Eleutherodactylus thorectes

Number of Pages: 2Integrative BiologyGeological Science

Eleutherodactylus amadeus

Number of Pages: 2Integrative BiologyGeological Science

Eleutherodactylus chlorophenax

Number of Pages: 2Integrative BiologyGeological Science

Evolutionary sequence analysis of complete eukaryote genomes

BACKGROUND: Gene duplication and gene loss during the evolution of eukaryotes have hindered attempts to estimate phylogenies and divergence times of species. Although current methods that identify clusters of orthologous genes in complete genomes have helped to investigate gene function and gene content, they have not been optimized for evolutionary sequence analyses requiring strict orthology and complete gene matrices. Here we adopt a relatively simple and fast genome comparison approach designed to assemble orthologs for evolutionary analysis. Our approach identifies single-copy genes representing only species divergences (panorthologs) in order to minimize potential errors caused by gene duplication. We apply this approach to complete sets of proteins from published eukaryote genomes specifically for phylogeny and time estimation. RESULTS: Despite the conservative criterion used, 753 panorthologs (proteins) were identified for evolutionary analysis with four genomes, resulting in a single alignment of 287,000 amino acids. With this data set, we estimate that the divergence between deuterostomes and arthropods took place in the Precambrian, approximately 400 million years before the first appearance of animals in the fossil record. Additional analyses were performed with seven, 12, and 15 eukaryote genomes resulting in similar divergence time estimates and phylogenies. CONCLUSION: Our results with available eukaryote genomes agree with previous results using conventional methods of sequence data assembly from genomes. They show that large sequence data sets can be generated relatively quickly and efficiently for evolutionary analyses of complete genomes

Tres especies nuevas de Pristimantis (Lissamphibia: Anura) en los bosques montanos de la Cordillera Yanachaga en el centro del Perú

We describe three additional new species of Pristimantis from the Cordillera Yanachaga, a part of the Andes in central Peru. Analyses of DNA sequences of the mitochondrial rRNA genes show that one species is a close relative of P. bipunctatus (P. conspicillatus Group), another is a close relative of P. stictogaster (P. peruvianus Group), and the third is related to several species in the P. unistrigatus Group. The first two species are morphologically similar to their closest relatives but occur at lower elevations. Twenty-nine species of Pristimantis and Phrynopus are known from the vicinity of the Cordillera Yanachaga. The number of species, especially of Pristimantis, is high in the humid montane forest in comparison with other sites in humid montane forests in Peru, but the number is lower than on the western slopes of the Andes in Ecuador.Describimos tres especies nuevas de Pristimantis provenientes de la Cordillera Yanachaga, en los Andes del centro del Perú. Los análisis de las secuencias de ADN mitocondrial de genes ribosomales muestran que una de las especies está cercanamente relacionada con P. bipunctatus (Grupo P. conspicillatus), la segunda especie con P. stictogaster (Grupo P. peruvianus) y la tercera con varias especies del Grupo P. unistrigatus. Las primeras dos especies son morfológicamente similares a sus respectivas especies hermanas, pero sin embargo habitan en elevaciones más bajas. Se conocen 29 especies de ranas del g´nero Phrynopus y Pristimantis en las inmediaciones de la Cordillera Yanachaga. Esta diversidad de especies, particularmente de Pristimantis, es elevada en comparación con otras localidades de características similares en el Perú; sin embargo, es menor a la reportada en la vertiente occidental de los Andes del Ecuador

The evolutionary position of nematodes

BACKGROUND: The complete genomes of three animals have been sequenced by global research efforts: a nematode worm (Caenorhabditis elegans), an insect (Drosophila melanogaster), and a vertebrate (Homo sapiens). Remarkably, their relationships have yet to be clarified. The confusion concerns the enigmatic position of nematodes. Traditionally, nematodes have occupied a basal position, in part because they lack a true body cavity. However, the leading hypothesis now joins nematodes with arthropods in a molting clade, Ecdysozoa, based on data from several genes. RESULTS: We tested the Ecdysozoa hypothesis with analyses of more than 100 nuclear protein alignments, under conditions that would expose biases, and found that it was not supported. Instead, we found significant support for the traditional hypothesis, Coelomata. Our result is robust to different rates of sequence change among genes and lineages, different numbers of taxa, and different species of nematodes. CONCLUSION: We conclude that insects (arthropods) are genetically and evolutionarily closer to humans than to nematode worms

A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land

BACKGROUND: The timescale of prokaryote evolution has been difficult to reconstruct because of a limited fossil record and complexities associated with molecular clocks and deep divergences. However, the relatively large number of genome sequences currently available has provided a better opportunity to control for potential biases such as horizontal gene transfer and rate differences among lineages. We assembled a data set of sequences from 32 proteins (~7600 amino acids) common to 72 species and estimated phylogenetic relationships and divergence times with a local clock method. RESULTS: Our phylogenetic results support most of the currently recognized higher-level groupings of prokaryotes. Of particular interest is a well-supported group of three major lineages of eubacteria (Actinobacteria, Deinococcus, and Cyanobacteria) that we call Terrabacteria and associate with an early colonization of land. Divergence time estimates for the major groups of eubacteria are between 2.5–3.2 billion years ago (Ga) while those for archaebacteria are mostly between 3.1–4.1 Ga. The time estimates suggest a Hadean origin of life (prior to 4.1 Ga), an early origin of methanogenesis (3.8–4.1 Ga), an origin of anaerobic methanotrophy after 3.1 Ga, an origin of phototrophy prior to 3.2 Ga, an early colonization of land 2.8–3.1 Ga, and an origin of aerobic methanotrophy 2.5–2.8 Ga. CONCLUSIONS: Our early time estimates for methanogenesis support the consideration of methane, in addition to carbon dioxide, as a greenhouse gas responsible for the early warming of the Earths' surface. Our divergence times for the origin of anaerobic methanotrophy are compatible with highly depleted carbon isotopic values found in rocks dated 2.8–2.6 Ga. An early origin of phototrophy is consistent with the earliest bacterial mats and structures identified as stromatolites, but a 2.6 Ga origin of cyanobacteria suggests that those Archean structures, if biologically produced, were made by anoxygenic photosynthesizers. The resistance to desiccation of Terrabacteria and their elaboration of photoprotective compounds suggests that the common ancestor of this group inhabited land. If true, then oxygenic photosynthesis may owe its origin to terrestrial adaptations