Peter Houde

Whole-genome analyses resolve early branches in the tree of life of modern birds

To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.

Comparative genomics reveals insights into avian genome evolution and adaptation

Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.

PARALLEL RADIATIONS IN THE PRIMARY CLADES OF BIRDS

Knowledge of avian phylogeny is prerequisite to understanding the circumstances and timing of the diversification of birds and the evolution of morphological, behavioral, and life-history traits. Recent molecular datasets have helped to elucidate the three most basal clades in the tree of living birds, but relationships among neoavian orders (the vast majority of birds) remain frustratingly vexing. Here, we examine intron 7 of the beta-fibrinogen gene in the most taxonomically inclusive survey of DNA sequences of nonpasserine bird families and orders to date. These data suggest that Neoaves consist of two sister clades with ecological parallelisms comparable to those found between marsupial and placental mammals. Some members of the putative respective clades have long been recognized as examples of convergent evolution, but it was not appreciated that they might be parts of diverse parallel radiations. In contrast, some traditional orders of birds are suggested by these data to be polyphyletic, with representative families in both radiations.

Critical Evaluation of DNA Hybridization Studies in Avian Systematics

-It is frequently claimed that equal rates of DNA evolution are observed in birds, but specific tests necessary to demonstrate this are rarely performed. I demonstrated statistically significant differences in rates of DNA evolution for a few passerine birds that vitiate the role of DNA hybridization as the direct indicator of kinship. The differences in evolutionary rates observed may be substantial enough to introduce ambiguity into the clustering of taxa. Researchers frequently fail to perform the specific experiments needed to distinguish between real differences in relative rates of DNA evolution vs. differences that can be attributed to experimental error. They also fail to draw attention to and account for either erroneous or problematical data for some birds, or fail to perform the experiments necessary to determine the cause of unexpectedly problematical results. The DNA molecular clock is shown to be calibrated using speculative and questionable data. It involves diverse organisms that cannot be shown to evolve at the same rate, and that probably did not. Yet, DNA hybridization is a valuable tool that probably cannot lead one to make major systematic errors providing the data are not incorrect because of technical or computational errors and are taken from a sufficient diversity of relevant taxa. Received 29 November 1985, accepted 8

The Fat Body Transcriptomes of the Yellow Fever Mosquito Aedes aegypti, Pre- and Post- Blood Meal

Background The fat body is the main organ of intermediary metabolism in insects and the principal source of hemolymph proteins. As part of our ongoing efforts to understand mosquito fat body physiology and to identify novel targets for insect control, we have conducted a transcriptome analysis of the fat body of Aedes aegypti before and in response to blood feeding. Results We created two fat body non-normalized EST libraries, one from mosquito fat bodies non-blood fed (NBF) and another from mosquitoes 24 hrs post-blood meal (PBM). 454 pyrosequencing of the non-normalized libraries resulted in 204,578 useable reads from the NBF sample and 323,474 useable reads from the PBM sample. Alignment of reads to the existing reference Ae. aegypti transcript libraries for analysis of differential expression between NBF and PBM samples revealed 116,912 and 115,051 matches, respectively. De novo assembly of the reads from the NBF sample resulted in 15,456 contigs, and assembly of the reads from the PBM sample resulted in 15,010 contigs. Collectively, 123 novel transcripts were identified within these contigs. Prominently expressed transcripts in the NBF fat body library were represented by transcripts encoding ribosomal proteins. Thirty-five point four percent of all reads in the PBM library were represented by transcripts that encode yolk proteins. The most highly expressed were transcripts encoding members of the cathepsin b, vitellogenin, vitellogenic carboxypeptidase, and vitelline membrane protein families. Conclusion The two fat body transcriptomes were considerably different from each other in terms of transcript expression in terms of abundances of transcripts and genes expressed. They reflect the physiological shift of the pre-feeding fat body from a resting state to vitellogenic gene expression after feeding.

Paleognathous Carinate Birds from the Early Tertiary of North America

Fossils newly discovered in the Paleocene and early Eocene of western North America document some of the oldest birds known from nearly complete skeletons. These were medium-sized carinates with powers of sustained flight but which had a paleognathous palate like that of the flightless ostrich-like birds and the tinamous. The fossils provide additional evidence that the paleognathous palate is probably primitive and therefore should not be cited as a derived character state to define the ostrich-like birds as a monophyletic group.

CHAPTER 5 – Phylogeny and Evolution of 12S rDNA in Gruiformes (Aves)

In this chapter, several observations and inferences about the evolutionary dynamics and character evolution of the 12S rDNA molecule have been presented. These include variation in secondary structure resulting from stem migration and uncompensated insertions and deletions within stems; replication slippage as a mechanism of sequence length variation in loops; differences in per-site substitution rates between birds and mammals; the process of compensatory substitution in stems; and differences in distributions of synapomorphies and homoplasies that are spatially correlated with functional and structural regions of 12S rDNA. A robust but simplified estimate of the instantaneous ratio of rates between transversions to transitions is calculated for the 12S rDNA of Gruiformes. 12S rDNA is not entirely saturated by homoplasious substitutions at the levels of gruiform divergence, because it performs well at resolving much older divergences. Yet it exhibits sufficient noise to hinder the resolution of a phylogeny that may be characterized by relatively short internodal branches. High rates of substitution thus are not confined to particular sites across taxa; they are found in different locations in different lineages.

Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor

BackgroundThe availability of multiple avian genome sequence assemblies greatly improves our ability to define overall genome organization and reconstruct evolutionary changes. In birds, this has previously been impeded by a near intractable karyotype and relied almost exclusively on comparative molecular cytogenetics of only the largest chromosomes. Here, novel whole genome sequence information from 21 avian genome sequences (most newly assembled) made available on an interactive browser (Evolution Highway) was analyzed.ResultsFocusing on the six best-assembled genomes allowed us to assemble a putative karyotype of the dinosaur ancestor for each chromosome. Reconstructing evolutionary events that led to each species’ genome organization, we determined that the fastest rate of change occurred in the zebra finch and budgerigar, consistent with rapid speciation events in the Passeriformes and Psittaciformes. Intra- and interchromosomal changes were explained most parsimoniously by a series of inversions and translocations respectively, with breakpoint reuse being commonplace. Analyzing chicken and zebra finch, we found little evidence to support the hypothesis of an association of evolutionary breakpoint regions with recombination hotspots but some evidence to support the hypothesis that microchromosomes largely represent conserved blocks of synteny in the majority of the 21 species analyzed. All but one species showed the expected number of microchromosomal rearrangements predicted by the haploid chromosome count. Ostrich, however, appeared to retain an overall karyotype structure of 2n = 80 despite undergoing a large number (26) of hitherto un-described interchromosomal changes.ConclusionsResults suggest that mechanisms exist to preserve a static overall avian karyotype/genomic structure, including the microchromosomes, with widespread interchromosomal change occurring rarely (e.g., in ostrich and budgerigar lineages). Of the species analyzed, the chicken lineage appeared to have undergone the fewest changes compared to the dinosaur ancestor.

POSTCRANIAL ANATOMY OF VIVERRAVUS (MAMMALIA, CARNIVORA) AND IMPLICATIONS FOR SUBSTRATE USE IN BASAL CARNIVORA

Abstract A postcranial skeleton of the viverravid carnivoran, Viverravus acutus from the early Eocene of Wyoming, is described and compared to contemporary carnivorans (the viverravid Didymictis, and the miacids Miacis and Vulpavus), and to extant taxa belonging to the families Mustelidae, Procyonidae, Canidae, Viverridae, and Herpestidae. Based on humeral and femoral midshaft diameters, body mass for this animal is estimated to have been about 250 g, less than all but a few living species of Carnivora. Shoulder and hip morphology indicate a considerable range of motion and the structure of the humeroulnar joint suggests habitually flexed postures, characteristics typical of extant carnivorans that are excellent climbers. These similarities are also shared with miacids, supporting the hypothesis that basal members of the order Carnivora were well adapted for exploiting arboreal habitats. An astragalus tentatively attributed to the middle Eocene species Viverravus gracilis, however, is similar to that of Didymictis and suggests a greater emphasis on terrestrial locomotion than is found in miacids.

Response to Comment on "Whole-genome analyses resolve early branches in the tree of life of modern birds"

Mitchell et al. argue that divergence-time estimates for our avian phylogeny were too young because of an “inappropriate” maximum age constraint for the most recent common ancestor of modern birds and that, as a result, most modern bird orders diverged before the Cretaceous-Paleogene mass extinction event 66 million years ago instead of after. However, their interpretations of the fossil record and timetrees are incorrect.