The genetic basis of conspicuous coloration in the Guadeloupean anole: Evolution by sexual and ecological selection.

Understanding how natural selection acts on the genome and contributes to the process of speciation is a primary aim of the study of evolution. Here we used natural variation in two subspecies of the Guadeloupean anole ( ssp.), from the island of Guadeloupe in the Lesser Antilles, to explore the genomic basis of adaptation and speciation in lizards.

Loci associated with skin pigmentation identified in African populations.

Despite the wide range of skin pigmentation in humans, little is known about its genetic basis in global populations. Examining ethnically diverse African genomes, we identify variants in or near , , , , , and that are significantly associated with skin pigmentation. Genetic evidence indicates that the light pigmentation variant at was introduced into East Africa by gene flow from non-Africans.

A phylogenomic analysis of turtles.

Molecular analyses of turtle relationships have overturned prevailing morphological hypotheses and prompted the development of a new taxonomy. Here we provide the first genome-scale analysis of turtle phylogeny. We sequenced 2381 ultraconserved element (UCE) loci representing a total of 1,718,154bp of aligned sequence.

Hybridization reveals the evolving genomic architecture of speciation.

The rate at which genomes diverge during speciation is unknown, as are the physical dynamics of the process. Here, we compare full genome sequences of 32 butterflies, representing five species from a hybridizing Heliconius butterfly community, to examine genome-wide patterns of introgression and infer how divergence evolves during the speciation process. Our analyses reveal that initial divergence is restricted to a small fraction of the genome, largely clustered around known wing-patterning genes.

Divergence in coloration and ecological speciation in the Anolis marmoratus species complex.

Adaptive divergence in coloration is expected to produce reproductive isolation in species that use colourful signals in mate choice and species recognition. Indeed, many adaptive radiations are characterized by differentiation in colourful signals, suggesting that divergent selection acting on coloration may be an important component of speciation. Populations in the Anolis marmoratus species complex from the Caribbean island of Guadeloupe display striking divergence in the colour and pattern of adult males that occurs over small geographic distances, suggesting strong divergent selection.

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.

More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs.

We present the first genomic-scale analysis addressing the phylogenetic position of turtles, using over 1000 loci from representatives of all major reptile lineages including tuatara. Previously, studies of morphological traits positioned turtles either at the base of the reptile tree or with lizards, snakes and tuatara (lepidosaurs), whereas molecular analyses typically allied turtles with crocodiles and birds (archosaurs). A recent analysis of shared microRNA families found that turtles are more closely related to lepidosaurs.

Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes.

The International Crocodilian Genomes Working Group (ICGWG) will sequence and assemble the American alligator (Alligator mississippiensis), saltwater crocodile (Crocodylus porosus) and Indian gharial (Gavialis gangeticus) genomes. The status of these projects and our planned analyses are described.

Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales.

Although massively parallel sequencing has facilitated large-scale DNA sequencing, comparisons among distantly related species rely upon small portions of the genome that are easily aligned. Methods are needed to efficiently obtain comparable DNA fragments prior to massively parallel sequencing, particularly for biologists working with non-model organisms. We introduce a new class of molecular marker, anchored by ultraconserved genomic elements (UCEs), that universally enable target enrichment and sequencing of thousands of orthologous loci across species separated by hundreds of millions of years of evolution.

Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis.

Phylogenomics offers the potential to fully resolve the Tree of Life, but increasing genomic coverage also reveals conflicting evolutionary histories among genes, demanding new analytical strategies for elucidating a single history of life. Here, we outline a phylogenomic approach using a novel class of phylogenetic markers derived from ultraconserved elements and flanking DNA. Using species-tree analysis that accounts for discord among hundreds of independent loci, we show that this class of marker is useful for recovering deep-level phylogeny in placental mammals.

Developing a community-based genetic nomenclature for anole lizards.

Background: Comparative studies of amniotes have been hindered by a dearth of reptilian molecular sequences. With the genomic assembly of the green anole, Anolis carolinensis available, non-avian reptilian genes can now be compared to mammalian, avian, and amphibian homologs. Furthermore, with more than 350 extant species in the genus Anolis, anoles are an unparalleled example of tetrapod genetic diversity and divergence.

smogd: software for the measurement of genetic diversity.

Software for the measurement of genetic diversity (SMOGD) is a web-based application for the calculation of the recently proposed genetic diversity indices G'(ST) and D(est) . SMOGD includes bootstrapping functionality for estimating the variance, standard error and confidence intervals of estimated parameters, and SMOGD also generates genetic distance matrices from pairwise comparisons between populations. SMOGD accepts standard, multilocus Genepop and Arlequin formatted input files and produces HTML and tab-delimited output.

Polymorphic microsatellite loci from Sprague's pipit (Anthus spragueii), a grassland endemic passerine bird.

We developed 11 novel microsatellite loci for Sprague's pipit (Anthus spragueii), a songbird endemic to the Northern Great Plains of central North America. These loci were screened in 21 individuals from southern Saskatchewan, Canada. All 11 loci were polymorphic, with the number of alleles per locus ranging from five to 23, polymorphic information content from 0.

Development and characterization of microsatellite loci in the American white pelican (Pelecanus erythrorhynchos).

We isolated and characterized nine microsatellite loci from the American white pelican, Pelecanus erythrorhynchos. The loci were screened in 23 individuals from the eastern and western populations of North America and were polymorphic, with the number of alleles per locus ranging from two to eight. Polymorphic information content ranged from 0.

PERMANENT GENETIC RESOURCES: Fifteen polymorphic microsatellite DNA loci from Hawaii's Metrosideros polymorpha (Myrtaceae: Myrtales), a model species for ecology and evolution.

We developed 15 polymorphic microsatellite loci from the Hawaiian tree Metrosideros polymorpha. These loci were screened against two varieties from several populations and from 23 individuals from one mid-elevation population on Hawaii Island. Loci were variable with the number of alleles per locus ranging from three to 24.

Thirteen polymorphic microsatellite DNA loci from whiptails of the genus Aspidoscelis (Teiidae: Squamata) and related cnemidophorine lizards.

We describe polymerase chain reaction primers and amplification conditions for 13 microsatellite DNA loci isolated from two bisexual species of whiptail lizards Aspidoscelis costata huico and Aspidoscelis inornata. Primers were tested on either 16 or 48 individuals of A. c.