Brett W. Benz

Tectonic collision and uplift of Wallacea triggered the global songbird radiation

Songbirds (oscine passerines) are the most species-rich and cosmopolitan bird group, comprising almost half of global avian diversity. Songbirds originated in Australia, but the evolutionary trajectory from a single species in an isolated continent to worldwide proliferation is poorly understood. Here, we combine the first comprehensive genome-scale DNA sequence data set for songbirds, fossil-based time calibrations, and geologically informed biogeographic reconstructions to provide a well-supported evolutionary hypothesis for the group. We show that songbird diversification began in the Oligocene, but accelerated in the early Miocene, at approximately half the age of most previous estimates. This burst of diversification occurred coincident with extensive island formation in Wallacea, which provided the first dispersal corridor out of Australia, and resulted in independent waves of songbird expansion through Asia to the rest of the globe. Our results reconcile songbird evolution with Earth history and link a major radiation of terrestrial biodiversity to early diversification within an isolated Australian continent.

Highly Pathogenic H5N1 Avian Influenza: Entry Pathways into North America via Bird Migration

Given the possibility of highly pathogenic H5N1 avian influenza arriving in North America and monitoring programs that have been established to detect and track it, we review intercontinental movements of birds. We divided 157 bird species showing regular intercontinental movements into four groups based on patterns of movement—one of these groups (breed Holarctic, winter Eurasia) fits well with the design of the monitoring programs (i.e., western Alaska), but the other groups have quite different movement patterns, which would suggest the importance of H5N1 monitoring along the Pacific, Atlantic, and Gulf coasts of North America.

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.

Molecular phylogenetics, vocalizations, and species limits in Celeus woodpeckers (Aves: Picidae).

Species limits and the evolutionary mechanisms that have shaped diversification of woodpeckers and allies (Picidae) remain obscure, as inter and intraspecific phylogenetic relationships have yet to be comprehensively resolved for most genera. Herein, we analyzed 5020 base pairs of nucleotide sequence data from the mitochondrial and nuclear genomes to reconstruct the evolutionary history of Celeus woodpeckers. Broad geographic sampling was employed to assess species limits in phenotypically variable lineages and provide a first look at the evolution of song and plumage traits in this poorly known Neotropical genus. Our results strongly support the monophyly of Celeus and reveal several novel relationships across a shallow phylogenetic topology. We confirm the close sister relationship between Celeus spectabilis and the enigmatic Celeus obrieni, both of which form a clade with Celeus flavus. The Mesoamerican Celeus castaneus was placed as sister to a Celeus undatus-grammicus lineage, with the species status of the latter drawn into question given the lack of substantial genetic, morphological, and vocal variation in these taxa. We recovered paraphyly in Celeus elegans; however, this result appears to be the consequence of mitochondrial introgression from Celeus lugubris considering the monophyly of elegans at the ß-FIBI7 locus. A second instance of paraphyly was observed in Celeus flavescens with deep genetic splits and substantial phenotypic variation indicating the presence of two distinct species in this broadly distributed lineage. As such, we advocate elevation of Celeus flavescens ochraceus to species status. Our analysis of Celeus vocalizations and plumage characters demonstrates a pattern of lability consistent with a relatively recent origin of the genus and potentially rapid speciation history.

Phylogenetic relationships of the Helmeted Woodpecker (Dryocopus galeatus): A case of interspecific mimicry?

ABSTRACT Examples of phenotypic convergence in plumage coloration have been reported in a wide diversity of avian taxonomic groups, yet the underlying evolutionary mechanisms driving this phenomenon have received little scientific inquiry. We document a striking new case of plumage convergence in the Helmeted Woodpecker (Dryocopus galeatus) and explore the possibility of visual mimicry among Atlantic Forest woodpeckers. Our multilocus phylogenetic analyses unequivocally place D. galeatus within Celeus, indicating that the former has subsequently converged in appearance upon the distantly related and syntopic Dryocopus lineatus, to which it bears a remarkable resemblance in plumage coloration and pattern. Although details of the Helmeted Woodpeckers ecology and natural history are only now beginning to emerge, its smaller size and submissive behavior are consistent with predictions derived from evolutionary game-theory models and the hypothesis of interspecific social-dominance mimicry (ISDM). Moreover, estimates of avian visual acuity suggest that size-related mimetic deception is plausible at distances ecologically relevant to Celeus and Dryocopus foraging behavior. In light of our results, we recommend taxonomic transfer of D. galeatus to Celeus and emphasize the need for detailed behavioral studies that examine the social costs and benefits of plumage convergence to explicitly test for ISDM and other forms of mimicry in these Atlantic Forest woodpecker communities. Future field studies examining potential cases of competitive mimicry should also take into account the mimics acoustic behavior, particularly in the presence of putative model species and other heterospecific competitors, as any discontinuity between morphological and behavioral mimicry would likely preclude the possibility of deception.

Song Rates, Mating Status, and Territory Size of Cerulean Warblers in Missouri Ozark Riparian Forest

Abstract We assessed song rates among male Cerulean Warblers (Dendroica cerulea) in Ozark riparian forest in southeastern Missouri to characterize song rate variation and estimate how many males may be missed during censuses. Average (± SD) songs per 5-min intervals for continuous 4-hr observation periods varied from 3.1 ± 4.8 (mated males) to 36.0 ± 18.7 (unmated males; n = 24 males). Unmated males averaged twice the number of songs per 5-min periods than mated males. Considerable song rate variation existed even among mated males. Song rates slightly declined over the 4-hr observation period. Song rate differences between Cerulean Warblers in Ontario and southeastern Missouri suggest caution when making assumptions about breeding status based on auditory surveys. Average male Cerulean Warbler territory size (n = 20) was 0.9 ± 0.1 ha with 27 of 31 males having at least one abutting conspecific territory. All males (n = 24) were silent for 32.7 ± 21.5 and 21.8 ± 17.4% of the 5-min and 10-min periods, respectively. Unpaired males (n = 5) were silent for 2.9 ± 3.15 and 1.2 ± 1.86% and mated males (n = 19) were silent for 37.9 ± 18.8 and 25.4 ± 16.2% of the 5-min and 10-min periods, respectively. These data demonstrate that when auditory clues are used for detection, not incorporating song rate will result in significant underestimates of density.

Aves, province of Guizhou, China.

We report our inventories of birds observed and collected at three field sites from the province of Guizhou, southeastern China. Our findings detailed herein complement our previous ornithological surveys from Guangxi province, as part of a comprehensive biotic survey of the region. Of 153 total bird species recorded, 17 were new for the province, among which several taxa of conservational importance, such as: Golden Pheasant Crysolophus pictus, Tawny Fish-Owl Ketupa flavipes, Black-breasted Thrush Turdus dissimilis, Fujian Flycatcher Niltava davidii, Red- tailed Laughingthrush Garrulax milnei, and Slaty Bunting Latoucheornis siemsseni. These records provide the most recent insight into the current status of the habitats and the avian biodiversity of an important, yet sparsely surveyed and reported biogeographic region.

River-Based Surveys for Assessing Riparian Bird Populations: Cerulean Warbler as a Test Case

Abstract Birds concentrated in riparian habitats are poorly sampled by traditional survey methods because of the difficulties associated with accessing these habitats. Our objectives were to test the effectiveness of river-based surveys to determine the status, distribution, and relative abundance for riparian bird species in Missouri and northern Arkansas, with special emphasis on Dendroica cerulea (Cerulean Warbler). Our canoe-based surveys revealed an average of 2.3 and 0.8 singing male Cerulean Warblers/river km along the Current River (128 river km surveyed), MO, and the Buffalo National River (96 river km), AR. Nonparametric estimates for repeated surveys of the same river stretches indicate that 69–79% of singing male Cerulean Warblers were detected. However, the bias associated with the estimate methodology and independent song rate data suggest those are conservative estimates. In comparison with land-based point-counts, this river-based protocol offers a quick and efficient assessment of Cerulean Warblers in riparian areas.

Comparative Genomics and Genome Evolution in Birds-of-paradise

The diverse array of phenotypes and courtship displays exhibited by the birds-of-paradise have long fascinated scientists and laymen alike. Remarkably, almost nothing is known about the genomics of this iconic radiation. There are 41 species in 16 genera currently recognized within the birds-of-paradise family (Paradisaeidae), most of which are endemic to the island of New Guinea. In this study, we sequenced genomes of representatives from all five major clades within this family to characterize genomic changes that may have played an important role in the evolution of the group’s extensive phenotypic diversity. We found genes important for coloration, morphology and feather development to be under positive selection. GO enrichment of positively selected genes in the birds-of-paradise showed an enrichment for collagen, glycogen synthesis and regulation, eye development and other categories. In the core birds-of-paradise, we found GO categories for ‘startle response’ (response to predators) and ‘olfactory receptor activity’ to be enriched among the gene families expanding significantly faster compared to the other birds in our study. Furthermore, we found novel families of retrovirus-like retrotransposons active in all three de novo genomes since the early diversification of the birds-of-paradise group, which could have potentially played a role in the evolution of this fascinating group of birds.Background The diverse array of phenotypes and lekking behaviors in birds-of-paradise have long excited scientists and laymen alike. Remarkably, almost nothing is known about the genomics underlying this iconic radiation. Currently, there are 41 recognized species of birds-of-paradise, most of which live on the islands of New Guinea. In this study we sequenced genomes of representatives from all five major clades recognized within the birds-of-paradise family (Paradisaeidae). Our aim was to characterize genomic changes that may have been important for the evolution of the groups extensive phenotypic diversity. Results We sequenced three de novo genomes and re-sequenced two additional genomes representing all major clades within the birds-of-paradise. We found genes important for coloration, morphology and feather development to be under positive selection. GO enrichment of positively selected genes on the branch leading to the birds-of-paradise shows an enrichment for collagen, glycogen synthesis and regulation, eye development and other categories. In the core birds-of-paradise, we found GO categories for startle response (response to predators) and olfactory receptor activity to be enriched among the gene families expanding significantly faster compared to the other birds in our study. Furthermore, we found novel families ofretrovirus-like retrotransposons active in all three de novo genomes since the early diversification of the birds-of-paradise group, which could have potentially played a role in the evolution of this fascinating group of birds. Conclusion Here we provide a first glimpse into the genomic changes underlying the evolution of birds-of- paradise. Our aim was to use comparative genomics to study to what degree the genomic landscape of birds-of-paradise deviates from other closely related passerine birds. Given the extreme phenotypic diversity in this family, our prediction was that genomes should be able to reveal features important for the evolution of this amazing radiation. Overall, we found a strong signal for evolution on mechanisms important for coloration, morphology, sensory systems, as well as genome structure.

Uneven missing data skews phylogenomic relationships within the lories and lorikeets

Resolution of the Tree of Life has accelerated with advances in DNA sequencing technology. To achieve dense sampling, it is often necessary to obtain DNA from historical museum specimens to supplement modern genetic samples. However, DNA from historical material is generally degraded and fragmented, which presents various challenges. In this study, we evaluated how the read depth at variant sites and missing data among historical and modern sample types impacts phylogenomic inference. We explored these patterns in the brush-tongued parrots (lories and lorikeets) of Australasia by sampling ultraconserved elements in 105 taxa. Trees estimated with low coverage sites had several clades where historical or modern samples clustered together, which were not observed in trees with more stringent filtering. To assess if the aberrant relationships were affected by missing data, we performed an outlier analysis of sites and genes for trees built with and without low coverage sites, and with and without missing data. Outlier analyses showed that 6.6% of total sites were driving the topological differences, and at these sites, historical samples had 7.5x more missing data. An examination of subclades found loci biased by missing data, and the exclusion of these loci shifted phylogenetic relationships. Predictive modeling found that outlier analysis scores were not correlated with summary statistics of locus alignments, indicating that outlier loci do not have characteristics differing from other loci. After accounting for biased loci and understanding the stability of relationships, we inferred a more robust phylogenetic hypothesis for lories and lorikeets.