under other tree species. Our data suggest that this invasive tree plays a critical role in the persistence of pale field rat populations in this degraded ecosystem, and that managers should maintain these trees (despite their alien origins) at least until feral horses have been removed.     

Indirect interactions among tropical tree species through shared rodent seed predators: a novel mechanism of tree species coexistence

The coexistence of numerous tree species in tropical forests is commonly explained by negative dependence of recruitment on the conspecific seed and tree density due to specialist natural enemies that attack seeds and seedlings (‘Janzen–Connell’ effects). Less known is whether guilds of shared seed predators can induce a negative dependence of recruitment on the density of different species of the same plant functional group. We studied 54 plots in tropical forest on Barro Colorado Island, Panama, with contrasting mature tree densities of three coexisting large seeded tree species with shared seed predators. Levels of seed predation were far better explained by incorporating seed densities of all three focal species than by conspecific seed density alone. Both positive and negative density dependencies were observed for different species combinations. Thus, indirect interactions via shared seed predators can either promote or reduce the coexistence of different plant functional groups in tropical forest.     

Global change‐type drought‐induced tree mortality: vapor pressure deficit is more important than temperature per se in causing decline in tree health

Drought‐induced tree mortality is occurring across all forested continents and is expected to increase worldwide during the coming century. Regional‐scale forest die‐off influences terrestrial albedo, carbon and water budgets, and land‐surface energy partitioning. Although increased temperatures during drought are widely identified as a critical contributor to exacerbated tree mortality associated with “global‐change‐type drought”, corresponding changes in vapor pressure deficit (D) have rarely been considered explicitly and have not been disaggregated from that of temperature per se. Here, we apply a detailed mechanistic soil–plant–atmosphere model to examine the impacts of drought, increased air temperature (+2°C or +5°C), and increased vapor pressure deficit (D; +1 kPa or +2.5 kPa), singly and in combination, on net primary productivity (NPP) and transpiration and forest responses, especially soil moisture content, leaf water potential, and stomatal conductance. We show that increased D exerts a larger detrimental effect on transpiration and NPP, than increased temperature alone, with or without the imposition of a 3‐month drought. Combined with drought, the effect of increased D on NPP was substantially larger than that of drought plus increased temperature. Thus, the number of days when NPP was zero across the 2‐year simulation was 13 or 14 days in the control and increased temperature scenarios, but increased to approximately 200 days when D was increased. Drought alone increased the number of days of zero NPP to 88, but drought plus increased temperature did not increase the number of days. In contrast, drought and increased D resulted in the number of days when NPP = 0 increasing to 235 (+1 kPa) or 304 days (+2.5 kPa). We conclude that correct identification of the causes of global change‐type mortality events requires explicit consideration of the influence of D as well as its interaction with drought and temperature.     

Genetic diversity and structure of natural populations of Plathymenia reticulata (Mimosoideae), a tropical tree from the Brazilian Cerrado

Plathymenia reticulata is a tropical tree native to the Brazilian Cerrado, one of the most important and endangered ecosystems in Brazil. This species presents high-quality wood and potential for recovery of degraded areas. Despite its importance, almost nothing is known about its genetic or ecological features. Random amplified polymorphic DNA (RAPD) markers were used to investigate the genetic diversity and structure of six natural populations of P. reticulata. DNAs from 117 adult individuals were amplified with 10 random primers and Shannon's index and amova were used to evaluate the levels of genetic diversity within and among populations. Through 72 markers, 70.8% of which were polymorphic, it was possible to obtain 117 unique RAPD phenotypes. The levels of genetic variability found in the six populations of P. reticulata were considerable and most of the genetic variation was found between individuals within populations, although pairwise PH(ST) values indicated significant divergence between populations. The among-population component accounted for, respectively, 12.3% and 16% of the genetic variation, according to amova and Shannon's index. These results were compared with other genetic studies on plant species and such a level of differentiation among populations corresponds to that which has usually been observed for outcrossing plants. The importance of maintenance of the P. reticulata populations and implications of the analysis of adult individuals, considering the longevity of this species and the relatively recent Cerrado fragmentation, are discussed.     

Local adaptation through genetic differentiation in highly fragmented Tilia cordata populations

We assessed the level of geographic differentiation of Tilia cordata in Denmark based on tests of 91 trees selected from 12 isolated populations. We used quantitative analysis of spring phenology and population genetic analysis based on SSR markers to infer the likely historical genetic processes within and among populations. High genetic variation within and among populations was observed in spring phenology, which correlated with spring temperatures at the origin of the tested T. cordata trees. The population genetic analysis revealed significant differentiation among the populations, but with no clear sign of isolation by distance. We infer the findings as indications of ongoing fine scale selection in favor of local growth conditions made possible by limited gene flow among the small and fragmented populations. This hypothesis fits well with reports of limited fruiting in the investigated Danish T. cordata populations, while the species is known for its ability to propagate vegetatively by root suckers. Our results suggest that both divergent selection and genetic drift may have played important roles in forming the genetic patterns of T. cordata at its northern distribution limit. However, we also speculate that epigenetic mechanism arising from the original population environment could have created similar patterns in regulating the spring phenology.     

A tree of tree frogs around the Black Sea

Speciation, the process by which one species evolves into two or more, is a major focus of ongoing debate, particularly regarding the geographic context in which it occurs. Geographic models of speciation tend to fall into discrete categories, typically referred to as allopatric, parapatric and sympatric speciation, according to whether two groups evolve reproductive isolation while geographically isolated, differentiated but connected by gene flow, or completely co‐occurring. Yet molecular studies indicate that full development of reproductive isolation can take very long compared with the timescale at which climatic oscillations occur, such that the geographic context of differentiating forms might change often during the long process to full species. Studies of genetic relationships across the ranges of organisms with low‐dispersal distances have the potential to reveal these complex histories. In a particularly elegant example in this issue, Dufresnes et al. ( 2016 ) use genetic variation and ecological niche modelling to show that a ring of populations of the eastern tree frog (Hyla orientalis) surrounding the Black Sea had a complex history of geographic differentiation. Alternating phases of geographic fragmentation and phases of gene flow between neighbouring populations have produced a pattern of gradual genetic change connecting the western, southern and eastern sides of the ring, with the northwestern and northeastern forms being most differentiated. In the north, a population in Crimea appears to have been produced through mixture of the two extreme forms. The overall genetic relationships are reminiscent of those found in ring species, which have been used as prime demonstrations of the process of speciation. The difference, however, is that the terminal forms appear to have mixed rather than be reproductively isolated, although more research is needed to infer whether there might be some reproductive isolation on the northern side of the ring.     

The genetic basis of drought tolerance in the high oil crop Sesamum indicum

Unlike most of the important food crops, sesame can survive drought but severe and repeated drought episodes, especially occurring during the reproductive stage, significantly curtail the productivity of this high oil crop. Genome‐wide association study was conducted for traits related to drought tolerance using 400 diverse sesame accessions, including landraces and modern cultivars. Ten stable QTLs explaining more than 40% of the phenotypic variation and located on four linkage groups were significantly associated with drought tolerance related traits. Accessions from the tropical area harboured higher numbers of drought tolerance alleles at the peak loci and were found to be more tolerant than those from the northern area, indicating a long‐term genetic adaptation to drought‐prone environments. We found that sesame has already fixed important alleles conferring survival to drought which may explain its relative high drought tolerance. However, most of the alleles crucial for productivity and yield maintenance under drought conditions are far from been fixed. This study also revealed that pyramiding the favourable alleles observed at the peak loci is of high potential for enhancing drought tolerance in sesame. In addition, our results highlighted two important pleiotropic QTLs harbouring known and unreported drought tolerance genes such as SiABI4, SiTTM3, SiGOLS1, SiNIMIN1 and SiSAM. By integrating candidate gene association study, gene expression and transgenic experiments, we demonstrated that SiSAM confers drought tolerance by modulating polyamine levels and ROS homeostasis, and a missense mutation in the coding region partly contributes to the natural variation of drought tolerance in sesame.     

Adaptive divergence in embryonic thermal plasticity among Atlantic salmon populations

In the context of global changes, the long‐term viability of populations of endangered ectotherms may depend on their adaptive potential and ability to cope with temperature variations. We measured responses of Atlantic salmon embryos from four populations to temperature variations and used a Q_ST–F_ST approach to study the adaptive divergence among these populations. Embryos were reared under two experimental conditions: a low temperature regime at 4 °C until eyed‐stage and 10 °C until the end of embryonic development and a high temperature regime with a constant temperature of 10 °C throughout embryonic development. Significant variations among populations and population × temperature interactions were observed for embryo survival, incubation time and length. Q_ST was higher than F_ST in all but one comparison suggesting an important effect of divergent selection. Q_ST was also higher under the high‐temperature treatment than at low temperature for length and survival due to a higher variance among populations under the stressful warmer treatment. Interestingly, heritability was lower for survival under high temperature in relation to a lower additive genetic variance under that treatment. Overall, these results reveal an adaptive divergence in thermal plasticity in embryonic life stages of Atlantic salmon suggesting that salmon populations may differentially respond to temperature variations induced by climate change. These results also suggest that changes in temperature may alter not only the adaptive potential of natural populations but also the selection regimes among them.     

Comparative analyses of clinical and environmental populations of Cryptococcus neoformans in Botswana

Cryptococcus neoformans var. grubii (Cng) is the most common cause of fungal meningitis, and its prevalence is highest in sub‐Saharan Africa. Patients become infected by inhaling airborne spores or desiccated yeast cells from the environment, where the fungus thrives in avian droppings, trees and soil. To investigate the prevalence and population structure of Cng in southern Africa, we analysed isolates from 77 environmental samples and 64 patients. We detected significant genetic diversity among isolates and strong evidence of geographic structure at the local level. High proportions of isolates with the rare MAT a allele were observed in both clinical and environmental isolates; however, the mating‐type alleles were unevenly distributed among different subpopulations. Nearly equal proportions of the MAT a and MATα mating types were observed among all clinical isolates and in one environmental subpopulation from the eastern part of Botswana. As previously reported, there was evidence of both clonality and recombination in different geographic areas. These results provide a foundation for subsequent genomewide association studies to identify genes and genotypes linked to pathogenicity in humans.