Robert G. Moyle

Explosive Pleistocene diversification and hemispheric expansion of a “great speciator”

Factors that influence speciation rates among groups of organisms are integral to deciphering macroevolutionary processes; however, they remain poorly understood. Here, we use molecular phylogenetic data and divergence time estimates to reconstruct the pattern and tempo of speciation within a widespread and homogeneous bird family (white-eyes, Zosteropidae) that contains an archetypal “great speciator.” Our analyses show that the majority of this species-rich family constitutes a clade that arose within the last 2 million years, yielding a per-lineage diversification rate among the highest reported for vertebrates (1.95–2.63 species per million years). However, unlike most rapid radiations reported to date, this burst of diversification was not limited in geographic scope, but instead spanned the entire Old World tropics, parts of temperate Asia, and numerous Atlantic, Pacific, and Indian Ocean archipelagos. The tempo and geographic breadth of this rapid radiation defy any single diversification paradigm, but implicate a prominent role for lineage-specific life-history traits (such as rapid evolutionary shifts in dispersal ability) that enabled white-eyes to respond rapidly and persistently to the geographic drivers of diversification.

Single origin of a pan-Pacific bird group and upstream colonization of Australasia

Oceanic islands have long served as natural laboratories for understanding the diversification of life. In particular, the many thousands of islands spanning the tropical Pacific support an unparalleled array of terrestrial communities whose patterns of diversity contributed fundamental insights to the development of classical speciation and biogeographic theory. Much of this work is founded on an assumption derived from traditional taxonomic approaches, namely that faunas on these widely separated archipelagos stem from a simple one-way, downstream flow of colonists from continents to islands. Here we show, with the use of molecular phylogenetic data from one of the original bird families used to justify this assumption, that a diverse array of endemic island genera and species are the product of a single radiation that diversified across all major Pacific archipelagos in a non-stepping-stone fashion, and recently recolonized continental areas. The geographic scope and lineage-specific approach of this study reveal evolutionary patterns long obscured by traditional taxonomic surveys and indicate that widely dispersed archipelagos can be sources of biological diversity.

The assembly of montane biotas: linking Andean tectonics and climatic oscillations to independent regimes of diversification in Pionus parrots

The mechanisms underlying the taxonomic assembly of montane biotas are still poorly understood. Most hypotheses have assumed that the diversification of montane biotas is loosely coupled to Earth history and have emphasized instead the importance of multiple long-distance dispersal events and biotic interactions, particularly competition, for structuring the taxonomic composition and distribution of montane biotic elements. Here we use phylogenetic and biogeographic analyses of species in the parrot genus Pionus to demonstrate that standing diversity within montane lineages is directly attributable to events of Earth history. Phylogenetic relationships confirm three independent biogeographic disjunctions between montane lineages, on one hand, and lowland dry-forest/wet-forest lineages on the other. Temporal estimates of lineage diversification are consistent with the interpretation that the three lineages were transported passively to high elevations by mountain building, and that subsequent diversification within the Andes was driven primarily by Pleistocene climatic oscillations and their large-scale effects on habitat change. These results support a mechanistic link between diversification and Earth history and have general implications for explaining high altitudinal disjuncts and the origin of montane biotas.

Plumage and song differences mediate species recognition between incipient flycatcher species of the Solomon Islands

Changes in mating signals among populations contribute to species formation. Often these signals involve a suite of display traits of different sensory modalities (“multimodal signals”); however, few studies have tested the consequences of multimodal signal divergence with most focusing on only a single divergent signal or suite of signals of the same sensory modality. Populations of the chestnut-bellied flycatcher Monarcha castaneiventris vary in song and plumage color across the Solomon Islands. Using taxidermic mount presentation and song playback experiments, we tested for the relative roles of divergent song and color in homotypic (“same type”) recognition between one pair of recently diverged sister taxa (the nominate chestnut-bellied M. c. castaneiventris and the white-capped M. c. richardsii forms). We found that both plumage and song type influenced the intensity of aggressive response by territory-owners, with plumage color playing a stronger role. These results indicate that differences in plumage and song are used in homotypic recognition, suggesting the importance of multimodal signal divergence in the evolution of premating reproductive isolation.

Difference in plumage color used in species recognition between incipient species is linked to a single amino acid substitution in the melanocortin-1 receptor.

Many studies demonstrate that differences in mating signals are used by incipient species in recognizing potential mates or sexual competitors (i.e., species recognition). Little is known, however, about the genetic changes responsible for these differences in mating signals. Populations of the Monarcha castaneiventris flycatcher vary in plumage color across the Solomon Islands, with a subspecies on Makira Island having chestnut bellies and blue‐black upper parts (Monarcha castaneiventris megarhynchus) and a subspecies on neighboring satellite islands being entirely blue‐black (melanic; Monarcha castaneiventris ugiensis). Here we show that a single nonsynonymous point mutation in the melanocortin‐1 receptor (MC1R) gene is present in all melanic birds from one island (Santa Ana) but absent in all chestnut‐bellied birds from Makira Island, implicating this mutation in causing melanism. Birds from a second satellite island (Ugi) do not show the same perfect association between this MC1R variant and plumage color, suggesting an alternative mechanism for melanism on this island. Finally, taxidermic mount presentation experiments in Makira (chestnut) and Santa Ana (melanic) suggest that the plumage difference mediates species recognition. Assuming that the signals used in species recognition are also used in mutual mate choice, our results indicate that a single amino acid substitution contributes to speciation.

Phylogeny and biogeography of the core babblers (Aves: Timaliidae).

The avian family Timaliidae is a species rich and morphologically diverse component of African and Asian tropical forests. The morphological diversity within the family has attracted interest from ecologists and evolutionary biologists, but systematists have long suspected that this diversity might also mislead taxonomy, and recent molecular phylogenetic work has supported this hypothesis. We produced and analyzed a data set of 6 genes and almost 300 individuals to assess the evolutionary history of the family. Although phylogenetic analysis required extensive adjustment of program settings, we ultimately produced a well-resolved phylogeny for the family. The resulting phylogeny provided strong support for major subclades within the family but extensive paraphyly of genera. Only 3 genera represented by more than 3 species were monophyletic. Biogeographic reconstruction indicated a mainland Asian origin for the family and most major clades. Colonization of Africa, Sundaland, and the Philippines occurred relatively late in the familys history and was mostly unidirectional. Several putative babbler genera, such as Robsonius, Malia, Leonardina, and Micromacronus are only distantly related to the Timaliidae.

Origin and diversification of Philippine bulbuls

We examine the origin and diversification of Philippine bulbuls using a phylogenetic framework. Maximum likelihood and Bayesian methods are used to construct trees from DNA sequences of two mitochondrial and two nuclear genes obtained from 11 Philippine bulbul species as well as 32 other Asian and African taxa. The study finds eight independent colonization events of bulbuls to the Philippines, including one clade comprising Philippine members of the genus Ixos that underwent extensive diversification within the archipelago. Each Philippine clade of bulbuls invaded either the Palawan region or the oceanic islands of the Philippines, but not both. Genetic data reveal at least five lineages that warrant recognition as full species. This study underscores how Philippine avian diversity is currently underestimated and highlights the need for further phylogenetic studies in other Philippine bird groups.

Phylogeny and phylogenetic classification of the tyrant flycatchers, cotingas, manakins, and their allies (Aves: Tyrannides)

Phylogenetic relationships among the Tyrannides were assessed using over 4000 base pairs of nuclear recombination activating 1 (RAG‐1) and 2 (RAG‐2) DNA sequence data from about 93% of all described genera, which represents the most complete assessment of relationships for this diverse New World radiation to date. With this sampling we propose a significantly expanded interpretation of higher‐level relationships within the group. The Tyrannides are shown to be comprised of six major lineages, all of which represent traditional family‐level taxa (sensu Fitzpatrick, 2004a and Snow, 2004a,b ; del Hoyo et al., 2004 ): (i) manakins (Pipridae); (ii) cotingas (Cotingidae); (iii) the sharpbill (Oxyruncus) + onychorhynchine flycatchers (Onychorhynchini); (iv) tityrines (Tityridae); (v) rhynchocycline flycatchers (Rhynchocyclidae); and (vi) the tyrant flycatchers (Tyrannidae). In addition, the RAG data recovered isolated lineages with uncertain relationships, including Neopipo, Platyrinchus, Piprites, and Tachuris. The Pipridae are the sister‐group to all the other Tyrannides. Within the latter, the clade ((Oxyruncidae + Tityridae) + Cotingidae) is the sister‐group of the Tyrannoidea. Within the Tyrannoidea, the Rhynchocyclidae and their allies are sisters to Neopipo + Tyrannidae. Using our phylogenetic hypothesis, we propose the first comprehensive phylogenetic classification that attempts to achieve isometry between the tree and a classification scheme using subordination and phyletic sequencing. This study thus provides a phylogenetic framework for understanding the evolution of this diverse New World assemblage, and identifies many avenues for further systematic study.

Phylogeny and phylogenetic classification of the antbirds, ovenbirds, woodcreepers, and allies (Aves: Passeriformes: infraorder Furnariides)

The infraorder Furnariides is a diverse group of suboscine passerine birds comprising a substantial component of the Neotropical avifauna. The included species encompass a broad array of morphologies and behaviours, making them appealing for evolutionary studies, but the size of the group (ca. 600 species) has limited well‐sampled higher‐level phylogenetic studies. Using DNA sequence data from the nuclear RAG‐1 and RAG‐2 exons, we undertook a phylogenetic analysis of the Furnariides sampling 124 (more than 88%) of the genera. Basal relationships among family‐level taxa differed depending on phylogenetic method, but all topologies had little nodal support, mirroring the results from earlier studies in which discerning relationships at the base of the radiation was also difficult. In contrast, branch support for family‐rank taxa and for many relationships within those clades was generally high. Our results support the Melanopareidae and Grallariidae as distinct from the Rhinocryptidae and Formicariidae, respectively. Within the Furnariides our data contradict some recent phylogenetic hypotheses and suggest that further study is needed to resolve these discrepancies. Of the few genera represented by multiple species, several were not monophyletic, indicating that additional systematic work remains within furnariine families and must include dense taxon sampling. We use this study as a basis for proposing a new phylogenetic classification for the group and in the process erect new family‐group names for clades having high branch support across methods.

REVISITING WALLACE'S HAUNT: COALESCENT SIMULATIONS AND COMPARATIVE NICHE MODELING REVEAL HISTORICAL MECHANISMS THAT PROMOTED AVIAN POPULATION DIVERGENCE IN THE MALAY ARCHIPELAGO.

Sundaland, a biogeographic region of Southeast Asia, is a major biodiversity hotspot. However, little is known about the relative importance of Pleistocene habitat barriers and rivers in structuring populations and promoting diversification here. We sampled 16 lowland rainforest bird species primarily from peninsular Malaysia and Borneo to test the long‐standing hypothesis that animals on different Sundaic landmasses intermixed extensively when lower sea‐levels during the Last Glacial Maximum (LGM) exposed land‐bridges. This hypothesis was rejected in all but five species through coalescent simulations. Furthermore, we detected a range of phylogeographic patterns; Bornean populations are often genetically distinct from each other, despite their current habitat connectivity. Environmental niche modeling showed that the presence of unsuitable habitats between western and eastern Sundaland during the LGM coincided with deeper interpopulation genetic divergences. The location of this habitat barrier had been hypothesized previously based on other evidence. Paleo‐riverine barriers are unlikely to have produced such a pattern, but we cannot rule out that they acted with habitat changes to impede population exchanges across the Sunda shelf. The distinctiveness of northeastern Borneo populations may be underlied by a combination of factors such as rivers, LGM expansion of montane forests and other aspects of regional physiography.