Eldredge Bermingham

Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species

The human genome project has been recently complemented by whole-genome assessment sequence of 32 mammals and 24 nonmammalian vertebrate species suitable for comparative genomic analyses. Here we anticipate a precipitous drop in costs and increase in sequencing efficiency, with concomitant development of improved annotation technology and, therefore, propose to create a collection of tissue and DNA specimens for 10,000 vertebrate species specifically designated for whole-genome sequencing in the very near future. For this purpose, we, the Genome 10K Community of Scientists (G10KCOS), will assemble and allocate a biospecimen collection of some 16,203 representative vertebrate species spanning evolutionary diversity across living mammals, birds, nonavian reptiles, amphibians, and fishes (ca. 60,000 living species). In this proposal, we present precise counts for these 16,203 individual species with specimens presently tagged and stipulated for DNA sequencing by the G10KCOS. DNA sequencing has ushered in a new era of investigation in the biological sciences, allowing us to embark for the first time on a truly comprehensive study of vertebrate evolution, the results of which will touch nearly every aspect of vertebrate biological enquiry.

Evolutionary Relationships, Cospeciation, and Host Switching in Avian Malaria Parasites

We used phylogenetic analyses of cytochrome b sequences of malaria parasites and their avian hosts to assess the coevolutionary relationships between host and parasite lineages. Many lineages of avian malaria parasites have broad host distributions, which tend to obscure cospeciation events. The hosts of a single parasite or of closely related parasites were nonetheless most frequently recovered from members of the same host taxonomic family, more so than expected by chance. However, global assessments of the relationship between parasite and host phylogenetic trees, using Component and ParaFit, failed to detect significant cospeciation. The event-based approach employed by TreeFitter revealed significant cospeciation and duplication with certain cost assignments for these events, but host switching was consistently more prominent in matching the parasite tree to the host tree. The absence of a global cospeciation signal despite conservative host distribution most likely reflects relatively frequent acquisition of new hosts by individual parasite lineages. Understanding these processes will require a more refined species concept for malaria parasites and more extensive sampling of parasite distributions across hosts. If parasites can disperse between allopatric host populations through alternative hosts, cospeciation may not have a strong influence on the architecture of host-parasite relationships. Rather, parasite speciation may happen more often in conjunction with the acquisition of new hosts followed by divergent selection between host lineages in sympatry. Detailed studies of the phylogeographic distributions of hosts and parasites are needed to characterize these events.

Molecular Systematic Analysis Reveals Cryptic Tertiary Diversification of a Widespread Tropical Rain Forest Tree

The broad geographic range of many Neotropical rain forest tree species implies excellent dispersal abilities or range establishment that preceded the formation of current dispersal barriers. In order to initiate historical analyses of such widespread Neotropical trees, we sequenced the nuclear ribosomal spacer (ITS) region of Symphonia globulifera L. f. (Clusiaceae) from populations spanning the Neotropics and western Africa. This rain forest tree has left unmistakable Miocene fossils in Mesoamerica (15.5–18.2 Ma) and in South America (∼15 Ma). Although marine dispersal of S. globulifera is considered improbable, our study establishes three marine dispersal events leading to the colonization of Mesoamerica, the Amazon basin, and the West Indies, thus supporting the paleontological data. Our phylogeographic analysis revealed the spatial extent of the three Neotropical S. globulifera clades, which represent trans‐Andes (ndocumentclass{aastex}nusepackage{amsbsy}nusepackage{amsfonts}nusepackage{amssymb}nusepackage{bm}nusepackage{mathrsfs}nusepackage{pifont}nusepackage{stmaryrd}nusepackage{textcomp}nusepackage{portland,xspace}nusepackage{amsmath,amsxtra}nusepackage[OT2,OT1]{fontenc}nnewcommandcyr{nrenewcommandrmdefault{wncyr}nrenewcommandsfdefault{wncyss}nrenewcommandencodingdefault{OT2}nnormalfontnselectfont}nDeclareTextFontCommand{textcyr}{cyr}npagestyle{empty}nDeclareMathSizes{10}{9}{7}{6}nbegin{document}nlandscapen

Host Specialization and Geographic Localization of Avian Malaria Parasites: A Regional Analysis in the Lesser Antilles

mathrm{Mesoamerica},+mathrm{west},

The Causes of Evolutionary Radiations in Archipelagoes: Passerine Birds in the Lesser Antilles

nend{document} Ecuador), cis‐Andes (ndocumentclass{aastex}nusepackage{amsbsy}nusepackage{amsfonts}nusepackage{amssymb}nusepackage{bm}nusepackage{mathrsfs}nusepackage{pifont}nusepackage{stmaryrd}nusepackage{textcomp}nusepackage{portland,xspace}nusepackage{amsmath,amsxtra}nusepackage[OT2,OT1]{fontenc}nnewcommandcyr{nrenewcommandrmdefault{wncyr}nrenewcommandsfdefault{wncyss}nrenewcommandencodingdefault{OT2}nnormalfontnselectfont}nDeclareTextFontCommand{textcyr}{cyr}npagestyle{empty}nDeclareMathSizes{10}{9}{7}{6}nbegin{document}nlandscapen

Hybridization in Large-Bodied New World Primates

mathrm{Amazonia},+mathrm{Guiana},