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Systematics of the Neopelminae (Aves: Passeriformes: Pipridae) with description of a new genus
Abstract
The genus Neopelma Sclater, 1860 contains five species of manakins found in humid tropical forests east of the Andes in South America. All five are cryptic in plumage and morphology. Neopelma chrysolophum Pinto, 1944 of SE Brazilian montane Atlantic Forests is so similar in appearance to the elevationally parapatric (Whitney et al. 1995) N. aurifrons Wied-Neuwied, 1831 occurring in lowland Atlantic Forest further north, that it was originally suggested to be a subspecies of the latter (Pinto 1944). In an examination of vocal data and habitat preference as well as morphology, Whitney et al. (1995) proposed that the genus Neopelma as currently defined is not monophyletic and hypothesized that N. aurifrons would be most closely related to the two species in Tyranneutes Sclater & Salvin, 1881. Capurucho et al. (2018) investigated the relationships in Neopelma and Tyranneutes and found that Neopelma was indeed paraphyletic. Their phylogenetic analysis indicated that Tyranneutes is nested within Neopelma, and that N. chrysolophum is sister to a clade containing Tyranneutes and the remainder of Neopelma. However, Capurucho et al. (2018) did not include N. aurifrons in their study and were therefore unable to conclusively settle on a proper taxonomic arrangement of the group. Capurucho et al. (2018) hypothesized that N. aurifrons would be sister to N. chrysolophum, based on biogeographical patterns and elevational replacement of N. aurifrons by N. chrysolophum. Harvey et al. (2020) included all species-level taxa of both Neopelma and Tyranneutes. Their topology was consistent with that of Capurucho et al. (2018), with Neopelma paraphyletic with respect to Tyranneutes. However, they found that Neopelma aurifrons is not sister to N. chrysolophum but instead represents the earliest divergence within the remaining Neopelma after the split with Tyranneutes. The paraphyly of Neopelma combined with the availability of information on all members of the genus provides an opportunity to revise taxonomy to better reflect evolutionary history. Tyranneutes is characterized by diminutive size, proportionally short tails, and differently structured vocalizations relative to Neopelma sensu lato (see below). They also prefer taller, more mature and more humid forest in general than Neopelma (Whitney et al. 1995). The two species of Tyranneutes are a morphologically, vocally, and ecologically coherent group, so we prefer to maintain them in a genus separate from other members of the complex. Resolving paraphyly therefore requires placement of Neopelma in two genera. Because aurifrons is the type species of Neopelma, a new genus name is required for N. chrysolophum:
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Functional traits offer a rich quantitative framework for developing and testing theories in evolutionary biology, ecology and ecosystem science. However, the potential of functional traits to drive theoretical advances and refine models of global change can only be fully realised when species-level information is complete. Here we present the AVONET dataset containing comprehensive functional trait data for all birds, including six ecological variables, 11 continuous morphological traits, and information on range size and location. Raw morphological measurements are presented from 90,020 individuals of 11,009 extant bird species sampled from 181 countries. These data are also summarised as species averages in three taxonomic formats, allowing integration with a global phylogeny, geographical range maps, IUCN Red List data and the eBird citizen science database. The AVONET dataset provides the most detailed picture of continuous trait variation for any major radiation of organisms, offering a global template for testing hypotheses and exploring the evolutionary origins, structure and functioning of biodiversity.
The White-crowned Manakin Pipra pipra was long considered congeneric with other members of the genus
Pipra, until Prum (1990, 1992, 1994) demonstrated that its display repertoire and syringeal morphology differ considerably from all other members of that genus. Subsequently, three different molecular phylogenies have all indicated that this manakin is more closely related to the genus Machaeropterus than to Pipra. Prum (1992) considered that the name Dixiphia Reichenbach, 1850, was available, and thus the combination Dixiphia pipra has since been in widespread use for this species. However, as first recognized more than 150 years ago, Dixiphia is a junior synonym of Arundinicola d’Orbigny, 1840. We show that no genus-group name is available for the manakin originally described as Parus pipra Linnaeus, 1758, and for which we therefore provide a new genus name.
Phylogenies are increasingly used in all fields of medical and biological research. Because of the next generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. We present ExaML version 3, a dedicated production-level code for inferring phylogenies on whole-transcriptome and whole-genome alignments using supercomputers.
We introduce several improvements and extensions to ExaML: Extensions of substitution models and supported data types, the integration of a novel load balance algorithm as well as a parallel I/O optimization that significantly improve parallel efficiency, and a production-level implementation for Intel MIC-based hardware platforms.
The code is available under GNU GPL at https://github.com/stamatak/ExaML.
Alexandros.Stamatakis@h-its.org.
© The Author(s) 2015. Published by Oxford University Press.
Ever larger phylogenies are being constructed due to the explosion of genetic data and development of high-performance phylogenetic reconstruction algorithms. However, most methods for calculating divergence times are limited to datasets that are orders of magnitude smaller than recently published large phylogenies. Here, we present an algorithm and implementation of a divergence time method using penalized likelihood that can handle datasets of thousands of taxa. We implement a method that combines the standard derivative-based optimization with a stochastic simulated annealing approach to overcome optimization challenges. We compare this approach with existing software including r8s, PATHd8 and BEAST.
Source code, example files, binaries and documentation for treePL are available at https://github.com/blackrim/treePL.
eebsmith@umich.edu
Supplementary data are available at Bioinformatics online.
Although massively parallel sequencing has facilitated large-scale DNA sequencing, comparisons among distantly related species rely upon small portions of the genome that are easily aligned. Methods are needed to efficiently obtain comparable DNA fragments prior to massively parallel sequencing, particularly for biologists working with non-model organisms. We introduce a new class of molecular marker, anchored by ultraconserved genomic elements (UCEs), that universally enable target enrichment and sequencing of thousands of orthologous loci across species separated by hundreds of millions of years of evolution. Our analyses here focus on use of UCE markers in Amniota because UCEs and phylogenetic relationships are well-known in some amniotes. We perform an in silico experiment to demonstrate that sequence flanking 2030 UCEs contains information sufficient to enable unambiguous recovery of the established primate phylogeny. We extend this experiment by performing an in vitro enrichment of 2386 UCE-anchored loci from nine, non-model avian species. We then use alignments of 854 of these loci to unambiguously recover the established evolutionary relationships within and among three ancient bird lineages. Because many organismal lineages have UCEs, this type of genetic marker and the analytical framework we outline can be applied across the tree of life, potentially reshaping our understanding of phylogeny at many taxonomic levels.
Diversity does not drive speciation
The role of the environment in the origin of new species has long been debated. Harvey et al. examined the evolutionary history and species diversity of suboscine birds in the tropics (see the Perspective by Morlon). Contrary to expectations that the tropics have higher rates of speciation, the authors observed that higher and more constant speciation rates occur in harsh environments relative to the tropics. Thus, for this group of birds, diversification in temperate to Arctic regions followed by the movement and retention of species in the tropics results in their higher local levels of species diversity.
Science , this issue p. 1343 ; see also p. 1268
Availability and implementation:
PHYLUCE is written for Python 2.7. PHYLUCE is supported on OSX and Linux (RedHat/CentOS) operating systems. PHYLUCE source code is distributed under a BSD-style license from https://www.github.com/faircloth-lab/phyluce/. PHYLUCE is also available as a package (https://binstar.org/faircloth-lab/phyluce) for the Anaconda Python distribution that installs all dependencies, and users can request a PHYLUCE instance on iPlant Atmosphere (tag: phyluce). The software manual and a tutorial are available from http://phyluce.readthedocs.org/en/latest/ and test data are available from doi: 10.6084/m9.figshare.1284521.
Contact:
brant@faircloth-lab.org SUPPLEMENTARY INFORMATION: Supplementary Figure 1.
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