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1.
Parasit Vectors ; 12(1): 473, 2019 Oct 11.
Artigo em Inglês | MEDLINE | ID: mdl-31604471

RESUMO

BACKGROUND: A considerable amount of evidence has favored ecological host-fitting, rather than coevolution, as the main mechanism responsible for trypanosome divergence. Nevertheless, beyond the study of human pathogenic trypanosomes, the genetic basis of host specificity among trypanosomes isolated from forest-inhabiting hosts remains largely unknown. METHODS: To test possible scenarios on ecological host-fitting and coevolution, we combined a host capture recapture strategy with parasite genetic data and studied the genetic variation, population dynamics and phylogenetic relationships of Trypanosoma terrestris, a recently described trypanosome species isolated from lowland tapirs in the Brazilian Pantanal and Atlantic Forest biomes. RESULTS: We made inferences of T. terrestris population structure at three possible sources of genetic variation: geography, tapir hosts and 'putative' vectors. We found evidence of a bottleneck affecting the contemporary patterns of parasite genetic structure, resulting in little genetic diversity and no evidence of genetic structure among hosts or biomes. Despite this, a strongly divergent haplotype was recorded at a microgeographical scale in the landscape of Nhecolândia in the Pantanal. However, although tapirs are promoting the dispersion of the parasites through the landscape, neither geographical barriers nor tapir hosts were involved in the isolation of this haplotype. Taken together, these findings suggest that either host-switching promoted by putative vectors or declining tapir population densities are influencing the current parasite population dynamics and genetic structure. Similarly, phylogenetic analyses revealed that T. terrestris is strongly linked to the evolutionary history of its perissodactyl hosts, suggesting a coevolving scenario between Perissodactyla and their trypanosomes. Additionally, T. terrestris and T. grayi are closely related, further indicating that host-switching is a common feature promoting trypanosome evolution. CONCLUSIONS: This study provides two lines of evidence, both micro- and macroevolutionary, suggesting that both host-switching by ecological fitting and coevolution are two important and non-mutually-exclusive processes driving the evolution of trypanosomes. In line with other parasite systems, our results support that even in the face of host specialization and coevolution, host-switching may be common and is an important determinant of parasite diversification.


Assuntos
Perissodáctilos/parasitologia , Trypanosoma/classificação , Jacarés e Crocodilos/parasitologia , Animais , Teorema de Bayes , Coevolução Biológica , Análise por Conglomerados , Fenômenos Ecológicos e Ambientais , Ecossistema , Variação Genética , Genética Populacional , Interações Hospedeiro-Parasita , Filogenia , Dinâmica Populacional , Trypanosoma/genética , Trypanosoma/crescimento & desenvolvimento
2.
Trends Ecol Evol ; 34(7): 641-654, 2019 07.
Artigo em Inglês | MEDLINE | ID: mdl-30904190

RESUMO

Aquatic species represent a vast diversity of metazoans, provide humans with the most abundant animal protein source, and are of increasing conservation concern, yet landscape genomics is dominated by research in terrestrial systems. We provide researchers with a roadmap to plan aquatic landscape genomics projects by aggregating spatial and software resources and offering recommendations from sampling to data production and analyses, while cautioning against analytical pitfalls. Given the unique properties of water, we discuss the importance of considering freshwater system structure and marine abiotic properties when assessing genetic diversity, population connectivity, and signals of natural selection. When possible, genomic datasets should be parsed into neutral, adaptive, and sex-linked datasets to generate the most accurate inferences of eco-evolutionary processes.


Assuntos
Genética Populacional , Genômica , Animais , Clima , Variação Genética , Seleção Genética
3.
Mol Phylogenet Evol ; 125: 78-84, 2018 08.
Artigo em Inglês | MEDLINE | ID: mdl-29555294

RESUMO

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.


Assuntos
Ecossistema , Filogenia , Urodelos/classificação , Urodelos/genética , Animais , Teorema de Bayes , Calibragem , México , Filogeografia , Fatores de Tempo
4.
Mol Phylogenet Evol ; 125: 243-254, 2018 08.
Artigo em Inglês | MEDLINE | ID: mdl-29555296

RESUMO

Rapid evolutionary radiations are difficult to resolve because divergence events are nearly synchronous and gene flow among nascent species can be high, resulting in a phylogenetic "bush". Large datasets composed of sequence loci from across the genome can potentially help resolve some of these difficult phylogenetic problems. A suitable test case is the Liolaemus fitzingerii species group of lizards, which includes twelve species that are broadly distributed in Argentinean Patagonia. The species in the group have had a complex evolutionary history that has led to high morphological variation and unstable taxonomy. We generated a sequence capture dataset for 28 ingroup individuals of 580 nuclear loci, alongside a mitogenomic dataset, to infer phylogenetic relationships among species in this group. Relationships among species were generally weakly supported with the nuclear data, and along with an inferred age of ∼2.6 million years old, indicate either rapid evolution, hybridization, incomplete lineage sorting, non-informative data, or a combination thereof. We inferred a signal of mito-nuclear discordance, indicating potential hybridization between L. melanops and L. martorii, and phylogenetic network analyses provided support for 5 reticulation events among species. Phasing the nuclear loci did not provide additional insight into relationships or suspected patterns of hybridization. Only one clade, composed of L. camarones, L. fitzingerii, and L. xanthoviridis was recovered across all analyses. Genomic datasets provide molecular systematists with new opportunities to resolve difficult phylogenetic problems, yet the lack of phylogenetic resolution in Patagonian Liolaemus is biologically meaningful and indicative of a recent and rapid evolutionary radiation. The phylogenetic relationships of the Liolaemus fitzingerii group may be best modeled as a reticulated network instead of a bifurcating phylogeny.


Assuntos
Genômica , Lagartos/genética , Filogenia , Animais , Sequência de Bases , DNA Mitocondrial/genética , Geografia , Hibridização Genética , Análise de Sequência de DNA , Especificidade da Espécie
5.
Mol Ecol ; 26(8): 2306-2316, 2017 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-28133829

RESUMO

Moving hybrid zones provide compelling examples of evolution in action, yet long-term studies that test the assumptions of hybrid zone stability are rare. Using replicated transect samples collected over a 10-year interval from 2002 to 2012, we find evidence for concerted movement of genetic clines in a plateau fence lizard hybrid zone (Sceloporus tristichus) in Arizona. Cline-fitting analyses of SNP and mtDNA data both provide evidence that the hybrid zone shifted northward by approximately 2 km during the 10-year interval. For each sampling period, the mtDNA cline centre is displaced from the SNP cline centre and maintaining an introgression distance of approximately 3 km. The northward expansion of juniper trees into the Little Colorado River Basin in the early 1900s provides a plausible mechanism for hybrid zone formation and movement, and a broadscale quantification of recent land cover change provides support for increased woody species encroachment at the southern end of the hybrid zone. However, population processes can also contribute to hybrid zone movement, and the current stability of the ecotone habitats in the centre of the hybrid zone suggests that movement could decelerate in the future.


Assuntos
Evolução Biológica , Hibridização Genética , Lagartos/genética , Animais , Arizona , Núcleo Celular/genética , DNA Mitocondrial/genética , Genética Populacional , Modelos Genéticos , Polimorfismo de Nucleotídeo Único
6.
Mol Ecol ; 24(7): 1523-42, 2015 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-25712551

RESUMO

Interspecific gene flow is pervasive throughout the tree of life. Although detecting gene flow between populations has been facilitated by new analytical approaches, determining the timing and geography of hybridization has remained difficult, particularly for historical gene flow. A geographically explicit phylogenetic approach is needed to determine the overlap of ancestral populations. In this study, we performed population genetic analyses, species delimitation, simulations and a recently developed approach of species tree diffusion to infer the phylogeographic history, timing and geographic extent of gene flow in lizards of the Sceloporus spinosus group. The two species in this group, S. spinosus and S. horridus, are distributed in eastern and western portions of Mexico, respectively, but populations of these species are sympatric in the southern Mexican highlands. We generated data consisting of three mitochondrial genes and eight nuclear loci for 148 and 68 individuals, respectively. We delimited six lineages in this group, but found strong evidence of mito-nuclear discordance in sympatric populations of S. spinosus and S. horridus owing to mitochondrial introgression. We used coalescent simulations to differentiate ancestral gene flow from secondary contact, but found mixed support for these two models. Bayesian phylogeography indicated more than 60% range overlap between ancestral S. spinosus and S. horridus populations since the time of their divergence. Isolation-migration analyses, however, revealed near-zero levels of gene flow between these ancestral populations. Interpreting results from both simulations and empirical data indicate that despite a long history of sympatry among these two species, gene flow in this group has only recently occurred.


Assuntos
Fluxo Gênico , Genética Populacional , Lagartos/genética , Filogenia , Simpatria , Animais , Teorema de Bayes , Núcleo Celular/genética , DNA Mitocondrial/genética , Funções Verossimilhança , México , Modelos Genéticos , Modelos Estatísticos , Dados de Sequência Molecular , Filogeografia , Análise de Sequência de DNA
7.
Genome Biol Evol ; 7(3): 706-19, 2015 Feb 07.
Artigo em Inglês | MEDLINE | ID: mdl-25663487

RESUMO

Sequence capture and restriction site associated DNA sequencing (RADseq) are popular methods for obtaining large numbers of loci for phylogenetic analysis. These methods are typically used to collect data at different evolutionary timescales; sequence capture is primarily used for obtaining conserved loci, whereas RADseq is designed for discovering single nucleotide polymorphisms (SNPs) suitable for population genetic or phylogeographic analyses. Phylogenetic questions that span both "recent" and "deep" timescales could benefit from either type of data, but studies that directly compare the two approaches are lacking. We compared phylogenies estimated from sequence capture and double digest RADseq (ddRADseq) data for North American phrynosomatid lizards, a species-rich and diverse group containing nine genera that began diversifying approximately 55 Ma. Sequence capture resulted in 584 loci that provided a consistent and strong phylogeny using concatenation and species tree inference. However, the phylogeny estimated from the ddRADseq data was sensitive to the bioinformatics steps used for determining homology, detecting paralogs, and filtering missing data. The topological conflicts among the SNP trees were not restricted to any particular timescale, but instead were associated with short internal branches. Species tree analysis of the largest SNP assembly, which also included the most missing data, supported a topology that matched the sequence capture tree. This preferred phylogeny provides strong support for the paraphyly of the earless lizard genera Holbrookia and Cophosaurus, suggesting that the earless morphology either evolved twice or evolved once and was subsequently lost in Callisaurus.


Assuntos
Lagartos/classificação , Filogenia , Análise de Sequência de DNA/métodos , Animais , Enzimas de Restrição do DNA , Genômica , Lagartos/genética
8.
Zootaxa ; 3790: 439-50, 2014 Apr 22.
Artigo em Inglês | MEDLINE | ID: mdl-24869877

RESUMO

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.


Assuntos
Biodiversidade , Lagartos/anatomia & histologia , Animais , Ecossistema , Feminino , Lagartos/classificação , Lagartos/genética , Masculino , México , Análise de Componente Principal
9.
Syst Biol ; 63(2): 119-33, 2014 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-24262383

RESUMO

Current molecular methods of species delimitation are limited by the types of species delimitation models and scenarios that can be tested. Bayes factors allow for more flexibility in testing non-nested species delimitation models and hypotheses of individual assignment to alternative lineages. Here, we examined the efficacy of Bayes factors in delimiting species through simulations and empirical data from the Sceloporus scalaris species group. Marginal-likelihood scores of competing species delimitation models, from which Bayes factor values were compared, were estimated with four different methods: harmonic mean estimation (HME), smoothed harmonic mean estimation (sHME), path-sampling/thermodynamic integration (PS), and stepping-stone (SS) analysis. We also performed model selection using a posterior simulation-based analog of the Akaike information criterion through Markov chain Monte Carlo analysis (AICM). Bayes factor species delimitation results from the empirical data were then compared with results from the reversible-jump MCMC (rjMCMC) coalescent-based species delimitation method Bayesian Phylogenetics and Phylogeography (BP&P). Simulation results show that HME and sHME perform poorly compared with PS and SS marginal-likelihood estimators when identifying the true species delimitation model. Furthermore, Bayes factor delimitation (BFD) of species showed improved performance when species limits are tested by reassigning individuals between species, as opposed to either lumping or splitting lineages. In the empirical data, BFD through PS and SS analyses, as well as the rjMCMC method, each provide support for the recognition of all scalaris group taxa as independent evolutionary lineages. Bayes factor species delimitation and BP&P also support the recognition of three previously undescribed lineages. In both simulated and empirical data sets, harmonic and smoothed harmonic mean marginal-likelihood estimators provided much higher marginal-likelihood estimates than PS and SS estimators. The AICM displayed poor repeatability in both simulated and empirical data sets, and produced inconsistent model rankings across replicate runs with the empirical data. Our results suggest that species delimitation through the use of Bayes factors with marginal-likelihood estimates via PS or SS analyses provide a useful and complementary alternative to existing species delimitation methods.


Assuntos
Teorema de Bayes , Simulação por Computador , Iguanas/classificação , Filogenia , Animais , Iguanas/anatomia & histologia , Iguanas/genética , Cadeias de Markov , Método de Monte Carlo , Proteínas de Répteis/genética , Especificidade da Espécie
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