Genomic divergence across ecological gradients in the Central African rainforest songbird (Andropadus virens)

The little greenbul, a common rainforest passerine from sub‐Saharan Africa, has been the subject of long‐term evolutionary studies to understand the mechanisms leading to rainforest speciation. Previous research found morphological and behavioural divergence across rainforest–savannah transition zones (ecotones), and a pattern of divergence with gene flow suggesting divergent natural selection has contributed to adaptive divergence and ecotones could be important areas for rainforests speciation. Recent advances in genomics and environmental modelling make it possible to examine patterns of genetic divergence in a more comprehensive fashion. To assess the extent to which natural selection may drive patterns of differentiation, here we investigate patterns of genomic differentiation among populations across environmental gradients and regions. We find compelling evidence that individuals form discrete genetic clusters corresponding to distinctive environmental characteristics and habitat types. Pairwise F_ST between populations in different habitats is significantly higher than within habitats, and this differentiation is greater than what is expected from geographic distance alone. Moreover, we identified 140 SNPs that showed extreme differentiation among populations through a genomewide selection scan. These outliers were significantly enriched in exonic and coding regions, suggesting their functional importance. Environmental association analysis of SNP variation indicates that several environmental variables, including temperature and elevation, play important roles in driving the pattern of genomic diversification. Results lend important new genomic evidence for environmental gradients being important in population differentiation.     

Testing alternative mechanisms of evolutionary divergence in an African rain forest passerine bird

Abstract Models of speciation in African rain forests have stressed either the role of isolation or ecological gradients. Here we contrast patterns of morphological and genetic divergence in parapatric and allopatric populations of the Little Greenbul, Andropadus virens, within different and similar habitats. We sampled 263 individuals from 18 sites and four different habitat types in Upper and Lower Guinea. We show that despite relatively high rates of gene flow among populations, A. virens has undergone significant morphological divergence across the savanna-forest ecotone and mountain-forest boundaries. These data support a central component of the divergence-with-gene-flow model of speciation by suggesting that despite large amounts of gene flow, selection is sufficiently intense to cause morphological divergence. Despite evidence of isolation based on neutral genetic markers, we find little evidence of morphological divergence in fitness-related traits between hypothesized refugial areas. Although genetic evidence suggests populations in Upper and Lower Guinea have been isolated for over 2 million years, morphological divergence appears to be driven more by habitat differences than geographic isolation and suggests that selection in parapatry may be more important than geographic isolation in causing adaptive divergence in morphology.     

GEOGRAPHIC VARIATION IN THE SONGS OF NEOTROPICAL SINGING MICE: TESTING THE RELATIVE IMPORTANCE OF DRIFT AND LOCAL ADAPTATION

Patterns of geographic variation in communication systems can provide insight into the processes that drive phenotypic evolution. Although work in birds, anurans, and insects demonstrates that acoustic signals are sensitive to diverse selective and stochastic forces, processes that shape variation in mammalian vocalizations are poorly understood. We quantified geographic variation in the advertisement songs of sister species of singing mice, montane rodents with a unique mode of vocal communication. We tested three hypotheses to explain spatial variation in the song of the lower altitude species, Scotinomys teguina: selection for species recognition in sympatry with congener, S. xerampelinus, acoustic adaptation to different environments, and stochastic divergence. Mice were sampled at seven sites in Costa Rica and Panamá; genetic distances were estimated from mitochondrial control region sequences, between‐site differences in acoustic environment were estimated from climatic data. Acoustic, genetic and geographic distances were all highly correlated in S. teguina, suggesting that population differentiation in song is largely shaped by genetic drift. Contrasts between interspecific genetic‐acoustic distances were significantly greater than expectations derived from intraspecific contrasts, indicating accelerated evolution of species‐specific song. We propose that, although much intraspecific acoustic variation is effectively neutral, selection has been important in shaping species differences in song.     

Habitat-dependent song divergence in the little greenbul: an analysis of environmental selection pressures on acoustic signals

Abstract.— Bird song is a sexual trait important in mate choice and known to be shaped by environmental selection. Here we investigate the ecological factors shaping song variation across a rainforest gradient in central Africa. We show that the little greenbul ( Andropadus virens ), previously shown to vary morphologically across the gradient in fitness-related characters, also varies with respect to song characteristics. Acoustic features, including minimum and maximum frequency, and delivery rate of song notes showed significant differences between habitats. In contrast, we found dialectal variation independent of habitat in population-typical songtype sequences. This pattern is consistent with ongoing gene flow across habitats and in line with the view that song variation in the order in which songtypes are produced is not dependent on habitat characteristics in the same way physical song characteristics are. Sound transmission characteristics of the two habitats did not vary significantly, but analyses of ambient noise spectra revealed dramatic and consistent habitat-dependent differences. Matching between low ambient noise levels for low frequencies in the rainforest and lower minimal frequencies in greenbul songs in this habitat suggests that part of the song divergence may be driven by habitat-dependent ambient noise patterns. These results suggest that habitat-dependent selection may act simultaneously on traits of ecological importance and those important in prezygotic isolation, leading to an association between morphological and acoustic divergence. Such an association may promote assortative mating and may be a mechanism driving reproductive divergence across ecological gradients.     

Testing for local adaptation and evolutionary potential along altitudinal gradients in rainforest Drosophila: beyond laboratory estimates

Predicting how species will respond to the rapid climatic changes predicted this century is an urgent task. Species distribution models (SDMs) use the current relationship between environmental variation and species’ abundances to predict the effect of future environmental change on their distributions. However, two common assumptions of SDMs are likely to be violated in many cases: (i) that the relationship of environment with abundance or fitness is constant throughout a species’ range and will remain so in future and (ii) that abiotic factors (e.g. temperature, humidity) determine species’ distributions. We test these assumptions by relating field abundance of the rainforest fruit fly Drosophila birchii to ecological change across gradients that include its low and high altitudinal limits. We then test how such ecological variation affects the fitness of 35 D. birchii families transplanted in 591 cages to sites along two altitudinal gradients, to determine whether genetic variation in fitness responses could facilitate future adaptation to environmental change. Overall, field abundance was highest at cooler, high‐altitude sites, and declined towards warmer, low‐altitude sites. By contrast, cage fitness (productivity) increased towards warmer, lower‐altitude sites, suggesting that biotic interactions (absent from cages) drive ecological limits at warmer margins. In addition, the relationship between environmental variation and abundance varied significantly among gradients, indicating divergence in ecological niche across the species’ range. However, there was no evidence for local adaptation within gradients, despite greater productivity of high‐altitude than low‐altitude populations when families were reared under laboratory conditions. Families also responded similarly to transplantation along gradients, providing no evidence for fitness trade‐offs that would favour local adaptation. These findings highlight the importance of (i) measuring genetic variation in key traits under ecologically relevant conditions, and (ii) considering the effect of biotic interactions when predicting species’ responses to environmental change.     

Isolation by distance,not incipient ecological speciation,explains genetic differentiation in an Andean songbird (Aves: Furnariidae: Cranioleuca antisiensis,Line‐cheeked Spinetail) despite near threefold body size change across an environmental gradient

During the process of ecological speciation, reproductive isolation results from divergent natural selection and leads to a positive correlation between genetic divergence and adaptive phenotypic divergence, that is, isolation by adaptation (IBA). In natural populations, phenotypic differentiation is often autocorrelated with geographic distance, making IBA difficult to distinguish from the neutral expectation of isolation by distance (IBD). We examined these two alternatives in a dramatic case of clinal phenotypic variation in an Andean songbird, the Line‐cheeked Spinetail (Cranioleuca antisiensis). At its geographic extremes, this species shows a near threefold difference in body mass (11.5 to 31.0 g) with marked plumage differences. We analysed phenotypic, environmental and genetic data (5,154 SNPs) from 172 individuals and 19 populations sampled along its linear distribution in the Andes. We found that body mass was tightly correlated with environmental temperature, consistent with local adaptation as per Bergmann's rule. Using a P_ST–F_ST analysis, we found additional support for natural selection driving body mass differentiation, but these results could also be explained by environment‐mediated phenotypic plasticity. When we assessed the relative support for patterns of IBA and IBD using variance partitioning, we found that IBD was the best explanation for genetic differentiation along the cline. Adaptive phenotypic or environmental divergence can reduce gene flow, a pattern interpreted as evidence of ecological speciation's role in diversification. Our results provide a counterexample to this interpretation. Despite conditions conducive to ecological speciation, our results suggest that dramatic size and environmental differentiation within C. antisiensis are not limiting gene flow.     

Testing for evolutionary trade-offs in a phylogenetic context: ecological diversification and evolution of locomotor performance in emydid turtles

The evolution of ecological trade-offs is an important component of ecological specialization and adaptive radiation. However, the pattern that would show that evolutionary trade-offs have occurred between traits among species has not been clearly defined. In this paper, we propose a phylogeny-based definition of an evolutionary trade-off, and apply it to an analysis of the evolution of trade-offs in locomotor performance in emydid turtles. We quantified aquatic and terrestrial speed and endurance for up to 16 species, including aquatic, semi-terrestrial and terrestrial emydids. Emydid phylogeny was reconstructed from morphological characters and nuclear and mitochondrial DNA sequences. Surprisingly, we find that there have been no trade-offs in aquatic and terrestrial speed among species. Instead, specialization to aquatic and terrestrial habitats seems to have involved trade-offs in speed and endurance. Given that trade-offs between speed and endurance may be widespread, they may underlie specialization to different habitats in many other groups.     

Elevational diversity patterns as an example for evolutionary and ecological dynamics in ferns and lycophytes

Evolutionary processes such as adaptation, ecological filtering, and niche conservatism involve the interaction of organisms with their environment and are thus commonly studied along environmental gradients. Elevational gradients have become among the most studied environmental gradients to understand large-scale patterns of species richness and composition because they are highly replicated with different combinations of geographical, environmental and historical factors. We here review the literature on using elevational gradients to understand evolutionary processes in ferns. Some phylogenetic studies of individual fern clades have considered elevation in the analysis or interpretation and postulated that fern diversification is linked to the colonization of mountain habitats. Other studies that have linked elevational community composition and hence ecological filtering with phylogenetic community composition and morphological traits, usually only found limited phylogenetic signal. However, these studies are ultimately only correlational, and there are few actual tests of the evolutionary mechanisms leading to these patterns. We identify a number of challenges for improving our understanding of how evolutionary and ecological processes are linked to elevational richness patterns in ferns: i) limited information on traits and their ecological relevance, ii) uncertainties on the dispersal kernels of ferns and hence the delimitation of regional species pools from which local assemblages are recruited, iii) limited genomic data to identify candidate genes under selection and hence actually document adaptation and selection, and iv) conceptual challenges in developing clear and testable hypotheses to how specific evolutionary processes can be linked to patterns in community composition and species richness.     

Testing Wallace's intuition: water type,reproductive isolation and divergence in an Amazonian fish

Alfred Russel Wallace proposed classifying Amazon rivers based on their colour and clarity: white, black and clear water. Wallace also proposed that black waters could mediate diversification and yield distinct fish species. Here, we bring evidence of speciation mediated by water type in the sailfin tetra (Crenuchus spilurus), a fish whose range encompasses rivers of very distinct hydrochemical conditions. Distribution of the two main lineages concords with Wallace's water types: one restricted to the acidic and nutrient‐poor waters of the Negro River (herein Rio Negro lineage) and a second widespread throughout the remaining of the species’ distribution (herein Amazonas lineage). These lineages occur over a very broad geographical range, suggesting that despite occurring in regions separated by thousands of kilometres, individuals of the distinct lineages fail to occupy each other's habitats, hundreds of metres apart and not separated by physical barrier. Reproductive isolation was assessed in isolated pairs exposed to black‐water conditions. All pairs with at least one individual of the lineage not native to black waters showed significantly lower spawning success, suggesting that the water type affected the fitness and contributed to reproductive isolation. Our results endorse Wallace's intuition and highlight the importance of ecological factors in shaping diversity of the Amazon fish fauna.     

Genomics of the divergence continuum in an African plant biodiversity hotspot,I: drivers of population divergence in Restio capensis (Restionaceae)

Understanding the drivers of population divergence, speciation and species persistence is of great interest to molecular ecology, especially for species‐rich radiations inhabiting the world's biodiversity hotspots. The toolbox of population genomics holds great promise for addressing these key issues, especially if genomic data are analysed within a spatially and ecologically explicit context. We have studied the earliest stages of the divergence continuum in the Restionaceae, a species‐rich and ecologically important plant family of the Cape Floristic Region (CFR) of South Africa, using the widespread CFR endemic Restio capensis (L.) H.P. Linder & C.R. Hardy as an example. We studied diverging populations of this morphotaxon for plastid DNA sequences and >14 400 nuclear DNA polymorphisms from Restriction site Associated DNA (RAD) sequencing and analysed the results jointly with spatial, climatic and phytogeographic data, using a Bayesian generalized linear mixed modelling (GLMM) approach. The results indicate that population divergence across the extreme environmental mosaic of the CFR is mostly driven by isolation by environment (IBE) rather than isolation by distance (IBD) for both neutral and non‐neutral markers, consistent with genome hitchhiking or coupling effects during early stages of divergence. Mixed modelling of plastid DNA and single divergent outlier loci from a Bayesian genome scan confirmed the predominant role of climate and pointed to additional drivers of divergence, such as drift and ecological agents of selection captured by phytogeographic zones. Our study demonstrates the usefulness of population genomics for disentangling the effects of IBD and IBE along the divergence continuum often found in species radiations across heterogeneous ecological landscapes.     

Toxic hydrogen sulfide and dark caves: phenotypic and genetic divergence across two abiotic environmental gradients in Poecilia mexicana

Divergent natural selection drives evolutionary diversification. It creates phenotypic diversity by favoring developmental plasticity within populations or genetic differentiation and local adaptation among populations. We investigated phenotypic and genetic divergence in the livebearing fish Poecilia mexicana along two abiotic environmental gradients. These fish typically inhabit nonsulfidic surface rivers, but also colonized sulfidic and cave habitats. We assessed phenotypic variation among a factorial combination of habitat types using geometric and traditional morphometrics, and genetic divergence using quantitative and molecular genetic analyses. Fish in caves (sulfidic or not) exhibited reduced eyes and slender bodies. Fish from sulfidic habitats (surface or cave) exhibited larger heads and longer gill filaments. Common-garden rearing suggested that these morphological differences are partly heritable. Population genetic analyses using microsatellites as well as cytochrome b gene sequences indicate high population differentiation over small spatial scale and very low rates of gene flow, especially among different habitat types. This suggests that divergent environmental conditions constitute barriers to gene flow. Strong molecular divergence over short distances as well as phenotypic and quantitative genetic divergence across habitats in directions classic to fish ecomorphology suggest that divergent selection is structuring phenotypic variation in this system.     

Morphological and genetic differentiation in anadromous smelt Osmerus mordax (Mitchill): disentangling the effects of geography and morphology on gene flow

Morphological analyses were combined with genetic analyses at nine microsatellite loci to examine the determinants of gene flow at 21 spawning locations of rainbow smelt Osmerus mordax along the east coast of Canada. Associations between morphology, geography and gene flow were examined using a computational geometric approach and partial Mantel tests. Significant barriers to gene flow and discontinuities in morphology were observed between Newfoundland and mainland Canada, as well as within Newfoundland samples. On regional scales, contrasting patterns were present with restricted gene flow between Newfoundland populations ( F _ST= c . 0·11) and high gene flow between mainland populations ( F _ST= c . 0·017). Within Newfoundland populations, geographic distance was significantly associated with gene flow ( r = 0·85, P < 0·001) contrasting mainland samples where gene flow was most associated with phenotypic divergence ( r = 0·33, P < 0·001). At large spatial scales, weak ( r = 0·19, P = 0·02) associations between gene flow and geographic distance were observed, and moderate associations were also observed between gene flow and morphology ( r = 0·28, P < 0·001). The presence of significant genetic isolation by distance in Newfoundland samples and the clear discontinuity associated with the Cabot Strait suggest geography may be the primary determinant of gene flow. Interestingly, the association between genetic and morphological divergence within mainland samples and overall, supports the hypothesis that gene flow may be moderated by morphological divergence at larger spatial scales even in high gene flow environments.     

Divergent natural selection with gene flow along major environmental gradients in Amazonia: insights from genome scans, population genetics and phylogeography of the characin fish Triportheus albus

The unparalleled diversity of tropical ecosystems like the Amazon Basin has been traditionally explained using spatial models within the context of climatic and geological history. Yet, it is adaptive genetic diversity that defines how species evolve and interact within an ecosystem. Here, we combine genome scans, population genetics and sequence-based phylogeographic analyses to examine spatial and ecological arrangements of selected and neutrally evolving regions of the genome of an Amazonian fish, Triportheus albus. Using a sampling design encompassing five major Amazonian rivers, three hydrochemical settings, 352 nuclear markers and two mitochondrial DNA genes, we assess the influence of environmental gradients as biodiversity drivers in Amazonia. We identify strong divergent natural selection with gene flow and isolation by environment across craton (black and clear colour)- and Andean (white colour)-derived water types. Furthermore, we find that heightened selection and population genetic structure present at the interface of these water types appears more powerful in generating diversity than the spatial arrangement of river systems and vicariant biogeographic history. The results from our study challenge assumptions about the origin and distribution of adaptive and neutral genetic diversity in tropical ecosystems. In addition, they have important implications for measures of biodiversity and evolutionary potential in one of the world's most diverse and iconic ecosystems.     

Autecological traits determined two evolutionary strategies in Mediterranean plants during the Quaternary: low differentiation and range expansion versus geographical speciation in Linaria

The evolutionary patterns of the Mediterranean flora during the Quaternary have been relatively well documented based on phylogenetic and biogeographic analyses, but few studies have addressed the evolutionary traits that determined diversification and range expansion success during this period. We analysed previously published and newly generated sequences of three plastid noncoding regions (rpl32‐trnL^UAG, trnS‐trnG and trnL‐trnF), the nuclear ribosomal internal transcribed spacer (ITS) and a low‐copy nuclear gene intron (AGT1) of Linaria sect. Supinae, a group of angiosperms that diversified in the Quaternary. The origin and recent colonization dynamics of closely related lineages were inferred by biogeographic reconstruction and phylogeographic analyses, while breeding system experiments coupled with ecological and morphological data were used to test association with range expansion and diversification. A combination of traits, including selfing, short lifespan and the ability to tolerate a wide variety of substrates, were key factors underlying range expansion after long‐distance dispersal throughout the Mediterranean basin. By contrast, self‐incompatibility may have promoted higher diversification rates in narrow ranges of the Iberian Peninsula. We argue that a few traits contributed to the adoption of two contrasting strategies that may have been predominant in the evolution of Mediterranean angiosperms.     

Adaptive divergence and the evolution of reproductive isolation in the wild: an empirical demonstration using introduced sockeye salmon

Populations exposed to different ecological environments should diverge for phenotypic traits that influence survival and reproduction. This adaptive divergence should reduce gene flow between populations because immigrants become less fit than residents and because hybrids perform poorly in either environment (i.e., ecologically-dependent reproductive isolation). Here I demonstrate adaptive divergence and the evolution of reproductive isolation in populations of sockeye salmon (Oncorhynchus nerka) introduced from a common ancestral source into a new lake system (Lake Washington, Washington). The introduced fish founded several new populations, two of which experience very different environments during breeding and early development (Cedar River v.s. Pleasure Point beach). Over 13 generations, the two populations diverged for adult traits (female body size, male body depth; measured in the wild) and embryo traits (survival to hatching, development rate, size at emergence; measured in a common environment). The rates of divergence for these characters were similar to those observed in other examples of rapid evolution, and can best be attributed to natural selection. Partial reproductive isolation has evolved in concert with adaptive divergence: the rate of exchange of adults between the populations (determined using natural tags) is higher than the rate of gene flow (determined using DNA microsatellites). The demonstration that adaptive divergence can initiate reproductive isolation in less than 13 generations suggests that the first signs of ecological speciation may appear soon after new environments are first colonized.     

The search for causal traits of speciation: Divergent female mate preferences target male courtship song,not pheromones,in Drosophila athabasca species complex

Understanding speciation requires the identification of traits that cause reproductive isolation. This remains a major challenge since it is difficult to determine which of the many divergent traits actually caused speciation. To overcome this difficulty, we studied the sexual cue traits and behaviors associated with rapid speciation between EA and WN sympatric behavioral races of Drosophila athabasca that diverged only 16,000–20,000 years ago. First, we found that sexual isolation was essentially complete and driven primarily by divergent female mating preferences. To determine the target of female mate choice, we found that, unlike cuticular hydrocarbons (CHCs), male courtship song is highly divergent between EA and WN in both allopatry and sympatry and is not affected by latitudinal variation. We then used pheromone rub‐off experiments to show no effect of CHCs on divergent female mate choice. In contrast, both male song differences and male mating success in hybrids exhibited a large X‐effect and playback song experiments confirmed that male courtship song is indeed the target of sexual isolation. These results show that a single secondary sexual trait is a major driver of speciation and suggest that we may be overestimating the number of traits involved in speciation when we study older taxa.     

Cranial variation in geographically widespread dwarf gerbil Gerbillus nanus (Gerbillinae,Rodentia) populations: Isolation by distance versus adaptation to local environments

The dwarf gerbil (Gerbillus nanus) is broadly distributed in Asia, with a range that encompasses altitudinally diverse terrain, including two major mountain ranges. Previous studies have shown this species to be generally varied across its geographic range, both genetically and morphologically. Physical barriers (e.g. mountains) and geographic distance (i.e. isolation by distance [IBD]) are expected to reduce dispersal rates, and consequently could lead to cranial morphological differentiation among populations. Adaptation to local environments is also expected to lead to cranial morphological differentiation among populations. Here, I test these hypotheses by examining variation in cranial shape and size across the geographic distribution of G. nanus using geometric morphometric analysis. Based on a sample of 473 specimens from throughout its distribution, G. nanus populations do not seem to show biologically meaningful variation in cranial shape. Cranial size, on the other hand, did show geographic variation—yet, this variation does not seem to show strong patterns of IBD nor adaptation to local environments, which could indicate that the geographic variation in the cranial size of G. nanus populations may be accounted for by factors unexamined in this study.