Origin and evolution of the unique Australo-Papuan mangrove- restricted avifauna: novel insights form molecular phylogenetic and comparative phylogeographic analyses

Coastal mangrove forests of Australo-Papua harbor the world's richest avifauna restricted to mangroves, however their biogeographic origins and evolutionary processes shaping their current distributions are not well understood. Building upon previous work based on field surveys and morphological characters, I am here focusing on elucidating the phylogenetic placement of mangrove-bound species from three different bird families as well as the comparative phylogeographic analysis of eight co-distributed mangrove restricted birds. In the first molecular phylogenetic analysis of fantails (Aves: Rhipiduride) I document six distinct clades, harboring members spread across large geographic extents. Rhipidura hypoxantha is not a true fantail, but rather a member of the Stenostiridae clade that is morphologically and behaviorally convergent with fantails. The Australian mangrove fantails R. phasiana and R. dryas both evolved recently from Pacific island radiations. A molecular phylogeny of all extant species of the honeyeater genus Lichenostomus (Aves: Meliphagidae) also addresses the relationship of the only mangrove-restricted honeyeaters on Australia's east coast, L. versicolor and L. fasciogularis. These species were not sisters but rather L. versicolor was sister to the pair comprising L. fasciogularis and the continental widespread Singing Honeyeater L. virescens. The genus Lichenostomus is not monophyletic, and instead comprises seven distinct lineages interdispersed within the larger meliphagid assemblage. Based on this taxonomic and nomenclatural revision, recognition of a novel genus of honeyeater is warranted. A multilocus molecular phylogeny of gerygones (Aves; Acanthizidae) establishes that the three mangrove endemic species do not form a monophyletic clade, instead indicating three distinct, temporally non-overlapping, radiations into magroves. Moreover, G. cinerea from New Guinea is in fact a member of the genus Acanthiza, with which it consistently grouped based on 13 distinct molecular loci analyzed. Comparative phylogeographic analyses of 8 co-distributed mangrove forest endemic birds concludes biogeographic barriers such as the Canning Gap, Bonaparte Gap, and the Carpentarian Gaps all had important, but varying degrees of impact on the species we analyzed. Species with more recent radiations into mangroves include Rhipidura phasiana, Myiagra ruficollis, and Myzomela erythrocephala, while Peneoenanthe pulverulenta, Pachycephala melanura, P. lanioides, Zosterops luteus, and Colluricincla megarhyncha all had more marked phylogeographic signatures

Phylogeography of the Rufous vanga and the role of bioclimatic transition zones in promoting speciation within Madagascar

Madagascar is known as a biodiversity hotspot, providing an ideal natural laboratory for investigating the processes of avian diversification. Yet, the phylogeography of Madagascar’s avifauna is still largely unexamined. In this study, we evaluated phylogeographic patterns and species limits within the Rufous Vanga, Schetba rufa, a monotypic genus of forest-dwelling birds endemic to the island. Using an integrative taxonomic approach, we synthesized data from over 4000 ultra-conserved element (UCE) loci, mitochondrial DNA, multivariate morphometrics, and ecological niche modeling to uncover two reciprocally monophyletic, geographically circumscribed, and morphologically distinct clades of Schetba. The two lineages are restricted to eastern and western Madagascar, respectively, with distributions broadly consistent with previously described subspecies. Based on their genetic and morphological distinctiveness, the two subspecies merit recognition as separate species. The bioclimatic transition between the humid east and dry west of Madagascar likely promoted population subdivision and drove speciation in Schetba during the Pleistocene. Our study is the first evidence that an East-West bioclimatic transition zone played a role in the speciation of birds within Madagascar

Phylogenetic relationships of flowerpeckers (Aves: Dicaeidae): Novel insights into the evolution of a tropical passerine clade

Understanding the relationships and evolution of flowerpeckers has been challenging, particularly as no phylogenetic study has as yet assessed the group. Here, we present a first such analysis of this clade based on sequences of two mitochondrial genes and one nuclear intron. Our analyses offer strong support for monophyly of the Dicaeidae. Within the family, 4 Dicaeum species (D. chrysorrheum, D. melanoxanthum, D. agile, and D. everetii) had closer affinity to Prionochilus, although tests of alternative topologies could not reject reciprocal monophyly of the two genera. Across the family, overall bill shape trends from more stout bills basally to more slender and medium bills, whereas sexual dichromatism and plumage patterns show much more homoplasy. Taxonomically, generic allocations may need to be changed to reflect historical relationships better

Evolution in Australasian Mangrove Forests: Multilocus Phylogenetic Analysis of the Gerygone Warblers (Aves: Acanthizidae)

The mangrove forests of Australasia have many endemic bird species but their evolution and radiation in those habitats has been little studied. One genus with several mangrove specialist species is Gerygone (Passeriformes: Acanthizidae). The phylogeny of the Acanthizidae is reasonably well understood but limited taxon sampling for Gerygone has constrained understanding of its evolution and historical biogeography in mangroves. Here we report on a phylogenetic analysis of Gerygone based on comprehensive taxon sampling and a multilocus dataset of thirteen loci spread across the avian genome (eleven nuclear and two mitochondrial loci). Since Gerygone includes three species restricted to Australia's coastal mangrove forests, we particularly sought to understand the biogeography of their evolution in that ecosystem. Analyses of individual loci, as well as of a concatenated dataset drawn from previous molecular studies indicates that the genus as currently defined is not monophyletic, and that the Grey Gerygone (G. cinerea) from New Guinea should be transferred to the genus Acanthiza. The multilocus approach has permitted the nuanced view of the group's evolution into mangrove ecosystems having occurred on multiple occasions, in three non-overlapping time frames, most likely first by the G. magnirostris lineage, and subsequently followed by those of G. tenebrosa and G. levigaster

Locating Pleistocene Refugia: Comparing Phylogeographic and Ecological Niche Model Predictions

Ecological niche models (ENMs) provide a means of characterizing the spatial distribution of suitable conditions for species, and have recently been applied to the challenge of locating potential distributional areas at the Last Glacial Maximum (LGM) when unfavorable climate conditions led to range contractions and fragmentation. Here, we compare and contrast ENM-based reconstructions of LGM refugial locations with those resulting from the more traditional molecular genetic and phylogeographic predictions. We examined 20 North American terrestrial vertebrate species from different regions and with different range sizes for which refugia have been identified based on phylogeographic analyses, using ENM tools to make parallel predictions. We then assessed the correspondence between the two approaches based on spatial overlap and areal extent of the predicted refugia. In 14 of the 20 species, the predictions from ENM and predictions based on phylogeographic studies were significantly spatially correlated, suggesting that the two approaches to development of refugial maps are converging on a similar result. Our results confirm that ENM scenario exploration can provide a useful complement to molecular studies, offering a less subjective, spatially explicit hypothesis of past geographic patterns of distribution

Comparative Phyloclimatic Analysis and Evolution of Ecological Niches in the Scimitar Babblers (Aves: Timaliidae: <em>Pomatorhinus</em>)

<div><p>We present the first extensive and integrative analysis of niche evolution based on climatic variables and a dated molecular phylogeny of a heterogeneous avian group of Southeast Asian scimitar babblers of the genus <em>Pomatorhinus</em>. The four main clades of scimitar babblers have species that co-occur in similar areas across southern Asia but some have diverged at different timeframes, with the most recently evolved clade harboring the highest number of species. Ecological niche models and analysis of contributing variables within a phylogenetic framework indicate instances of convergent evolution of members of different clades onto similar ecological parameter space, as well as divergent evolution of members from within clades. <em>Pomatorhinus</em> species from different clades occupying Himalayan foothills show convergence towards similar climatic tolerances, whereas within a clade, allopatric sister-species occurring in the Himalayas have diverged to occupy different climatic parameter spaces. Comparisons of climatic tolerances of Himalayan foothills taxa with species distributed further south in Assam/Burma and Burma/Thailand indicate convergence towards similar parameter spaces in several climatic variables. Niche overlap was observed to be lower among species of the youngest clade (<em>ruficollis</em>) and higher among species of older clades (<em>ferruginosus</em>). Analysis of accumulation of ecological disparity through time indicates rapid divergence within recent time frames. As a result, Himalayan taxa originating at different temporal scales within the four main scimitar babbler clades have differentiated ecologically only in recently diverged taxa. Our study suggests that the repeated orogenic and climatic fluctuations of the Pliocene and Pleistocene within mainland Southeast Asia served as an important ecological speciation driver within scimitar babblers, by providing opportunities for rapid geographic expansion and filling of novel environmental niches.</p> </div

Phylogenetic estimates of gene trees obtained via Bayesian and Maximum Likelihood analysis of individual loci.

<p>Locus acronyms follow <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031840#pone-0031840-t002" target="_blank">Table 2</a> and references therein. Nodal support is indicated by circles, where the upper half corresponds to Bayesian posterior probabilities (BPP) and the lower half depicts ML bootstrap values (MLBV). BPP support values greater than 95% are given in bold above branches, and indicated by dark upper half-circles. MLBV greater than 80 are in bold below branches, and indicated by dark lower half-circles. Support values below these thresholds are in regular font and depicted with an open circle half. Values below 50% BPP and 50 MLBV are denoted by double dashes or not at all where both algorithms failed to recover that value at a node. The mitochondrial protein coding genes ND2 and ND3 have been combined in a single partition, indicated as “mtDNA”. Mangrove specialists are highlighted in bold.</p

Summary of the thirteen loci included in the present study.

a<p>Locus information and chromosome number was inferred from the genome map of the chicken genome on GenBank.</p