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 molecular timescale of eukaryote evolution and the rise of complex multicellular life

BACKGROUND: The pattern and timing of the rise in complex multicellular life during Earth's history has not been established. Great disparity persists between the pattern suggested by the fossil record and that estimated by molecular clocks, especially for plants, animals, fungi, and the deepest branches of the eukaryote tree. Here, we used all available protein sequence data and molecular clock methods to place constraints on the increase in complexity through time. RESULTS: Our phylogenetic analyses revealed that (i) animals are more closely related to fungi than to plants, (ii) red algae are closer to plants than to animals or fungi, (iii) choanoflagellates are closer to animals than to fungi or plants, (iv) diplomonads, euglenozoans, and alveolates each are basal to plants+animals+fungi, and (v) diplomonads are basal to other eukaryotes (including alveolates and euglenozoans). Divergence times were estimated from global and local clock methods using 20–188 proteins per node, with data treated separately (multigene) and concatenated (supergene). Different time estimation methods yielded similar results (within 5%): vertebrate-arthropod (964 million years ago, Ma), Cnidaria-Bilateria (1,298 Ma), Porifera-Eumetozoa (1,351 Ma), Pyrenomycetes-Plectomycetes (551 Ma), Candida-Saccharomyces (723 Ma), Hemiascomycetes-filamentous Ascomycota (982 Ma), Basidiomycota-Ascomycota (968 Ma), Mucorales-Basidiomycota (947 Ma), Fungi-Animalia (1,513 Ma), mosses-vascular plants (707 Ma), Chlorophyta-Tracheophyta (968 Ma), Rhodophyta-Chlorophyta+Embryophyta (1,428 Ma), Plantae-Animalia (1,609 Ma), Alveolata-plants+animals+fungi (1,973 Ma), Euglenozoa-plants+animals+fungi (1,961 Ma), and Giardia-plants+animals+fungi (2,309 Ma). By extrapolation, mitochondria arose approximately 2300-1800 Ma and plastids arose 1600-1500 Ma. Estimates of the maximum number of cell types of common ancestors, combined with divergence times, showed an increase from two cell types at 2500 Ma to ~10 types at 1500 Ma and 50 cell types at ~1000 Ma. CONCLUSIONS: The results suggest that oxygen levels in the environment, and the ability of eukaryotes to extract energy from oxygen, as well as produce oxygen, were key factors in the rise of complex multicellular life. Mitochondria and organisms with more than 2–3 cell types appeared soon after the initial increase in oxygen levels at 2300 Ma. The addition of plastids at 1500 Ma, allowing eukaryotes to produce oxygen, preceded the major rise in complexity