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"Evolutionary history"

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https://www.readbyqxmd.com/read/28918554/genome-wide-identification-classification-evolutionary-analysis-and-gene-expression-patterns-of-the-protein-kinase-gene-family-in-wheat-and-aegilops-tauschii
#1
Jun Yan, Peisen Su, Zhaoran Wei, Eviatar Nevo, Lingrang Kong
In this study we systematically identified and classified PKs in Triticum aestivum, Triticum urartu and Aegilops tauschii. Domain distribution and exon-intron structure analyses of PKs were performed, and we found conserved exon-intron structures within the exon phases in the kinase domain. Collinearity events were determined, and we identified various T. aestivum PKs from polyploidizations and tandem duplication events. Global expression pattern analysis of T. aestivum PKs revealed that some PKs might participate in the signaling pathways of stress response and developmental processes...
September 16, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/28916791/genomic-structure-and-evolution-of-the-mating-type-locus-in-the-green-seaweed-ulva-partita
#2
Tomokazu Yamazaki, Kensuke Ichihara, Ryogo Suzuki, Kenshiro Oshima, Shinichi Miyamura, Kazuyoshi Kuwano, Atsushi Toyoda, Yutaka Suzuki, Sumio Sugano, Masahira Hattori, Shigeyuki Kawano
The evolution of sex chromosomes and mating loci in organisms with UV systems of sex/mating type determination in haploid phases via genes on UV chromosomes is not well understood. We report the structure of the mating type (MT) locus and its evolutionary history in the green seaweed Ulva partita, which is a multicellular organism with an isomorphic haploid-diploid life cycle and mating type determination in the haploid phase. Comprehensive comparison of a total of 12.0 and 16.6 Gb of genomic next-generation sequencing data for mt(-) and mt(+) strains identified highly rearranged MT loci of 1...
September 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28911112/integrative-and-conjugative-elements-and-their-hosts-composition-distribution-and-organization
#3
Jean Cury, Marie Touchon, Eduardo P C Rocha
Conjugation of single-stranded DNA drives horizontal gene transfer between bacteria and was widely studied in conjugative plasmids. The organization and function of integrative and conjugative elements (ICE), even if they are more abundant, was only studied in a few model systems. Comparative genomics of ICE has been precluded by the difficulty in finding and delimiting these elements. Here, we present the results of a method that circumvents these problems by requiring only the identification of the conjugation genes and the species' pan-genome...
September 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28904788/biogeography-and-systematics-of-endemic-island-damselflies-the-nesobasis-and-melanesobasis-odonata-zygoptera-of-fiji
#4
Christopher D Beatty, Melissa Sánchez Herrera, Jeffrey H Skevington, Arash Rashed, Hans Van Gossum, Scott Kelso, Thomas N Sherratt
The study of island fauna has greatly informed our understanding of the evolution of diversity. We here examine the phylogenetics, biogeography, and diversification of the damselfly genera Nesobasis and Melanesobasis, endemic to the Fiji Islands, to explore mechanisms of speciation in these highly speciose groups. Using mitochondrial (COI, 12S) and nuclear (ITS) replicons, we recovered garli-part maximum likelihood and mrbayes Bayesian phylogenetic hypotheses for 26 species of Nesobasis and eight species/subspecies of Melanesobasis...
September 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28904786/phylogenetic-position-and-age-of-lake-baikal-candonids-crustacea-ostracoda-inferred-from-multigene-sequence-analyzes-and-molecular-dating
#5
Ivana Karanovic, Tatiana Ya Sitnikova
With 104 endemic species family Candonidae is one of the most diverse crustacean groups in Lake Baikal, yet their phylogenetic relationships and position in the family have not been addressed so far. Here, we study the phylogenetic position of Baikal candonids within the family and their evolutionary history using molecular markers for the first time since their original description. We choose 10 Baikal and 28 species from around the world, and three ribosomal RNA-s (18S, 28S, and 16S), and analyze individual and concatenated datasets using Bayesian Inference in MrBayes and BEAST...
September 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28903620/phylogenetic-relationships-of-three-representative-sea-krait-species-genus-laticauda-elapidae-serpentes-based-on-13-mitochondrial-genes
#6
Il-Hun Kim, Jaejin Park, Ho Young Suk, Han-Gyu Bae, Mi-Sook Min, Tein-Shun Tsai, Daesik Park
To investigate the phylogenetic relationships of the genus Laticauda to related higher taxa, we compared the sequences of four mitochondrial genes (12S rRNA, 16S rRNA, ND4, Cytb) from three Laticauda species (L. colubrina, L. laticaudata, and L. semifasciata) with those of 55 Asian and Australo-Melanesian elapid species. We also characterized the complete mitogenomes of the three Laticauda species and compared the sequences of 13 mitochondrial genes from Laticauda species with five terrestrial elapid and one viperid species to estimate phylogenetic relationships and divergence times...
September 13, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/28903468/a-case-for-the-protection-of-saline-and-hypersaline-environments-a-microbiological-perspective
#7
Varun G Paul, Melanie R Mormile
Saline and hypersaline environments are known for their unique geochemical properties, microbial populations and aesthetic appeal. Microbial activities and a spectrum of diversity seen in hypersaline environments are distinct with many novel species being identified and reported on a regular basis. Many distinguishing characteristics about the adaptation, morphology, evolutionary history, and potential environmental and biotechnological applications of these organisms are continually investigated. An abundance of interdisciplinary activities and opportunities exist to explore and understand the importance of these environments that potentially hold promising solutions for current and future global issues...
August 1, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28903461/comparative-genomics-reveals-two-major-bouts-of-gene-retroposition-coinciding-with-crucial-periods-of-symbiodinium-evolution
#8
Bo Song, David Morse, Yue Song, Yuan Fu, Xin Lin, Wenliang Wang, Shifeng Cheng, Wenbin Chen, Xin Liu, Senjie Lin
Gene retroposition is an important mechanism of genome evolution but the role it plays in dinoflagellates, a critical player in marine ecosystems, is not known. Until recently, when the genomes of two coral-symbiotic dinoflagellate genomes, Symbiodinium kawagutii and S. minutum, were released, it has not been possible to systematically study these retrogenes. Here we examine the abundant retrogenes (∼23% of the total genes) in these species. The hallmark of retrogenes in the genome is the presence of DCCGTAGCCATTTTGGCTCAAG, a spliced leader (DinoSL) constitutively trans-spliced to the 5'-end of all nucleus-encoded mRNAs...
August 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28902843/the-apostasia-genome-and-the-evolution-of-orchids
#9
Guo-Qiang Zhang, Ke-Wei Liu, Zhen Li, Rolf Lohaus, Yu-Yun Hsiao, Shan-Ce Niu, Jie-Yu Wang, Yao-Cheng Lin, Qing Xu, Li-Jun Chen, Kouki Yoshida, Sumire Fujiwara, Zhi-Wen Wang, Yong-Qiang Zhang, Nobutaka Mitsuda, Meina Wang, Guo-Hui Liu, Lorenzo Pecoraro, Hui-Xia Huang, Xin-Ju Xiao, Min Lin, Xin-Yi Wu, Wan-Lin Wu, You-Yi Chen, Song-Bin Chang, Shingo Sakamoto, Masaru Ohme-Takagi, Masafumi Yagi, Si-Jin Zeng, Ching-Yu Shen, Chuan-Ming Yeh, Yi-Bo Luo, Wen-Chieh Tsai, Yves Van de Peer, Zhong-Jian Liu
Constituting approximately 10% of flowering plant species, orchids (Orchidaceae) display unique flower morphologies, possess an extraordinary diversity in lifestyle, and have successfully colonized almost every habitat on Earth. Here we report the draft genome sequence of Apostasia shenzhenica, a representative of one of two genera that form a sister lineage to the rest of the Orchidaceae, providing a reference for inferring the genome content and structure of the most recent common ancestor of all extant orchids and improving our understanding of their origins and evolution...
September 13, 2017: Nature
https://www.readbyqxmd.com/read/28902834/alternative-evolutionary-histories-in-the-sequence-space-of-an-ancient-protein
#10
Tyler N Starr, Lora K Picton, Joseph W Thornton
To understand why molecular evolution turned out as it did, we must characterize not only the path that evolution followed across the space of possible molecular sequences but also the many alternative trajectories that could have been taken but were not. A large-scale comparison of real and possible histories would establish whether the outcome of evolution represents an optimal state driven by natural selection or the contingent product of historical chance events; it would also reveal how the underlying distribution of functions across sequence space shaped historical evolution...
September 13, 2017: Nature
https://www.readbyqxmd.com/read/28900436/molecular-resources-from-transcriptomes-in-the-brassicaceae-family
#11
Lua Lopez, Eva M Wolf, J Chris Pires, Patrick P Edger, Marcus A Koch
The rapidly falling costs and the increasing availability of large DNA sequence data sets facilitate the fast and affordable mining of large molecular markers data sets for comprehensive evolutionary studies. The Brassicaceae (mustards) are an important species-rich family in the plant kingdom with taxa distributed worldwide and a complex evolutionary history. We performed Simple Sequence Repeats (SSRs) mining using de novo assembled transcriptomes from 19 species across the Brassicaceae in order to study SSR evolution and provide comprehensive sets of molecular markers for genetic studies within the family...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28899837/an-integrative-taxonomic-study-of-pavanelliella-spp-monogenoidea-dactylogyridae-with-the-description-of-a-new-species-from-the-nasal-cavities-of-an-amazon-pimelodid-catfish
#12
Julio C Aguiar, Antônio A M Maia, Marcia R M Silva, Paulo S Ceccarelli, Marcus V Domingues, Edson A Adriano
The present study is an integrative taxonomic analysis of Pavanelliella spp. (Monogenoidea, Dactylogyridae), and describes a new species from the nasal cavities of the Amazonian pimelodid catfish Brachyplatystoma rousseauxii (Siluriformes Pimelodidae) from the Tapajós River (Amazon Basin, Pará state, Brazil). Pavanelliella jarii sp. n. is characterized by the presence of 3-4 rings in the male copulatory organ, the absence of rings around the vaginal atrium and by its sinuous vaginal canal, which sometimes forms 0...
September 9, 2017: Parasitology International
https://www.readbyqxmd.com/read/28899345/phylogeographic-structure-cryptic-speciation-and-demographic-history-of-the-sharpbelly-hemiculter-leucisculus-a-freshwater-habitat-generalist-from-southern-china
#13
Weitao Chen, Zaixuan Zhong, Wei Dai, Qi Fan, Shunping He
BACKGROUND: Species with broad distributions frequently divide into multiple genetic forms and may therefore be viewed as "cryptic species". Here, we used the mitochondrial cytochrome b (Cytb) and 12 nuclear DNA loci to investigate phylogeographic structures of the sharpbelly (Hemiculter leucisculus) in rivers in southern China and explored how the geological and climatic factors have shaped the genetic diversity and evolutionary history of this species. RESULTS: Our mitochondrial phylogenetic analysis identified three major lineages (lineages A, B, and C)...
September 12, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28898663/late-palaeozoic-plants
#14
Zhuo Feng
Land plants are one of the major constituents of terrestrial ecosystems on Earth, and play an irreplaceable role in human activities today. If we are to understand the extant plants, it is imperative that we have some understanding of the fossil plants from the deep geological past, particularly those that occurred during their early evolutionary history, in the late Palaeozoic.
September 11, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28895124/ecological-opportunity-alters-the-timing-and-shape-of-adaptive-radiation
#15
Edward D Burress, Milton Tan
The uneven distribution of diversity is a conspicuous phenomenon across the tree of life. Ecological opportunity is a prominent catalyst of adaptive radiation and therefore may alter patterns of diversification. We evaluated the distribution of shifts in diversification rates across the cichlid phylogeny and the distribution of major clades across phylogenetic space. We also tested if ecological opportunity influenced these patterns. Colonization-associated ecological opportunity altered the tempo and mode of diversification during the adaptive radiation of cichlid fishes...
September 12, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28894925/alligator-wrestling-morphological-molecular-and-phylogenetic-data-on-odhneriotrema-incommodum-leidy-1856-digenea-clinostomidae-from-alligator-mississippiensis-daudin-1801-in-mississippi-usa
#16
Ethan T Woodyard, Thomas Graham Rosser, Scott A Rush
Based on specimens collected from harvested American alligator Alligator mississippiensis Daudin, 1801 in Mississippi, USA, novel molecular data for both nuclear ribosomal genes (18S, ITS1-5.8S, ITS2, and 28S) and mitochondrial genes (cytochrome c oxidase subunit 1 and nicotinamide adenine dinucleotide dehydrogenase subunit 1) are provided for Odhneriotrema incommodum (Leidy, 1856), a trematode of the family Clinostomidae Lühe, 1901 infecting A. mississippiensis and the Florida spotted gar Lepisosteus platyrhincus DeKay, 1842...
September 11, 2017: Parasitology Research
https://www.readbyqxmd.com/read/28892502/rapid-and-recent-diversification-patterns-in-anseriformes-birds-inferred-from-molecular-phylogeny-and-diversification-analyses
#17
Zhonglou Sun, Tao Pan, Chaochao Hu, Lu Sun, Hengwu Ding, Hui Wang, Chenling Zhang, Hong Jin, Qing Chang, Xianzhao Kan, Baowei Zhang
The Anseriformes is a well-known and widely distributed bird order, with more than 150 species in the world. This paper aims to revise the classification, determine the phylogenetic relationships and diversification patterns in Anseriformes by exploring the Cyt b, ND2, COI genes and the complete mitochondrial genomes (mito-genomes). Molecular phylogeny and genetic distance analyses suggest that the Dendrocygna species should be considered as an independent family, Dendrocygnidae, rather than a member of Anatidae...
2017: PloS One
https://www.readbyqxmd.com/read/28890940/phylotranscriptomic-consolidation-of-the-jawed-vertebrate-timetree
#18
Iker Irisarri, Denis Baurain, Henner Brinkmann, Frédéric Delsuc, Jean-Yves Sire, Alexander Kupfer, Jörn Petersen, Michael Jarek, Axel Meyer, Miguel Vences, Hervé Philippe
Phylogenomics is extremely powerful but introduces new challenges as no agreement exists on "standards" for data selection, curation and tree inference. We use jawed vertebrates (Gnathostomata) as model to address these issues. Despite considerable efforts in resolving their evolutionary history and macroevolution, few studies have included a full phylogenetic diversity of gnathostomes and some relationships remain controversial. We tested a novel bioinformatic pipeline to assemble large and accurate phylogenomic datasets from RNA sequencing and find this phylotranscriptomic approach successful and highly cost-effective...
September 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28890856/the-semi-aquatic-pondweed-bugs-of-a-cretaceous-swamp
#19
Alba Sánchez-García, André Nel, Antonio Arillo, Mónica M Solórzano Kraemer
Pondweed bugs (Hemiptera: Mesoveliidae), considered a sister group to all other Gerromorpha, are exceedingly rare as fossils. Therefore, each new discovery of a fossil mesoveliid is of high interest, giving new insight into their early evolutionary history and diversity and enabling the testing of their proposed relationships. Here, we report the discovery of new mesoveliid material from Spanish Lower Cretaceous (Albian) amber, which is the first such find in Spanish amber. To date, fossil records of this family only include one species from French Kimmeridgian as compression fossils, two species in French amber (Albian-Cenomanian boundary), and one in Dominican amber (Miocene)...
2017: PeerJ
https://www.readbyqxmd.com/read/28887534/phylogeographic-studies-of-schizothoracine-fishes-on-the-central-qinghai-tibet-plateau-reveal-the-highest-known-glacial-microrefugia
#20
Yangyang Liang, Dekui He, Yintao Jia, Heying Sun, Yifeng Chen
Pleistocene climatic oscillations have greatly influenced the evolutionary history and distribution pattern of most extant species. However, their effects on species on the Qinghai-Tibet Plateau (QTP) are not well understood. To investigate the effects of past climatic shifts, particularly the Last Glacial Maximum (LGM), on plateau fish, we analysed the phylogeographic structure and demographic history of five closely related taxa of the subfamily Schizothoracinae, a representative endemic taxon of the QTP, from nine endorheic lakes on the central QTP and three peripheral exorheic rivers using the mitochondrial control region (D-loop) sequence and 12 microsatellite (SSR) markers...
September 8, 2017: Scientific Reports
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