Modeling environmentally associated morphological and genetic variation in a rainforest bird, and its application to conservation prioritization

Influence of geographic isolation and the environment on gene flow among phenotypically diverse lizards

Lizards in the genus Anolis comprise hundreds of species that display a wide range of phenotypic variation closely related to their environment. One example is the Guadeloupean anole (Anolis marmoratus ssp.) that display extreme phenotypic variation, primarily in adult male color and pattern, with twelve described subspecies on the archipelago. Here we examine the relationship between phenotypic and genetic divergence among five subspecies on the two main islands and test the role of geographic isolation and the environment in reducing gene flow. We also examined two offshore island populations to assess the impact of complete geographic isolation on gene flow. We analyzed color phenotypes by measuring spectral reflectance and genomic diversity using SNPs. Genetic divergence was correlated with dorsolateral head and body color phenotypes, and slope and geographic distance were nearly equivalent at explaining this divergence. There was minimal genome-wide divergence at neutral loci among phenotypically disparate subspecies on the two main islands and their differentiation is consistent with a model of divergence with gene flow. Our spatial visualization of gene flow showed an impact of environmental features consistent with a hypothesis of ecologically driven divergence. Nonetheless, subspecies on the two main islands remain interconnected by substantial gene flow and their phenotypic variation is likely maintained at selection-gene flow equilibrium by divergent selection at loci associated with their color phenotypes. Greater isolation, such as inhabiting a remote island, may be required for reducing gene flow. Our findings highlight the role of the environment, adaptation, and geographic isolation on gene flow.

Patterns of morphological differentiation within Manacus manacus (Aves: Pipridae) in Colombia: revisiting hypotheses of isolation and secondary contact

Determining the factors responsible for phenotypic variation within species is a fundamental task in evolutionary ecology. Isolation by distance, isolation by environment and clines along secondary contact zones between formerly isolated populations are common patterns of morphological variation. In this study, we evaluated whether patterns of morphological variation exhibit association with isolation by distance, isolation by environment or secondary contact in populations of Manacus manacus with contrasting plumage colour. We used field and museum measurements of five morphological characters from 311 individuals from 88 localities distributed across a highly heterogeneous environmental range within Colombia. Climatic variables explained a higher proportion of the variation than geographic distance among localities. We found differences in wing and culmen length between white and yellow phenotypes of M. manacus in Colombia. Overall morphology did not change in a clinal fashion in relation to the contact zone and the few traits that exhibit clinal variation suggest a distant locality for the contact zone, not in line with our expectations by secondary contact between differentiated populations, suggesting alternative mechanisms for differentiation between subspecies. Our results suggest that this species exhibits marked morphological variation associated with changes in temperature and precipitation. These associations are consistent throughout the geographic range analysed, leading us to postulate that dispersal and local adaptation jointly shape the distribution of phenotypic variation.

Anthropogenic load іs a leading factor in the morphological variability of Chondrula tridens (Gastropoda, Enidae) in the northwestern Azov Sea region

Morphometric data are widely used in biology to assess intraspecific and inter-population variability and for bioindication and environmental condition assessment. The following hypotheses have been experimentally tested in the paper: 1) the vegetation type affects the change in the shell shape of Chondrula tridens martynovi Gural-Sverlova & Gural, 2010; 2) the change in the shell shape of this species is influenced by the biotope moisture regime; 3) the shell shape changes depending on the anthropogenic load level. The material in the form of empty, fully formed Ch. tridens shells was collected in 2019 in the north-western Azov region within the basin of the Molochna River. The collection points were located in settlements and outside them and differed in vegetation, moisture regime and level of anthropogenic load. The vegetation has been expertly attributed to two alternative types: herbaceous vegetation and tree plantations. By moisture level, the locations have been assessed as xerophytic and mesoxerophytic. The anthropogenic load levels have been assessed as low, medium and high. The study revealed that the morphological characteristics of Ch. tridens demonstrate a significant component of variability, which is due to the shell size. The shell size depends on the anthropogenic impact level. Under conditions of high anthropogenic impact, the shell size increases. Mollusks from locations with low and medium anthropogenic impact levels did not differ in shell size. After extraction of the size component, morphological properties develop three main trends of variability. The mouth apparatus development of mollusks does not depend on the vegetation type, but depends on the biotope moisture level and the anthropogenic transformation level. The mollusk shell elongation was observed to have the opposite dynamics of the height parameters in relation to the width and depended on the level of anthropogenic load. Rearrangement in the mouth apparatus depended on the biotope moisture level and the anthropogenic load level. There were distinguished four clusters, the quantitative morphological features of which allowed us to identify them as morphotypes. Each location was characterized by a combination of different morphotypes, according to which the sampling points may be classified. Morphotype 1 corresponds to biotopes with low level of anthropogenic load, morphotype 4 corresponded to biotopes with high anthropogenic load. Morphotypes 2 and 3 corresponded to moderate level of anthropogenic load. Vegetation type is not an important factor in determining the morphotypic diversity of populations. Under xerophytic conditions, morphotypes 2 and 3 are more common, and under mesoxerophytic conditions, morphotypes 1 and 4 are more common. The range of molluscs in different habitats needs to be expanded in the future to clarify climatic and other patterns.

Precipitation and vegetation shape patterns of genomic and craniometric variation in the central African rodent Praomys misonnei

Predicting species' capacity to respond to climate change is an essential first step in developing effective conservation strategies. However, conservation prioritization schemes rarely take evolutionary potential into account. Ecotones provide important opportunities for diversifying selection and may thus constitute reservoirs of standing variation, increasing the capacity for future adaptation. Here, we map patterns of environmentally associated genomic and craniometric variation in the central African rodent Praomys misonnei to identify areas with the greatest turnover in genomic composition. We also project patterns of environmentally associated genomic variation under future climate change scenarios to determine where populations may be under the greatest pressure to adapt. While precipitation gradients influence both genomic and craniometric variation, vegetation structure is also an important determinant of craniometric variation. Areas of elevated environmentally associated genomic and craniometric variation overlap with zones of rapid ecological transition underlining their importance as reservoirs of evolutionary potential. We also find that populations in the Sanaga river basin, central Cameroon and coastal Gabon are likely to be under the greatest pressure from climate change. Lastly, we make specific conservation recommendations on how to protect zones of high evolutionary potential and identify areas where populations may be the most susceptible to climate change.

Fragmented and isolated: limited gene flow coupled with weak isolation by environment in the paleoendemic giant sequoia (Sequoiadendron giganteum)

PREMISE

Patterns of genetic structure across a species' range reflect the long-term interplay between genetic drift, gene flow, and selection. Given the importance of gene flow in preventing the loss of diversity through genetic drift among spatially isolated populations, understanding the dynamics of gene flow and the factors that influence connectivity across a species' range is a major goal for conservation of genetic diversity. Here we present a detailed look at gene flow dynamics of Sequoiadendron giganteum, a paleoendemic tree species that will likely face numerous threats due to climate change.

METHODS

We used microsatellite markers to examine nineteen populations of S. giganteum for patterns of genetic structure and to estimate admixture and rates of gene flow between eight population pairs. Also, we used Generalized Dissimilarity Models to elucidate landscape factors that shape genetic differentiation among populations.

RESULTS

We found minimal gene flow between adjacent groves in the northern disjunct range. In most of the southern portion of the range, groves showed a signal of connectivity which degrades to isolation in the extreme south. Geographic distance was the most important predictor of genetic dissimilarity across the range, with environmental conditions related to precipitation and temperature explaining a small, but significant, portion of the genetic variance.

CONCLUSIONS

Due to their isolation and unique genetic composition, northern populations of S. giganteum should be considered a high conservation priority. In this region, we suggest germplasm conservation as well as restoration planting to enhance genetic diversity.

Temperature and Rainfall Are Separate Agents of Selection Shaping Population Differentiation in a Forest Tree

Research highlights: We present evidence indicating that covariation of functional traits among populations of a forest tree is not due to genetic constraints, but rather selective covariance arising from local adaptation to different facets of the climate, namely rainfall and temperature. Background and Aims: Traits frequently covary among natural populations. Such covariation can be caused by pleiotropy and/or linkage disequilibrium, but also may arise when the traits are genetically independent as a direct consequence of natural selection, drift, mutation and/or gene flow. Of particular interest are cases of selective covariance, where natural selection directly generates among-population covariance in a set of genetically independent traits. We here studied the causes of population-level covariation in two key traits in the Australian tree Eucalyptus pauciflora. Materials and Methods: We studied covariation in seedling lignotuber size and vegetative juvenility using 37 populations sampled from throughout the geographic and ecological ranges of E. pauciflora on the island of Tasmania. We integrated evidence from multiple sources: (i) comparison of patterns of trait covariation within and among populations; (ii) climate-trait modelling using machine-learning algorithms; and (iii) selection analysis linking trait variation to field growth in an arid environment. Results: We showed strong covariation among populations compared with the weak genetic correlation within populations for the focal traits. Population differentiation in these genetically independent traits was correlated with different home-site climate variables (lignotuber size with temperature; vegetative juvenility with rainfall), which spatially covaried. The role of selection in shaping the population differentiation in lignotuber size was supported by its relationship with fitness measured in the field. Conclusions: Our study highlights the multi-trait nature of adaptation likely to occur as tree species respond to spatial and temporal changes in climate.

Everything you always wanted to know about gene flow in tropical landscapes (but were afraid to ask)

The bulk of the world’s biodiversity is found in tropical regions, which are increasingly threatened by the human-led degradation of natural habitats. Yet, little is known about tropical biodiversity responses to habitat loss and fragmentation. Here we review all available literature assessing landscape effects on gene flow in tropical species, aiming to help unravel the factors underpinning functional connectivity in the tropics. We map and classify studies by focus species, the molecular markers employed, statistical approaches to assess landscape effects on gene flow, and the evaluated landscape and environmental variables. We then compare qualitatively and quantitatively landscape effects on gene flow across species and units of analysis. We found 69 articles assessing landscape effects on gene flow in tropical organisms, most of which were published in the last five years, were concentrated in the Americas, and focused on amphibians or mammals. Most studies employed population-level approaches, microsatellites were the preferred type of markers, and Mantel and partial Mantel tests the most common statistical approaches used. While elevation, land cover and forest cover were the most common gene flow predictors assessed, habitat suitability was found to be a common predictor of gene flow. A third of all surveyed studies explicitly assessed the effect of habitat degradation, but only 14 of these detected a reduced gene flow with increasing habitat loss. Elevation was responsible for most significant microsatellite-based isolation by resistance effects and a single study reported significant isolation by non-forested areas in an ant. Our study reveals important knowledge gaps on the study of landscape effects on gene flow in tropical organisms, and provides useful guidelines on how to fill them.

Where does diversity come from? Linking geographical patterns of morphological, genetic, and environmental variation in wall lizards

BACKGROUND

Understanding how phenotypic variation scales from individuals, through populations, up to species, and how it relates to genetic and environmental factors, is essential for deciphering the evolutionary mechanisms that drive biodiversity. We used two species of Podarcis wall lizards to test whether phenotypic diversity within and divergence across populations follow concordant patterns, and to examine how phenotypic variation responds to genetic and environmental variability across different hierarchical levels of biological organization, in an explicit geographic framework.

RESULTS

We found a general concordance of phenotypic variation across hierarchical levels (i.e. individuals and populations). However, we also found that within-population diversity does not exhibit a coherent geographic structure for most traits, while among-population divergence does, suggesting that different mechanisms may underlie the generation of diversity at these two levels. Furthermore, the association of phenotypic variation with genetic and environmental factors varied extensively between hierarchical levels and across traits, hampering the identification of simple rules to explain what yields diversity.

CONCLUSIONS

Our results in some cases comply with general ecological and evolutionary predictions, but in others they are difficult to explain in the geographic framework used, suggesting that habitat characteristics and other regulatory mechanisms may have a more substantial contribution in shaping phenotypic diversity.

Environmental selection is a main driver of divergence in house sparrows (Passer domesticus) in Romania and Bulgaria

Both neutral and adaptive evolutionary processes can cause population divergence, but their relative contributions remain unclear. We investigated the roles of these processes in population divergence in house sparrows (Passer domesticus) from Romania and Bulgaria, regions characterized by high landscape heterogeneity compared to Western Europe. We asked whether morphological divergence, complemented with genetic data in this human commensal species, was best explained by environmental variation, geographic distance, or landscape resistance—the effort it takes for an individual to disperse from one location to the other—caused by either natural or anthropogenic barriers. Using generalized dissimilarity modeling, a matrix regression technique that fits biotic beta diversity to both environmental predictors and geographic distance, we found that a small set of climate and vegetation variables explained up to ~30% of the observed divergence, whereas geographic and resistance distances played much lesser roles. Our results are consistent with signals of selection on morphological traits and of isolation by adaptation in genetic markers, suggesting that selection by natural environmental conditions shapes population divergence in house sparrows. Our study thus contributes to a growing body of evidence that adaptive evolution may be a major driver of diversification.

Tackling intraspecific genetic structure in distribution models better reflects species geographical range

Genetic diversity provides insight into heterogeneous demographic and adaptive history across organisms' distribution ranges. For this reason, decomposing single species into genetic units may represent a powerful tool to better understand biogeographical patterns as well as improve predictions of the effects of GCC (global climate change) on biodiversity loss. Using 279 georeferenced Iberian accessions, we used classes of three intraspecific genetic units of the annual plant Arabidopsis thaliana obtained from the genetic analyses of nuclear SNPs (single nucleotide polymorphisms), chloroplast SNPs, and the vernalization requirement for flowering. We used SDM (species distribution models), including climate, vegetation, and soil data, at the whole-species and genetic-unit levels. We compared model outputs for present environmental conditions and with a particularly severe GCC scenario. SDM accuracy was high for genetic units with smaller distribution ranges. Kernel density plots identified the environmental variables underpinning potential distribution ranges of genetic units. Combinations of environmental variables accounted for potential distribution ranges of genetic units, which shrank dramatically with GCC at almost all levels. Only two genetic clusters increased their potential distribution ranges with GCC. The application of SDM to intraspecific genetic units provides a detailed picture on the biogeographical patterns of distinct genetic groups based on different genetic criteria. Our approach also allowed us to pinpoint the genetic changes, in terms of genetic background and physiological requirements for flowering, that Iberian A. thaliana may experience with a GCC scenario applying SDM to intraspecific genetic units.

The dual role of Andean topography in primary divergence: functional and neutral variation among populations of the hummingbird, Metallura tyrianthina

Background

The ridges and valleys of the Andes create physical barriers that limit animal dispersal and cause deterministic local variation in rainfall. This has resulted in physical isolation of animal populations and variation in habitats, each of which has likely contributed to the evolution of high species diversity in the region. However, the relative influences of geographic isolation, ecoclimatic conditions, and their potential interactions remain poorly understood. To address this, we compared patterns of genetic and morphological diversity in Peruvian populations of the hummingbird Metallura tyrianthina.

Results

Phylogenetic and variation partitioning analyses showed that geographic isolation rather than climatic dissimilarity explained the greatest proportion of genetic variance. In contrast, bill length variation was explained by climatic seasonality, but not by genetic divergence. We found that mutation-scaled migration rate (m) between persistently humid and semi-humid environments was nearly 20 times higher when the habitats were contiguous (m = 39.9) than when separated by a barrier, the Cordillera de Vilcanota (m = 2.1). Moreover, the population experiencing more gene flow exhibited a lesser degree of bill length divergence despite similar differences in climate.

Conclusions

Geographic isolation is necessary for genetic divergence. Ecological differences, represented here by climate characteristics, are necessary for functional divergence. Gene flow appears to hinder the evolution of functional traits toward local adaptive optima. This suggests that functional diversification requires geographic isolation followed or accompanied by a shift in ecological conditions. Andean topography causes both isolation and climatic variation, underscoring its dual role in biotic diversification.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-016-0595-2) contains supplementary material, which is available to authorized users.

Lineage range estimation method reveals fine-scale endemism linked to Pleistocene stability in Australian rainforest herpetofauna

Areas of suitable habitat for species and communities have arisen, shifted, and disappeared with Pleistocene climate cycles, and through this shifting landscape, current biodiversity has found paths to the present. Evolutionary refugia, areas of relative habitat stability in this shifting landscape, support persistence of lineages through time, and are thus crucial to the accumulation and maintenance of biodiversity. Areas of endemism are indicative of refugial areas where diversity has persisted, and endemism of intraspecific lineages in particular is strongly associated with late-Pleistocene habitat stability. However, it remains a challenge to consistently estimate the geographic ranges of intraspecific lineages and thus infer phylogeographic endemism, because spatial sampling for genetic analyses is typically sparse relative to species records. We present a novel technique to model the geographic distribution of intraspecific lineages, which is informed by the ecological niche of a species and known locations of its constituent lineages. Our approach allows for the effects of isolation by unsuitable habitat, and captures uncertainty in the extent of lineage ranges. Applying this method to the arc of rainforest areas spanning 3500 km in eastern Australia, we estimated lineage endemism for 53 species of rainforest dependent herpetofauna with available phylogeographic data. We related endemism to the stability of rainforest habitat over the past 120,000 years and identified distinct concentrations of lineage endemism that can be considered putative refugia. These areas of lineage endemism are strongly related to historical stability of rainforest habitat, after controlling for the effects of current environment. In fact, a dynamic stability model that allows movement to track suitable habitat over time was the most important factor in explaining current patterns of endemism. The techniques presented here provide an objective, practical method for estimating geographic ranges below the species level, and including them in spatial analyses of biodiversity.

Environmental variation and rivers govern the structure of chimpanzee genetic diversity in a biodiversity hotspot

Background

The mechanisms that underlie the diversification of tropical animals remain poorly understood, but new approaches that combine geo-spatial modeling with spatially explicit genetic data are providing fresh insights on this topic. Data about the diversification of tropical mammals remain particularly sparse, and vanishingly few opportunities exist to study endangered large mammals that increasingly exist only in isolated pockets. The chimpanzees of Cameroon represent a unique opportunity to examine the mechanisms that promote genetic differentiation in tropical mammals because the region is home to two chimpanzee subspecies: Pan troglodytes ellioti and P. t. trogolodytes. Their ranges converge in central Cameroon, which is a geographically, climatically and environmentally complex region that presents an unparalleled opportunity to examine the roles of rivers and/or environmental variation in influencing the evolution of chimpanzee populations.

Results

We analyzed microsatellite genotypes and mtDNA HVRI sequencing data from wild chimpanzees sampled at a fine geographic scale across Cameroon and eastern Nigeria using a spatially explicit approach based upon Generalized Dissimilarity Modeling. Both the Sanaga River and environmental variation were found to contribute to driving separation of the subspecies. The importance of environmental variation differed among subspecies. Gene-environment associations were weak in P. t. troglodytes, whereas environmental variation was found to play a much larger role in shaping patterns of genetic differentiation in P. t. ellioti.

Conclusions

We found that both the Sanaga River and environmental variation likely play a role in shaping patterns of chimpanzee genetic diversity. Future studies using single nucleotide polymorphism (SNP) data are necessary to further understand how rivers and environmental variation contribute to shaping patterns of genetic variation in chimpanzees.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-014-0274-0) contains supplementary material, which is available to authorized users.

Mapping evolutionary process: a multi-taxa approach to conservation prioritization

Human-induced land use changes are causing extensive habitat fragmentation. As a result, many species are not able to shift their ranges in response to climate change and will likely need to adapt in situ to changing climate conditions. Consequently, a prudent strategy to maintain the ability of populations to adapt is to focus conservation efforts on areas where levels of intraspecific variation are high. By doing so, the potential for an evolutionary response to environmental change is maximized. Here, we use modeling approaches in conjunction with environmental variables to model species distributions and patterns of genetic and morphological variation in seven Ecuadorian amphibian, bird, and mammal species. We then used reserve selection software to prioritize areas for conservation based on intraspecific variation or species-level diversity. Reserves selected using species richness and complementarity showed little overlap with those based on genetic and morphological variation. Priority areas for intraspecific variation were mainly located along the slopes of the Andes and were largely concordant among species, but were not well represented in existing reserves. Our results imply that in order to maximize representation of intraspecific variation in reserves, genetic and morphological variation should be included in conservation prioritization.

New host and lineage diversity of avian haemosporidia in the northern Andes

The northern Andes, with their steep elevational and climate gradients, are home to an exceptional diversity of flora and fauna, particularly rich in avian species that have adapted to divergent ecological conditions. With this diversity comes the opportunity for parasites to exploit a wide breadth of avian hosts. However, little research has focused on examining the patterns of prevalence and lineage diversity of avian parasites in the Andes. Here, we screened a total of 428 birds from 19 species (representing nine families) and identified 133 infections of avian haemosporidia (31%), including lineages of Plasmodium, Haemoproteus, and Leucocytozoon. We document a higher prevalence of haemosporidia at higher elevations and lower temperatures, as well as an overall high diversity of lineages in the northern Andes, including the first sequences of haemosporidians reported in hummingbirds (31 sequences found in 11 species within the family Trochilidae). Double infections were distinguished using PHASE, which enables the separation of distinct parasite lineages. Results suggest that the ecological heterogeneity of the northern Andes that has given rise to a rich diversity of avian hosts may also be particularly conducive to parasite diversification and specialization.

Intraspecific morphological and genetic variation of common species predicts ranges of threatened ones

Predicting where threatened species occur is useful for making informed conservation decisions. However, because they are usually rare, surveying threatened species is often expensive and time intensive. Here, we show how regions where common species exhibit high genetic and morphological divergence among populations can be used to predict the occurrence of species of conservation concern. Intraspecific variation of common species of birds, bats and frogs from Ecuador were found to be a significantly better predictor for the occurrence of threatened species than suites of environmental variables or the occurrence of amphibians and birds. Fully 93 per cent of the threatened species analysed had their range adequately represented by the geographical distribution of the morphological and genetic variation found in seven common species. Both higher numbers of threatened species and greater genetic and morphological variation of common species occurred along elevation gradients. Higher levels of intraspecific divergence may be the result of disruptive selection and/or introgression along gradients. We suggest that collecting data on genetic and morphological variation in common species can be a cost effective tool for conservation planning, and that future biodiversity inventories include surveying genetic and morphological data of common species whenever feasible.

The role of ecological variation in driving divergence of sexual and non-sexual traits in the red-backed fairy-wren (Malurus melanocephalus)

Background

Many species exhibit geographic variation in sexual signals, and divergence in these traits may lead to speciation. Sexual signals may diverge due to differences in ecology if the environment constrains signal production or transmission. Alternatively, sexual signals may diverge stochastically through sexual selection or genetic drift, with little environmental influence. To distinguish between these alternatives we quantified variation in two putative sexual signals – tail length and plumage color – and a suite of non-sexual morphometric traits across the geographic range of the red-backed fairy-wren (Malurus melanocephalus). We then tested for associations between these traits and a number of environmental variables using generalized dissimilarity models.

Results

Variation in morphometric traits was explained well by environmental variation, irrespective of geographic distance between sites. Among putative signals, variation in plumage color was best explained by geographic distance, whereas tail length was best explained by environmental variation. Divergence in male plumage color was not coincident with the boundary between genetic lineages, but was greatest across a contact zone located 300 km east of the genetic boundary.

Conclusions

Morphometric traits describing size and shape have likely been subject to ecological selection and thus appear to track local environmental variation regardless of subspecies identity. Ecological selection appears to have also influenced the evolution of tail length as a signal, but has played a limited role in shaping geographic variation in plumage color, consistent with stochastic divergence in concert with Fisherian selection on this trait. The lack of coincidence between the genetic boundary and the contact zone between plumage types suggests that the sexual plumage signal of one subspecies has introgressed into the genetic background of the other. Thus, this study provides insight into the various ways in which signal evolution may occur within a species, and the geographic patterns of signal variation that can arise, especially following secondary contact.

Local genetic structure on breeding grounds of a long-distance migrant passerine: the bluethroat (Luscinia svecica) in Spain

Breeding site fidelity can be determined by environmental features, which depending on their heterogeneous distribution may shape the genetic landscape of a population. We used 10 microsatellite loci to study the genetic variation of 83 bluethroats (Luscinia svecica azuricollis) across 14 localities within the Spanish breeding population and assess the relative influence of different habitat characteristics (physiography and vegetation) on genetic differentiation. Based on the genetic variation of this population, we identified 3 geographically consistent genetic clusters that on average showed a higher genetic differentiation than among other north European populations, even those belonging to different subspecies. The inferred genetic clusters occurred in geographic areas that significantly differed in elevation. The highest genetic differentiation was observed between sites at different mountain ranges, as well as between the highest altitude sites in the northeastern locale, whereas vegetation type did not explain a significant percentage of genetic variation. The lack of correlation between geographic and genetic distances suggests that this pattern of genetic structure cannot be explained as a consequence of isolation by distance. Finally, we discuss the importance of preserving areas encompassing high environmental and genetic variation as a means of preserving evolutionary processes and adaptive potential.

A trans-Amazonian screening of mtDNA reveals deep intraspecific divergence in forest birds and suggests a vast underestimation of species diversity

The Amazonian avifauna remains severely understudied relative to that of the temperate zone, and its species richness is thought to be underestimated by current taxonomy. Recent molecular systematic studies using mtDNA sequence reveal that traditionally accepted species-level taxa often conceal genetically divergent subspecific lineages found to represent new species upon close taxonomic scrutiny, suggesting that intraspecific mtDNA variation could be useful in species discovery. Surveys of mtDNA variation in Holarctic species have revealed patterns of variation that are largely congruent with species boundaries. However, little information exists on intraspecific divergence in most Amazonian species. Here we screen intraspecific mtDNA genetic variation in 41 Amazonian forest understory species belonging to 36 genera and 17 families in 6 orders, using 758 individual samples from Ecuador and French Guiana. For 13 of these species, we also analyzed trans-Andean populations from the Ecuadorian Chocó. A consistent pattern of deep intraspecific divergence among trans-Amazonian haplogroups was found for 33 of the 41 taxa, and genetic differentiation and genetic diversity among them was highly variable, suggesting a complex range of evolutionary histories. Mean sequence divergence within families was the same as that found in North American birds (13%), yet mean intraspecific divergence in Neotropical species was an order of magnitude larger (2.13% vs. 0.23%), with mean distance between intraspecific lineages reaching 3.56%. We found no clear relationship between genetic distances and differentiation in plumage color. Our results identify numerous genetically and phenotypically divergent lineages which may result in new species-level designations upon closer taxonomic scrutiny and thorough sampling, although lineages in the tropical region could be older than those in the temperate zone without necessarily representing separate species. In-depth phylogeographic surveys are urgently needed to avoid underestimating tropical diversity, and the use of mtDNA markers can be instrumental in identifying and prioritizing taxa for species discovery.

Integrative analyses of speciation and divergence in Psammodromus hispanicus (Squamata: Lacertidae)

BACKGROUND

Genetic, phenotypic and ecological divergence within a lineage is the result of past and ongoing evolutionary processes, which lead ultimately to diversification and speciation. Integrative analyses allow linking diversification to geological, climatic, and ecological events, and thus disentangling the relative importance of different evolutionary drivers in generating and maintaining current species richness.

RESULTS

Here, we use phylogenetic, phenotypic, geographic, and environmental data to investigate diversification in the Spanish sand racer (Psammodromus hispanicus). Phylogenetic, molecular clock dating, and phenotypic analyses show that P. hispanicus consists of three lineages. One lineage from Western Spain diverged 8.3 (2.9-14.7) Mya from the ancestor of Psammodromus hispanicus edwardsianus and P. hispanicus hispanicus Central lineage. The latter diverged 4.8 (1.5-8.7) Mya. Molecular clock dating, together with population genetic analyses, indicate that the three lineages experienced northward range expansions from southern Iberian refugia during Pleistocene glacial periods. Ecological niche modelling shows that suitable habitat of the Western lineage and P. h. edwardsianus overlap over vast areas, but that a barrier may hinder dispersal and genetic mixing of populations of both lineages. P. h. hispanicus Central lineage inhabits an ecological niche that overlaps marginally with the other two lineages.

CONCLUSIONS

Our results provide evidence for divergence in allopatry and niche conservatism between the Western lineage and the ancestor of P. h. edwardsianus and P. h. hispanicus Central lineage, whereas they suggest that niche divergence is involved in the origin of the latter two lineages. Both processes were temporally separated and may be responsible for the here documented genetic and phenotypic diversity of P. hispanicus. The temporal pattern is in line with those proposed for other animal lineages. It suggests that geographic isolation and vicariance played an important role in the early diversification of the group, and that lineage diversification was further amplified through ecological divergence.