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https://www.readbyqxmd.com/read/27919705/the-complete-mitochondrial-genome-of-thitarodes-sejilaensis-lepidoptera-hepialidae-a-host-insect-of-ophiocordyceps-sinensis-and-its-implication-in-taxonomic-revision-of-hepialusadopted-in-china
#1
Zhiwen Zou, Qiang Min, Shiyu Cheng, Tianrong Xin, Bin Xia
The mitochondrial genome is widely used for phylogenetic analyses and evolutionary biology. The complete mitochondrial genome of Thitarodes sejilaensis (Lepidoptera: Hepialidae) was sequenced and analyzed in this study. This mitogenome is a typical circular molecule of 15,290bp, with the gene content, orientation and order identical to other insects in the family Hepialidae. The genome nucleotide composition is heavily biased towards As and Ts, accounting for 80.87% of total nucleotide content. The major strand shows a positive AT-skew and negative GC-skew...
December 2, 2016: Gene
https://www.readbyqxmd.com/read/27907107/a-time-calibrated-mitogenome-phylogeny-of-catfish-teleostei-siluriformes
#2
Ilias Kappas, Spiros Vittas, Chrysoula N Pantzartzi, Elena Drosopoulou, Zacharias G Scouras
A very significant part of the world's freshwater ichthyofauna is represented by ancient, exceptionally diverse and cosmopolitan ray-finned teleosts of the order Siluriformes. Over the years, catfish have been established as an exemplary model for probing historical biogeography at various scales. Yet, several tantalizing gaps still exist in their phylogenetic history, timeline and mode of diversification. Here, we re-examine the phylogeny of catfish by assembling and analyzing almost all publicly available mitogenome data...
2016: PloS One
https://www.readbyqxmd.com/read/27904151/phylogenetic-and-population-based-approaches-to-mitogenome-variation-do-not-support-association-with-male-infertility
#3
Alberto Gómez-Carballa, Jacobo Pardo-Seco, Federico Martinón-Torres, Antonio Salas
Infertility has a complex multifactorial etiology and a high prevalence worldwide. Several studies have pointed to variation in the mitochondrial DNA (mtDNA) molecule as a factor responsible for the different disease phenotypes related to infertility. We analyzed 53 mitogenomes of infertile males from Galicia (northwest Spain), and these haplotypes were meta-analyzed phylogenetically with 43 previously reported from Portugal. Taking advantage of the large amount of information available, we additionally carried out association tests between patient mtDNA single-nucleotide polymorphisms (mtSNPs) and haplogroups against Iberian matched controls retrieved from The 1000 Genomes Project and the literature...
December 1, 2016: Journal of Human Genetics
https://www.readbyqxmd.com/read/27886369/genomic-data-reveals-potential-for-hybridization-introgression-and-incomplete-lineage-sorting-to-confound-phylogenetic-relationships-in-an-adaptive-radiation-of-narrow-mouth-frogs
#4
A M Alexander, Y-C Su, C H Oliveros, K V Olson, S L Travers, R M Brown
The microhylid frog genus Kaloula is an adaptive radiation spanning the edge of the Asian mainland and multiple adjacent island archipelagos, with much of the clade's diversity associated with an endemic Philippine radiation. Relationships among clades from the Philippines, however, remain unresolved. With ultraconserved element (UCE) and mitogenomic data, we identified highly-supported differences in topology and areas of poor resolution, for each marker set. Using the UCE data, we then identified possible instances of contemporary hybridization, past introgression and incomplete lineage sorting (ILS) within the Philippine Kaloula...
November 25, 2016: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/27881087/intraspecific-rearrangement-of-mitochondrial-genome-suggests-the-prevalence-of-the-tandem-duplication-random-loss-tdlr-mechanism-in-quasipaa-boulengeri
#5
Yun Xia, Yuchi Zheng, Robert W Murphy, Xiaomao Zeng
BACKGROUND: Tandem duplication followed by random loss (TDRL) is the most frequently invoked model to explain the diversity of gene rearrangements in metazoan mitogenomes. The initial stages of gene rearrangement are difficult to observe in nature, which limits our understanding of incipient duplication events and the subsequent process of random loss. Intraspecific gene reorganizations may represent intermediate states, and if so they potentially shed light on the evolutionary dynamics of TDRL...
November 24, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27867038/comparative-mitogenomic-analysis-of-three-species-of-periwinkles-littorina-fabalis-l-obtusata-and-l-saxatilis
#6
João P Marques, Graciela Sotelo, Tomas Larsson, Kerstin Johannesson, Marina Panova, Rui Faria
The flat periwinkles, Littorina fabalis and L.obtusata, offer an interesting system for local adaptation and ecological speciation studies. In order to provide genomic resources for these species, we sequenced their mitogenomes together with that of the rough periwinkle L.saxatilis by means of next-generation sequencing technologies. The three mitogenomes present the typical repertoire of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and a putative control region. Although the latter could not be fully recovered in flat periwinkles using short-reads due to a highly repetitive fragment, in L...
November 17, 2016: Marine Genomics
https://www.readbyqxmd.com/read/27864912/inferring-contemporary-and-historical-genetic-connectivity-from-juveniles
#7
Pierre Feutry, Oliver Berry, Peter M Kyne, Richard D Pillans, Rich Hillary, Peter M Grewe, James R Marthick, Grant Johnson, Rasanthi M Gunasekera, Nicholas J Bax, Mark Bravington
Measuring population connectivity is a critical task in conservation biology. While genetic markers can provide reliable long-term historical estimates of population connectivity, scientists are still limited in their ability to determine contemporary patterns of gene flow, the most practical time frame for management. Here, we tackled this issue by developing a new approach that only requires juvenile sampling at a single time period. To demonstrate the usefulness of our method, we used the Speartooth shark (Glyphis glyphis), a critically endangered species of river sharks found only in tropical northern Australia and southern Papua New Guinea...
November 19, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27853549/two-species-of-southeast-asian-cats-in-the-genus-catopuma-with-diverging-histories-an-island-endemic-forest-specialist-and-a-widespread-habitat-generalist
#8
Riddhi P Patel, Daniel W Förster, Andrew C Kitchener, Mark D Rayan, Shariff W Mohamed, Laura Werner, Dorina Lenz, Hans Pfestorf, Stephanie Kramer-Schadt, Viktoriia Radchuk, Jörns Fickel, Andreas Wilting
Background. The bay cat Catopuma badia is endemic to Borneo, whereas its sister species the Asian golden cat Catopuma temminckii is distributed from the Himalayas and southern China through Indochina, Peninsular Malaysia and Sumatra. Based on morphological data, up to five subspecies of the Asian golden cat have been recognized, but a taxonomic assessment, including molecular data and morphological characters, is still lacking. Results. We combined molecular data (whole mitochondrial genomes), morphological data (pelage) and species distribution projections (up to the Late Pleistocene) to infer how environmental changes may have influenced the distribution of these sister species over the past 120 000 years...
October 2016: Royal Society Open Science
https://www.readbyqxmd.com/read/27833437/two-complete-mitochondrial-genomes-from-praticolella-mexicana-perez-2011-polygyridae-and-gene-order-evolution-in-helicoidea-mollusca-gastropoda
#9
Russell L Minton, Marco A Martinez Cruz, Mark L Farman, Kathryn E Perez
Helicoidea is a diverse group of land snails with a global distribution. While much is known regarding the relationships of helicoid taxa, comparatively little is known about the evolution of the mitochondrial genome in the superfamily. We sequenced two complete mitochondrial genomes from Praticolella mexicana Perez, 2011 representing the first such data from the helicoid family Polygyridae, and used them in an evolutionary analysis of mitogenomic gene order. We found the mitochondrial genome of Praticolella mexicana to be 14,008 bp in size, possessing the typical 37 metazoan genes...
2016: ZooKeys
https://www.readbyqxmd.com/read/27822711/the-complete-mitogenome-of-a-jumping-spider-carrhotus-xanthogramma-araneae-salticidae-and-comparative-analysis-in-four-salticid-mitogenomes
#10
Wen-Yuan Fang, Zheng-Liang Wang, Chao Li, Xiao-Qing Yang, Xiao-Ping Yu
The complete mitogenome of the jumping spider Carrhotus xanthogramma was determined and comparative analysis among four salticid mitogenomes was conducted. The circular genome is 14,563 bp in size and contains a complete set of genes that usually present in the metazoa. All of the 13 protein-coding genes begin with a typical ATN codon and stop with the canonical stop codons, except for ND4 and ND4L genes with an incomplete stop codon T. All of the tRNAs cannot be formed the fully paired acceptor stems and seven out of them cannot be folded into the typical cloverleaf-shaped secondary structures...
December 2016: Genetica
https://www.readbyqxmd.com/read/27812024/the-first-complete-mitochondrial-genome-of-dacus-longicornis-diptera-tephritidae-using-next-generation-sequencing-and-mitochondrial-genome-phylogeny-of-dacini-tribe
#11
Fan Jiang, Xubin Pan, Xuankun Li, Yanxue Yu, Junhua Zhang, Hongshan Jiang, Liduo Dou, Shuifang Zhu
The genus Dacus is one of the most economically important tephritid fruit flies. The first complete mitochondrial genome (mitogenome) of Dacus species - D. longicornis was sequenced by next-generation sequencing in order to develop the mitogenome data for this genus. The circular 16,253 bp mitogenome is the typical set and arrangement of 37 genes present in the ancestral insect. The mitogenome data of D. longicornis was compared to all the published homologous sequences of other tephritid species. We discovered the subgenera Bactrocera, Daculus and Tetradacus differed from the subgenus Zeugodacus, the genera Dacus, Ceratitis and Procecidochares in the possession of TA instead of TAA stop codon for COI gene...
November 4, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27808159/limited-mitogenomic-degradation-in-response-to-a-parasitic-lifestyle-in-orobanchaceae
#12
Weishu Fan, Andan Zhu, Melisa Kozaczek, Neethu Shah, Natalia Pabón-Mora, Favio González, Jeffrey P Mower
In parasitic plants, the reduction in plastid genome (plastome) size and content is driven predominantly by the loss of photosynthetic genes. The first completed mitochondrial genomes (mitogenomes) from parasitic mistletoes also exhibit significant degradation, but the generality of this observation for other parasitic plants is unclear. We sequenced the complete mitogenome and plastome of the hemiparasite Castilleja paramensis (Orobanchaceae) and compared them with additional holoparasitic, hemiparasitic and nonparasitic species from Orobanchaceae...
November 3, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27792534/polymorphism-in-mitochondrial-coding-regions-of-mediterranean-loggerhead-turtles-evolutionary-relevance-and-structural-effects
#13
Andrea Novelletto, Letizia Testa, Federico Iacovelli, Paola Blasi, Luisa Garofalo, Toni Mingozzi, Mattia Falconi
We sequenced coding portions (1.6 kb) of the mtDNA in 170 loggerhead (Caretta caretta) turtles sampled in the central Mediterranean. The sequences spanned the entire ND1 and ND3 genes, the tRNAGly and tRNAArg, plus the 3' and 5' termini of COXIII and ND4L genes, respectively. Based on our sequencing results and published complete mitogenomes, we constructed a maximum parsimony phylogeny of C. caretta matrilines that sheds new light on the evolutionary relationships within the collection of lineages found in the Mediterranean and so far recognized by D-loop haplotypes only...
November 2016: Physiological and Biochemical Zoology: PBZ
https://www.readbyqxmd.com/read/27782189/molecular-phylogeny-of-polyneoptera-insecta-inferred-from-expanded-mitogenomic-data
#14
Nan Song, Hu Li, Fan Song, Wanzhi Cai
The Polyneoptera represents one of the earliest insect radiations, comprising the majority of hemimetabolous orders, in which many species have great economic importance. Here, we sequenced eleven mitochondrial genomes of the polyneopteran insects by using high throughput pooled sequencing technology, and presented a phylogenetic reconstruction for this group based on expanded mitochondrial genome data. Our analyses included 189 taxa, of which 139 species represent all the major polyneopteran lineages. Multiple results support the monophyly of Polyneoptera, the monophyly of Dictyoptera, and the monophyly of Orthoptera...
October 26, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27781569/the-complete-mitochondrial-genome-of-great-cormorant-phalacrocorax-carbo-phalacrocorax-phalacrocoracidae
#15
Letong Zhang, Ming Zhang, Shiyang He
The great cormorant (Phalacrocorax carbo) is widely distributed in the world. Here, we report the complete mitogenome sequence of P. carbo, which was 18,995 bp long and composed of 15 protein-coding genes, 25 tRNA genes, 2 rRNA genes and 2 control regions. Most genes were located on H-strand except for 10 tRNAs and 2 ND6 genes. In protein-coding genes, ATG, ATC and GTG were used as initiation codons, and TAA, AGA, AGG and TAG were used as stop codons. The 25 tRNA genes ranged in size from 67 to 75 bp. And 12S and 16S rRNA were respectively 983 and 1517 bp...
October 26, 2016: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/27770241/the-complete-mitochondrial-genome-of-trabala-vishnou-guttata-lepidoptera-lasiocampidae-and-the-related-phylogenetic-analyses
#16
Liuyu Wu, Xiao Xiong, Xuming Wang, Tianrong Xin, Jing Wang, Zhiwen Zou, Bin Xia
The bluish yellow lappet moth, Trabala vishnou guttata is an extraordinarily important pest in China. The complete mitochondrial genome is sequenced and determined firstly, which is based on traditional PCR amplification and primer walking methods with a length of 15,281 bp, including 13 protein-coding (PCG) genes, 22 transfer RNA (rRNA) genes, two ribosomal RNA (tRNA) genes, and an A + T-rich region. The gene order and orientation of the T. vishnou guttata mitogenome were identical to the other sequenced Lasiocampidae species...
December 2016: Genetica
https://www.readbyqxmd.com/read/27769298/past-climate-changes-population-dynamics-and-the-origin-of-bison-in-europe
#17
Diyendo Massilani, Silvia Guimaraes, Jean-Philip Brugal, E Andrew Bennett, Malgorzata Tokarska, Rose-Marie Arbogast, Gennady Baryshnikov, Gennady Boeskorov, Jean-Christophe Castel, Sergey Davydov, Stéphane Madelaine, Olivier Putelat, Natalia N Spasskaya, Hans-Peter Uerpmann, Thierry Grange, Eva-Maria Geigl
BACKGROUND: Climatic and environmental fluctuations as well as anthropogenic pressure have led to the extinction of much of Europe's megafauna. The European bison or wisent (Bison bonasus), one of the last wild European large mammals, narrowly escaped extinction at the onset of the 20th century owing to hunting and habitat fragmentation. Little is known, however, about its origin, evolutionary history and population dynamics during the Pleistocene. RESULTS: Through ancient DNA analysis we show that the emblematic European bison has experienced several waves of population expansion, contraction, and extinction during the last 50,000 years in Europe, culminating in a major reduction of genetic diversity during the Holocene...
October 21, 2016: BMC Biology
https://www.readbyqxmd.com/read/27767191/the-first-complete-mitochondrial-genome-for-the-subfamily-limacodidae-and-implications-for-the-higher-phylogeny-of-lepidoptera
#18
Qiu-Ning Liu, Zhao-Zhe Xin, Dan-Dan Bian, Xin-Yue Chai, Chun-Lin Zhou, Bo-Ping Tang
The mitochondrial genome (mitogenome) provides important information for understanding molecular evolution and phylogeny. To determine the systematic status of the family Limacodidae within Lepidoptera, we infer a phylogenetic hypothesis based on the complete mitogenome of Monema flavescens (Lepidoptera: Limacodidae). The mitogenome of M. flavescens is 15,396 base pairs (bp), and includes 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a control region (CR)...
October 21, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27762445/phylogeny-of-the-jacchus-group-of-callithrix-marmosets-based-on-complete-mitochondrial-genomes
#19
Joanna Malukiewicz, Crystal M Hepp, Katerina Guschanski, Anne C Stone
OBJECTIVES: Two subgroups make up the marmoset genus Callithrix. The "aurita" group is composed of two species, whereas evolutionary relationships among the four species of the "jacchus" group remain unclear. To uncover these relationships, we first sequenced mitochondrial genomes for C. kuhlii and C. penicillata to complement data available for congeners. We then constructed a phylogenetic tree based on mtDNA heavy chain protein coding genes from several primates to untangle species relationships and estimate divergence times of the jacchus group...
October 20, 2016: American Journal of Physical Anthropology
https://www.readbyqxmd.com/read/27760787/phylogenomic-reconstruction-of-sportive-lemurs-genus-lepilemur-recovered-from-mitogenomes-with-inferences-for-madagascar-biogeography
#20
Runhua Lei, Cynthia L Frasier, Melissa T R Hawkins, Shannon E Engberg, Carolyn A Bailey, Steig E Johnson, Adam T McLain, Colin P Groves, George H Perry, Stephen D Nash, Russell A Mittermeier, Edward E Louis
The family Lepilemuridae includes 26 species of sportive lemurs, most of which were recently described. The cryptic morphological differences confounded taxonomy until recent molecular studies; however, some species' boundaries remain uncertain. To better understand the genus Lepilemur, we analyzed 35 complete mitochondrial genomes representing all recognized 26 sportive lemur taxa and estimated divergence dates. With our dataset we recovered 25 reciprocally monophyletic lineages, as well as an admixed clade containing Lepilemur mittermeieri and Lepilemur dorsalis Using modern distribution data, an ancestral area reconstruction and an ecological vicariance analysis were performed to trace the history of diversification and to test biogeographic hypotheses...
October 3, 2016: Journal of Heredity
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