Temporal and spatial diversification of Pteroglossus araçaris (AVES: Ramphastidae) in the neotropics: Constant rate of diversification does not support an increase in radiation during the Pleistocene

Department of Biology, Northwestern University, Evanston, IL 60208, USA.
Molecular Phylogenetics and Evolution (Impact Factor: 3.92). 11/2010; 58(1):105-15. DOI: 10.1016/j.ympev.2010.10.016
Source: PubMed


We use the small-bodied toucan genus Pteroglossus to test hypotheses about diversification in the lowland Neotropics. We sequenced three mitochondrial genes and one nuclear intron from all Pteroglossus species and used these data to reconstruct phylogenetic trees based on maximum parsimony, maximum likelihood, and Bayesian analyses. These phylogenetic trees were used to make inferences regarding both the pattern and timing of diversification for the group. We used the uplift of the Talamanca highlands of Costa Rica and western Panama as a geologic calibration for estimating divergence times on the Pteroglossus tree and compared these results with a standard molecular clock calibration. Then, we used likelihood methods to model the rate of diversification. Based on our analyses, the onset of the Pteroglossus radiation predates the Pleistocene, which has been predicted to have played a pivotal role in diversification in the Amazon rainforest biota. We found a constant rate of diversification in Pteroglossus evolutionary history, and thus no support that events during the Pleistocene caused an increase in diversification. We compare our data to other avian phylogenies to better understand major biogeographic events in the Neotropics. These comparisons support recurring forest connections between the Amazonian and Atlantic forests, and the splitting of cis/trans Andean species after the final uplift of the Andes. At the subspecies level, there is evidence for reciprocal monophyly and groups are often separated by major rivers, demonstrating the important role of rivers in causing or maintaining divergence. Because some of the results presented here conflict with current taxonomy of Pteroglossus, new taxonomic arrangements are suggested.

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    • "We choose to use the nuclear b-fibint7 because it has proven useful to investigate the phylogenetic relationships and phylogeographic patterns of several avian species (e.g. Derryberry et al., 2011; Patel et al., 2011; Prychitko and Moore, 1997; Ribas et al., 2012). Amplification and sequencing of the ND2 fragments required an internal primer specifically designed for this study (ND2xg; Table 2). "
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    ABSTRACT: The genus Xiphorhynchus is a species rich avian group widely distributed in Neotropical forests of Central and South America. Although recent molecular studies have improved our understanding of the spatial patterns of genetic diversity in some species of this genus, most are still poorly known, including their taxonomy. Here, we address the historical diversification and phylogenetic relationships of the X. guttatus / susurrans complex, using data from two mitochondrial (cyt b and ND2) and one nuclear (β-fibint7) genes. Phylogenetic relationships were inferred with both gene trees and a Bayesian-based species tree under a coalescent framework (∗BEAST). With exception of the nuclear β-fibint7 gene that produced an unresolved tree, both mtDNA and the species tree showed a similar topology and were congruent in recovering five main clades with high statistical support. These clades, however, are not fully concordant with traditional delimitation of some X. guttatus subspecies, since X. g. polystictus, X. g. guttatus, and X. connectens are not supported as distinct clades. Interestingly, these three taxa are more closely related to the mostly trans-Andean X. susurrans than the other southern and western Amazonian subspecies of X. guttatus, which constitutes a paraphyletic species. Timing estimates based on the species tree indicated that diversification in X. guttatus occurred between the end of the Pliocene and early Pleistocene, likely associated with the formation of the modern Amazon River and its main southern tributaries (Xingu, Tocantins, and Madeira), in addition to climate-induced changes in the distribution of rainforest biomes. Our study supports with an enlarged dataset a previous proposal for recognizing at least three species level taxa in the X. guttatus / susurrans complex: X. susurrans, X. guttatus, and X. guttatoides. Copyright © 2015 Elsevier Inc. All rights reserved.
    Molecular Phylogenetics and Evolution 02/2015; 85. DOI:10.1016/j.ympev.2015.02.004 · 3.92 Impact Factor
    • "Despite the large number of distinct hypotheses to explain Amazonian biodiversity (e.g., refuge hypothesis, Haffer, 1969; riverine hypothesis, Wallace, 1852; Ayres and Clutton-Brock, 1992; riverine-refuge hypothesis, Ayres and Clutton-Brock, 1992; Haffer, 1993, 2001; ecological gradients hypothesis, Endler, 1977; ''museum'' hypothesis, Roy et al., 1997; and marine incursions, Bates, 2001), and the common sense that many causations have operated for the formation of such diversity (Bush, 1994; Haffer, 2001; Miller et al., 2008), recent phylogeographic and paleobiogeographic reconstructions (Aleixo and Rossetti 2007; Patel et al., 2011; Weir and Price, 2011; Ribas et al., 2012) have postulated the formation of the current Amazonian physical landscape as the main source of cladogenetic events among the studied lineages. "
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    ABSTRACT: The growing knowledge on paleogeography and the recent applications of molecular biology and phylogeography to the study of the Amazonian biota have provided a framework for testing competing hypotheses of biotic diversification in this region. Here, we reconstruct the spatio-temporal context of diversification of a widespread understory polytypic Amazonian bird species (Thamnophilus aethiops) and contrast it with different hypotheses of diversification and the taxonomy currently practiced in the group. Sequences of mtDNA (cytochrome b and ND2) and nuclear (β-fibrinogen introns 5 and 7 and the Z-liked Musk4) genes, adding up to 4,093 bp of 89 individuals covering the Amazonian, Andean, and Atlantic forest populations of T. aethiops were analyzed. Phylogenetic and population genetics analyses revealed ten reciprocally monophyletic and genetically isolated or nearly-isolated lineages in T. aethiops, highlighting several inconsistencies between taxonomy and evolutionary history in this group. Our data suggest that the diversification of T. aethiops started in the Andean highlands, and then proceeded into the Amazonian lowlands probably after the consolidation of the modern Amazonian drainage. The main cladogenetic events in T. aethiops may be related to the formation and structuring of large Amazonian rivers during the Late Miocene - Early Pleistocene, coinciding with the dates proposed for other lineages of Amazonian organisms. Population genetics data do not support climatic fluctuations as a major source of diversification in T. aethiops. Even though not entirely concordant with paleobiogeographic models derived from phylogenies of other vertebrate lineages, our results support a prominent role for rivers as major drivers of diversification in Amazonia, while underscoring that different diversification scenarios are probably related to the distinct evolutionary origins of groups being compared.
    Molecular Phylogenetics and Evolution 10/2014; 82. DOI:10.1016/j.ympev.2014.09.023 · 3.92 Impact Factor
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    • "The diversification analysis indicated a best topological-fit to a diversity-dependent model (c and AIC RC ; Tables 2 and 3) and a slight decrease of the diversification rates within Conopophaga (see lineage through time plot in Fig. 3). However, such decrease of diversification in Conopophaga is not in accordance with other Neotropical groups that exhibited a pattern of constant diversification rate through the late Tertiary to Quaternary (Derryberry et al., 2011; d'Horta et al., 2013; Patel et al., 2011). Our diversification result thus corroborates the relictual status of Conopophaga, which seems to have filled a limited ecological space in the South America (a diversity-dependent pattern). "
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    ABSTRACT: We inferred the phylogenetic relationships, divergence time and biogeography of Conopophagidae (gnateaters) based on sequence data of mitochondrial genes (ND2, ND3 and cytb) and nuclear introns (TGFB2 and G3PDH) from 45 tissue samples (43 Conopophaga and 2 Pittasoma) representing all currently recognized species of the family and the majority of subspecies. Phylogenetic relationships were estimated by maximum likelihood and Bayesian inference. Divergence time estimates were obtained based on a Bayesian relaxed clock model. These chronograms were used to calculate diversification rates and reconstruct ancestral areas of Conopophaga. The phylogenetic analyses support the reciprocal monophyly of Conopophaga and Pittasoma. All species were monophyletic with the exception of C. lineata, as C. lineata cearae did not cluster with the other two C. lineata subspecies. Divergence time estimates for Conopophagidae suggested that diversification took place during the Neogene, and that the diversification rate within Conopophaga was highest in the late Miocene, suggesting a diversity-dependent pattern. Our analyses of the diversification of Conopophagidae provided a scenario for evolution in Terra Firme forest across tropical South America. The spatio-temporal pattern suggests that Conopophaga originated in the Brazilian Shield and that a complex sequence of events possibly related to the Andean uplift and infilling of former sedimentation basins and erosion cycles shaped the current distribution and diversity of this genus.
    Molecular Phylogenetics and Evolution 07/2014; 79(1). DOI:10.1016/j.ympev.2014.06.025 · 3.92 Impact Factor
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