Fábio Raposo do Amaral

Out of Amazonia again and again: episodic crossing of the Andes promotes diversification in a lowland forest flycatcher

Most Neotropical lowland forest taxa occur exclusively on one side of the Andes despite the availability of appropriate habitat on both sides. Almost all molecular phylogenies and phylogenetic analyses of species assemblages (i.e. area cladograms) have supported the hypothesis that Andean uplift during the Late Pliocene created a vicariant barrier affecting lowland lineages in the region. However, a few widespread plant and animal species occurring in lowland forests on both sides of the Andes challenge the generality of this hypothesis. To understand the role of the Andes in the history of such organisms, we reconstructed the phylogeographic history of a widespread Neotropical flycatcher (Mionectes oleagineus) in the context of the other four species in the genus. A molecular phylogeny based on nuclear and mitochondrial sequences unambiguously showed an early basal split between montane and lowland Mionectes. The phylogeographic reconstruction of lowland taxa revealed a complex history, with multiple cases in which geographically proximate populations do not represent sister lineages. Specifically, three populations of M. oleagineus west of the Andes do not comprise a monophyletic clade; instead, each represents an independent lineage with origins east of the Andes. Divergence time estimates suggest that at least two cross-Andean dispersal events post-date Andean uplift.

Multilocus tests of Pleistocene refugia and ancient divergence in a pair of Atlantic Forest antbirds (Myrmeciza)

The Atlantic Forest (AF) harbours one of the most diverse vertebrate faunas of the world, including 199 endemic species of birds. Understanding the evolutionary processes behind such diversity has become the focus of many recent, primarily single locus, phylogeographic studies. These studies suggest that isolation in forest refugia may have been a major mechanism promoting diversification, although there is also support for a role of riverine and geotectonic barriers, two sets of hypotheses that can best be tested with multilocus data. Here we combined multilocus data (one mtDNA marker and eight anonymous nuclear loci) from two species of parapatric antbirds, Myrmeciza loricata and M. squamosa, and Approximate Bayesian Computation to determine whether isolation in refugia explains current patterns of genetic variation and their status as independent evolutionary units. Patterns of population structure, differences in intraspecific levels of divergence and coalescent estimates of historical demography fit the predictions of a recently proposed model of refuge isolation in which climatic stability in the northern AF sustains higher diversity and demographic stability than in the southern AF. However, a pre‐Pleistocene divergence associated with their abutting range limits in a region of past tectonic activity also suggests a role for rivers or geotectonic barriers. Little or no gene flow between these species suggests the development of reproductive barriers or competitive exclusion. Our results suggests that limited marker sampling in recent AF studies may compromise estimates of divergence times and historical demography, and we discuss the effects of such sampling on this and other studies.

Patterns and processes of diversification in a widespread and ecologically diverse avian group, the buteonine hawks (Aves, Accipitridae).

Buteonine hawks represent one of the most diverse groups in the Accipitridae, with 58 species distributed in a variety of habitats on almost all continents. Variations in migratory behavior, remarkable dispersal capability, and unusual diversity in Central and South America make buteonine hawks an excellent model for studies in avian evolution. To evaluate the history of their global radiation, we used an integrative approach that coupled estimation of the phylogeny using a large sequence database (based on 6411 bp of mitochondrial markers and one nuclear intron from 54 species), divergence time estimates, and ancestral state reconstructions. Our findings suggest that Neotropical buteonines resulted from a long evolutionary process that began in the Miocene and extended to the Pleistocene. Colonization of the Nearctic, and eventually the Old World, occurred from South America, promoted by the evolution of seasonal movements and development of land bridges. Migratory behavior evolved several times and may have contributed not only to colonization of the Holarctic, but also derivation of insular species. In the Neotropics, diversification of the buteonines included four disjunction events across the Andes. Adaptation of monophyletic taxa to wet environments occurred more than once, and some relationships indicate an evolutionary connection among mangroves, coastal and várzea environments. On the other hand, groups occupying the same biome, forest, or open vegetation habitats are not monophyletic. Refuges or sea-level changes or a combination of both was responsible for recent speciation in Amazonian taxa. In view of the lack of concordance between phylogeny and classification, we propose numerous taxonomic changes.

Ultraconserved Elements Sequencing as a Low-Cost Source of Complete Mitochondrial Genomes and Microsatellite Markers in Non-Model Amniotes.

Sequence capture of ultraconserved elements (UCEs) associated with massively parallel sequencing has become a common source of nuclear data for studies of animal systematics and phylogeography. However, mitochondrial and microsatellite variation are still commonly used in various kinds of molecular studies, and probably will complement genomic data in years to come. Here we show that besides providing abundant genomic data, UCE sequencing is an excellent source of both sequences for microsatellite loci design and complete mitochondrial genomes with high sequencing depth. Identification of dozens of microsatellite loci and assembly of complete mitogenomes is exemplified here using three species of Poospiza warbling finches from southern and southeastern Brazil. This strategy opens exciting opportunities to simultaneously analyze genome-wide nuclear datasets and traditionally used mtDNA and microsatellite markers in non-model amniotes at no additional cost.

NEW LOCALITIES FOR THE BLACK-FACED HAWK (LEUCOPTERNIS MELANOPS) SOUTH OF THE AMAZON RIVER AND DESCRIPTION OF THE IMMATURE PLUMAGE OF THE WHITE-BROWED HAWK (LEUCOPTERNIS KUHLI)

Abstract The Black-faced Hawk (Leucopternis melanops) and White-browed Hawk (L. kuhli) are forest-based, Amazonian raptors whose distributions have been considered to be mutually exclusive north and south of the Amazon River, respectively. The occurrence of L. melanops south of the river was first indicated by a specimen collected by A. M. Olalla on the lower Tapajós River >70 years ago. The provenience of this specimen has been contested by diverse authors but both species were recently captured at localities along the lower Tapajós, corroborating the coexistence of L. melanops and L. kuhli in this region. We present four new specimen localities for L. melanops in southern Amazonia, greatly amplifying its known distribution. We also describe the immature plumage of L. kuhli based on three specimens that had been identified as L. melanops.

The “Atlantis Forest hypothesis” does not explain Atlantic Forest phylogeography

Leite et al. (1) conclude that isolation according to the forest refuge hypothesis (FRH) may have had a minor, if any, role on Atlantic Forest (AF) biotic evolution based on genetic data from five mammal species. Their evidence comes from signatures of population expansion during both glacial and interglacial periods, and fragmentation of reconstructed distributions during interglacial periods. Despite its novelty (i.e., the influence of sea-level changes in AF phylogeography), Leite et al.’s study presents many issues that need a critical appraisal. First, analyses based on a single locus are prone to stochastic error and often lack sufficient variation for detecting historical processes, such as bottlenecks and shallow population structure, which are key in contrasting refugium vs. nonrefugium hypotheses. Leite et al.’s (1 … [↵][1]1To whom correspondence should be addressed. Email: fabioraposo{at}gmail.com. [1]: #xref-corresp-1-1

Phenotypic and Genetic Structure Support Gene Flow Generating Gene Tree Discordances in an Amazonian Floodplain Endemic Species

Abstract Before populations become independent evolutionary lineages, the effects of micro evolutionary processes tend to generate complex scenarios of diversification that may affect phylogenetic reconstruction. Not accounting for gene flow in species tree estimates can directly impact topology, effective population sizes and branch lengths, and the resulting estimation errors are still poorly understood in wild populations. In this study, we used an integrative approach, including sequence capture of ultra‐conserved elements (UCEs), mtDNA Sanger sequencing and morphological data to investigate species limits and phylogenetic relationships in face of gene flow in an Amazonian endemic species (Myrmoborus lugubris: Aves). We used commonly implemented species tree and model‐based approaches to understand the potential effects of gene flow in phylogenetic reconstructions. The genetic structure observed was congruent with the four recognized subspecies of M. lugubris. Morphological and UCEs data supported the presence of a wide hybrid zone between M. l. femininus from the Madeira river and M. l. lugubris from the Middle and lower Amazon river, which were recovered as sister taxa by species tree methods. When fitting gene flow into simulated demographic models with different topologies, the best‐fit model indicated these two taxa as non‐sister lineages, a finding that is in agreement with the results of mitochondrial and morphological analyses. Our results demonstrated that failing to account for gene flow when estimating phylogenies at shallow divergence levels can generate topological uncertainty, which can nevertheless be statistically well supported, and that model testing approaches using simulated data can be useful tools to test alternative phylogenetic hypotheses.

Eight anonymous nuclear loci for the squamate antbird ( Myrmeciza squamosa ), cross-amplifiable in other species of typical antbirds (Aves, Thamnophilidae)

Typical antbirds (~209 species) represent a diverse radiation of Neotropical birds that includes many species of conservation concern. Here we present eight anonymous nuclear loci designed for the squamate antbird Myrmeciza squamosa, a species endemic to the Atlantic Forest of Brazil. We also show that those anonymous nuclear loci are amplifiable in a number of other typical antbird species from related genera (Myrmeciza, Percnostola, Gymnocichla, Myrmoborus, Pyriglena and Formicivora), including three threatened species (Myrmeciza ruficauda, Formicivora littoralis, and Pyriglena atra). Those markers will be useful not only to help management of threatened species of typical antbirds, but also to explore their evolutionary histories, both at intra and interspecific levels.

Towards an assessment of character interdependence in avian RNA phylogenetics: A general secondary structure model for the avian mitochondrial 16S rRNA

RNA has been a major source of information for animal phylogenetics for 20 years (see early examples in Carmean et al., 1992; Hillis and Dixon, 1989). Avian phylogenetics has benefited from comparisons of RNA in studies of a wide range of taxa at varying hierarchical levels. These comparisons have focused particularly on mitochondrial rRNA (i.e., 12S and 16S) and tRNA genes (e.g., Houde et al., 1997; Pereira et al., 2007; Tavares et al., 2006). The power of RNA genes as sources of phylogenetic information derives from their heterogeneous rates of evolution in different structural regions, which have the potential to resolve both recent and early phylogenetic events. In eukaryotes, the base-pairing regions of rRNA, or stems, evolve more slowly than loops, which are nonbase-pairing regions (Smit et al., 2007). Base-pairing patterns in RNA reflect complex secondary structures that consist of adjacent and anti-parallel Watson–Crick strands and G–U base-pairs (Brown and Ellis, 2005). Evolution of paired bases in RNA stems occurs, in part, via compensatory nucleotide changes, i.e., substitutions that maintain or restore base pairing following a base change on a complementary strand (Dixon and Hillis, 1993). This structural constraint has important consequences for phylogenetics, because paired bases may evolve in a non-independent fashion, a violation of the assumption of site-independent evolution common to most phylogenetic methods (Dixon and Hillis, 1993).

Striking pseudogenization in avian phylogenetics: Numts are large and common in falcons

Nuclear copies of mitochondrial genes (numts) are a well-known feature of eukaryotic genomes and a concern in systematics, as they can mislead phylogenetic inferences when inadvertently used. Studies on avian numts initially based on the chicken genome suggest that numts may be uncommon and relatively short among birds. Here we ask how common numts are in falcons, based on recently sequenced genomes of the Saker falcon (Falco cherrug) and Peregrine falcon (F. peregrinus). We identified numts by BLASTN searches and then extracted CYTB, ND2 and COI sequences from them, which were then used for phylogeny inference along with several sequences from other species in Falconiformes. Our results indicate that avian numts may be much more frequent and longer than previously thought. Phylogenetic inferences revealed multiple independent nuclear insertions throughout the history of the Falconiformes, including cases of sequences available in public databases and wrongly identified as authentic mtDNA. New sequencing technologies and ongoing efforts for whole genome sequencing will provide exciting opportunities for avian numt research in the near future.