Genomic data reveal a protracted window of introgression during the diversification of a neotropical woodcreeper radiation

The incidence of introgression during the diversification process and the timespan following divergence when introgression is possible are poorly understood in the neotropics where high species richness could provide extensive opportunities for genetic exchange. We used thousands of genome-wide SNPs to infer phylogenetic relationships, calculate ages of splitting, and to estimate the timing of introgression in a widespread avian neotropical genus of woodcreepers. Five distinct introgression events were reconstructed involving taxa classified both as subspecies and species including lineages descending from the basal-most split, dated to 7.3 million years ago. Introgression occurred between just a few hundred thousand to about 2.5 million years following divergence, suggesting substantial portions of the genome are capable of introgressing across taxa boundaries during a protracted time window of a few million years following divergence. Despite this protracted time window, we found that the proportion of the genome introgressing (6-11%) declines with the time of introgression following divergence, suggesting that the genome becomes progressively more immune to introgression as reproductive isolation increases.Peer reviewe

Description of the immature stages of Platycoelia puncticollis (Scarabaeidae: Rutelinae: Anoplognathini), DNA barcode and a key for the third instar larvae of the genus

Se describen la larva del tercer estadio y la pupa de Platycoelia puncticollis. Se presentan nuevos datos sobre la biología, genética y distribución de esta especie en Colombia y una clave para la identificación de las larvas del tercer estadio de las especies conocidas para el género Platycoelia Dejean (Coleoptera: Scarabaeidae). Se reporta, por primera vez para la especie, un fragmento de 658 pb del gen COI (código de barras de ADN) mitocondrial.The third instar larvae and the pupae of Platycoelia puncticollis are described. New data on the biology, genetics, and distribution of this species in Colombia are reported and a key to identification of third instar larvae of the known species of Platycoelia Dejean (Coleoptera: Scarabaeidae) is provided. A 658 bp fragment of the mitochondrial COI (DNA barcode) gene is reported for the first time for the species.Fil: Neita Moreno, Jhon. Instituto Alexander Von Humboldt; ColombiaFil: Castro Vargas, María Isabel. Instituto Alexander Von Humboldt; ColombiaFil: Ibarra Polesel, Mario Gabriel. Universidad Nacional del Nordeste. Facultad de Ciencias Exactas y Naturales y Agrimensura; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste; ArgentinaFil: Pulido Santacruz, Paola. Instituto Alexander Von Humboldt; Colombi

Protocolos de genómica para monitoreo ambiental asociado a acciones de respuesta por impacto o contingencia ambiental formalizados y listos para ser transferidos a usuarios interesados

En este documento se describen los aspectos más relevantes para aplicar la técnica de metabarcoding en estudios de biodiversidad. En la primera sección se realiza un recuento de los aspectos relevantes en el diseño experimental propios a la técnica. En la segunda se plantea una propuesta de protocolo para la aplicación del metabarcoding, incluyendo la toma de muestra, el procesamiento molecular y el procesamiento o depuración bioinformática. El diseño de muestreo y los análisis ecológicos no son incluidos desde que estos son totalmente contexto-dependientes. En la tercera sección se describe un estudio de caso usando metabarcoding en la caracterización de microorganismos de una zona altamente contaminada por actividades relacionadas a la extracción convencional de hidrocarburos. En la cuarta parte se realiza una revisión del potencial uso del metabarcoding en el monitoreo ambiental a través insectos. Finalmente, en la quinta y última parte se exponen algunas de las perspectivas y limitaciones del uso de la técnica en Colombia. El objetivo de este documento es fomentar el uso de esta herramienta en escenarios colombianos, generando datos cuantitativos de diversidad que puedan ser incluidos en la toma de decisiones.Bogotá, ColombiaPrograma de Ciencias de la Biodiversida

Aves del Parque Nacional Natural Chingaza y zona de amortiguación, Cordillera Oriental de Colombia

We describe the bird species composition in the Chingaza National Park and its buffer zone, based on a revision of 10 published studies, recent fieldwork between 2008-2017, and the Colombia Bio expedition on 2018. We report 531 species for the Chingaza National Park and its buffer zone, grouped in 339 genera and 57 families. Six species are endemic to Colombia, 14 are near-endemic, 1 is critically endangered, 6 are endangered, 4 are vulnerable, 3 are near-threatened and 37 are migratory. This list includes 149 species more than those comprised in previous information from published datasets and ornithological collections. Additionally, we generated genetic barcodes, based sequences of the mtDNA gene COI, for 74 species, and present the first genetic record from Colombia in Barcode of Life Datasystems (BOLD) for Dysithamnus leucostictus, Chamaeza turdina, Rupicola peruvianus, Atlapetes semirufus, Euphonia mesochrysa and Chlorospingus flavopectus olsoni. This list is a tool to promote the study and conservation of birds in this area of the Colombian Eastern Cordillera.Describimos la composición de especies de aves del Parque Nacional Natural (PNN) Chingaza y su zona de amortiguación, a partir de la revisión de 10 estudios ornitológicos, trabajo de campo entre 2008–2017 y la expedición Colombia Bio en 2018. Reportamos para el PNN Chingaza y su zona de amortiguación un total de 531 especies, agrupadas en 339 géneros y 57 familias. Seis especies presentes en el parque son endémicas de Colombia, 14 casi endémicas, 1 en peligro crítico, 6 en peligro, 4 vulnerables, 3 casi amenazadas y 37 migratorias. Esta lista incluye 149 especies adicionales a la información previamente conocida por datos publicados y colecciones ornitológicas. Adicionalmente, generamos códigos de barras genéticos, con base en secuencias del gen mitocondrial COI, para 74 especies y presentamos los primeros registros genéticos de Colombia en la plataforma para códigos de barra genéticos Barcode of Life Datasystems (BOLD) para Dysithamnus leucostictus, Chamaeza turdina, Rupicola peruvianus, Atlapetes semirufus, Euphonia mesochrysa y Chlorospingus flavopectus olsoni.  El presente listado es una herramienta para incentivar el estudio y conservación de las aves en este sector de la Cordillera Oriental colombiana

Las cercas vivas : herramienta clave para la conservación de la biodiversidad en un paisaje rural de la cordillera central de los Andes Colombianos

Las cercas vivas son elementos del paisaje rural que han recibido una atención especial por el papel que desempeñan en los sistemas productivos y la función que pueden desarrollar para el mantenimiento de la diversidad nativa de plantas y animales. En este estudio se evaluó el efecto de la composición florística, estructura y contexto espacial en el que se encuentran las cercas vivas, sobre el uso y la riqueza de la comunidad de aves, en el Municipio de Aranzazu, Caldas, Colombia.Live fences are elements in rural landscapes that have received particular attention due to the role that they play in productive systems and their importance for native biodiversity maintenance. The effect of live fence attributes such as floristic composition, structure, and connection to forest fragments on bird species richness and use of fences was evaluated in a study area located in the municipality of Aranzazu, Caldas, Colombia.Biólogo (a)Pregrad

Diversidade cr?ptica e diverg?ncia profunda no tapaculo preto Scytalopus speluncae (Aves: Rhinocryptidae)

Made available in DSpace on 2015-04-14T13:09:25Z (GMT). No. of bitstreams: 1 431115.pdf: 40111 bytes, checksum: 341f5e66198379e8e905a199036cafa5 (MD5) Previous issue date: 2011-03-28A Mata Atl?ntica abriga uma das maiores riquezas de esp?cies de aves do mundo, mas at? agora, pouco ? conhecido sobre seus padr?es espaciais de diversidade gen?tica e sua hist?ria evolutiva neste bioma. Utilizando-se de dados de sequ?ncias de genes mitocondriais (Cyt b e ND2), foi estimada a hist?ria evolutiva e populacional do complexo Scytalopus speluncae de 56 localidades ao longo de toda sua distribui??o na Mata Atl?ntica. Os resultados mostram que S. speluncae ? um complexo de pelo menos sete linhagens cr?pticas, alop?tricas e bem suportadas, que se originaram no Pleistoceno Tardio e M?dio. O padr?o filogeogr?fico do grupo ? amplamente concordante com a hip?tese dos ref?gios est?veis e antigos da parte norte da Mata Atl?ntica. Ao mesmo tempo, os resultados refutam o cen?rio de n?opersist?ncia ao longo dos ciclos glaciais nos ref?gios da parte sul, que por este cen?rio teriam sido colonizados muito recentemente por popula??es do norte. Al?m disso, a diversifica??o em S. speluncae mostrou-se muito maior do que era previsto atrav?s de an?lises fenot?picas, sugerindo um elevado n?vel de diverg?ncia e isolamento entre algumas linhagens. A exist?ncia de tais linhagens distintas que podem at? representar esp?cies diferentes, portanto, implica que a conserva??o de cada linhagem deve ser avaliada de forma independent

Dynamics of Speciation in Neotropical Birds: Diversification Rates, Introgression and Reproductive Isolation

Tropical rainforests â covering 7% of the earth's surface â are areas of exceptionally high biodiversity compared to other ecosystems. However, no consensus has been reached as to the primal cause of high tropical diversity. In this thesis, I used a combination of phylogenetic and population genetic methods to address whether speciation is an important driver of diversification patterns and to determine the genetic architecture of reproductive isolation and the frequency of introgression during the diversification process in the species-rich Neotropics. I developed and fit a character-state dependent diversification model to a global avian phylogeny and found consistent support across replicate clades for extinction as a key driver of species richness gradients. In contrast, an association between speciation or dispersal rates with species richness was not consistently found. To better understand the process of speciation in the tropics, I studied reproductive isolation in two genera of suboscine birds. My results showed that pre-zygotic reproductive barriers play a less important role in the tropical speciation process than at high latitudes, with reproductive isolation driven largely by post-zygotic genetic incompatibilities. I also found evidence of frequent introgression events during the diversification process in the Neotropical genus Dendrocincla. My analyses showed different instances of historical introgression events among closely and distantly related lineages of Dendrocincla, demonstrating that introgression may often be a common phenomenon during the diversification process in the Neotropics. These results contribute to our understanding of the evolutionary processes that drive diversification and how speciation evolves in areas of high species richness.Ph.D.2019-11-06 00:00:0

Diversidade críptica e divergência profunda no tapaculo preto Scytalopus speluncae (Aves: Rhinocryptidae)

A Mata Atlântica abriga uma das maiores riquezas de espécies de aves do mundo, mas até agora, pouco é conhecido sobre seus padrões espaciais de diversidade genética e sua história evolutiva neste bioma. Utilizando-se de dados de sequências de genes mitocondriais (Cyt b e ND2), foi estimada a história evolutiva e populacional do complexo Scytalopus speluncae de 56 localidades ao longo de toda sua distribuição na Mata Atlântica. Os resultados mostram que S. speluncae é um complexo de pelo menos sete linhagens crípticas, alopátricas e bem suportadas, que se originaram no Pleistoceno Tardio e Médio. O padrão filogeográfico do grupo é amplamente concordante com a hipótese dos refúgios estáveis e antigos da parte norte da Mata Atlântica. Ao mesmo tempo, os resultados refutam o cenário de nãopersistência ao longo dos ciclos glaciais nos refúgios da parte sul, que por este cenário teriam sido colonizados muito recentemente por populações do norte. Além disso, a diversificação em S. speluncae mostrou-se muito maior do que era previsto através de análises fenotípicas, sugerindo um elevado nível de divergência e isolamento entre algumas linhagens. A existência de tais linhagens distintas que podem até representar espécies diferentes, portanto, implica que a conservação de cada linhagem deve ser avaliada de forma independente.The Brazilian Atlantic Forest harbors one of the world´s highest bird species richness, but to date there is a deficient understanding of the spatial patterns of genetic diversity and the evolutionary history of this biome. Here we estimated the phylogenetic and populational history of the wide-spread mouse-colored Tapaculo Scytalopus speluncae complex from 56 localities throughout its range across the Atlantic Forest, using data from two mitochondrial gene sequences (Cyt b and ND2). Our findings uncover at least seven cryptic, allopatric and well-supported lineages within S. speluncae that have originated in Early to Middle Pleistocene. Its phylogeographic pattern is broadly concordant with the hypothesis of more stable and ancient refugia in the northern region. At the same time our results refuted the scenario of non-persistence throughout glacial cycles of southern Atlantic Forest refugia in which they would have been very recently colonized from northern areas. Our results shown cryptic diversification in S. speluncae much higher than could be suspected by phenotypic analysis and suggest the high level of divergence and isolation among some lineages reflect potential species-level differences. The existence of such distinct lineages that could even represent different species suggests that the conservation of these lineages must be accessed in an independent way

Data from: Extinction as a driver of avian latitudinal diversity gradients

The role of historical factors in driving latitudinal diversity gradients is poorly understood. Here we used an updated global phylogeny of terrestrial birds to test the role of three key historical factors – speciation, extinction and dispersal rates – in generating latitudinal diversity gradients for eight major clades. We fit a model that allows speciation, extinction and dispersal rates to differ, both with latitude and between the New and Old World. Our results consistently support extinction (all clades had lowest extinction where species richness was highest) as a key driver of species richness gradients across each of eight major clades. In contrast, speciation and dispersal rates showed no consistent latitudinal patterns across replicate bird clades, and thus are unlikely to represent general underlying drivers of latitudinal diversity gradients

A new species of Caecilia (Gymnophiona, Caeciliidae) from the Magdalena valley region of Colombia

A new species of the genus Caecilia (Caeciliidae) from the western foothills of the Serranía de los Yariguíes in Colombia is described. Caecilia pulchraserrana sp. nov. is similar to C. degenerata and C. corpulenta but differs from these species in having fewer primary annular grooves and a shorter body length. With this new species, the currently recognized species in the genus are increased to 35. Mitochondrial DNA sequences, including newly sequenced terminals representing two additional, previously unanalyzed species, corroborate the phylogenetic position of the new species within Caecilia and the monophyly of the genus. This analysis also included newly sequenced terminals of Epicrionops aff. parkeri (Rhinatrematidae) and trans-Andean Microcaecilia nicefori (Siphonopidae). Evidence was found for the non-monophyly of the family Siphonopidae and the siphonopid genera Microcaecilia and Siphonops. The implications of these results for caecilian systematics are discussed and the status of the trans-Andean populations of Caecilia degenerata is commented upon