Espécies crípticas em Pagamea coriacea sensu lato (Rubiaceae): evidências morfológicas, ecológicas e de comportamento reprodutivo em um contexto simpátrico

In this study we explore morphological and ecological variation in sympatric populations of Pagamea coriacea s.l. - a species complex from white-sand vegetation in the Amazon. A total of 147 trees were sampled and monitored at three nearby sites in Central Amazon, Brazil. Multivariate analyses of morphology indicated two distinct groups (A and B), which also differed in bark type, each containing subgroups associated with sexual dimorphism. However, a single hermaphroditic individual was observed within group B. As expected, all pistillate plants produced fruits, but 23% of the staminate plants of group B, and 5% of group A also produced fruits. This variation suggests that the sexual systems of both groups are between dioecy and gynodioecy. There was an overlap in flowering phases between the two groups, but the pattern of floral maturation differed. Ecologically, plants of group B were found in more shaded habitats and over sandstone bedrocks, while group A was prevalent in deeper sandy soils as canopy plants. The significances of morphological and environmental differences were tested by a multivariate analysis of variance, and a canonical discriminant analysis assessed the importance of variables. The coexistence in sympatry of two discrete morphological groups in the P. coriacea s.l., with different habitat preferences and reproductive behaviors, indicates they represent distinct species.O objetivo deste estudo foi testar se o complexo de espécies Pagamea coriacea inclui múltiplas espécies, usando evidências morfológicas, ecológicas e de comportamento reprodutivo. Um total de 147 árvores foram amostradas e monitoradas em três locais próximos na Amazônia Central, Brasil. Análises multivariadas de dados morfológicos indicaram dois grupos discretos (A e B), que coincidem com diferenças no tipo de casca, cada um por sua vez com subgrupos que representam dimorfismo sexual. Contudo, um indivíduo distintamente hermafrodita foi encontrado no grupo B. Todas as plantas pistiladas produziram frutos, mas também foram observados frutos para 23% das plantas estaminadas do grupo B, e para 5% das estaminadas do grupo A. Essa variação sugere que ambos grupos possuem um sistema sexual entre dioicia e ginodioicia. Houve sobreposição das fases de floração e frutificação entre os dois grupos, mas o padrão de maturação de flores foi diferente. Quanto ao hábitat, o grupo B predominou em situações de sombra e em solos arenosos rasos sobre lajes de pedra, enquanto o grupo A ocorreu em solos arenosos mais profundos e no dossel da vegetação. A coexistência de dois grupos morfológicos discretos no complexo P. coriacea s.l., com diferenças ecológicas e de comportamento reprodutivo, indica que correspondem a duas espécies distintas

Two waves of diversification in mammals and reptiles of Baja California revealed by hierarchical Bayesian analysis

Many species inhabiting the Peninsular Desert of Baja California demonstrate a phylogeographic break at the mid-peninsula, and previous researchers have attributed this shared pattern to a single vicariant event, a mid-peninsular seaway. However, previous studies have not explicitly considered the inherent stochasticity associated with the gene-tree coalescence for species preceding the time of the putative mid-peninsular divergence. We use a Bayesian analysis of a hierarchical model to test for simultaneous vicariance across co-distributed sister lineages sharing a genealogical break at the mid-peninsula. This Bayesian method is advantageous over traditional phylogenetic interpretations of biogeography because it considers the genetic variance associated with the coalescent and mutational processes, as well as the among-lineage demographic differences that affect gene-tree coalescent patterns. Mitochondrial DNA data from six small mammals and six squamate reptiles do not support the perception of a shared vicariant history among lineages exhibiting a north–south divergence at the mid-peninsula, and instead support two events differentially structuring genetic diversity in this region

Evaluación empírica de un protocolo para el ensamble de datos genómicos obtenidos mediante ddRADseq

La secuenciación de fragmentos de ADN asociado a fragmentos de restricción (RADseq) está siendo cada vez más empleada en estudios poblacionales y filogenéticos puesto que permite la obtención de cientos a miles de loci, lo que es ventajoso en situaciones en donde los marcadores tradicionalmente empleados arrojan resultados ambiguos. Sin embargo, la robustez de las inferencias realizadas depende de un cuidadoso procesamiento bioinformático de los datos (ej. remoción de regiones parálogas). Un desafío metodológico clave es determinar el porcentaje de similitud a partir del cual dos alelos son considerados homólogos y por ende son agrupados en el mismo locus (umbral de similitud). Este umbral define la divergencia máxima permitida entre variantes alélicas y la divergencia mínima entre posibles parálogos, y por ende es central para los análisis posteriores. En este trabajo pusimos a prueba un conjunto de métricas para determinar los umbrales de similitud entre secuencias que maximizan la remoción correcta de regiones parálogas, y minimizan la separación incorrecta de variantes alélicas distantes en diferentes loci. Para ello se ensamblaron loci empleando diferentes valores de este parámetro y se observaran atributos tales como: número de regiones parálogas identificadas, número de SNPs recuperados, proporción de heterocigosis, variabilidad explicada, correlación entre divergencia genética y falta de datos y resolución filogenética. Probamos este enfoque en un conjunto de datos genómicos de lagartijas del grupo Liolaemus kingii obtenidos mediante ddRADseq. Las métricas infieren un patrón de aproximadamente 90% de similitud entre alelos del mismo loci, como un umbral por encima del cual la divergencia genética y la falta de datos se correlacionan de manera creciente. Este protocolo posibilita una selección objetiva de parámetros, a la vez que es aplicable a cualquier sistema biológico tanto modelo como no modelo (cuando no se dispone de un genoma de referenciaFil: Sánchez, Kevin Imanol. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico para el Estudio de los Ecosistemas Continentales; ArgentinaFil: Avila, Luciano J.. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico para el Estudio de los Ecosistemas Continentales; ArgentinaFil: Sites Jr., J. W.. University Brigham Young; Estados UnidosFil: Leaché, A.D.. University of Washington; Estados UnidosFil: Morando, Mariana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico para el Estudio de los Ecosistemas Continentales; Argentina9na Jornada de Becarios y 1er Encuentro Patagónico de BecariosPuerto MadrynArgentinaCentro Nacional Patagónic

Species Delimitation using Genome-Wide SNP Data

The multispecies coalescent has provided important progress for evolutionary inferences, including increasing the statistical rigor and objectivity of comparisons among competing species delimitation models. However, Bayesian species delimitation methods typically require brute force integration over gene trees via Markov chain Monte Carlo (MCMC), which introduces a large computation burden and precludes their application to genomic-scale data. Here we combine a recently introduced dynamic programming algorithm for estimating species trees that bypasses MCMC integration over gene trees with sophisticated methods for estimating marginal likelihoods, needed for Bayesian model selection, to provide a rigorous and computationally tractable technique for genome-wide species delimitation. We provide a critical yet simple correction that brings the likelihoods of different species trees, and more importantly their corresponding marginal likelihoods, to the same common denominator, which enables direct and accurate comparisons of competing species delimitation models using Bayes factors. We test this approach, which we call Bayes factor delimitation (*with genomic data; BFD*), using common species delimitation scenarios with computer simulations. Varying the numbers of loci and the number of samples suggest that the approach can distinguish the true model even with few loci and limited samples per species. Misspecification of the prior for population size θ has little impact on support for the true model. We apply the approach to West African forest geckos (Hemidactylus fasciatus complex) using genome-wide SNP data. This new Bayesian method for species delimitation builds on a growing trend for objective species delimitation methods with explicit model assumptions that are easily tested. [Bayes factor; model testing; phylogeography; RADseq; simulation; speciation.

Resolving complex phylogeographic patterns in the Balkan Peninsula using closely related wall-lizard species as a model system

The Balkan Peninsula constitutes a biodiversity hotspot with high levels of species richness and endemism. The complex geological history of the Balkans in conjunction with the climate evolution are hypothesized as the main drivers generating this biodiversity. We investigated the phylogeography, historical demography, and population structure of closely related wall-lizard species from the Balkan Peninsula and southeastern Europe to better understand diversification processes of species with limited dispersal ability, from Late Miocene to the Holocene. We used several analytical methods integrating genome-wide SNPs (ddRADseq), microsatellites, mitochondrial and nuclear DNA data, as well as species distribution modelling. Phylogenomic analysis resulted in a completely resolved species level phylogeny, population level analyses confirmed the existence of at least two cryptic evolutionary lineages and extensive within species genetic structuring. Divergence time estimations indicated that the Messinian Salinity Crisis played a key role in shaping patterns of species divergence, whereas intraspecific genetic structuring was mainly driven by Pliocene tectonic events and Quaternary climatic oscillations. The present work highlights the effectiveness of utilizing multiple methods and data types coupled with extensive geographic sampling to uncover the evolutionary processes that shaped the species over space and time. © 2018 Elsevier Inc