Assembling the Tree of Life in Europe (AToLE)

A network of scientists under the umbrella of 'Assembling the Tree of Life in Europe (AToLE)' seeks funding under the FP7-Theme: Cooperation - Environment (including Climate Change and Biodiversity Conservation) programme of the European Commission.
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A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing

Evolutionary relationships among birds in Neoaves, the clade comprising the vast majority of avian diversity, have vexed systematists due to the ancient, rapid radiation of numerous lineages. We applied a new phylogenomic approach to resolve relationships in Neoaves using target enrichment (sequence capture) and high-throughput sequencing of ultraconserved elements (UCEs) in avian genomes. We collected sequence data from UCE loci for 32 members of Neoaves and one outgroup (chicken) and analyzed data sets that differed in their amount of missing data. An alignment of 1,541 loci that allowed missing data was 87% complete and resulted in a highly resolved phylogeny with broad agreement between the Bayesian and maximum-likelihood (ML) trees. Although results from the 100% complete matrix of 416 UCE loci were similar, the Bayesian and ML trees differed to a greater extent in this analysis, suggesting that increasing from 416 to 1,541 loci led to increased stability and resolution of the tree. Novel results of our study include surprisingly close relationships between phenotypically divergent bird families, such as tropicbirds (Phaethontidae) and the sunbittern (Eurypygidae) as well as between bustards (Otididae) and turacos (Musophagidae). This phylogeny bolsters support for monophyletic waterbird and landbird clades and also strongly supports controversial results from previous studies, including the sister relationship between passerines and parrots and the non-monophyly of raptorial birds in the hawk and falcon families. Although significant challenges remain to fully resolving some of the deep relationships in Neoaves, especially among lineages outside the waterbirds and landbirds, this study suggests that increased data will yield an increasingly resolved avian phylogeny.Comment: 30 pages, 1 table, 4 figures, 1 supplementary table, 3 supplementary figure

The fossil tragulids of the Siwalik Formations of Southern Asia

Tragulids are common in the Early Miocene through Pliocene Siwalik faunas of the Indian Subcontinent where they are represented by as many as 17 species. Large collections of Siwalik fossils have recently been made by collaborative projects from Harvard University, the University of Arizona, the Geological Survey of Pakistan, and the Pakistan Museum of Natural History. The collections together comprise over 3700 specimens, including dental, cranial, and postcranial elements. Most of this fossil material is from northern and southwestern Pakistan from well-dated stratigraphic sections. The oldest definite tragulids are from the Early Miocene Vihowa Formation and are around 18.7 Ma, while the youngest are in the Pliocene Tatrot Formation and are 3.3 Ma. The fossil tragulids of the Siwaliks differ from the extant species in a number of ways. Importantly, they have a much wider range of body sizes, ranging from 1 to nearly 76 kg. Consequently the small species overlap with the smallest species of extant Tragulus, while the large species approach medium size bovids and cervids. Compared to other ruminants, Siwalik tragulids are also relatively abundant and species rich. Although the status of some described species is uncertain, preliminary analysis indicates there are many as yet undescribed species. Three genera are known and typically at least four species co-exist at any one time during the Miocene. The history of the south Asian tragulids can be correlated to documented environmental changes. The Siwalik deposits formed in a large fluvial system, with mostly forested or wooded low relief floodplains having abundant cover and fruit. Isotopic analyses of tooth enamel and soil carbonates indicate the vegetation was dominated by C3 plants until 9 Ma, after which there was a shift to a more seasonally dry monsoon climate, undoubtedly accounting for a Late Miocene change in the relative abundance of tragulids