Tarphonomus, a new genus of ovenbird (Aves: Passeriformes: Furnariidae) from South America

Tarphonomus, a new genus of ovenbird (Aves: Passeriformes: Furnariidae) from South America, is described. Species included in the new genus, formerly placed in Upucerthia, are T. certhioides and T. harterti

Genomic insights into adaptation to high-altitude environments

Elucidating the molecular genetic basis of adaptive traits is a central goal of evolutionary genetics. The cold, hypoxic conditions of high-altitude habitats impose severe metabolic demands on endothermic vertebrates, and understanding how high-altitude endotherms cope with the combined effects of hypoxia and cold can provide important insights into the process of adaptive evolution. The physiological responses to high-altitude stress have been the subject of over a century of research, and recent advances in genomic technologies have opened up exciting opportunities to explore the molecular genetic basis of adaptive physiological traits. Here, we review recent literature on the use of genomic approaches to study adaptation to high-altitude hypoxia in terrestrial vertebrates, and explore opportunities provided by newly developed technologies to address unanswered questions in high-altitude adaptation at a genomic scale. © 2012 Macmillan Publishers Limited All rights reserved

A Reference Genome For The Nectar-Robbing Black-Throated Flowerpiercer (Diglossa Brunneiventris)

Black-throated Flowerpiercers (Diglossa brunneiventris) are one species representing a phenotypically specialized group of tanagers (Thraupidae) that have hooked bills which allow them to feed by stealing nectar from the base of flowers. Members of the genus are widely distributed in montane regions from Mexico to northern Argentina, and previous studies of Diglossa have focused on their systematics, phylogenetics, and interesting natural history. Despite numerous studies of species within the genus, no genome assembly exists to represent these nectivorous tanagers. We described the assembly of a genome sequence representing a museum-vouchered, wild, female D. brunneiventris collected in Peru. By combining Pacific Biosciences Sequel long-read technology with 10x linked-read and reference-based scaffolding, we produced a 1.08 Gbp pseudochromosomal assembly including 600 scaffolds with a scaffold N50 of 67.3 Mbp, a scaffold L50 of 6, and a BUSCO completeness score of 95%. This new assembly improves representation of the diverse species that comprise the tanagers, improves on scaffold lengths and contiguity when compared to existing genomic resources for tanagers, and provides another avenue of research into the genetic basis of adaptations common to a nectivorous lifestyle among vertebrates

Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis

The multi-species coalescent provides an elegant theoretical framework for estimating species trees and species demographics from genetic markers. Practical applications of the multi-species coalescent model are, however, limited by the need to integrate or sample over all gene trees possible for each genetic marker. Here we describe a polynomial-time algorithm that computes the likelihood of a species tree directly from the markers under a finite-sites model of mutation, effectively integrating over all possible gene trees. The method applies to independent (unlinked) biallelic markers such as well-spaced single nucleotide polymorphisms (SNPs), and we have implemented it in SNAPP, a Markov chain Monte-Carlo sampler for inferring species trees, divergence dates, and population sizes. We report results from simulation experiments and from an analysis of 1997 amplified fragment length polymorphism (AFLP) loci in 69 individuals sampled from six species of {\em Ourisia} (New Zealand native foxglove)

Andean Land Use And Biodiversity: Humanized Landscapes In A Time Of Change

Some landscapes Cannot be understood without reference., to the kinds. degrees, kinds, degrees, and history of human-caused modifications to the Earth's surface. The tropical latitudes of the Andes represent one such place, with agricultural land-use systems appearing in the Early Holocene. Current land use includes both intensive and extensive grazing and crop- or tree-based agricultural systems found across virtually the, entire range of possible elevations and humidity regimes. Biodiversity found in or adjacent to such humanized landscapes will have been altered in abundance. composition, and distribution in relation to the resiliency of the native Species to harvest, hold cover modifications, and other deliberate or inadvertent human land uses. In addition, the geometries of land cover, resulting flout difference among the shapes, sizes, connectivities, and physical structures of the patches, corridors, and matrices that compose landscape mosaics, will constrain biodiversity, often in predictable ways. This article proposes a conceptual model that alter ins that the Continued persistence of native species may depend as much oil the shifting Of Andean landscape mosaics as on species characteristics, themselves. Furthermore, mountains such as the Andes display long gradients of environmental Conditions that after in relation to latitude, soil moisture, aspect, and elevation. Global environmental change will shift these, especially temperature and humidity regimes along elevational gradients, causing Changes outside the historical range of variation for some species. Both land-use systems and Conservation efforts will need to respond spatially to these shifts in the future, at both landscape and regional scales.Geography and the Environmen

Phylogeny and phylogenetic classification of the antbirds, ovenbirds, woodcreepers, and allies (Aves: Passeriformes: Infraorder Furnariides)

The infraorder Furnariides is a diverse group of suboscine passerine birds comprising a substantial component of the Neotropical avifauna. The included species encompass a broad array of morphologies and behaviours, making them appealing for evolutionary studies, but the size of the group (ca. 600 species) has limited well-sampled higher-level phylogenetic studies. Using DNA sequence data from the nuclear RAG-1 and RAG-2 exons, we undertook a phylogenetic analysis of the Furnariides sampling 124 (more than 88%) of the genera. Basal relationships among family-level taxa differed depending on phylogenetic method, but all topologies had little nodal support, mirroring the results from earlier studies in which discerning relationships at the base of the radiation was also difficult. In contrast, branch support for family-rank taxa and for many relationships within those clades was generally high. Our results support the Melanopareidae and Grallariidae as distinct from the Rhinocryptidae and Formicariidae, respectively. Within the Furnariides our data contradict some recent phylogenetic hypotheses and suggest that further study is needed to resolve these discrepancies. Of the few genera represented by multiple species, several were not monophyletic, indicating that additional systematic work remains within furnariine families and must include dense taxon sampling. We use this study as a basis for proposing a new phylogenetic classification for the group and in the process erect new family-group names for clades having high branch support across methods. © 2009 The Willi Hennig Society

Epinecrophylla, a new genus of antwrens (Aves: Passeriformes: Thamnophilidae)

We offer a new generic name for the stipple-throated assemblage of antwrens (Thamnophilidae) currently placed in the genus Myrmotherula. Molecular studies demonstrated that Myrmotherula is polyphyletic, with the stippled-throated group forming a clade that is not sister to any other currently recognized Myrmotherula species. The stipple-throated assemblage is distinguished morphologically by at least one sex having a black throat stippled white or buffy white combined with a comparatively long, unmarked tail, although three populations considered subspecies have lost one of these characters. The distinct evolution of this assemblage is supported by diagnostic behavioral characters derived from foraging behaviors, vocal repertoires, and nest architecture