RESUMEN
The niche comprises the set of abiotic and biotic environmental conditions in which a species can live. Consequently, those species that present broader niches are expected to be more tolerant to changes in climatic variations than those species that present reduced niches. In this study, we estimate the amplitude of the climatic niche of fourteen species of rattlesnakes of the genus Crotalus to evaluate whether those species that present broader niches are less susceptible to the loss of climatically suitable zones due to the projected climate change for the time period 2021-2040. Our results suggest that for the species under study, the breadth of the niche is not a factor that determines their vulnerability to climatic variations. However, 71.4% of the species will experience increasingly inadequate habitat conditions, mainly due to the increase in temperature and the contribution that this variable has in the creation of climatically suitable zones for most of these species.
Asunto(s)
Cambio Climático , Crotalus , Animales , Ecosistema , América del Norte , TemperaturaRESUMEN
Sceloporus subniger Poglaygen Smith is a montane bunchgrass lizard distributed across pine-oak forests of central Mexico. Prompted by the discovery of a new population of this lizard in far western Mexico, and by recent studies suggesting S. subniger may be a composite of several distinct species, we examined in more detail the genetic structure of S. subniger. We generated a mitochondrial DNA (mtDNA) dataset from 81 specimens and an ultraconserved elements (UCE) dataset representing thousands of genomic regions from 12 specimens to specifically evaluate the genetic distinctiveness of populations from western Michoacán and adjacent Jalisco along with the newly discovered population in the Sierra de Mascota in western Jalisco. We also recorded morphological data from 47 museum specimens to compare to our genetic data. Results from our analyses of the genetic data, augmented by specimen measurements and scale counts, support the notion that S. subniger is indeed a composite of distinct species. Montane bunchgrass lizards from western Michoacán and adjacent Jalisco, and from the Sierra de Mascota in western Jalisco, each represent distinct new species, which we describe and name here.
Asunto(s)
Biodiversidad , Lagartos , Animales , Secuencia Conservada/genética , ADN Mitocondrial/genética , Bosques , Lagartos/clasificación , Lagartos/genética , MéxicoRESUMEN
Incomplete or geographically biased sampling poses significant problems for research in phylogeography, population genetics, phylogenetics, and species delimitation. Despite the power of using genome-wide genetic markers in systematics and related fields, approaches such as the multispecies coalescent remain unable to easily account for unsampled lineages. The Empidonax difficilis/Empidonax occidentalis complex of small tyrannid flycatchers (Aves: Tyrannidae) is a classic example of widely distributed species with limited phenotypic geographic variation that was broken into two largely cryptic (or "sibling") lineages following extensive study. Though the group is well-characterized north of the US Mexico border, the evolutionary distinctiveness and phylogenetic relationships of southern populations remain obscure. In this article, we use dense genomic and geographic sampling across the majority of the range of the E. difficilis/E. occidentalis complex to assess whether current taxonomy and species limits reflect underlying evolutionary patterns, or whether they are an artifact of historically biased or incomplete sampling. We find that additional samples from Mexico render the widely recognized species-level lineage E. occidentalis paraphyletic, though it retains support in the best-fit species delimitation model from clustering analyses. We further identify a highly divergent unrecognized lineage in a previously unsampled portion of the group's range, which a cline analysis suggests is more reproductively isolated than the currently recognized species E. difficilis and E. occidentalis. Our phylogeny supports a southern origin of these taxa. Our results highlight the pervasive impacts of biased geographic sampling, even in well-studied vertebrate groups like birds, and illustrate what is a common problem when attempting to define species in the face of recent divergence and reticulate evolution.
Asunto(s)
Marcadores Genéticos/genética , Filogenia , Pájaros Cantores/clasificación , Pájaros Cantores/genética , Animales , Variación Genética , México , Sesgo de Selección , Estados UnidosRESUMEN
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.
Asunto(s)
Biodiversidad , Crotalus/clasificación , Crotalus/genética , Filogenia , Animales , Biología Computacional/métodos , Crotalus/crecimiento & desarrollo , MéxicoRESUMEN
Integrative taxonomy has been generally considered as a goal in systematics for more than a decade. Here, we employed environmental, molecular, and morphological data to evaluate the species boundaries within the short-nosed skink Plestiodon brevirostris from south-central Mexico, one member of the morphologically conservative P. brevirostris group. Our molecular dataset includes one mitochondrial and two nuclear loci. The mitochondrial fragment includes the full length of the gene coding for the NADH dehydrogenase subunit 1 protein, a segment of the gene coding for 16S ribosomal RNA, and flanking tRNAs. The nuclear dataset includes fragments of the genes coding for the megakaryoblastic leukemia 1 and RNA fingerprint 35 proteins. We employed phylogenetic reconstruction, analyses of population structure and morphological variation, and species delimitation methods (including the integration of the three kinds of data in a unified probabilistic framework) to evaluate species limits. Our results suggest that P. brevirostris represents four distinct species. The information provided by each kind of data allowed us to discern between alternative explanations for the observed patterns of geographic structure. Two of the newly recognized lineages are poorly differentiated morphologically but apparently differ in environmental preferences and are allopatric. Additionally, one lineage is microendemic and parapatric with respect to another one. Moreover, our phylogenetic analyses suggest that other taxa within the P. brevirostris group may represent species complexes. We discuss our results in the context of integrative species delimitation.
Asunto(s)
Lagartos/clasificación , Filogenia , Animales , Teorema de Bayes , ADN Mitocondrial/genética , Sitios Genéticos , Geografía , Lagartos/genética , México , Mitocondrias/genética , ARN Ribosómico 16S/genética , Reproducibilidad de los Resultados , Especificidad de la Especie , Factores de TiempoRESUMEN
As trophic adaptations, rattlesnake venoms can vary in composition depending on several intrinsic and extrinsic factors. Ontogenetic changes in venom composition have been documented for numerous species, but little is known of the potential age-related changes in many rattlesnake species found in México. In the current study, venom samples collected from adult and neonate Crotalus polystictus from Estado de México were subjected to enzymatic and electrophoretic analyses, toxicity assays (LD50), and MALDI-TOF mass spectrometry, and a pooled sample of adult venom was analyzed by shotgun proteomics. Electrophoretic profiles of adult males and females were quite similar, and only minor sex-based variation was noted. However, distinct differences were observed between venoms from adult females and their neonate offspring. Several prominent bands, including P-I and P-III snake venom metalloproteinases (SVMPs) and disintegrins (confirmed by MS/MS) were present in adult venoms and absent/greatly reduced in neonate venoms. Age-dependent differences in SVMP, kallikrein-like, phospholipase A2 (PLA2), and L-amino acid oxidase (LAAO) activity levels were confirmed by enzymatic activity assays, and like many other rattlesnake species, venoms from adult snakes have higher SVMP activity than neonate venoms. Conversely, PLA2 activity was approximately 2.5 × greater in venoms from neonates, likely contributing to the increased toxicity (neonate venom LD50 = 4.5 μg/g) towards non-Swiss albino mice when compared to adult venoms (LD50 = 5.5 μg/g). Thrombin-like (TLE) and phosphodiesterase activities did not vary significantly with age. A significant effect of sex (between adult male and adult female venoms) was also observed for SVMP, TLE, and LAAO activities. Analysis of pooled adult venom by LC-MS/MS identified 14 toxin protein families, dominated by bradykinin-inhibitory peptides, SVMPs (P-I, P-II and P-III), disintegrins, PLA2s, C-type-lectins, CRiSPs, serine proteinases, and LAAOs (96% of total venom proteins). Neonate and adult C. polystictus in this population consume almost exclusively mammals, suggesting that age-based differences in composition are related to physical differences in prey (e.g., surface-to-volume ratio differences) rather than taxonomic differences between prey. Venoms from adult C. polystictus fit a Type I pattern (high SVMP activity, lower toxicity), which is characteristic of many larger-bodied rattlesnakes of North America.
Asunto(s)
Venenos de Crotálidos/química , Venenos de Crotálidos/toxicidad , Animales , Cromatografía Liquida , Crotalus , Femenino , Dosificación Letal Mediana , Masculino , Ratones , Proteómica , Proteínas de Reptiles/análisis , Espectrometría de Masa por Láser de Matriz Asistida de Ionización Desorción , Espectrometría de Masas en TándemRESUMEN
The Mojave rattlesnake (Crotalus scutulatus) inhabits deserts and arid grasslands of the western United States and Mexico. Despite considerable interest in its highly toxic venom and the recognition of two subspecies, no molecular studies have characterized range-wide genetic diversity and population structure or tested species limits within C. scutulatus. We used mitochondrial DNA and thousands of nuclear loci from double-digest restriction site associated DNA sequencing to infer population genetic structure throughout the range of C. scutulatus, and to evaluate divergence times and gene flow between populations. We find strong support for several divergent mitochondrial and nuclear clades of C. scutulatus, including splits coincident with two major phylogeographic barriers: the Continental Divide and the elevational increase associated with the Central Mexican Plateau. We apply Bayesian clustering, phylogenetic inference, and coalescent-based species delimitation to our nuclear genetic data to test hypotheses of population structure. We also performed demographic analyses to test hypotheses relating to population divergence and gene flow. Collectively, our results support the existence of four distinct lineages within C. scutulatus, and genetically defined populations do not correspond with currently recognized subspecies ranges. Finally, we use approximate Bayesian computation to test hypotheses of divergence among multiple rattlesnake species groups distributed across the Continental Divide, and find evidence for co-divergence at this boundary during the mid-Pleistocene.
Asunto(s)
Crotalus/genética , Flujo Génico , Variación Genética , Animales , Secuencia de Bases , Teorema de Bayes , Núcleo Celular/genética , Crotalus/clasificación , ADN Mitocondrial/genética , Ecosistema , Genética de Población , México , Filogenia , Filogeografía , Factores de Tiempo , Estados UnidosRESUMEN
Mountain formation in Mexico has played an important role in the diversification of many Mexican taxa. The Trans-Mexican Volcanic Belt in particular has served as both a cradle of diversification and conduit for dispersal. We investigated the evolutionary history of the Isthmura bellii group of salamanders, a widespread amphibian across the Mexican highlands, using sequence capture of ultraconserved elements. Results suggest that the I. bellii group probably originated in southeastern Mexico in the late Miocene and later dispersed across the Trans-Mexican Volcanic Belt and into the Sierra Madre Occidental. Pre-Pleistocene uplift of the Trans-Volcanic Belt likely promoted early diversification by serving as a mesic land-bridge across central Mexico. These findings highlight the importance of the Trans-Volcanic Belt in generating Mexico's rich biodiversity.
Asunto(s)
Ecosistema , Filogenia , Urodelos/clasificación , Urodelos/genética , Animales , Teorema de Bayes , Calibración , México , Filogeografía , Factores de TiempoRESUMEN
Although the Mexican Highlands has the highest diversity of small-bodied rattlesnakes in the world, studies on the species found throughout this region have been relatively scarce. This has led to challenges with examining venom phenotypic characteristics, as well as species misidentifications and misclassifications. In the current study we investigated venom variation among four subspecies of Crotalus lepidus (C. l. klaluberi, C. l. lepidus, C. l. maculosus, C. l. morulus) and four subspecies of C. willardi (C. w. amabilis, C. w. obscurus, C. w. silus, and C. w. willardi) that inhabit regions of southwestern United States and central México. SDS-PAGE patterns show the presence of many of the major compounds found in other rattlesnake venoms, although minor variations in protein banding patterns and intensity are recognizable. Most notably, PI-metalloproteinase (SVMP) bands appear to be very faint to absent in northern C. l. lepidus and C. l. klauberi subspecies, but are fairly prominent in all other C. lepidus and C. willardi subspecies. Enzyme activity assays revealed that C. lepidus subspecies exhibit higher SVMP and thrombin-like activities when compared to C. willardi subspecies. Significant differences between subspecies were also observed for kallikrein-like serine protease, L-amino acid oxidase, and phosphodiesterase activities, although these differences appear to be random and fail to follow a geographical or phylogenetic trend. The same relationship was also observed for fibrinogenolytic and coagulation assays. Toxicity assays conducted on lab mice (Mus musculus), house geckos (Hemidactylus frenatus), and house crickets (Acheta domestica) revealed varying toxicities between subspecies, with C. l klauberi being the most toxic towards mice (LD50 = 1.36 µg/g) and house geckos (LD50 = 0.17 µg/g), and C. w. silus being most toxic to house crickets (LD50 = 1.94 µg/g). These results provide additional evidence that geographical isolation, natural selection, and adaptive evolution in response to diets may be driving forces contributing to population-level variation in venom composition.
Asunto(s)
Venenos de Crotálidos/química , Venenos de Crotálidos/toxicidad , Crotalus/clasificación , Animales , Venenos de Crotálidos/enzimología , Electroforesis en Gel de Poliacrilamida , Gryllidae , Lagartos , Metaloproteasas/metabolismo , México , Ratones , Fenotipo , Sudoeste de Estados UnidosRESUMEN
Genomic studies are revealing that divergence and speciation are marked by gene flow, but it is not clear whether gene flow has played a prominent role during the generation of biodiversity in species-rich regions of the world where vicariance is assumed to be the principal mode by which new species form. We revisit a well-studied organismal system in the Mexican Highlands, Aphelocoma jays, to test for gene flow among Mexican sierras. Prior results from mitochondrial DNA (mtDNA) largely conformed to the standard model of allopatric divergence, although there was also evidence for more obscure histories of gene flow in a small sample of nuclear markers. We tested for these 'hidden histories' using genomic markers known as ultraconserved elements (UCEs) in concert with phylogenies, clustering algorithms and newer introgression tests specifically designed to detect ancient gene flow (e.g. ABBA/BABA tests). Results based on 4303 UCE loci and 2500 informative SNPs are consistent with varying degrees of gene flow among highland areas. In some cases, gene flow has been extensive and recent (although perhaps not ongoing today), whereas in other cases there is only a trace signature of ancient gene flow among species that diverged as long as 5 million years ago. These results show how a species complex thought to be a model for vicariance can reveal a more reticulate history when a broader portion of the genome is queried. As more organisms are studied with genomic data, we predict that speciation-with-bouts-of-gene-flow will turn out to be a common mode of speciation.
Asunto(s)
Flujo Génico , Especiación Genética , Genética de Población , Passeriformes/genética , Animales , ADN Mitocondrial/genética , Genómica , México , Modelos Genéticos , Filogenia , Polimorfismo de Nucleótido Simple , Análisis de Secuencia de ADNRESUMEN
A new species of Vaejovis is described from the Mexican state of Aguascalientes. It is assigned to the "mexicanus" group and compared with similar species from Jalisco, Guanajuato, and San Luis Potosí. A map with their known distributions is provided.
Asunto(s)
Escorpiones/clasificación , Animales , Femenino , Geografía , Masculino , México , Escorpiones/anatomía & histologíaRESUMEN
A new species of bunchgrass lizard in the Sceloporus scalaris group is described from the southern portion of the Sierra Madre Occidental in Mexico. The new species, Sceloporus aurantius sp. nov., was previously confused with S. brownorum but differs from this and all but one species within the S. scalaris group by a lack of blue belly patches in males. It shares with S. chaneyi an absence of blue belly patches, but differs from this species in size, number of dorsal scales, number of scales around midbody, and presence of an un-patterned morph. The new species further differs from S. chaneyi, and all other species in the S. scalaris species group, by unique phylogenetic position revealed through species delimitation based on multi-locus nuclear DNA. Principal component analyses of 24 traditional morphological characters used to describe previous S. scalaris group taxa indicate that these characters may be of limited use to delineate species in this species group. However, male lateral and ventral coloration may still be an important character for diagnosing species.
Asunto(s)
Biodiversidad , Lagartos/anatomía & histología , Animales , Ecosistema , Femenino , Lagartos/clasificación , Lagartos/genética , Masculino , México , Análisis de Componente PrincipalRESUMEN
Interpretations of phylogeographic patterns can change when analyses shift from single gene-tree to multilocus coalescent analyses. Using multilocus coalescent approaches, a species tree and divergence times can be estimated from a set of gene trees while accounting for gene-tree stochasticity. We utilized the conceptual strengths of a multilocus coalescent approach coupled with complete range-wide sampling to examine the speciation history of a broadly distributed, North American warm-desert toad, Anaxyrus punctatus. Phylogenetic analyses provided strong support for three major lineages within A. punctatus. Each lineage broadly corresponded to one of three desert regions. Early speciation in A. punctatus appeared linked to late Miocene-Pliocene development of the Baja California peninsula. This event was likely followed by a Pleistocene divergence associated with the separation of the Chihuahuan and Sonoran Deserts. Our multilocus coalescent-based reconstruction provides an informative contrast to previous single gene-tree estimates of the evolutionary history of A. punctatus.
Asunto(s)
Bufonidae/clasificación , Especiación Genética , Filogenia , Animales , Bufonidae/genética , ADN Mitocondrial/genética , Clima Desértico , México , Análisis de Secuencia de ADNRESUMEN
The widespread montane Mexican horned lizard Phrynosoma orbiculare (Squamata: Phrynosomatidae) represents an ideal species to investigate the relative impacts of Neogene vicariance and Quaternary climate change on lineage diversification across the Mexican highlands. We used mitochondrial DNA to examine the maternal history of P. orbiculare and estimate the timing and tempo of lineage diversification. Based on our results, we inferred 11 geographically structured, well supported mitochondrial lineages within this species, suggesting P. orbiculare represents a species complex. Six divergences between lineages likely occurred during the Late Miocene and Pliocene, and four splits probably happened during the Pleistocene. Diversification rate appeared relatively constant through time. Spatial and temporal divergences between lineages of P. orbiculare and co-distributed taxa suggest that a distinct period of uplifting of the Transvolcanic Belt around 7.5-3 million years ago broadly impacted diversification in taxa associated with this mountain range. To the north, several river drainages acting as filter barriers differentially subdivided co-distributed highland taxa through time. Diversification patterns observed in P. orbiculare provide additional insight into the mechanisms that impacted differentiation of highland taxa across the complex Mexican highlands.
Asunto(s)
Especiación Genética , Iguanas/genética , Adenosina Trifosfatasas/genética , Animales , Teorema de Bayes , Evolución Molecular , Genes Mitocondriales , Variación Genética , Iguanas/clasificación , Funciones de Verosimilitud , México , NADH Deshidrogenasa/genética , Filogenia , Filogeografía , Proteínas de Reptiles/genética , Análisis de Secuencia de ADNRESUMEN
Neogene vicariance during the Miocene and Pliocene and Quaternary climate change have synergistically driven diversification in Mexican highland taxa. We investigated the impacts of these processes on genetic diversification in the widely distributed bunchgrass lizards in the Sceloporus scalaris group. We searched for correlations between timing in diversification and timing of (1) a period of marked volcanism across the Trans-Mexican Volcanic Belt in central Mexico 3-7.5million years ago (Ma) and (2) a transition to larger glacial-interglacial cycles during the mid-Pleistocene. From our phylogenetic analyses of mitochondrial DNA we identified two major clades that contained 13 strongly supported lineages. One clade contained lineages from the two northern sierras of Mexico, and the other clade included lineages associated with the Trans-Mexican Volcanic Belt and Central Mexican Plateau. Results provided support for Neogene divergences within the S. scalaris group in response to uplift of the Trans-Mexican Volcanic Belt, a pattern observed in several co-distributed taxa, and suggested that Quaternary climate change likely had little effect on diversification between lineages. Uplift of the Trans-Mexican Volcanic Belt during specific time periods appears to have strongly impacted diversification in Mexican highland taxa.
Asunto(s)
Cambio Climático , Especiación Genética , Lagartos/genética , Animales , Teorema de Bayes , Calibración , Femenino , Fósiles , Funciones de Verosimilitud , Lagartos/clasificación , Masculino , Cadenas de Markov , México , ATPasas de Translocación de Protón Mitocondriales/genética , NADH Deshidrogenasa/genética , Filogenia , Filogeografía , ARN de Transferencia/genética , Proteínas de Reptiles/genética , Pigmentación de la PielRESUMEN
We investigate the evolutionary history of the wide-ranging Nearctic treefrog Hyla arenicolor through the integration of extensive range-wide sampling, phylogenetic analyses of multilocus genetic data, and divergence dating. Previous phylogeographic studies of this frog documented a potential signature of introgressive hybridization from an ecologically and morphologically divergent sister species. Based on our Bayesian phylogenetic analyses of mitochondrial DNA, we inferred strong phylogeographic structure in H. arenicolor as indicated by seven well-supported clades, five of which correspond to well-defined biogeographic regions. Clades from the Balsas Basin and southwestern Central Mexican Plateau in Mexico, and the Grand Canyon of Arizona, group with the morphologically, behaviorally, and ecologically divergent mountain treefrogs in the H. eximia group, rendering H. arenicolor as paraphyletic. The phylogenetic position of at least two of these three H. arenicolor clades within the H. eximia group, however, is most likely the result of several episodes of introgressive hybridization and subsequent mitochondrial gene capture separated in time and space, as supported by evidence from the nuclear genes. Hyla arenicolor from the Balsas Basin appear to be deeply divergent from other H. arenicolor and represent a distinctly different species. Results suggests that introgressive hybridization events, both ancient and contemporary, coupled with late Neogene vicariance and Pleistocene climate-driven range shifts, have all played a role in the historical diversification of H. arenicolor.
Asunto(s)
Anuros/genética , Biodiversidad , Genes Mitocondriales , Animales , Anuros/fisiología , Geografía , México , Filogenia , Alineación de Secuencia , Análisis de Secuencia de ADN , Sudoeste de Estados UnidosRESUMEN
The systematic relationships of snakes in the Lampropeltis mexicana complex (L. mexicana, L. alterna, and L. ruthveni) are poorly known despite several taxonomic studies over the last 80 years. Mitochondrial DNA sequences were used to infer the phylogeny of the L. mexicana complex. At least one representative sample from the nine currently recognized species of Lampropeltis was sequenced. Our results suggest that a deep basal split resulted in the divergence of two groups of Lampropeltis, with one group occupying the upland areas of western United States and most of western and central Mexico, and the other northeastern Mexico and the lowland areas of the southern United States. Results also revealed that the L. mexicana complex and Lampropeltis triangulum are polyphyletic, with taxa from both groups nested together in deeply divergent northern and southern clades. These results are incongruent with previous hypotheses of phylogenetic relationships based on morphology, and suggest that morphological characters shared among the various tri-colored Lampropeltis (e.g., hemipenal structure and tri-colored pattern) may be difficult to interpret phylogenetically.