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Molecular Phylogenetics and Evolution

David Ortiz, Oscar F Francke, Jason E Bond
Tarantula spider systematics has long been considered problematic. Species diagnosis and phylogenetic hypotheses have historically relied on morphological features, which are known to be relatively conserved and/or highly homoplastic across the family. Morphology-based attempts to clarify the phylogeny of the highly diverse New World Theraphosinae, have only been moderately successful, and the time-frame of tarantulas' evolution is nearly terra incognita. Here we present a molecular phylogenetic analysis of the Theraphosinae genus Bonnetina and related lineages, employing one mitochondrial (COI) and five nuclear (ITS1, EF1G, MID1IP1, MRPL44, and I3568) loci...
May 17, 2018: Molecular Phylogenetics and Evolution
Fengyuan Li, Shuqiang Li
Sea-level change has been viewed as a primary driver in the formation of biodiversity. Early studies confirmed that Plio-Pleistocene sea-level changes led to the isolation and subsequent genetic differentiation of Southeast (SE) Asian organisms over short geological timescales. However, long-time consequences of sea-level fluctuations remain unclear. Herein, we analyze the evolutionary history of Althepus (spiders) whose distribution encompasses Indo-Burma and the Sunda shelf islands to understand how sea-level changes over shallow and deep timescales effected their history...
May 17, 2018: Molecular Phylogenetics and Evolution
Jacqueline Heckenhauer, Rosabelle Samuel, Peter S Ashton, Kamariah Abu Salim, Ovidiu Paun
A supra-annual, community-level synchronous flowering prevails in several parts of the tropical forests of Southeast Asia and its evolution has been hypothesized to be linked to pollinator shifts. The aseasonal Southeast Asian lowland rainforests are dominated by Dipterocarpaceae, which exhibit great floral diversity, a range of pollination syndromes and include species with annual and supra-annual gregarious flowering. Phylogenetic relationships within this family are still unclear, especially in the tribe Shoreeae...
May 17, 2018: Molecular Phylogenetics and Evolution
Michael Tessler, Danielle de Carle, Madeleine L Voiklis, Olivia A Gresham, Johannes Neumann, Stanisław Cios, Mark E Siddall
Annelids possessing a posterior sucker and a fixed number of somites - most famously leeches (Hirudinida), but also crayfish worms (Branchiobdellida) and salmonid parasites (Acanthobdellida) - form a clade; however, determining the relationships between these orders has proven challenging. Here, we compile the largest molecular phylogenetic dataset yet analysed for these groups, including new sequences for key taxa. We find robust model-based support for a clade formed by Hirudinida and Acanthobdellida, contrasting the largest prior studies...
May 17, 2018: Molecular Phylogenetics and Evolution
Savel R Daniels, Sebastian Klaus
We examined the colonization history and phylogeographic structure of the two endemic freshwater crab species (Potamonautes margaritarius and P. principe) inhabiting the volcanic islands of São Tomé and Príncipe, respectively, using mitochondrial and nuclear DNA sequence data. All samples were sequenced for the mtDNA COI locus and used in the phylogeographic analyses, while a single specimen per lineage was sequenced for the two remaining loci (16S rRNA and histone 3) and used in the phylogenetic reconstruction...
May 14, 2018: Molecular Phylogenetics and Evolution
Ľubomír Rajter, Peter Vďačný
The class Litostomatea represents a highly diverse but monophyletic group, uniting both free-living and endosymbiotic ciliates. Ribosomal RNA genes and ITS-region sequences helped to recognize and define the main litostomatean lineages, but did not provide enough phylogenetic signal to unambiguously resolve their interrelationships. In this study, we attempted to improve the resolution among main free-living predatory lineages by adding the gene coding for alpha-tubulin. However, our phylogenetic analyses challenged the performance of alpha-tubulin in reconstruction of evolutionary history of free-living litostomateans...
May 12, 2018: Molecular Phylogenetics and Evolution
Alexander K Brazenor, Terry Bertozzi, Terrence L Miller, Ian D Whittington, Kate S Hutson
Accurate identification of parasite species and strains is crucial to mitigate the risk of epidemics and emerging disease. Species of Neobenedenia are harmful monogenean ectoparasites that infect economically important bony fishes in aquaculture worldwide, however, the species boundaries between two of the most notorious taxa, N. melleni and N. girellae, has been a topic of contention for decades. Historically, identifications of Neobenedenia isolates have overwhelmingly been attributed to N. melleni, and it has been proposed that N...
May 12, 2018: Molecular Phylogenetics and Evolution
Nikisha Patel, Chun-Xiang Li, Li-Bing Zhang, David S Barrington
No abstract text is available yet for this article.
May 12, 2018: Molecular Phylogenetics and Evolution
Artemis G Korovesi, Maria Ntertilis, Vassili N Kouvelis
The nuclear ribosomal protein S3 (Rps3) is implicated in the assembly of the ribosomal small subunit. Fungi and plants present a gene copy in their mitochondrial (mt) genomes. An analysis of 303 complete fungal mt genomes showed that, when rps3 is found, it is either a free-standing gene or an anchored gene within the omega intron of the rnl gene. Early divergent fungi, Basidiomycota and all yeasts but the CTG group belong to the first case, and Pezizomycotina to the second. Its position, size and genetic code employed are conserved within species of the same Order...
May 12, 2018: Molecular Phylogenetics and Evolution
Rachel S Jabaily, Kelly A Shepherd, Pryce S Michener, Caroline J Bush, Rodrigo Rivero, Andrew G Gardner, Emily B Sessa
Goodeniaceae is a primarily Australian flowering plant family with a complex taxonomy and evolutionary history. Previous phylogenetic analyses have successfully resolved the backbone topology of the largest clade in the family, Goodenia s.l., but have failed to clarify relationships within the species-rich and enigmatic Goodenia clade C, a prerequisite for taxonomic revision of the group. We used genome skimming to retrieve sequences for chloroplast, mitochondrial, and nuclear markers for 24 taxa representing Goodenia s...
May 11, 2018: Molecular Phylogenetics and Evolution
Qian Tang, Scott V Edwards, Frank E Rheindt
Multi-locus data have proven invaluable in phylogenetic reconstruction and species delimitation. However, the mixed genetic signal from different loci can make inference of evolutionary history challenging and may produce incongruences depending on analytical and marker choice. Aside from incomplete lineage sorting (ILS) following diversification events that have had little time for deep differentiation, the most common causes of incongruent phylogenies are genetic introgression confounding a bifurcating evolutionary trajectory...
May 11, 2018: Molecular Phylogenetics and Evolution
Ali Mohammad Moner, Agnelo Furtado, Robert J Henry
Whole chloroplast genome sequence analysis of 58 wild and domesticated rice samples was used to investigate their phylogeny providing more detail on the biogeography of the major groups of wild A genome rices globally. An optimized chloroplast assembly method was developed and applied to extracting high quality whole chloroplast genome sequences from shot gun whole DNA sequencing data. Forty complete high quality chloroplast genome sequences were assembled (including; temperate japonica, tropical japonica and aus)...
May 10, 2018: Molecular Phylogenetics and Evolution
Anna Mácová, Aneta Hoblíková, Václav Hypša, Michal Stanko, Jana Martinů, Jana Kvičerová
Recent studies show that host switching is much more frequent than originally believed and constitutes an important driver in evolution of host-parasite associations. However, its frequency and ecological mechanisms at the population level have been rarely investigated. We address this issue by analyzing phylogeny and population genetics of an extensive sample, from a broad geographic area, for commonly occurring parasites of the genus Eimeria within the abundant rodent genera Apodemus, Microtus and Myodes, using two molecular markers...
May 10, 2018: Molecular Phylogenetics and Evolution
Noemí Buján, Sabela Balboa, Jesús L Romalde, Alicia E Toranzo, Beatriz Magariños
At present, the genus Edwardsiella compiles five species: E. tarda, E. hoshinae, E. ictaluri, E. piscicida and E. anguillarum. Some species of this genus such us E. ictaluri and E. piscicida are important pathogens of numerous fish species. With the description of the two latter species, the phylogeny of Edwardsiella became more complicated. With the aim to clarify the relationships among all species in the genus, a multilocus sequence typing (MLST) approach was developed and applied to characterize 56 isolates and 6 reference strains belonging to the five Edwardsiella species...
May 8, 2018: Molecular Phylogenetics and Evolution
Emmanuel F A Toussaint, Andrew Short
Beetles have colonized freshwater habitats multiple times throughout their evolutionary history. Some of these aquatic lineages are associated exclusively with waterfall-like habitats, often with modified morphologies to cope with their unusual way of life. The historical biogeography of such cascade beetle lineages has been shown to strongly reflect ancient tectonic events. We focus on the pantropical genus Oocyclus of which species dwell in waterfalls and associated habitats. We infer the first molecular phylogeny of Oocyclus using a dataset of seven gene fragments...
May 7, 2018: Molecular Phylogenetics and Evolution
Genki Kobayashi, Ryutaro Goto, Tsuyoshi Takano, Shigeaki Kojima
Inter-familial relationships of the phylum Annelida have been widely studied using molecular phylogenetic/genomic approaches; however, intra-familial relationships remain scarcely investigated in most annelid families. The Maldanidae (bamboo worms) comprise more than 280 species of 40 genera and six subfamilies that occur in various environments from intertidal to hadal zones. Within this family, the taxon Maldanoplaca, which consists of four subfamilies (Maldaninae, Notoproctinae, Nicomachinae, and Euclymeninae), was proposed based on the presence of cephalic and anal plates...
May 4, 2018: Molecular Phylogenetics and Evolution
Lucie Bauret, Ashley R Field, Myriam Gaudeul, Marc-André Selosse, Germinal Rouhan
We explored the biogeographical history of a group of spore-bearing plants focusing on Phlegmariurus (Lycopodiaceae), a genus of lycophytes comprising ca. 250 species. Given its wide distribution in the Southern Hemisphere, Phlegmariurus provides a good model to address questions about the biogeographical processes underlying southern distributions, notably in Madagascar and surrounding islands (WIO). Our aims were i) to discuss the systematics of the Malagasy species in the light of molecular phylogenetic results, ii) to provide the first dating analysis focused on Phlegmariurus and iii) to understand the relative role of vicariance, dispersal and diversification in the origin of the Malagasy Phlegmariurus species...
May 4, 2018: Molecular Phylogenetics and Evolution
Manuel Lopes-Lima, Ivan N Bolotov, Van Tu Do, David C Aldridge, Miguel M Fonseca, Han Ming Gan, Mikhail Y Gofarov, Alexander V Kondakov, Vincent Prié, Ronaldo Sousa, Simone Varandas, Ilya V Vikhrev, Amílcar Teixeira, Rui-Wen Wu, Xiaoping Wu, Alexandra Zieritz, Elsa Froufe, Arthur E Bogan
Two Unionida (freshwater mussel) families are present in the Northern Hemisphere; the Margaritiferidae, representing the most threatened of unionid families, and the Unionidae, which include several genera of unresolved taxonomic placement. The recent reassignment of the poorly studied Lamprotula rochechouartii from the Unionidae to the Margaritiferidae motivated a new search for other potential species of margaritiferids from members of Gibbosula and Lamprotula. Based on molecular and morphological analyses conducted on newly collected specimens from Vietnam, we here assign Gibbosula crassa to the Margaritiferidae...
May 3, 2018: Molecular Phylogenetics and Evolution
Tiago P Carvalho, H Mariangeles Arce, Roberto E Reis, Mark H Sabaj
The family Aspredinidae is a moderately diverse and broadly distributed group of freshwater fishes endemic to South America. Commonly known as Banjo Catfishes, Aspredinidae currently includes 44 valid species divided among 13 genera. The first species-comprehensive hypothesis on phylogenetic relationships among aspredinids is presented. The phylogeny is based on DNA sequence data for five gene fragments (mitochondrial 16S and COI; nuclear RAG1, MYH6 and SH3PX3) from 114 individuals representing 31 species in 12 aspredinid genera...
April 30, 2018: Molecular Phylogenetics and Evolution
Ki-Oug Yoo, Andrew A Crowl, Kyung-Ah Kim, Kyeong-Sik Cheon, Nico Cellinese
The Campanulaceae comprises approximately 2300 species that are distributed among five major lineages, i.e., Campanuloideae, Cyphioideae, Cyphocarpoideae, Lobelioideae, and Nemacladoideae. Of these, the Campanuloideae, an Old World clade centered in East Asia, is the largest. In this study, we reconstruct the phylogeny of East Asian Campanuloideae (Campanulaceae) based on one nuclear gene (i.e., PPR70) and five plastid markers (i.e., atpB, matK, petD, rbcL, and trnL-trnF). We then use this phylogenetic framework to reconstruct the biogeographical history of the genus...
April 30, 2018: Molecular Phylogenetics and Evolution
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