TESTING ECOLOGICAL EXPLANATIONS FOR BIOGEOGRAPHIC BOUNDARIES

Genetic structure and climate niche differentiation among populations of Leopardus geoffroyi

Geoffroy's cat (Leopardus geoffroyi) is a small-sized felid native to South America. Given the species' distribution covering a wide variety of habitats, and the presence of high levels of anthropization in part of its range, it is possible that genetically differentiated groups exist and that they occupy different climatic niches. We assessed patterns of contemporary genetic diversity and structure in the species across most of its range, characterizing each inferred genetic group based on ecological niche models. We genotyped 11 microsatellites for 142 samples covering most of Geoffroy's cat distribution, and investigated patterns of genetic structure and diversity, applying spatial and nonspatial Bayesian clustering methods and a spatial principal component analysis. We created ecological niche models for each genetic cluster, evaluating whether these clusters occupy different climatic spaces and display differences in the suitability of different values of the climatic variables analyzed. We identified two genetic clusters, one in the north-northeast and the other in the south-southwest of the species' distribution. These clusters showed moderate FST values between them and differences in dispersal/genetic diversity. We found isolation-by-distance patterns globally and within each cluster. We observed lower expected heterozygosity compared with other studies and a north-south gradient in allelic richness. The southern cluster showed lower genetic variability and a more restricted climatic niche suggesting that this group is more vulnerable to the effects of the current context of climate change. Individuals from the southern genetic cluster are under different pressures, likely a product of the particularly dry habitat they occupy. Climatic variables associated with habitat suitability suggest the southern cluster has affinity for the arid and semiarid conditions present in its distribution. Conservation measures should consider the genetic structure observed and differences in climatic spaces to maintain the evolutionary potential of the species.

Gene Flow and Isolation in the Arid Nearctic Revealed by Genomic Analyses of Desert Spiny Lizards

The opposing forces of gene flow and isolation are two major processes shaping genetic diversity. Understanding how these vary across space and time is necessary to identify the environmental features that promote diversification. The detection of considerable geographic structure in taxa from the arid Nearctic has prompted research into the drivers of isolation in the region. Several geographic features have been proposed as barriers to gene flow, including the Colorado River, Western Continental Divide (WCD), and a hypothetical Mid-Peninsular Seaway in Baja California. However, recent studies suggest that the role of barriers in genetic differentiation may have been overestimated when compared to other mechanisms of divergence. In this study, we infer historical and spatial patterns of connectivity and isolation in Desert Spiny Lizards (Sceloporus magister) and Baja Spiny Lizards (Sceloporus zosteromus), which together form a species complex composed of parapatric lineages with wide distributions in arid western North America. Our analyses incorporate mitochondrial sequences, genomic-scale data, and past and present climatic data to evaluate the nature and strength of barriers to gene flow in the region. Our approach relies on estimates of migration under the multispecies coalescent to understand the history of lineage divergence in the face of gene flow. Results show that the S. magister complex is geographically structured, but we also detect instances of gene flow. The WCD is a strong barrier to gene flow, while the Colorado River is more permeable. Analyses yield conflicting results for the catalyst of differentiation of peninsular lineages in S. zosteromus. Our study shows how large-scale genomic data for thoroughly sampled species can shed new light on biogeography. Furthermore, our approach highlights the need for the combined analysis of multiple sources of evidence to adequately characterize the drivers of divergence.

Ecological niche contributes to the persistence of the western × glaucous-winged gull hybrid zone

Hybrid zones occur in nature when populations with limited reproductive barriers overlap in space. Many hybrid zones persist over time, and different models have been proposed to explain how selection can maintain hybrid zone stability. More empirical studies are needed to elucidate the role of ecological adaptation in maintaining stable hybrid zones. Here, we investigated the role of exogenous factors in maintaining a hybrid zone between western gulls (Larus occidentalis) and glaucous-winged gulls (L. glaucescens). We used ecological niche models (ENMs) and niche similarity tests to quantify and examine the ecological niches of western gulls, glaucous-winged gulls, and their hybrids. We found evidence of niche divergence between all three groups. Our results support the bounded superiority model, providing further evidence that exogenous selection favoring hybrids may be an important factor in maintaining this stable hybrid zone.

Divergence and reticulation in the Mexican white oaks: ecological and phylogenomic evidence on species limits and phylogenetic networks in the Quercus laeta complex (Fagaceae)

BACKGROUND AND AIMS

Introgressive hybridization poses a challenge to taxonomic and phylogenetic understanding of taxa, particularly when there are high numbers of co-occurring, intercrossable species. The genus Quercus exemplifies this situation. Oaks are highly diverse in sympatry and cross freely, creating syngameons of interfertile species. Although a well-resolved, dated phylogeny is available for the American oak clade, evolutionary relationships within many of the more recently derived clades remain to be defined, particularly for the young and exceptionally diverse Mexican white oak clade. Here, we adopted an approach bridging micro- and macroevolutionary scales to resolve evolutionary relationships in a rapidly diversifying clade endemic to Mexico.

METHODS

Ecological data and sequences of 155 low-copy nuclear genes were used to identify distinct lineages within the Quercus laeta complex. Concatenated and coalescent approaches were used to assess the phylogenetic placement of these lineages relative to the Mexican white oak clade. Phylogenetic network methods were applied to evaluate the timing and genomic significance of recent or historical introgression among lineages.

KEY RESULTS

The Q. laeta complex comprises six well-supported lineages, each restricted geographically and with mostly divergent climatic niches. Species trees corroborated that the different lineages are more closely related to other species of Mexican white oaks than to each other, suggesting that this complex is polyphyletic. Phylogenetic networks estimated events of ancient introgression that involved the ancestors of three present-day Q. laeta lineages.

CONCLUSIONS

The Q. laeta complex is a morphologically and ecologically related group of species rather than a clade. Currently, oak phylogenetics is at a turning point, at which it is necessary to integrate phylogenetics and ecology in broad regional samples to figure out species boundaries. Our study illuminates one of the more complicated of the Mexican white oak groups and lays groundwork for further taxonomic study.

Ecological niche divergence or ecological niche partitioning in a widespread Neotropical bird lineage

Ecological niche divergence is generally considered to be a facet of evolution that may accompany geographic isolation and diversification in allopatry, contributing to species' evolutionary distinctiveness through time. The null expectation for any two diverging species in geographic isolation is that of niche conservatism, wherein populations do not rapidly shift to or adapt to novel environments. Here, I test ecological niche divergence for a widespread, pan-American lineage, the avian genus of martins (Progne). The genus Progne includes migrant and resident species, as well as geographically restricted taxa and widespread, intercontinentally distributed taxa, thus providing an ideal group in which to study the nature of niche divergence within a broad geographic mosaic. I obtained distributional information for the genus from publicly available databases and created ecological niche models for each species to create pairwise comparisons of environmental space. I combined these data with the most up-to-date phylogeny of Progne currently available to examine the patterns of niche evolution within the genus. I found limited evidence for niche divergence across the breeding distributions of Progne, and much stronger support for niche conservatism with patterns of niche partitioning. The ancestral Progne had a relatively broad ecological niche, like extant basal Progne lineages, and several geographically localized descendant species occupy only portions of this larger ancestral niche. I recovered strong evidence of breeding niche divergence for four of 36 taxon pairs but only one of these divergent pairs involved two widespread species (Southern Martin P. elegans vs. Gray-breasted Martin P. chalybea). Potential niche expansion from the ancestral species was observed in the most wide-ranging present-day species, namely the North American Purple Martin P. subis and P. chalybea. I analyzed populations of P. subis separately, as a microcosm of Progne evolution, and again found only limited evidence of niche divergence. This study adds to the mounting evidence for niche conservatism as a dominant feature of diversifying lineages, and sheds light on the ways in which apparently divergent niches may arise through allopatry while not involving any true niche shifts through evolutionary time. Even taxa that appear unique in terms of habitat or behavior may not be diversifying with respect to their ecological niches, but merely partitioning ancestral niches among descendant taxa.

Ecological niche divergence or ecological niche partitioning in a widespread Neotropical bird lineage

Ecological niche divergence is generally considered to be a facet of evolution that may accompany geographic isolation and diversification in allopatry, contributing to species' evolutionary distinctiveness through time. The null expectation for any two diverging species in geographic isolation is that of niche conservatism, wherein populations do not rapidly shift to or adapt to novel environments. Here, I test ecological niche divergence for a widespread, pan-American lineage, the avian genus of martins (Progne). Despite containing species with distributions that go from continent-spanning to locally endemic, I found limited evidence for niche divergence across the breeding distributions of Progne, and much stronger support for niche conservatism with patterns of niche partitioning. The ancestral Progne had a relatively broad ecological niche, similar to extant basal Progne lineages, and several geographically localized descendant species occupy only portions of the larger ancestral Progne niche. I recovered strong evidence of breeding niche divergence for four of 36 taxon pairs but only one of these divergent pairs involved two widespread, continental species (Southern Martin P. elegans vs. Gray-breasted Martin P. chalybea). Potential niche expansion from the ancestral species was observed in the most wide-ranging present-day species, namely the North American Purple Martin P. subis and P. chalybea. I analyzed populations of P. subis separately, as a microcosm of Progne evolution, and again found only limited evidence of niche divergence. This study adds to the mounting evidence for niche conservatism as a dominant feature of diversifying lineages. Even taxa that appear unique in terms of habitat or behavior may still not be diversifying with respect to their ecological niches, but merely partitioning ancestral niches among descendant taxa.

Ecological niche contributes to the persistence of the Western x Glaucous-winged Gull hybrid zone

Hybrid zones occur in nature when populations with limited reproductive barriers overlap in space. Many hybrid zones persist over time, and different models have been proposed to explain how selection can maintain hybrid zone stability. More empirical studies are needed to elucidate the role of ecological adaptation in maintaining stable hybrid zones. Here, we investigated the role of exogenous factors in maintaining a hybrid zone between western gulls (Larus occidentalis) and glaucous-winged gulls (L. glaucescens). We used ecological niche models (ENMs) and niche similarity tests to quantify and examine the ecological niches of western gulls, glaucous-winged gulls, and their hybrids. We found evidence of niche divergence between all three groups. Our results best support the bounded superiority model, providing further evidence that exogenous selection favoring hybrids may be an important factor in maintaining this stable hybrid zone.

Modelling the effects of climate and land-cover changes on the potential distribution and landscape connectivity of three earth snakes (Genus Conopsis, Günther 1858) in central Mexico

Anthropogenic land use and climate change are the greatest threats to biodiversity, especially for many globally endangered reptile species. Earth snakes (Conopsis spp.) are a poorly studied group endemic to Mexico. They have limited dispersal abilities and specialized niches, making them particularly vulnerable to anthropogenic threats. Species distribution models (SDMs) were used to assess how future climate and land-cover change scenarios might influence the distribution and habitat connectivity of three earth snakes: Conopsis biserialis (Taylor and Smith), C. lineata (Kennicott), and C. nasus (Günther). Two climate models, CNRM-CM5 (CN) and MPI-ESM-LR (MP) (Representative Concentration Pathway 85), were explored with ENMeval Maxent modelling. Important SDM environmental variables and environmental niche overlap between species were also examined. We found that C. biserialis and C. lineata were restricted by maximum temperatures whereas C. nasus was restricted by minimum ones and was more tolerant to arid vegetation. C. biserialis and C. lineata were primarily distributed in the valleys and mountains of the highlands of the TMBV, while C. nasus was mainly distributed in the Altiplano Sur (Zacatecano-Potosino). C. lineata had the smallest potential distribution and suffered the greatest contraction in the future whereas C. nasus was the least affected species in future scenarios. The Sierra de las Cruces and the Sierra Chichinautzin were identified as very important areas for connectivity. Our results suggest that C. lineata may be the most vulnerable of the three species to anthropogenic and climate changes whereas C. nasus seems to be less affected by global warming than the other species.

Potential Distribution and Connectivity for Two Plethodontid Salamanders: Conservation Areas and Landscape Corridors for Two Endemic Species of México and Guatemala

Habitat loss is one of the most important threats to biodiversity; it alters the habitat connectivity of species and is among the main causes of the global amphibian extinction crisis. Identifying the potential areas of distribution and connectivity of species is of the utmost importance so that informed decisions can be made for the conservation of vulnerable amphibian populations. In this study, we performed species distribution models and used circuit theory to model omnidirectional connectivity for two plethodontid salamanders of conservation concern distributed in the forests of Chiapas, Mexico, and Guatemala (Bolitoglossa franklini and Bolitoglossa lincolni). Potential distribution maps show an affinity for well-preserved montane forests for both species. Likewise, we found that the niches of the species are not similar. The connectivity models show that the main areas of connectivity are in the Meseta Central de Chiapas, Sierra Madre de Chiapas, and the Cordillera Volcánica Guatemalense, in this last range, important areas of connectivity were located, as well as least-cost paths and barriers to the movement of both species. We identified that important areas of climatic suitability and connectivity are not within the protected natural areas and may be threatened by the increasing influence of anthropogenic activities. The results of our study show the importance of preserving the regional forests to ensure the persistence of species with arboreal habits and high sensitivity to habitat transformation, as well as to recognize and prioritize potential areas for management and protection in both southern Mexico and Guatemala.

Cordyceps cicadae and Cordyceps gunnii have closer species correlation with Cordyceps sinensis: from the perspective of metabonomic and MaxEnt models

Cordyceps sinensis is a second-class nationally-protected medicinal fungus and functional food. Cordyceps sinensis resources are endangered, and finding new medicinal materials is a fast and economical way to meet the current demonstrated demand, which can effectively solve the shortage of C. sinensis resources. In this study, the metabolite characteristics of Cordyceps were comprehensively revealed by LC-QTOF-MS technology. The maxent model can be used to predict the habitat suitability distribution of Cordyceps and screen out the main climatic factors affecting its distribution. The correlation model between climate factors and chemical components was established by Pearson correlation analysis. Finally, based on the analysis of climate factors and metabolites, we will analyze the high correlation species with C. sinensis, and develop them as possible alternative species of C. sinensis in the future. The results showed that the suitable area of Cordyceps cicadae demonstrated a downward trend, while that of C. sinensis, Cordyceps militaris and Cordyceps gunnii demonstrated an upwards trend. The suitable areas all shifted to the northwest. The temperature seasonality and max temperature of the warmest month are the maximum climatic factors affecting nucleosides. Compared with C. sinensis, the metabolic spectrum similarities of C. cicadae, C. militaris, and C. gunnii were 94.42%, 80.82%, and 91.00%, respectively. Cordyceps sinensis, C. cicadae, and C. gunnii were correlated well for compounds and climate factors. This study will explore whether C. cicadae, C. militaris and C. gunnii can be used as substitutes for C. sinensis. Our results may provide a reference for resource conservation and sustainable utilization of endangered C. sinensis.

Niche diversification of Mediterranean and southwestern Asian tortoises

Background

Tortoises of the genus Testudo are widely distributed throughout the Mediterranean region and southwestern Asia. However, the evolutionary mechanisms of diversification in this genus are still poorly understood.

Methods

In this study, we assessed the evolutionary patterns in the climate niches of five species and 11 subspecies of the genus Testudo using ecological niche models and evaluated the niche overlap based on species phylogenetic distances.

Results

The ecological models indicated that most species differ in their climate niches, but show overlap, with gradual transitions at range boundaries. As expected, the ecological divergence among subspecies was lower than that among species. Evaluation of the phylogenetic signal indicated that climate niches have been weakly conserved, but sister species also show high evolutionary divergence.

Fighting climate change: soil bacteria communities and topography play a role in plant colonization of desert areas

Global warming has exacerbated desertification in arid regions. Exploring the environmental variables and microbial communities that drive the dynamics of geographic patterns of desert crops is important for large-scale standardization of crops that can control desertification. Here, predictions based on future climate data from CMIP6 show that a steady expand in the suitable production areas for three desert plants (Cistanche deserticola, Cynomorium songaricum and Cistanche salsa) under global warming, demonstrating their high adaptability to future climate change. We examined the biogeography of three desert plant soil bacteria communities and assessed the environmental factors affecting the community assembly process. The α-diversity significantly decreased along elevated latitudes, indicating that the soil bacterial communities of the three species have latitude diversity patterns. The neutral community model evaluated 66.6% of the explained variance of the bacterial community in the soil of desert plants and Modified Stochasticity Ratio <0.5, suggesting that deterministic processes dominate the assembly of bacterial communities in three desert plants. Moreover, topography (longitude, elevation) and precipitation as well as key OTUs (OTU4911: Streptomyces eurythermus and OTU4672: Streptomyces flaveus) drive the colonization of three desert plants. This research offers a promising solution for desert management in arid areas under global warming.

Climatic dissimilarity associated with phylogenetic breaks

Shared phylogenetic breaks often are associated with clear geographic barriers but some common phylogeographic breaks may lack obvious underlying mechanisms. A phylogenetic break involving multiple taxa was found in the Baja California Peninsula that was associated with a past sea barrier. However, geological evidence is lacking for this barrier’s past existence, and despite its current absence, the genetic breaks have persisted. This work explores the relationships between the current climatic niches for matrilineages of 11 vertebrate species as a possible explanation for the current geographic partitioning of matrilineages. We evaluated the climatic occupancy of each matrilineage through ecological niche models, background similarity, niche overlap, niche divergence, and Mantel tests. We found disparities in the climatic occupancy between north and south matrilineage of each taxon. Northern matrilineages are associated with lower temperatures and winter rains, while southern matrilineages reside in areas with higher temperatures and summer rains.

The effects of climate and demographic history in shaping genomic variation across populations of the Desert Horned Lizard (Phrynosoma platyrhinos)

Species often experience spatial environmental heterogeneity across their range, and populations may exhibit signatures of adaptation to local environmental characteristics. Other population genetic processes, such as migration and genetic drift, can impede the effects of local adaptation. Genetic drift in particular can have a pronounced effect on population genetic structure during large-scale geographic expansions, where a series of founder effects leads to decreases in genetic variation in the direction of the expansion. Here, we explore the genetic diversity of a desert lizard that occupies a wide range of environmental conditions and that has experienced post-glacial expansion northwards along two colonization routes. Based on our analyses of a large SNP data set, we find evidence that both climate and demographic history have shaped the genetic structure of populations. Pronounced genetic differentiation was evident between populations occupying cold versus hot deserts, and we detected numerous loci with significant associations with climate. The genetic signal of founder effects, however, is still present in the genomes of the recently expanded populations, which comprise subsets of genetic variation found in the southern populations.

Ring distribution patterns-diversification or speciation? Comparative phylogeography of two small mammals in the mountains surrounding the Sichuan Basin

Studying the genetic differentiation in a unique geographical area contributes to understanding the process of speciation. Here, we explore the spatial genetic structure and underlying formation mechanism of two congeneric small mammal species (Apodemus draco and A. chevrieri), which are mainly distributed in the mountains surrounding the lowland Sichuan Basin, southwest China. We applied a set of comparative phylogeographical analyses to determine their genetic diversification patterns, combining mitochondrial (Cytb and COI) and nuclear (microsatellite loci) markers, with dense sampling throughout the range (411 A. draco from 21 sites and 191 A. chevrieri from 22 sites). Moreover, we performed three complementary statistical methods to investigate the correlation between genotype and geographical and environmental components, and predicted the potential suitable distributional range under the present and historical climate conditions. Our results suggest that both species have experienced allopatric differentiation and admixture in historical periods, resulting in a ring-shape diversification, under the barrier effect of the Sichuan Basin. We infer that the tectonic events of the Qinghai-Tibetan Plateau and climatic oscillations during the Quaternary played an important role on the genetic divergence of the two species by providing environmental heterogeneity and geographical variation. Our study reveals a case of two sympatric small mammals following a ring-shaped diversification pattern and provides insight into the process of differentiation.

Niche divergence of evolutionarily significant units with implications for repopulation programs of the world's largest amphibians

The niche divergence and potential climate change-induced loss of evolutionarily significant units (ESUs) of flagship amphibian species in China, the Chinese giant salamander clade, were investigated. We tested niche-related ecological hypotheses and identified suitable habitats that are essential for the conservation of ESUs in response to future climate change according to ecological niche models (ENMs). We predicted the localized habitat loss crisis of ESUs induced by global climate heating using the predicted climate derived from two representative concentration pathway (RCP) scenarios 2.6 and 8.5, respectively. In our study, a niche conservatism pattern was found between the two distinctive northern and southern ESUs with sufficient distributional records, but their niches were not equivalent. Furthermore, there was neither abrupt environmental change in nor remarkable biogeographic barriers between the suitable habitats of the species, as indicated by random linear, blob and ribbon range-breaking tests. Under the low-emission scenario RCP2.6, the northern ESU had a moderate loss of suitable range, while the southern ESU had range expansion in the 2070s. The climatic velocities were low in the ranges of both ESUs. However, under the high-emission scenario RCP8.5, the climatic velocities were found to become larger in the suitable ranges of both ESUs. Moreover, the northern ESU had severe habitat loss, bringing it to the edge of extinction, while the southern ESU also had intensified range loss. Considering this, climatic velocity can be an effective indicator of range loss. We argued conclusively that conservation prioritization of ESUs should effectively take into account the underlying geographic and ecological mechanisms driving the speciation process. The conservation of ESUs should consider the conservation of both evolutionary potential and ecological adaptation capacity of each lineage. The present study provided practical guidelines for repopulation programs for endangered species and the conservation of evolutionary diversity.

High dispersal capacity and biogeographic breaks shape the genetic diversity of a globally distributed reef-dwelling calcifier

Understanding the role of dispersal and adaptation in the evolutionary history of marine species is essential for predicting their response to changing conditions. We analyzed patterns of genetic differentiation in the key tropical calcifying species of large benthic foraminifera Amphistegina lobifera to reveal the evolutionary processes responsible for its biogeographic distribution. We collected specimens from 16 sites encompassing the entire range of the species and analyzed hypervariable fragments of the 18S SSU rDNA marker. We identified six hierarchically organized genotypes with mutually exclusive distribution organized along a longitudinal gradient. The distribution is consistent with diversification occurring in the Indo-West Pacific (IWP) followed by dispersal toward the periphery. This pattern can be explained by: (a) high dispersal capacity of the species, (b) habitat heterogeneity driving more recent differentiation in the IWP, and (c) ecological-scale processes such as niche incumbency reinforcing patterns of genotype mutual exclusion. The dispersal potential of this species drives the ongoing range expansion into the Mediterranean Sea, indicating that A. lobifera is able to expand its distribution by tracking increases in temperature. The genetic structure reveals recent diversification and high rate of extinction in the evolutionary history of the clade suggesting a high turnover rate of the diversity at the cryptic level. This diversification dynamic combined with high dispersal potential, allowed the species to maintain a widespread distribution over periods of geological and climatic upheaval. These characteristics are likely to allow the species to modify its geographic range in response to ongoing global warming without requiring genetic differentiation.

Genetic diversity and biogeographic determinants of population structure in Araucaria angustifolia (Bert.) O. Ktze

Araucaria (Araucaria angustifolia (Bert.) O. Ktze) is a primarily dioecious species threatened with extinction that plays an important social and economic role especially in the southern region of Brazil. The aim of this work is to investigate the diversity and likely determinants of genetic lineages in this species for conservation management. For this, a collection of 30-year-old Araucaria was used. Accessions collected from 12 sites across the species range were analyzed, with ten individuals per site. The SSR genotyping was conducted with 15 loci and the data were analyzed using several complementary approaches. Descriptive statistics among sampling sites were used and diversity was partitioned non-hierarchically to estimate the size and composition of genetic clusters using a Bayesian assignment method. To explore possible biological implications of differences between Niche Models and habitat suitability, a series of statistical procedures were used, and tests were carried out using the software ENM Tools and Maxent. Populations from the southernmost zone showed higher genetic variation and a lower inbreeding coefficient compared to the northernmost zone, which may correlate with their isolation. A positive relation between genetic differentiation and geographic distance was observed. Two genetic groups (southernmost and northernmost zones) were evident. The Niche modelling showed separate ranges for each genetic lineage suggesting that differences in selection pressure may be playing a role in the apparent differentiation and may be adaptive. Finally, an evident correlation was observed between genetic data and habitat suitability. The two distinct groups observed must be considered as independent units for conservation and hybridization in breeding programs.

Niche modeling reveals life history shifts in birds at La Brea over the last twenty millennia

A species presence at a particular site can change over time, resulting in temporally dynamic species pools. Ecological niche models provide estimates of species presence at different time intervals. The avifauna of La Brea includes approximately 120 species dating to approximately 15,000 years ago. Niche models predicted presence at the Last Glacial Maximum for over 90% of 89 landbird species. This confirms that niche modeling produces sensible range estimates at the Last Glacial Maximum. For 97 currently local species that are as yet undocumented at La Brea over 90% were predicted to occur; absence is due to insufficient study, lack of the ecological niche, transient occurrence or a behavioral ability to avoid entrapment. Our 366 niche models provide a prospective checklist of the landbird fauna of La Brea. The models indicate fluidity in life history strategies and a higher proportion of resident birds at the LGM (88% to 60%). We evaluated a subset of 103 species in breeding and winter periods using two climate models (MIROC-ESM, CCSM4) with a variety of differing parameters, finding differences in 5% of the niche models. Niche breadths in bark-foraging birds changed little between the present and LGM, suggesting that greater species diversity at the LGM was due to greater niche availability rather than contractions of niche breadths (i.e., niche partitioning).

Transcontinental dispersal of Anopheles gambiae occurred from West African origin via serial founder events

The mosquito Anopheles gambiae s.s. is distributed across most of sub-Saharan Africa and is of major scientific and public health interest for being an African malaria vector. Here we present population genomic analyses of 111 specimens sampled from west to east Africa, including the first whole genome sequences from oceanic islands, the Comoros. Genetic distances between populations of A. gambiae are discordant with geographic distances but are consistent with a stepwise migration scenario in which the species increases its range from west to east Africa through consecutive founder events over the last ~200,000 years. Geological barriers like the Congo River basin and the East African rift seem to play an important role in shaping this process. Moreover, we find a high degree of genetic isolation of populations on the Comoros, confirming the potential of these islands as candidate sites for potential field trials of genetically engineered mosquitoes for malaria control.

Regional patterns of genetic structure and environmental differentiation in willow populations (Salix humboldtiana Willd.) from Central Mexico

AIM

To infer the geological and climatic factors that have shaped the genetic diversity and structure of a willow species (Salix humboldtiana) in three basins of Central Mexico.

LOCATION

Central Mexico.

METHODS

We collected samples from 11 populations across two hydrological basins (Balsas and Lerma) and one population from another basin (Ameca) within the Mexican Central Plateau (MCP). Individuals were analyzed using sequences of two chloroplast DNA (cpDNA) regions and eight nuclear simple sequence repeats (nSSR). Population genetic diversity and structure were determined from these data. To evaluate whether genetic structure was associated with ecological niche differentiation, we determined whether there is niche equivalence, overlap, or divergence between the Balsas and Lerma basins. Also, we evaluated the relative contributions of geographic distribution and climatic variation on population genetic structuring through redundancy analysis (RDA) and partial RDA.

RESULTS

Both cpDNA and nSSRs data indicated the presence of three highly differentiated genetic groups, mostly geographically congruent with the three main hydrological basins. According to nSSRs, the three genetic groups can be further subdivided into eight subgroups corresponding to different rivers within the main basins. The niche equivalency test showed that the niches of the species in the Balsas and Lerma basins are significantly nonequivalent. The RDA indicated a significant association of genetic variation among populations with climate variables (particularly those related to the precipitation regime), while controlling for geographic distribution.

MAIN CONCLUSIONS

The genetic structure of S. humboldtiana is strongly associated with the historical and current geological configuration of the basins and the rivers within basins. The observed hierarchical genetic differentiation can be due to gene flow limitation resulting from physical barriers to the dispersal of S. humboldtiana, but also to some degree of isolation by environment, as suggested by the significant association between genetic variation among populations and precipitation regime.

Invasive Plant Species Establishment and Range Dynamics in Sri Lanka under Climate Change

Plant invasion has been widely recognized as an agent of global change that has the potential to have severe impacts under climate change. The challenges posed by invasive alien plant species (IAPS) on biodiversity and ecosystem stability is growing and not adequately studied, especially in developing countries. Defining climate suitability for multiple invasive plants establishment is important for early and strategic interventions to control and manage plant invasions. We modeled priority IAPS in Sri Lanka to identify the areas of greatest climatic suitability for their establishment and observed how these areas could be altered under projected climate change. We used Maximum Entropy method to model 14 nationally significant IAPS under representative concentration pathways 4.5 and 8.5 for 2050 and 2070. The combined climate suitability map produced by summing up climatic suitability of 14 IAPS was further classified into five classes in ArcMap as very high, high, moderate, low, and very low. South and west parts of Sri Lanka are projected to have potentially higher climatic suitability for a larger number of IAPS. We observed suitable area changes (gains and losses) in all five classes of which two were significant enough to make an overall negative impact i.e., (i) contraction of the very low class and (ii) expansion of the moderate class. Both these changes trigger the potential risk from IAPS in Sri Lanka in the future.

Genomic data reject the hypothesis of sympatric ecological speciation in a clade of Desmognathus salamanders

Closely related taxa with dissimilar morphologies are often considered to have diverged via natural selection favoring different phenotypes. However, some studies have found these scenarios to be paired with limited or no genetic differentiation. Desmognathus quadramaculatus and D. marmoratus are sympatric salamander species thought to represent a case of ecological speciation based on distinct morphologies, but the results of previous studies have not resolved corresponding patterns of lineage divergence. Here, we use genome-wide data to test this hypothesis of ecological speciation. Population structure analyses partitioned individuals geographically, but not morphologically, into two adjacent regions of western North Carolina: Pisgah and Nantahala. Phylogenetic analyses confirmed the nominal species are nonmonophyletic and resolved deep divergence between the two geographic clusters. Model-testing overwhelmingly supported the hypothesis that lineage divergence followed geography. Finally, ecological niche modeling showed that Pisgah and Nantahala individuals occupy different climatic niches, and geographic boundaries for the two lineages correspond to differences in precipitation regimes across southern Appalachia. Overall, we reject the previous hypothesis of ecological speciation based on microhabitat partitioning. Instead, our results suggest that there are two cryptic lineages, each containing the same pair of morphotypes.

Evolutionary relationships and climatic niche evolution in the genus Handleyomys (Sigmodontinae: Oryzomyini)

Mesoamerica is considered a biodiversity hot spot with levels of endemism and species diversity likely underestimated. Unfortunately, the region continues to experience some of the highest deforestation rates in the world. For mammals, the evolutionary relationships of many endemic taxa are controversial, as it is the case for members of the genus Handleyomys. Estimation of a time-calibrated hypothesis for the evolution of these six genera (Euryoryzomys, Handleyomys, Hylaeamys, Nephelomys, Oecomys and Transandinomys) supported a monophyletic Handleyomys sensu lato. Based on their distinctive morphology and the amount of inter-generic genetic divergence, Handleyomys sensu stricto, H. alfaroi, the H. chapmani, and the H. melanotis species groups warrant recognition as separate genera. In addition, species delimitation documents the existence of cryptic species-level lineages within H. alfaroi and H. rostratus. Cryptic lineages within H. rostratus exhibited significant niche differentiation, but this was not the pattern among species-level clades within H. alfaroi. Similarly, age-range correlations revealed that niche evolution within Handleyomys is not correlated with evolutionary time, instead, ancestral climate tolerance reconstructions show niche disparities at specific diversification events within the chapmani and melanotis species groups, while the climatic niche of the rest of species of Handleyomys tended to be conservative.

Inferring ecological explanations for biogeographic boundaries of parapatric Asian mountain frogs

Background

Identifying and understanding the mechanisms that shape barriers to dispersal and resulting biogeographic boundaries has been a longstanding, yet challenging, goal in ecology, evolution and biogeography. Characterized by stable, adjacent ranges, without any intervening physical barriers, and limited, if any, range overlap in a narrow contact zone, parapatric species are an interesting system for studying biogeographic boundaries. The geographic ranges of two parapatric frog species, Feirana quadranus and F. taihangnica, meet in a contact zone within the Qinling Mountains, an important watershed for East Asia. To identify possible ecological determinants of the parapatric range boundaries for two closely related frog species, we quantified the extent of their niche differentiation in both geographical and environmental space combining ecological niche models with an ordination technique. We tested two alternative null hypotheses (sharp environmental gradients versus a ribbon of unsuitable habitat dividing two highly suitable regions) for biogeographic boundaries, against the null expectation that environmental variation across a given boundary is no greater than expected by chance.

Results

We found that the niches of these two parapatric species are more similar than expected by chance, but not equivalent. No sharp environmental gradient was found, while a ribbon of unsuitable habitat did act as a barrier for F. quadranus, but not for F. taihangnica.

Conclusions

Integrating our findings with historical biogeographic information, our results suggest that at a contact zone, environmental tolerance restricted F. quadranus from dispersing further north, while interspecific competition most likely prevented the southward expansion of F. taihangnica. This study highlights the importance of both climate and competition in exploring ecological explanations for parapatric range boundaries between ecologically similar frog species, in particular under the effects of changing climate.

Electronic supplementary material

The online version of this article (10.1186/s12898-018-0160-5) contains supplementary material, which is available to authorized users.

Ecological and Genetic Divergences with Gene Flow of Two Sister Species (Leucomeris decora and Nouelia insignis) Driving by Climatic Transition in Southwest China

Understanding of the processes of divergence and speciation is a major task for biodiversity researches and may offer clearer insight into mechanisms generating biological diversity. Here, we employ an integrative approach to explore genetic and ecological differentiation of Leucomeris decora and Nouelia insignis distributed allopatrically along the two sides of the biogeographic boundary 'Tanaka Line' in Southwest China. We addressed these questions using ten low-copy nuclear genes and nine plastid DNA regions sequenced among individuals sampled from 28 populations across their geographic ranges in China. Phylogenetic, coalescent-based population genetic analyses, approximate Bayesian computation (ABC) framework and ecological niche models (ENMs) were conducted. We identified a closer phylogenetic relationship in maternal lineage of L. decora with N. insignis than that between L. decora and congeneric Leucomeris spectabilis. A deep divergence between the two species was observed and occurred at the boundary between later Pliocene and early Pleistocene. However, the evidence of significant chloroplast DNA gene flow was also detected between the marginal populations of L. decora and N. insignis. Niche models and statistical analyses showed significant ecological differentiation, and two nuclear loci among the ten nuclear genes may be under divergent selection. These integrative results imply that the role of climatic shift from Pliocene to Pleistocene may be the prominent factor for the divergence of L. decora and N. insignis, and population expansion after divergence may have given rise to chloroplast DNA introgression. The divergence was maintained by differential selection despite in the face of gene flow.

Phylogenetic and Functional Structure of Wintering Waterbird Communities Associated with Ecological Differences

Ecological differences may be related to community component divisions between Oriental (west) and Sino-Japanese (east) realms, and such differences may result in weak geographical breaks in migratory species that are highly mobile. Here, we conducted comparative phylogenetic and functional structure analyses of wintering waterbird communities in southern China across two realms and subsequently examined possible climate drivers of the observed patterns. An analysis based on such highly migratory species is particularly telling because migration is bound to reduce or completely eliminate any divergence between communities. Phylogenetic and functional structure of eastern communities showed over-dispersion while western communities were clustered. Basal phylogenetic and functional turnover of western communities was significant lower than that of eastern communities. The break between eastern and western communities was masked by these two realms. Geographic patterns were related to mean temperature changes and temperature fluctuations, suggesting that temperature may filter waterbird lineages and traits, thus underlying geographical community divisions. These results suggest phylogenetic and functional divisions in southern China, coinciding with biogeography. This study shows that temperature fluctuations constitute an essential mechanism shaping geographical divisions that have largely gone undetected previously, even under climate change.

Geographic patterns of phenotypic diversity in incipient species of North American blister beetles (Coleoptera: Meloidae) are not determined by species niches, but driven by demography along the speciation process

The Epicauta stigmata complex is a group of blister beetles composed of three parapatric or sympatric species that occur in central Mexico to southern USA: E. stigmata, E. uniforma and E. melanochroa. These species are morphologically very similar, and are mainly distinguished by body colour differences. Here we assessed whether phenotypic divergence in coloration patterns define evolutionary units within the complex. We studied the phylogenetic relationships, demographic history and concordances between morphological and ecological traits in the group. The complex apparently had a demographic history of recent population expansion during the last glaciation period 75000 to 9500 years ago. The three species show no reciprocal monophyly, and thus their allospecificity was not confirmed. The current distribution of haplotypes and the genetic divergences in these taxa can be explained by either recent mitochondrial introgression events caused by hybridisation or by incomplete lineage sorting. Colour pattern differences in the complex are not likely a product of local selection acting over a common genetic background. We suggest that phenotypic divergence in colour patterns during an incipient speciation process might be seen as an enhancing factor of cohesion within each of the three evolutionary units.

Genetic diversity and structure related to expansion history and habitat isolation: stone marten populating rural-urban habitats

Background

Population genetic diversity and structure are determined by past and current evolutionary processes, among which spatially limited dispersal, genetic drift, and shifts in species distribution boundaries have major effects. In most wildlife species, environmental modifications by humans often lead to contraction of species’ ranges and/or limit their dispersal by acting as environmental barriers. However, in species well adapted to anthropogenic habitat or open landscapes, human induced environmental changes may facilitate dispersal and range expansions. In this study, we analysed whether isolation by distance and deforestation, among other environmental features, promotes or restricts dispersal and expansion in stone marten (Martes foina) populations.

Results

We genotyped 298 martens from eight sites at twenty-two microsatellite loci to characterize the genetic variability, population structure and demographic history of stone martens in Poland. At the landscape scale, limited genetic differentiation between sites in a mosaic of urban, rural and forest habitats was mostly influenced by isolation by distance. Statistical clustering and multivariate analyses showed weak genetic structuring with two to four clusters and a high rate of gene flow between them. Stronger genetic differentiation was detected for one stone marten population (NE1) located inside a large forest complex. Genetic differentiation between this site and all others was 20% higher than between other sites separated by similar distances. The genetic uniqueness index of NE1 was also twofold higher than in other sites. Past demographic history analyses showed recent expansion of this species in north-eastern Poland. A decrease in genetic diversity from south to north, and MIGRAINE analyses indicated the direction of expansion of stone marten.

Conclusions

Our results showed that two processes, changes in species distribution boundaries and limited dispersal associated with landscape barriers, affect genetic diversity and structure in stone marten. Analysis of local barriers that reduced dispersal and large scale analyses of genetic structure and demographic history highlight the importance of isolation by distance and forest cover for the past colonization of central Europe by stone marten. This confirmed the hypothesis that human-landscape changes (deforestation) accelerated stone marten expansion, to which climate warming probably has also been contributing over the last few decades.

Electronic supplementary material

The online version of this article (10.1186/s12898-017-0156-6) contains supplementary material, which is available to authorized users.

Continuation of the genetic divergence of ecological speciation by spatial environmental heterogeneity in island endemic plants

Divergent selection plays a critical role not only as a speciation driver but also in maintaining post-speciation divergence. In the absence of direct evidence, ancestral interspecific gene flow between incipient species can reflect ancient selective pressure for ecological speciation. In the present study, two late-Pleistocene diverged species endemic to Taiwan, Scutellaria playfairii and S. tashiroi, were spatially and ecologically partitioned with partial overlap. Multilocus genome-scan analyses and in silico evaluation revealed ancestral interspecific gene flow but distinct genetic compositions, implying that adaptive divergence contributed to their speciation. Ecological niche modeling and principal component analysis suggested incomplete divergent niches between the two species; the species distribution is therefore consistent with Hutchinson's metaphor of multidimensional hypervolume niches rather than attributable to a single factor. Constraint ordination analysis supported this inference of a combination of variables explaining the genetic structure. The rare occurrence of hybrids in the sympatric population suggested hybrid breakdown, providing further evidence of divergent selection blocking gene flow. The correlation of environmental variables with integrated genetic components demonstrated that environmental heterogeneity maintains the species and population differentiation. This study highlights the importance of environmental heterogeneity and divergent selection for the rapid speciation and recent diversification of island plants.

Phylogeographical structure and demographic expansion in the endemic alpine stream salamander (Hynobiidae: Batrachuperus) of the Qinling Mountains

The Qinling Mountains of China provide an excellent study area for assessing the effect of Pleistocene climatic oscillations and paleogeological events on intraspecific diversification. To assess genetic diversity of an endemic stream salamander, Batrachuperus tibetanus, for its conservation, a phylogeographical survey was performed based on mitochondrial DNA and morphological data. The mitochondrial data revealed three lineages of B. tibetanus in the Qinling Mountains. A lineage present in the northwestern Qinling Mountains groups with the Tibet lineage of B. tibetanus, and the remaining Qinling populations are eastern and western lineages that separated ~3–4 million years ago (Ma). The eastern and western Qinling lineage delineation is supported by three morphological variables (snout length, eye diameter and axilla-groin length). The divergence of the two major lineages was likely caused by orogenesis of the Qinling Mountains during the late Cenozoic, and the two lineages were subsequently affected at different levels by Pleistocene climatic oscillations showing different signals of demographic expansion. A large suitable area of B. tibetanus through the Qinling Mountains since the last glacial maximum (LGM) indicated the adaptation of this species to the climatic changes. However, low genetic diversity within populations indicate the urgency of preserving the vulnerable populations and endemic lineages.

A genomic assessment of species boundaries and hybridization in a group of highly polymorphic anoles (distichus species complex)

Delimiting young species is one of the great challenges of systematic biology, particularly when the species in question exhibit little morphological divergence. Anolis distichus, a trunk anole with more than a dozen subspecies that are defined primarily by dewlap color, may actually represent several independent evolutionary lineages. To test this, we utilized amplified fragment length polymorphisms (AFLP) genome scans and genetic clustering analyses in conjunction with a coalescent‐based species delimitation method. We examined a geographically widespread set of samples and two heavily sampled hybrid zones. We find that genetic divergence is associated with a major biogeographic barrier, the Hispaniolan paleo‐island boundary, but not with dewlap color. Additionally, we find support for hypotheses regarding colonization of two Hispaniolan satellite islands and the Bahamas from mainland Hispaniola. Our results show that A. distichus is composed of seven distinct evolutionary lineages still experiencing a limited degree of gene flow. We suggest that A. distichus merits taxonomic revision, but that dewlap color cannot be relied upon as the primary diagnostic character.

Congruent biogeographical disjunctions at a continent-wide scale: Quantifying and clarifying the role of biogeographic barriers in the Australian tropics

AIM

To test whether novel and previously hypothesized biogeogaphic barriers in the Australian Tropics represent significant disjunction points or hard barriers, or both, to the distribution of plants.

LOCATION

Australian tropics: Australian Monsoon Tropics and Australian Wet Tropics.

METHODS

The presence or absence of 6,861 plant species was scored across 13 putative biogeographic barriers in the Australian Tropics, including two that have not previously been recognised. Randomizations of these data were used to test whether more species showed disjunctions (gaps in distribution) or likely barriers (range limits) at these points than expected by chance.

RESULTS

Two novel disjunctions in the Australian Tropics flora are identified in addition to eleven putative barriers previously recognized for animals. Of these, eleven disjunction points (all within the Australian Monsoon Tropics) were found to correspond to range-ending barriers to a significant number of species, while neither of the two disjunctions found within the Australian Wet Tropics limited a significant number of species' ranges.

MAIN CONCLUSIONS

Biogeographic barriers present significant distributional limits to native plant species in the Australian Monsoon Tropics but not in the Australian Wet Tropics.

Are we overestimating the niche? Removing marginal localities helps ecological niche models detect environmental barriers

Correlative ecological niche models (ENMs) estimate species niches using occurrence records and environmental data. These tools are valuable to the field of biogeography, where they are commonly used to infer potential connectivity among populations. However, a recent study showed that when locally relevant environmental data are not available, records from patches of suitable habitat protruding into otherwise unsuitable regions (e.g., gallery forests within dry areas) can lead to overestimations of species niches and their potential distributions. Here, we test whether this issue obfuscates detection of an obvious environmental barrier existing in northern Venezuela - that of the hot and xeric lowlands separating the Península de Paraguaná from mainland South America. These conditions most likely promote isolation between mainland and peninsular populations of three rodent lineages occurring in mesic habitat in this region. For each lineage, we calibrated optimally parameterized ENMs using mainland records only, and leveraged existing habitat descriptions to assess whether those assigned low suitability values corresponded to instances where the species was collected within locally mesic conditions amidst otherwise hot dry areas. When this was the case, we built an additional model excluding these records. We projected both models onto the peninsula and assessed whether they differed in their ability to detect the environmental barrier. For the two lineages in which we detected such problematic records, only the models built excluding them detected the barrier, while providing additional insights regarding peninsular populations. Overall, the study reveals how a simple procedure like the one applied here can deal with records problematic for ENMs, leading to better predictions regarding the potential effects of the environment on lineage divergence.

The Species versus Subspecies Conundrum: Quantitative Delimitation from Integrating Multiple Data Types within a Single Bayesian Approach in Hercules Beetles

With the recent attention and focus on quantitative methods for species delimitation, an overlooked but equally important issue regards what has actually been delimited. This study investigates the apparent arbitrariness of some taxonomic distinctions, and in particular how species and subspecies are assigned. Specifically, we use a recently developed Bayesian model-based approach to show that in the Hercules beetles (genus Dynastes) there is no statistical difference in the probability that putative taxa represent different species, irrespective of whether they were given species or subspecies designations. By considering multiple data types, as opposed to relying exclusively on genetic data alone, we also show that both previously recognized species and subspecies represent a variety of points along the speciation spectrum (i.e., previously recognized species are not systematically further along the continuum than subspecies). For example, based on evolutionary models of divergence, some taxa are statistically distinguishable on more than one axis of differentiation (e.g., along both phenotypic and genetic dimensions), whereas other taxa can only be delimited statistically from a single data type. Because both phenotypic and genetic data are analyzed in a common Bayesian framework, our study provides a framework for investigating whether disagreements in species boundaries among data types reflect (i) actual discordance with the actual history of lineage splitting, or instead (ii) differences among data types in the amount of time required for differentiation to become apparent among the delimited taxa. We discuss what the answers to these questions imply about what characters are used to delimit species, as well as the diverse processes involved in the origin and maintenance of species boundaries. With this in mind, we then reflect more generally on how quantitative methods for species delimitation are used to assign taxonomic status.