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Molecular Phylogenetics and Evolution

Hong-Juan Wang, Wei-Tao Li, Ya-Nan Liu, Fu-Sheng Yang, Xiao-Quan Wang
Phylogenomics has shown great potential in resolving evolutionary relationships at different taxonomical levels. However, it remains controversial whether all orthologous genes under different selective pressures can be concatenated for phylogenomic reconstruction. Here we used sect. Cyathophora of Pedicularis, one of the most species-rich genera of angiosperms in the alpine and arctic regions of the Northern Hemisphere, as a model to investigate the efficiency of RNA-seq in resolving relationships of closely related congeneric species...
November 28, 2016: Molecular Phylogenetics and Evolution
David S Portnoy, Stuart C Willis, Elizabeth Hunt, Dominic G Swift, John R Gold, Kevin W Conway
Phylogenetic relationships among members of the New World searobin genera Bellator and Prionotus (Family Triglidae, Subfamily Prionotinae) and among other searobins in the families Triglidae and Peristediidae were investigated using both mitochondrial and nuclear DNA sequences. Phylogenetic hypotheses derived from maximum likelihood and Bayesian methodologies supported a monophyletic Prionotinae that included four well resolved clades of uncertain relationship; three contained species in the genus Prionotus and one contained species in the genus Bellator...
November 28, 2016: Molecular Phylogenetics and Evolution
Hamid Reza Rezaei, Saeid Naderi, Ioana Cristina Chintauan-Marquier, Steve Jordan, Pierre Taberlet, Amjad Tahir Virk, Hamid Reza Naghash, Delphine Rioux, Mohammad Kaboli, Gordon Luikart, François Pompanon
No abstract text is available yet for this article.
November 26, 2016: Molecular Phylogenetics and Evolution
Debayan Dey, Valakunja Nagaraja, Suryanarayanarao Ramakumar
Nucleoid-associated proteins (NAPs) are chromosome-organizing factors, which affect the transcriptional landscape of a bacterial cell. HU is an NAP, which binds to DNA with a broad specificity while homologous IHF (Integration Host Factor), binds DNA with moderately higher specificity. Specificity and differential binding affinity of HU/IHF proteins towards their target binding sites play a crucial role in their regulatory dynamics. Decades of biochemical and genomic studies have been carried out for HU and IHF like proteins...
November 25, 2016: Molecular Phylogenetics and Evolution
Julieta M Manrique, Leandro R Jones
This work set out to shed light on the phylogeography of the SAR11 clade of Alphaproteobacteria, which is probably the most abundant group of heterotrophic bacteria on Earth. In particular, we assessed the degree to which empirical evidence (environmental DNA sequences) supports the concept that SAR11 lineages evolve faster than they are dispersed thus generating vicariant distributions, as predicted by recent simulation efforts. We generated 16S rRNA gene sequences from surface seawater collected at the South West Atlantic Ocean and combined these data with previously published sequences from similar environments from elsewhere...
November 25, 2016: Molecular Phylogenetics and Evolution
Amanda A Dick, Tim J Harlow, J Peter Gogarten
Long Branch Attraction (LBA) is a well-known artifact in phylogenetic reconstruction when dealing with branch length heterogeneity. Here we show another phenomenon, Short Branch Attraction (SBA), which occurs when BLAST searches, a phenetic analysis, are used as a surrogate method for phylogenetic analysis. This error also results from branch length heterogeneity, but this time it is the short branches that are attracting. The SBA artifact is reciprocal and can be returned 100% of the time when multiple branches differ in length by a factor of more than two...
November 25, 2016: Molecular Phylogenetics and Evolution
Jorge L Ramirez, José L O Birindelli, Pedro M Galetti
A new genus of Anostomidae (Characiformes) is described to include ten valid extant species previously classified in Leporinus or Hypomasticus and distributed throughout most major river basins in South America: L. brinco, L. conirostris, L. elongatus, H. garmani, L. macrocephalus, L. muyscorum, L. obtusidens, L. piavussu, L. reinhardti, and L. trifasciatus. The monophyly of Megaleporinus is well-supported in a phylogenetic analysis based on two mitochondrial and three nuclear genes, as well as its sister group relationship to Abramites...
November 25, 2016: Molecular Phylogenetics and Evolution
Dadáková Eva, Chrudimský Tomáš, Brožová Kristýna, Modrý David, Celer Vladimír, Hrazdilová Kristýna
The knowledge of the closest human relatives of human adenoviruses (AdVs) such as adenoviruses found in nonhuman primates is still limited, despite the growing importance of adenoviruses in vaccine development, gene and cancer therapy. We examined 153 stool samples of 17 non-human primate species and detected adenoviral DNA sequences of DNA polymerase (DPOL) gene in 54 samples (35 %), originating from 12 out of 17 primate species. We further sequenced 15 hexon gene fragments and based on the phylogenetic analysis we propose two new provisional species SAdV-H and SAdV-I...
November 25, 2016: Molecular Phylogenetics and Evolution
Nishma Dahal, Andrey A Lissovsky, Zhenzhen Lin, Katherine Solari, Elizabeth A Hadly, Xiangjiang Zhan, Uma Ramakrishnan
No abstract text is available yet for this article.
November 23, 2016: Molecular Phylogenetics and Evolution
Jeffrey A Rosenfeld, Sara Oppenheim, Rob DeSalle
Construction of stringent gene content matrices was accomplished for 21 Anopheline mosquito species and strains and four outgroups species. The presence absence matrix using e(-75) as a cutoff in single linkage clustering had over 17,000 ortholog groups. We used the gene content matrix to generate a phylogenetic hypothesis that is in general agreement with gene sequence based phylogenies. In addition to establishing a congruent gene content phylogeny we examined the consistency of three methods for analyzing presence absence data - unweighted parsimony, dollo parsimonly and maximum likelihood using a BINGAMMA model...
November 16, 2016: Molecular Phylogenetics and Evolution
M Bharathi, P Chellapandi
Methanobrevibacter ruminantium M1 (MRU) is a rumen methanogenic archaean that can be able to utilize formate and CO2/H2 as growth substrates. Extensive analysis on the evolutionary genomic contexts considered herein to unravel its intergenomic relationship and metabolic adjustment acquired from the genomic content of Methanothermobacter thermautotrophicus ΔH. We demonstrated its intergenomic distance, genome function, synteny homologs and gene families, origin of replication, and methanogenesis to reveal the evolutionary relationships between Methanobrevibacter and Methanothermobacter...
November 15, 2016: Molecular Phylogenetics and Evolution
Xiao-Yang Zhi, Zhao Jiang, Ling-Ling Yang, Ying Huang
The pangenome of a bacterial species population is formed by genetic reduction and genetic expansion over the long course of evolution. Gene loss is a pervasive source of genetic reduction, and (exogenous and endogenous) gene gain is the main driver of genetic expansion. To understand the genetic innovation and speciation of the family Corynebacteriaceae, which cause a wide range of serious infections in humans and animals, we analyzed the pangenome of this family, and reconstructed its phylogeny using a phylogenomics approach...
November 15, 2016: Molecular Phylogenetics and Evolution
A A Lisenkova, A P Grigorenko, T V Tyazhelova, T V Andreeva, F E Gusev, A D Manakhov, A Yu Goltsov, S Piraino, M P Miglietta, E I Rogaev
Turritopsis dohrnii (Cnidaria, Hydrozoa, Hydroidolina, Anthoathecata) is the only known metazoan that is capable of reversing its life cycle via morph rejuvenation from the adult medusa stage to the juvenile polyp stage. Here, we present a complete mitochondrial (mt) genome sequence of T. dohrnii, which harbors genes for 13 proteins, two transfer RNAs, and two ribosomal RNAs. The T. dohrnii mt genome is characterized by typical features of species in the Hydroidolina subclass, such as a high A+T content (71...
November 11, 2016: Molecular Phylogenetics and Evolution
David J Combosch, Timothy M Collins, Emily A Glover, Daniel L Graf, Elizabeth M Harper, John M Healy, Gisele Y Kawauchi, Sarah Lemer, Erin McIntyre, Ellen E Strong, John D Taylor, John D Zardus, Paula M Mikkelsen, Gonzalo Giribet, Rüdiger Bieler
The systematics of the molluscan class Bivalvia are explored using a 5-gene Sanger-based approach including the largest taxon sampling to date, encompassing 219 ingroup species spanning 93 (or 82%) of the 113 currently accepted bivalve families. This study was designed to populate the bivalve Tree of Life at the family level and to place many genera into a clear phylogenetic context, but also pointing to several major clades where taxonomic work is sorely needed. Despite not recovering monophyly of Bivalvia or Protobranchia-as in most previous Sanger-based approaches to bivalve phylogeny-our study provides increased resolution in many higher-level clades, and supports the monophyly of Autobranchia, Pteriomorphia, Heteroconchia, Palaeoheterodonta, Heterodonta, Archiheterodonta, Euheterodonta, Anomalodesmata, Imparidentia, and Neoheterodontei, in addition to many other lower clades...
November 10, 2016: Molecular Phylogenetics and Evolution
Narayan Prasad Koju, Kai He, Mukesh Kumar Chalise, Chris Ray, Zhongzheng Chen, Bin Zhang, Tao Wan, Shunde Chen, Xuelong Jiang
The phylogeny of living pikas (Ochotonidae, Ochotona) remains obscure, and pika species diversity in southwestern China has never been well explored. In this study, 96 tissue samples from 11 valid species in three classified subgenera (Pika, Ochotona and Conothoa) from 23 locations were characterized using multilocus sequences of 7031bp. Two mitochondrial (CYT B and COI) and five nuclear gene segments (RAG1, RAG2, TTN, OXAIL and IL1RAPL1) were sequenced. We analysed evolutionary histories using maximum likelihood (RAxML) and Bayesian analyses (BEAST), and we also used molecular species delimitation analyses (BPP) to explore species diversity...
November 9, 2016: Molecular Phylogenetics and Evolution
Armel S L Donkpegan, Jean-Louis Doucet, Jérémy Migliore, Jérôme Duminil, Kasso Dainou, Rosalía Piñeiro, Jan J Wieringa, Dominique Champluvier, Olivier J Hardy
Polyploidy has rarely been documented in rain forest trees but it has recently been found in African species of the genus Afzelia (Leguminosae), which is composed of four tetraploid rain forest species and two diploid dry forest species. The genus Afzelia thus provides an opportunity to examine how and when polyploidy and habitat shift occurred in Africa, and whether they are associated. In this study, we combined three plastid markers (psbA, trnL, ndhF), two nuclear markers (ribosomal ITS and the single-copy PEPC E7 gene), plastomes (obtained by High Throughput Sequencing) and morphological traits, with an extensive taxonomic and geographic sampling to explore the evolutionary history of Afzelia...
November 5, 2016: Molecular Phylogenetics and Evolution
Eitan Reem, Jacob Douek, Guy Paz, Gadi Katzir, Baruch Rinkevich
The wide distribution of the ascidian Botryllus schlosseri along the Mediterranean coasts has been documented since the eighteenth century. However, despite copious documentation, analyses of dispersal modes and genetic profiles were limited to local populations or restricted regions. In order to get a pan-Mediterranean overview, 288 specimens from 11 populations of B. schlosseri from the western and eastern Mediterranean basins were sampled and analyzed using five microsatellite loci and COI sequences. Both molecular markers revealed high polymorphisms, with 182 microsatellites alleles and 54 COI haplotypes...
November 4, 2016: Molecular Phylogenetics and Evolution
Zeev Frenkel, Yosef Kiat, Ido Izhaki, Sagi Snir
: With the availability of enormous quantities of genetic data it has become common to construct very accurate trees describing the evolutionary history of the species under study, as well as every single gene of these species. These trees allow us to examine the evolutionary compliance of given markers (characters). A marker compliant with the history of the species investigated, has undergone mutations along the species tree branches, such that every subtree of that tree exhibits a different state...
November 3, 2016: Molecular Phylogenetics and Evolution
Masami Hasegawa
A circular phylogeny with photos or drawings of species is named a phylogeny mandala. This is one of the ways for illustrating the Tree of Life, and is suitable to show visually how the biodiversity has developed in the course of evolution as clarified by the molecular phylogenetics. To demonstrate the recent progress of molecular phylogenetics, six phylogeny mandalas for various taxonomic groups of life were presented; i.e., (1) Eukaryota, (2) Metazoa, (3) Hexapoda, (4) Tetrapoda, (5) Eutheria, and (6) Primates...
November 2, 2016: Molecular Phylogenetics and Evolution
Adrián Nieto-Montes de Oca, Anthony J Barley, Rubi N Meza-Lázaro, Uri O García-Vázquez, Joan G Zamora-Abrego, Robert C Thomson, Adam D Leaché
No abstract text is available yet for this article.
November 2, 2016: Molecular Phylogenetics and Evolution
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