Accurate Reconstruction of Molecular Phylogenies for Proteins Using Codon and Amino Acid Unified Sequence Alignments (CAUSA)

Based on molecular clock hypothesis, and neutral theory of molecular evolution, molecular phylogenies have been widely used for inferring evolutionary history of organisms and individual genes. Traditionally, alignments and phylogeny trees of proteins and their coding DNA sequences are constructed separately, thus often different conclusions were drawn. Here we present a new strategy for sequence alignment and phylogenetic tree reconstruction, codon and amino acid unified sequence alignment (CAUSA), which aligns DNA and protein sequences and draw phylogenetic trees in a unified manner. We demonstrated that CAUSA improves both the accuracy of multiple sequence alignments and phylogenetic trees by solving a variety of molecular evolutionary problems in virus, bacteria and mammals. Our results support the hypothesis that the molecular clock for proteins has two pointers existing separately in DNA and protein sequences. It is more accurate to read the molecular clock by combination (additive) of these two pointers, since the ticking rates of them are sometimes consistent, sometimes different. CAUSA software were released as Open Source under GNU/GPL license, and are downloadable free of charge from the website www.dnapluspro.com

W(h)ither Fossils? Studying Morphological Character Evolution in the Age of Molecular Sequences

A major challenge in the post-genomics era will be to integrate molecular sequence data from extant organisms with morphological data from fossil and extant taxa into a single, coherent picture of phylogenetic relationships; only then will these phylogenetic hypotheses be effectively applied to the study of morphological character evolution. At least two analytical approaches to solving this problem have been utilized: (1) simultaneous analysis of molecular sequence and morphological data with fossil taxa included as terminals in the analysis, and (2) the molecular scaffold approach, in which morphological data are analyzed over a molecular backbone (with constraints that force extant taxa into positions suggested by sequence data). The perceived obstacles to including fossil taxa directly in simultaneous analyses of morphological and molecular sequence data with extant taxa include: (1) that fossil taxa are missing the molecular sequence portion of the character data; (2) that morphological characters might be misleading due to convergence; and (3) character weighting, specifically how and whether to weight characters in the morphological partition relative to characters in the molecular sequence data partition. The molecular scaffold has been put forward as a potential solution to at least some of these problems. Using examples of simultaneous analyses from the literature, as well as new analyses of previously published morphological and molecular sequence data matrices for extant and fossil Chiroptera (bats), we argue that the simultaneous analysis approach is superior to the molecular scaffold approach, specifically addressing the problems to which the molecular scaffold has been suggested as a solution. Finally, the application of phylogenetic hypotheses including fossil taxa (whatever their derivation) to the study of morphological character evolution is discussed, with special emphasis on scenarios in which fossil taxa are likely to be most enlightening: (1) in determining the sequence of character evolution; (2) in determining the timing of character evolution; and (3) in making inferences about the presence or absence of characteristics in fossil taxa that may not be directly observable in the fossil record. Published By: Missouri Botanical Garde

Introgressive Hybridization and the Evolution of Lake-Adapted Catostomid Fishes.

Hybridization has been identified as a significant factor in the evolution of plants as groups of interbreeding species retain their phenotypic integrity despite gene exchange among forms. Recent studies have identified similar interactions in animals; however, the role of hybridization in the evolution of animals has been contested. Here we examine patterns of gene flow among four species of catostomid fishes from the Klamath and Rogue rivers using molecular and morphological traits. Catostomus rimiculus from the Rogue and Klamath basins represent a monophyletic group for nuclear and morphological traits; however, the Klamath form shares mtDNA lineages with other Klamath Basin species (C. snyderi, Chasmistes brevirostris, Deltistes luxatus). Within other Klamath Basin taxa, D. luxatus was largely fixed for alternate nuclear alleles relative to C. rimiculus, while Ch. brevirostris and C. snyderi exhibited a mixture of these alleles. Deltistes luxatus was the only Klamath Basin species that exhibited consistent covariation of nuclear and mitochondrial traits and was the primary source of mismatched mtDNA in Ch. brevirostris and C. snyderi, suggesting asymmetrical introgression into the latter species. In Upper Klamath Lake, D. luxatus spawning was more likely to overlap spatially and temporally with C. snyderi and Ch. brevirostris than either of those two with each other. The latter two species could not be distinguished with any molecular markers but were morphologically diagnosable in Upper Klamath Lake, where they were largely spatially and temporally segregated during spawning. We examine parallel evolution and syngameon hypotheses and conclude that observed patterns are most easily explained by introgressive hybridization among Klamath Basin catostomids

Reconstructing phylogeny from RNA secondary structure via simulated evolution

DNA sequences of genes encoding functional RNA molecules (e.g., ribosomal RNAs) are commonly used in phylogenetics (i.e. to infer evolutionary history). Trees derived from ribosomal RNA (rRNA) sequences, however, are inconsistent with other molecular data in investigations of deep branches in the tree of life. Since much of te functional constraints on the gene products (i.e. RNA molecules) relate to three-dimensional structure, rather than their actual sequences, accumulated mutations in the gene sequences may obscure phylogenetic signal over very large evolutionary time-scales. Variation in structure, however, may be suitable for phylogenetic inference even under extreme sequence divergence. To evaluate qualitatively the manner in which structural evolution relates to sequence change, we simulated the evolution of RNA sequences under various constraints on structural change

First detection of kobuvirus in farm animals in Brazil and the Netherlands.

Animal kobuviruses have been described in pigs, cattle, sheep and bats in countries in Asia and Europe. The virus can be detected in fecal and serum samples of infected animals with or without diarrhea, but most of the clinical as well as epidemiological features of kobuvirus infection are still unknown. This study reports the first detection of kobuvirus in farm animals from Brazil and the Netherlands and the molecular analysis of the detected strains. In Brazil, 53% (61/115) of the pigs (suckling, weaned and sows) were shedding porcine kobuvirus in feces, while in the Netherlands 16.7% (3/18) of the tested weaned pigs were infected. Kobuviruses detected in fecal samples of pigs in Brazil showed association (p = 0.0002) with diarrhea. In pig serum, kobuvirus was detected at different ages (3, 21, 36, 60, 75, and 180 days), with an overall rate of 76.7% (23/30). The sequencing of amplicons detected in serum of pigs of different ages suggested reinfection and no persistent infection. Kobuvirus was also detected in sheep and cattle feces from Brazil and the Netherlands, respectively. Phylogenetic analyses of Brazilian and Dutch kobuviruses from pig, cattle and sheep revealed genetic variability, particularly in one strain detected in sheep feces, which was more closely related to human Aichi virus. The molecular and phylogenetic analyses performed with other published kobuvirus strains and the strains presented in this study, showed that, in most of the cases, kobuvirus seems to group according to host species, but not to geographical region of origin. The data presented in this study contribute to the comprehension of kobuvirus epidemiology and also to the molecular identification of kobuvirus strains circulating worldwide

Global distribution of two fungal pathogens threatening endangered sea turtles

This work was supported by grants of Ministerio de Ciencia e Innovación, Spain (CGL2009-10032, CGL2012-32934). J.M.S.R was supported by PhD fellowship of the CSIC (JAEPre 0901804). The Natural Environment Research Council and the Biotechnology and Biological Sciences Research Council supported P.V.W. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Thanks Machalilla National Park in Ecuador, Pacuare Nature Reserve in Costa Rica, Foundations Natura 2000 in Cape Verde and Equilibrio Azul in Ecuador, Dr. Jesus Muñoz, Dr. Ian Bell, Dr. Juan Patiño for help and technical support during samplingPeer reviewedPublisher PD