Bilaterian Phylogeny Based on Analyses of a Region of the Sodium-potassium ATPase beta-subunit Gene

Molecular investigations of deep-level relationships within and among the animal phyla have been hampered by a lack of slowly evolving genes that are amenable to study by molecular systematists. To provide new data for use in deep-level metazoan phylogenetic studies, primers were developed to amplify a 1.3-kb region of the alpha subunit of the nuclear-encoded sodium-potassium ATPase gene from 31 bilaterians representing several phyla. Maximum parsimony, maximum likelihood, and Bayesian analyses of these sequences (combined with ATPase sequences for 23 taxa downloaded from GenBank) yield congruent trees that corroborate recent findings based on analyses of other data sets (e.g., the 18S ribosomal RNA gene). The ATPase-based trees support monophyly for several clades (including Lophotrochozoa, a form of Ecdysozoa, Vertebrata, Mollusca, Bivalvia, Gastropoda, Arachnida, Hexapoda, Coleoptera, and Diptera) but do not support monophyly for Deuterostomia, Arthropoda, or Nemertea. Parametric bootstrapping tests reject monophyly for Arthropoda and Nemertea but are unable to reject deuterostome monophyly. Overall, the sodium-potassium ATPase alpha-subunit gene appears to be useful for deep-level studies of metazoan phylogeny

Taxonomy, biogeography and DNA barcodes of Geodiaspecies (Porifera, Demospongiae, Tetractinellida) in the Atlantic boreo-arctic region

Geodia species north of 60°N in the Atlantic appeared in the literature for the first time when Bowerbank described Geodia barretti and G. macandrewii in 1858 from western Norway. Since then, a number of species have been based on material from various parts of the region: G. simplex, Isops phlegraei, I. pallida, I. sphaeroides, Synops pyriformis, G. parva, G. normani, G. atlantica, Sidonops mesotriaena (now called G. hentscheli), and G. simplicissima. In addition to these 12 nominal species, four species described from elsewhere are claimed to have been identified in material from the northeast Atlantic, namely G. nodastrella and G. cydonium (and its synonyms Cydonium muelleri and Geodia gigas ). In this paper, we revise the boreo-arctic Geodia species using morphological, molecular, and biogeographical data. We notably compare northwest and northeast Atlantic specimens. Biological data (reproduction, biochemistry, microbiology, epibionts) for each species are also reviewed. Our results show that there are six valid species of boreo-arctic Atlantic Geodia while other names are synonyms or mis-identifications. Geodia barretti, G. atlantica, G. macandrewii, and G. hentscheli are well established and widely distributed. The same goes for Geodia phlegraei, but this species shows a striking geographical and bathymetric variation, which led us to recognize two species, G. phlegraei and G. parva(here resurrected). Some Geodia are arctic species (G. hentscheli, G. parva), while others are typically boreal (G. atlantica, G. barretti, G. phlegraei , G. macandrewii). No morphological differences were found between specimens from the northeast and northwest Atlantic, except for G. parva . The Folmer cytochrome oxidase subunit I (COI) fragment is unique for every species and invariable over their whole distribution range, except for G. barretti which had two haplotypes. 18S is unique for four species but cannot discriminate G. phlegraei and G. parva. Two keys to the boreo-arctic Geodia are included, one based on external morphology, the other based on spicule morphology

SPRIT: Identifying horizontal gene transfer in rooted phylogenetic trees

<p>Abstract</p> <p>Background</p> <p>Phylogenetic trees based on sequences from a set of taxa can be incongruent due to horizontal gene transfer (HGT). By identifying the HGT events, we can reconcile the gene trees and derive a taxon tree that adequately represents the species' evolutionary history. One HGT can be represented by a rooted Subtree Prune and Regraft (<smcaps>R</smcaps>SPR) operation and the number of <smcaps>R</smcaps>SPRs separating two trees corresponds to the minimum number of HGT events. Identifying the minimum number of <smcaps>R</smcaps>SPRs separating two trees is NP-hard, but the problem can be reduced to fixed parameter tractable. A number of heuristic and two exact approaches to identifying the minimum number of <smcaps>R</smcaps>SPRs have been proposed. This is the first implementation delivering an exact solution as well as the intermediate trees connecting the input trees.</p> <p>Results</p> <p>We present the SPR Identification Tool (SPRIT), a novel algorithm that solves the fixed parameter tractable minimum <smcaps>R</smcaps>SPR problem and its GPL licensed Java implementation. The algorithm can be used in two ways, exhaustive search that guarantees the minimum <smcaps>R</smcaps>SPR distance and a heuristic approach that guarantees finding a solution, but not necessarily the minimum one. We benchmarked SPRIT against other software in two different settings, small to medium sized trees i.e. five to one hundred taxa and large trees i.e. thousands of taxa. In the small to medium tree size setting with random artificial incongruence, SPRIT's heuristic mode outperforms the other software by always delivering a solution with a low overestimation of the <smcaps>R</smcaps>SPR distance. In the large tree setting SPRIT compares well to the alternatives when benchmarked on finding a minimum solution within a reasonable time. SPRIT presents both the minimum <smcaps>R</smcaps>SPR distance and the intermediate trees.</p> <p>Conclusions</p> <p>When used in exhaustive search mode, SPRIT identifies the minimum number of <smcaps>R</smcaps>SPRs needed to reconcile two incongruent rooted trees. SPRIT also performs quick approximations of the minimum <smcaps>R</smcaps>SPR distance, which are comparable to, and often better than, purely heuristic solutions. Put together, SPRIT is an excellent tool for identification of HGT events and pinpointing which taxa have been involved in HGT.</p

A Phylometagenomic Exploration of Oceanic Alphaproteobacteria Reveals Mitochondrial Relatives Unrelated to the SAR11 Clade

BACKGROUND: According to the endosymbiont hypothesis, the mitochondrial system for aerobic respiration was derived from an ancestral Alphaproteobacterium. Phylogenetic studies indicate that the mitochondrial ancestor is most closely related to the Rickettsiales. Recently, it was suggested that Candidatus Pelagibacter ubique, a member of the SAR11 clade that is highly abundant in the oceans, is a sister taxon to the mitochondrial-Rickettsiales clade. The availability of ocean metagenome data substantially increases the sampling of Alphaproteobacteria inhabiting the oxygen-containing waters of the oceans that likely resemble the originating environment of mitochondria. METHODOLOGY/PRINCIPAL FINDINGS: We present a phylogenetic study of the origin of mitochondria that incorporates metagenome data from the Global Ocean Sampling (GOS) expedition. We identify mitochondrially related sequences in the GOS dataset that represent a rare group of Alphaproteobacteria, designated OMAC (Oceanic Mitochondria Affiliated Clade) as the closest free-living relatives to mitochondria in the oceans. In addition, our analyses reject the hypothesis that the mitochondrial system for aerobic respiration is affiliated with that of the SAR11 clade. CONCLUSIONS/SIGNIFICANCE: Our results allude to the existence of an alphaproteobacterial clade in the oxygen-rich surface waters of the oceans that represents the closest free-living relative to mitochondria identified thus far. In addition, our findings underscore the importance of expanding the taxonomic diversity in phylogenetic analyses beyond that represented by cultivated bacteria to study the origin of mitochondria

Addition to Sweden’s freshwater sponge fauna and a phylogeographic study of &lt;i&gt;Spongilla lacustris&lt;/i&gt; (Spongillida, Porifera) in southern Sweden

Freshwater sponges constitute an overlooked part of the freshwater fauna in Sweden and there has been no recent systematic survey. Hitherto three species have been found in Sweden: Spongilla lacustris (Linnaeus, 1759), Ephydatia fluviatilis (Linnaeus, 1759) and E. muelleri (Lieberkühn, 1856). Neighbouring countries (Norway, Denmark, Estonia) harbour at least one additional species. We present a study on freshwater sponge diversity and distribution in the southern half of Sweden. We hypothesized dispersal within catchments to be less constrained than between, even at shorter intercatchment than intracatchment distances, and, as result, genetic distances being greater between than within catchments. We collected and identified freshwater sponges from 34 sites, using morphological and molecular data (coxI, 28S rRNA gene). We can report the presence of Eunapius fragilis (Leidy, 1851) in Sweden for the first time, and that S. lacustris is the most abundant and widely distributed freshwater sponge in Sweden. Genetic markers were tested on S. lacustris individuals for a phylogeographic study. From the 47 primers (24 markers), one pair presented successful amplification and enough variation for phylogeographic studies – i56, an intron located in a conserved gene. Seven different variants were found in the sampling area, but no clear population structure was observed.</p

Addition to Sweden’s freshwater sponge fauna and a phylogeographic study of Spongilla lacustris (Spongillida, Porifera) in southern Sweden

Freshwater sponges constitute an overlooked part of the freshwater fauna in Sweden and there has been no recent systematic survey. Hitherto three species have been found in Sweden: Spongilla lacustris (Linnaeus, 1759), Ephydatia fluviatilis (Linnaeus, 1759) and E. muelleri (Lieberkühn, 1856). Neighbouring countries (Norway, Denmark, Estonia) harbour at least one additional species. We present a study on freshwater sponge diversity and distribution in the southern half of Sweden. We hypothesized dispersal within catchments to be less constrained than between, even at shorter intercatchment than intracatchment distances, and, as result, genetic distances being greater between than within catchments. We collected and identified freshwater sponges from 34 sites, using morphological and molecular data (coxI, 28S rRNA gene). We can report the presence of Eunapius fragilis (Leidy, 1851) in Sweden for the first time, and that S. lacustris is the most abundant and widely distributed freshwater sponge in Sweden. Genetic markers were tested on S. lacustris individuals for a phylogeographic study. From the 47 primers (24 markers), one pair presented successful amplification and enough variation for phylogeographic studies – i56, an intron located in a conserved gene. Seven different variants were found in the sampling area, but no clear population structure was observed