Árpád S. Nyári

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.

ECOLOGICAL NICHE CONSERVATISM AND PLEISTOCENE REFUGIA IN THE THRUSH-LIKE MOURNER, SCHIFFORNIS SP., IN THE NEOTROPICS

Abstract Recent studies have increasingly implicated deep (pre-Pleistocene) events as key in the vertebrate speciation, downplaying the importance of more recent (Pleistocene) climatic shifts. This work, however, has been based almost exclusively on evidence from molecular clock inferences of splitting dates. We present an independent perspective on this question, using ecological niche model reconstructions of Pleistocene Last Glacial Maximum (LGM) potential distributions for the Thrush-like Mourner (Schiffornis turdina) complex in the neotropics. LGM distributional patterns reconstructed from the niche models relate significantly to phylogroups identified in previous molecular systematic analyses. As such, patterns of differentiation and speciation in this complex are consistent with Pleistocene climate and geography, although further testing will be necessary to establish dates of origin firmly and unambiguously.

Phylogeography of the Buarremon brush-finch complex (Aves, Emberizidae) in Mesoamerica

The Buarremon brush-finches represent a complex suite of populations distributed in the montane New World Tropics from Mexico south to South America. Traditional taxonomic arrangements have separated populations of this genus into three species, based on plumage variation, although plumage patterns are well known to exhibit homoplasy. We present a first detailed phylogeographic and phylogenetic study, focused on Mesoamerican populations, and signal the existence of strong differentiation among populations with a clear geographic structure. We find well differentiated clades for (1) the Sierra Madre Oriental and Sierra Madre del Sur in Oaxaca, (2) western Mexican populations, including the B. brunneinucha populations in the Sierra Madre del Sur and B. virenticeps, (3) Sierra Madre Oriental and Sierra de los Tuxtlas, (4) northern Central America, (5) southern Central America, (6) middle Central America, and (7) South America. We demonstrate a lack of concordance with plumage patterns, and argue for several additional species to be recognized in the complex.

Phylogenetic relationships of fantails (Aves: Rhipiduridae)

We explore the phylogenetic relationships of fantails (Aves: Rhipiduridae) using molecular characters derived from two nuclear introns and two mitochondrial genes. Our results indicate that Rhipidura hypoxantha is not a true fantail, but rather a member of the Stenostiridae clade that is morphologically and behaviourally convergent with fantails. Within the true Rhipiduridae, we identified six distinct clades; however, phylogenetic relationships among these groups were unresolved. The only well‐supported sister relationship was between members of the grey and the rufous fantail complexes. Clades recovered through our model‐based phylogenetic analyses generally correspond to previously proposed fantail complexes based on morphological characters. The phylogenetic position of R. atra and R. diluta remain unclear, as sister relationships varied between analyses for the prior whereas the latter was placed as sister to the New Guinea thicket fantails, R. leucothorax and R. threnothorax; yet significant node support was not recovered for either taxa. Biogeographically, fantails appear to have radiated rapidly and the six clades are not geographically restricted, but instead span South‐east Asia, New Guinea, Australia and Pacific Islands.

The differential effect of lowlands on the phylogeographic pattern of a Mesoamerican montane species (Lepidocolaptes affinis, Aves: Furnariidae).

We sequenced 1869 bp of mtDNA (cyt b and ND2) from 80 specimens of Lepidocolaptes affinis, a montane bird species of Mesoamerica, sampled at 34 localities from Mexico to Costa Rica. The species showed moderate genetic diversity (π=0.0045) and phylogeographic structure (Φ(ST)=0.12-0.95). The phylogeographic pattern indicated the Nicaragua Depression has prevented gene flow whereas populations on the two sides of the Isthmus of Tehuantepec did not show strong genetic differentiation. In Mexico, the population of the Sierra Madre Oriental was composed of two different lineages. In general, our data did not support a scenario of historical demographic expansion, and matched partially the phylogeographic patterns of other Mesoamerica montane species.

A new synthesis of the molecular systematics and biogeography of honeyeaters (Passeriformes: Meliphagidae) highlights biogeographical and ecological complexity of a spectacular avian radiation

The passerine family Meliphagidae (the honeyeaters) comprises 175–180 species in 40–50 genera. It is an iconic element of the Australo‐Papuan avifauna and also occurs in Indonesia and on remote Pacific Ocean islands. Building on previous molecular studies that have pioneered a renewed understanding of the familys circumscription and systematics, we present an updated phylogenetic and systematics synthesis of honeyeaters derived from 112 mostly Australian, New Guinean and Wallacean species‐ and subspecies‐rank taxa aligned across 9246 positions spanning four mitochondrial and four nuclear genes. We affirm many of the recent changes advocated to the groups genus‐level systematics and offer some further refinements. The groups radiation appears to coincide broadly with the aridification of Australia in the Miocene, consistent with the time of origin of diversification of extant lineages in several other groups of Australian organisms. Most importantly, the complexity of the biogeography underlying the groups spectacular radiation, especially within Australia, is now apparent. Foremost among such examples is the robust evidence indicating that multiple, independent lineages of honeyeaters, including several monotypic genera, are endemic to the Australian arid zone, presumably having diverged and evolved within it. Also apparent and warranting further study are the phenotypic diversity among close relatives and the remarkably disjunct distributions within some clades, perhaps implying extinction of geographically intermediate lineages. Given such complexity, understanding the evolution of this radiation, which has thus far been intractable, relies on integration of molecular data with morphology, ecology and behaviour.

Comparative phyloclimatic analysis and evolution of ecological niches in the scimitar babblers (Aves: Timaliidae: Pomatorhinus)

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 Pomatorhinus. 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. Pomatorhinus 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 (ruficollis) and higher among species of older clades (ferruginosus). 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.

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.

Systematic dismantlement of Lichenostomus improves the basis for understanding relationships within the honeyeaters (Meliphagidae) and the historical development of Australo-Papuan bird communities

Abstract Evaluations of relationships among honeyeaters (Passeriformes: Meliphagidae) have used dense taxon and nucleotide sampling. Here we focus on the systematically contentious meliphagid genus Lichenostomus. We use data from two molecular markers that were common to two major recent studies, the mitochondrial protein-coding gene ND2 and the nuclear intron Fib5. Based on complete species-level sampling of Lichenostomus, we confirm the recent finding that Lichenostomus is not monophyletic. We recover seven distinct lineages dispersed within the meliphagid assemblage. Two uniform and unadorned species, the White-gaped (L. unicolor) and Yellow (L. flavus) Honeyeaters, were sister species close to some other taxa currently placed in Lichenostomus. The only two mangrove specialists, the Varied (L. versicolor) and Mangrove (L. fasciogularis) Honeyeaters from north-eastern and central-eastern Australia respectively, were not sisterspecies, but the former was sister to the pair comprising Mangrove Honeyeater and the widespread Singing Honeyeater (L. virescens). Two endemic New Guinean species, the Obscure (L. obscurus) and Black-throated (L. subfrenatus) Honeyeaters, are a sister pair to the Yellow-faced Honeyeater (L. chrysops) of eastern Australia. We suggest a revised generic nomenclature for the species recently placed in Lichenostomus and erect one new genus-group name, Bolemoreus, to include two species that have been previously grouped in Caligavis.

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 Australias 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 groups 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.