RESUMO
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.
Assuntos
Fluxo Gênico , Lagartos , Animais , Lagartos/genética , Lagartos/classificação , Clima Desértico , Filogenia , México , GenômicaRESUMO
We compile a Mexican insular herpetofaunal checklist to estimate endemism, conservation status, island threats, net taxonomic turnover among six biogeographic provinces belonging to the Nearctic and Neotropical regions, and the relationships between island area and mainland distance versus species richness. We compile a checklist of insular herpetofaunal through performing a literature and collection review. We define the conservation status according to conservation Mexican law, the Red List of International Union for Conservation of Nature, and Environmental Vulnerability Scores. We determine threat percentages on islands according to the 11 major classes of threats to biodiversity. We estimate the net taxonomic turnover with beta diversity analysis between the Nearctic and Neotropical provinces. The Mexican insular herpetofauna is composed of 18 amphibian species, 204 species with 101 subspecies of reptiles, and 263 taxa in total. Endemism levels are 11.76% in amphibians, 53.57% in reptiles, and 27.91% being insular endemic taxa. Two conservation status systems classify the species at high extinction risk, while the remaining system suggests less concern. However, all systems indicate species lacking assessment. Human activities and exotic alien species are present on 60% of 131 islands. The taxonomic turnover value is high (0.89), with a clear herpetofaunal differentiation between the two biogeographic regions. The species-area and species-mainland distance relationships are positive. Insular herpetofauna faces a high percentage of threats, with the Neotropical provinces more heavily impacted. It is urgent to explore the remaining islands (3,079 islands) and better incorporate insular populations and species in ecological, evolutionary, and systematic studies. In the face of the biodiversity crisis, islands will play a leading role as a model to apply restoration and conservation strategies.
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We utilize the efficient GBS technique to obtain thousands of nuclear loci and SNPs to reconstruct the evolutionary history of Mexican leaf-toed geckos (Phyllodactylus). Through the incorporation of unprecedented sampling for this group of geckos, in combination with genomic data analysis, we generate mostly consistent phylogenetic hypotheses using two approaches: supermatrix and coalescent-based inference. All topologies depict three, mutually exclusive major clades. Clade I comprises P. bordai and all species closer to P. bordai than to any other Phyllodactylus. Clade II comprises P. nocticolus and all species closer to P. nocticolus than to any other Phyllodactylus. Clade III comprises P. tuberculosus and all species closer to P. tuberculosus than to any other Phyllodactylus. Analyses estimate the age for the most recent common ancestor of Phyllodactylus in the Eocene (~43 mya), and the ancestors of each major clade date to the Eocene-Oligocene transition (32-36 mya). This group includes one late-Eocene lineage (P. bordai), Oligocene lineages (P. paucituberculatus, P. delcampi), but also topological patterns that indicate a recent radiation occurred during the Pleistocene on islands in the Gulf of California. The wide spatial and temporal scale indicates a complex and unique biogeographic history for each major clade. The 33 species delimited by BPP and stepping-stone BFD*coalescent based genomic approaches reflect this history. This diversity delimited for Mexican leaf-toed geckos demonstrates a vast underestimation in the number of species based on morphological data alone.
Assuntos
Variação Genética , Lagartos/classificação , Animais , Teorema de Bayes , Evolução Biológica , Lagartos/genética , México , FilogeniaRESUMO
A new species of treefrog from the genus Charadrahyla is described from the cloud forest of western Sierra Madre del Sur of Oaxaca, Mexico. Charadrahyla sakbah sp. nov., is distinguished from the rest of the species in the genus by the large body size (81.15-85.75 mm and 67.91-73.21 mm in adult females and males respectively), axillary membrane, adult males with hypertrophied webbings between toes I and II, nuptial excrescences, one enlarged conical tubercle on either side of vent, vocal slits absent, and sexual dimorphism in the snout shape in dorsal profile (rounded and acuminate in females and males respectively). The hypertrophied webbings are a unique character among other hylids of Middle America, and are only present in C. trux, C. tecuani and the species described herein. These three species inhabit the cloud forest of the Sierra Madre del Sur, and are probably closely related. However, more detailed phylogenetic analyses are needed to define the internal relationships of the genus. The cloud forest in the Sierra Madre del Sur continues to be known for a high number of endemic species. However, the cloud forest faces several threats due to its limited distribution that make it a priority ecosystem for conservation.
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Anuros , Florestas , Animais , Ecossistema , Feminino , Masculino , México , FilogeniaRESUMO
Small-scale farming may have large impacts on the selection and spread of antimicrobial resistance to humans. We conducted an observational study to evaluate antibiotic-resistant Escherichia coli populations from poultry and humans in rural northwestern Esmeraldas, Ecuador. Our study site is a remote region with historically low resistance levels of third-generation antibiotics such cefotaxime (CTX), a clinically relevant antibiotic, in both poultry and humans. Our study revealed 1) high CTX resistance (66.1%) in farmed broiler chickens, 2) an increase in CTX resistance over time in backyard chicken not fed antibiotics (2.3-17.9%), and 3) identical bla CTX-M sequences from human and chicken bacteria, suggesting a spillover event. These findings provide evidence that small-scale meat production operations have direct impacts on the spread and selection of clinically important antibiotics among underdeveloped settings.
Assuntos
Farmacorresistência Bacteriana Múltipla/genética , Infecções por Escherichia coli/veterinária , Proteínas de Escherichia coli/genética , Escherichia coli/genética , Doenças das Aves Domésticas/epidemiologia , beta-Lactamases/genética , Agricultura/métodos , Animais , Antibacterianos/farmacologia , Cefotaxima/farmacologia , Galinhas , Equador/epidemiologia , Escherichia coli/efeitos dos fármacos , Escherichia coli/enzimologia , Infecções por Escherichia coli/epidemiologia , Infecções por Escherichia coli/microbiologia , Infecções por Escherichia coli/transmissão , Proteínas de Escherichia coli/metabolismo , Expressão Gênica , Humanos , Testes de Sensibilidade Microbiana , Aves Domésticas , Doenças das Aves Domésticas/microbiologia , Doenças das Aves Domésticas/transmissão , Prevalência , Resistência beta-Lactâmica/genética , beta-Lactamases/metabolismoRESUMO
With the continued adoption of genome-scale data in evolutionary biology comes the challenge of adequately harnessing the information to make accurate phylogenetic inferences. Coalescent-based methods of species tree inference have become common, and concatenation has been shown in simulation to perform well, particularly when levels of incomplete lineage sorting are low. However, simulation conditions are often overly simplistic, leaving empiricists with uncertainty regarding analytical tools. We use a large ultraconserved element data set (>3,000 loci) from rattlesnakes of the Crotalus triseriatus group to delimit lineages and estimate species trees using concatenation and several coalescent-based methods. Unpartitioned and partitioned maximum likelihood and Bayesian analysis of the concatenated matrix yield a topology identical to coalescent analysis of a subset of the data in bpp. ASTRAL analysis on a subset of the more variable loci also results in a tree consistent with concatenation and bpp, whereas the SVDquartets phylogeny differs at additional nodes. The size of the concatenated matrix has a strong effect on species tree inference using SVDquartets, warranting additional investigation on optimal data characteristics for this method. Species delimitation analyses suggest up to 16 unique lineages may be present within the C. triseriatus group, with divergences occurring during the Neogene and Quaternary. Network analyses suggest hybridization within the group is relatively rare. Altogether, our results reaffirm the Mexican highlands as a biodiversity hotspot and suggest that coalescent-based species tree inference on data subsets can provide a strongly supported species tree consistent with concatenation of all loci with a large amount of missing data.
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Biodiversidade , Crotalus/classificação , Crotalus/genética , Filogenia , Animais , Biologia Computacional/métodos , Crotalus/crescimento & desenvolvimento , MéxicoRESUMO
Rattlesnakes (Crotalus and Sistrurus) represent a radiation of approximately 42 species distributed throughout the New World from southern Canada to Argentina. Interest in this enigmatic group of snakes continues to accrue due, in part, to their ecomorphological diversity, contributions to global envenomations, and potential medicinal importance. Although the group has garnered substantial attention from systematists and evolutionary biologists for decades, little is still known regarding patterns of lineage diversification. In addition, few studies have statistically quantified broad-scale biogeographic patterns in rattlesnakes to ascertain how dispersal occurred throughout the New World, particularly among the different major biomes of the Americas. To examine diversification and biogeographic patterns in this group of snakes we assemble a multilocus data set consisting of over 6700bp encompassing three nuclear loci (NT-3, RAG-1, C-mos) and seven mitochondrial genes (12S, 16S, ATPase6, ATPase8, ND4, ND5, cytb). Fossil-calibrated phylogenetic and subsequent diversification rate analyses are implemented using maximum likelihood and Bayesian inference, to examine their evolutionary history and temporal dynamics of diversity. Based on ancestral area reconstructions we explore dispersal patterns throughout the New World. Cladogenesis occurred predominantly during the Miocene and Pliocene with only two divergences during the Pleistocene. Two different diversification rate models, advocating diversity-dependence, are strongly supported. These models indicate an early rapid radiation followed by a recent speciation rate decline. Biogeographic analyses suggest that the high elevation pine-oak forests of western Mexico served as a major speciation pump for the majority of lineages, with the desert biome of western North America colonized independently at least twice. All together, these results provide evidence for rapid diversification of rattlesnakes throughout the Mexican highlands during the Neogene, likely in response to continual orogenesis of Mexico's major mountain systems, followed by more recent dispersal into desert and tropical biomes.
Assuntos
Crotalus/classificação , Crotalus/genética , Especiação Genética , Filogenia , Animais , Teorema de Bayes , Núcleo Celular/genética , Clima Desértico , Florestas , Fósseis , Genes Mitocondriais/genética , Funções Verossimilhança , México , América do Norte , FilogeografiaRESUMO
Methods and approaches for accurate species delimitation continue to be a highly controversial subject in the systematics community. Inaccurate assessment of species' limits precludes accurate inference of historical evolutionary processes. Recent evidence suggests that multilocus coalescent methods show promise in delimiting species in cryptic clades. We combine multilocus sequence data with coalescence-based phylogenetics in a hypothesis-testing framework to assess species limits and elucidate the timing of diversification in leaf-toed geckos (Phyllodactylus) of Mexico's dry forests. Tropical deciduous forests (TDF) of the Neotropics are among the planet's most diverse ecosystems. However, in comparison to moist tropical forests, little is known about the mode and tempo of biotic evolution throughout this threatened biome. We find increased speciation and substantial, cryptic molecular diversity originating following the formation of Mexican TDF 30-20million years ago due to orogenesis of the Sierra Madre Occidental and Mexican Volcanic Belt. Phylogenetic results suggest that the Mexican Volcanic Belt, the Rio Fuerte, and Isthmus of Tehuantepec may be important biogeographic barriers. Single- and multilocus coalescent analyses suggest that nearly every sampling locality may be a distinct species. These results suggest unprecedented levels of diversity, a complex evolutionary history, and that the formation and expansion of TDF vegetation in the Miocene may have influenced subsequent cladogenesis of leaf-toed geckos throughout western Mexico.
Assuntos
Florestas , Especiação Genética , Lagartos/classificação , Filogenia , Animais , Teorema de Bayes , México , Modelos Genéticos , Análise de Sequência de DNARESUMO
Habitat fragmentation due to both natural and anthropogenic forces continues to threaten the evolution and maintenance of biological diversity. This is of particular concern in tropical regions that are experiencing elevated rates of habitat loss. Although less well-studied than tropical rain forests, tropical dry forests (TDF) contain an enormous diversity of species and continue to be threatened by anthropogenic activities including grazing and agriculture. However, little is known about the processes that shape genetic connectivity in species inhabiting TDF ecosystems. We adopt a landscape genetic approach to understanding functional connectivity for leaf-toed geckos (Phyllodactylus tuberculosus) at multiple sites near the northernmost limit of this ecosystem at Alamos, Sonora, Mexico. Traditional analyses of population genetics are combined with multivariate GIS-based landscape analyses to test hypotheses on the potential drivers of spatial genetic variation. Moderate levels of within-population diversity and substantial levels of population differentiation are revealed by FST and Dest. Analyses using structure suggest the occurrence of from 2 to 9 genetic clusters depending on the model used. Landscape genetic analysis suggests that forest cover, stream connectivity, undisturbed habitat, slope, and minimum temperature of the coldest period explain more genetic variation than do simple Euclidean distances. Additional landscape genetic studies throughout TDF habitat are required to understand species-specific responses to landscape and climate change and to identify common drivers. We urge researchers interested in using multivariate distance methods to test for, and report, significant correlations among predictor matrices that can impact results, particularly when adopting least-cost path approaches. Further investigation into the use of information theoretic approaches for model selection is also warranted.