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https://www.readbyqxmd.com/read/29777194/the-bony-labyrinth-of-toothed-whales-reflects-both-phylogeny-and-habitat-preferences
#1
Loïc Costeur, Camille Grohé, Gabriel Aguirre-Fernández, Eric Ekdale, Georg Schulz, Bert Müller, Bastien Mennecart
The inner ear of toothed whales (odontocetes) is known to have evolved particular shapes related to their abilities to echolocate and move under water. While the origin of these capacities is now more and more examined, thanks to new imaging techniques, little is still known about how informative inner ear shape could be to tackle phylogenetic issues or questions pertaining to the habitat preferences of extinct species. Here we show that the shape of the bony labyrinth of toothed whales provides key information both about phylogeny and habitat preferences (freshwater versus coastal and fully marine habitats)...
May 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29776969/identifying-genetic-players-in-cell-sheet-morphogenesis-using-a-drosophila-deficiency-screen-for-genes-on-chromosome-2r-involved-in-dorsal-closure
#2
Richard D Mortensen, Regan P Moore, Stephanie M Fogerson, Hellen Y Chiou, Chimdindu V Obinero, Neel K Prabhu, Angela H Wei, Janice M Crawford, Daniel P Kiehart
Cell sheet morphogenesis characterizes key developmental transitions and homeostasis, in vertebrates and throughout phylogeny, including gastrulation, neural tube formation and wound healing. Dorsal closure, a process during Drosophila embryogenesis, has emerged as a model for cell sheet morphogenesis. ∼140 genes are currently known to affect dorsal closure and new genes are identified each year. Many of these genes were identified in screens that resulted in arrested development. Dorsal closure is remarkably robust and many questions regarding the molecular mechanisms involved in this complex biological process remain...
May 18, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29774245/evaluation-of-phylogenetic-reconstruction-methods-using-bacterial-whole-genomes-a-simulation-based-study
#3
John A Lees, Michelle Kendall, Julian Parkhill, Caroline Colijn, Stephen D Bentley, Simon R Harris
Background : Phylogenetic reconstruction is a necessary first step in many analyses which use whole genome sequence data from bacterial populations. There are many available methods to infer phylogenies, and these have various advantages and disadvantages, but few unbiased comparisons of the range of approaches have been made. Methods : We simulated data from a defined "true tree" using a realistic evolutionary model. We built phylogenies from this data using a range of methods, and compared reconstructed trees to the true tree using two measures, noting the computational time needed for different phylogenetic reconstructions...
2018: Wellcome Open Research
https://www.readbyqxmd.com/read/29774232/multiple-origins-of-green-blood-in-new-guinea-lizards
#4
Zachary B Rodriguez, Susan L Perkins, Christopher C Austin
Several species of lizards from the megadiverse island of New Guinea have evolved green blood. An unusually high concentration of the green bile pigment biliverdin in the circulatory system of these lizards makes the blood, muscles, bones, tongue, and mucosal tissues bright green in color, eclipsing the crimson color from their red blood cells. This is a remarkable physiological feature because bile pigments are toxic physiological waste products of red blood cell catabolism and, when chronically elevated, cause jaundice in humans and all other vertebrates...
May 2018: Science Advances
https://www.readbyqxmd.com/read/29773135/discrimination-molecular-characterisation-and-phylogenetic-comparison-of-porcine-eimeria-spp-in-india
#5
Devina Sharma, Nirbhay K Singh, Harkirat Singh, Anja Joachim, Shitanshu S Rath, Damer P Blake
Infections with Eimeria spp. are common in pigs worldwide, occasionally affecting animals clinically after weaning or during the fattening period when diarrhoea and weight loss can be observed upon infection with the more pathogenic species. Molecular characterization of pathogens is valuable to accurately delimit species and development novel diagnostics, although sequences which define Eimeria species that infect pigs are scarce. Only three of the eight common species are currently represented in GenBank...
May 15, 2018: Veterinary Parasitology
https://www.readbyqxmd.com/read/29771363/multiple-sequence-alignment-averaging-improves-phylogeny-reconstruction
#6
Haim Ashkenazy, Itamar Sela, Eli Levy Karin, Giddy Landan, Tal Pupko
The classic methodology of inferring a phylogenetic tree from sequence data is composed of two steps. First, a multiple sequence alignment (MSA) is computed. Then, a tree is reconstructed assuming the MSA is correct. Yet, inferred MSAs were shown to be inaccurate and alignment errors reduce tree inference accuracy. It was previously proposed that filtering unreliable alignment regions can increase the accuracy of tree inference. However, it was also demonstrated that the benefit of this filtering is often obscured by the resulting loss of phylogenetic signal...
May 15, 2018: Systematic Biology
https://www.readbyqxmd.com/read/29771235/bordetella-pertussis-population-dynamics-and-phylogeny-in-japan-after-adoption-of-acellular-pertussis-vaccines
#7
Aldert Zomer, Nao Otsuka, Yukihiro Hiramatsu, Kazunari Kamachi, Naoko Nishimura, Takao Ozaki, Jan Poolman, Jeroen Geurtsen
Bordetella pertussis, the causative agent of whooping cough, has experienced a resurgence in the past 15 years, despite the existence of both whole-cell and acellular vaccines. Here, we performed whole genome sequencing analysis of 149 clinical strains, provided by the National Institute of Infectious Diseases (NIID), Japan, isolated in 1982-2014, after Japan became the first country to adopt acellular vaccines against B. pertussis. Additionally, we sequenced 39 strains provided by the Konan Kosei Hospital in Aichi prefecture, Japan, isolated in 2008-2013...
May 17, 2018: Microbial Genomics
https://www.readbyqxmd.com/read/29769032/live-neighbor-joining
#8
Guilherme P Telles, Graziela S Araújo, Maria E M T Walter, Marcelo M Brigido, Nalvo F Almeida
BACKGROUND: In phylogenetic reconstruction the result is a tree where all taxa are leaves and internal nodes are hypothetical ancestors. In a live phylogeny, both ancestral and living taxa may coexist, leading to a tree where internal nodes may be living taxa. The well-known Neighbor-Joining heuristic is largely used for phylogenetic reconstruction. RESULTS: We present Live Neighbor-Joining, a heuristic for building a live phylogeny. We have investigated Live Neighbor-Joining on datasets of viral genomes, a plausible scenario for its application, which allowed the construction of alternative hypothesis for the relationships among virus that embrace both ancestral and descending taxa...
May 16, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29768482/sequencing-of-complete-mitochondrial-genomes-confirms-synonymization-of-hyalomma-asiaticum-asiaticum-and-kozlovi-and-advances-phylogenetic-hypotheses-for-the-ixodidae
#9
Zhi-Qiang Liu, Yan-Feng Liu, Nuer Kuermanali, Deng-Feng Wang, Shi-Jun Chen, Hui-Ling Guo, Li Zhao, Jun-Wei Wang, Tao Han, Yuan-Zhi Wang, Jie Wang, Chen-Feng Shen, Zhuang-Zhi Zhang, Chuang-Fu Chen
Phylogeny of hard ticks (Ixodidae) remains unresolved. Mitochondrial genomes (mitogenomes) are increasingly used to resolve phylogenetic controversies, but remain unavailable for the entire large Hyalomma genus. Hyalomma asiaticum is a parasitic tick distributed throughout the Asia. As a result of great morphological variability, two subspecies have been recognised historically; until a morphological data-based synonymization was proposed. However, this hypothesis was never tested using molecular data. Therefore, objectives of this study were to: 1...
2018: PloS One
https://www.readbyqxmd.com/read/29768420/molecular-phylogeny-of-planaltina-b%C3%A3-hlke-characidae-stevardiinae-and-comments-on-the-definition-and-geographic-distribution-of-the-genus-with-description-of-a-new-species
#10
Gabriel de Carvalho Deprá, Weferson Júnio da Graça, Carla Simone Pavanelli, Gleisy Semencio Avelino, Claudio Oliveira
A molecular phylogeny of Planaltina, including the three previously described species and an undescribed species, is presented. The monophyly of the genus, included in Diapomini, is strongly supported. Its sister group, the remaining Diapomini, includes only species without modified caudal-fin squamation in the present analysis (species of Diapoma with caudal organs were not sampled). Creagrutus is sister to Planaltina plus remaining Diapomini instead of Planaltina being sister to Creagrutus plus Diapomini, as a previous analysis had suggested...
2018: PloS One
https://www.readbyqxmd.com/read/29765689/a-new-archaic-baleen-whale-toipahautea-waitaki-early-late-oligocene-new-zealand-and-the-origins-of-crown-mysticeti
#11
Cheng-Hsiu Tsai, R Ewan Fordyce
A new genus and species of extinct baleen whale † Toipahautea waitaki (Late Oligocene, New Zealand) is based on a skull and associated bones, from the lower Kokoamu Greensand, about 27.5 Ma (local upper Whaingaroan Stage, early Chattian). The upper jaw includes a thin, elongate and apparently toothless maxilla, with evidence of arterial supply for baleen. Open sutures with the premaxilla suggest a flexible (kinetic) upper jaw. The blowhole is well forward. The mandible is bowed laterally and slightly dorsally; unlike the Eomysticetidae, there are no mandibular alveoli, and the coronoid process is tapered and curved laterally...
April 2018: Royal Society Open Science
https://www.readbyqxmd.com/read/29765686/phylogeography-of-hydrothermal-vent-stalked-barnacles-a-new-species-fills-a-gap-in-the-indian-ocean-dispersal-corridor-hypothesis
#12
Hiromi Kayama Watanabe, Chong Chen, Daniel P Marie, Ken Takai, Katsunori Fujikura, Benny K K Chan
Phylogeography of animals provides clues to processes governing their evolution and diversification. The Indian Ocean has been hypothesized as a 'dispersal corridor' connecting hydrothermal vent fauna of Atlantic and Pacific oceans. Stalked barnacles of the family Eolepadidae are common associates of deep-sea vents in Southern, Pacific and Indian oceans, and the family is an ideal group for testing this hypothesis. Here, we describe Neolepas marisindica sp. nov. from the Indian Ocean, distinguished from N. zevinae and N...
April 2018: Royal Society Open Science
https://www.readbyqxmd.com/read/29765649/dietary-specialization-is-linked-to-reduced-species-durations-in-north-american-fossil-canids
#13
Mairin Balisi, Corinna Casey, Blaire Van Valkenburgh
How traits influence species persistence is a fundamental question in ecology, evolution and palaeontology. We test the relationship between dietary traits and both species duration and locality coverage over 40 million years in North American canids, a clade with considerable ecomorphological disparity and a dense fossil record. Because ecomorphological generalization-broad resource use-may enable species to withstand disturbance, we predicted that canids of average size and mesocarnivory would exhibit longer durations and wider distributions than specialized larger or smaller species...
April 2018: Royal Society Open Science
https://www.readbyqxmd.com/read/29765358/get_phylomarkers-a-software-package-to-select-optimal-orthologous-clusters-for-phylogenomics-and-inferring-pan-genome-phylogenies-used-for-a-critical-geno-taxonomic-revision-of-the-genus-stenotrophomonas
#14
Pablo Vinuesa, Luz E Ochoa-Sánchez, Bruno Contreras-Moreira
The massive accumulation of genome-sequences in public databases promoted the proliferation of genome-level phylogenetic analyses in many areas of biological research. However, due to diverse evolutionary and genetic processes, many loci have undesirable properties for phylogenetic reconstruction. These, if undetected, can result in erroneous or biased estimates, particularly when estimating species trees from concatenated datasets. To deal with these problems, we developed GET_PHYLOMARKERS, a pipeline designed to identify high-quality markers to estimate robust genome phylogenies from the orthologous clusters, or the pan-genome matrix (PGM), computed by GET_HOMOLOGUES...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29764943/microscopic-and-molecular-evidence-of-the-first-elasmobranch-adomavirus-the-cause-of-skin-disease-in-a-giant-guitarfish-rhynchobatus-djiddensis
#15
Jennifer A Dill, Alvin C Camus, John H Leary, Terry Fei Fan Ng
Only eight families of double-stranded DNA (dsDNA) viruses are known to infect vertebrate animals. During an investigation of papillomatous skin disease in an elasmobranch species, the giant guitarfish ( Rhynchobatus djiddensis ), a novel virus, distinct from all known viral families in regard to particle size, morphology, genome organization, and helicase phylogeny was discovered. Large inclusion bodies containing 75-nm icosahedral viral particles were present within epithelial cell nuclei in the proliferative skin lesions...
May 15, 2018: MBio
https://www.readbyqxmd.com/read/29764366/phylogenetic-signal-from-rearrangements-in-18-anopheles-species-by-joint-scaffolding-extant-and-ancestral-genomes
#16
Yoann Anselmetti, Wandrille Duchemin, Eric Tannier, Cedric Chauve, Sèverine Bérard
BACKGROUND: Genomes rearrangements carry valuable information for phylogenetic inference or the elucidation of molecular mechanisms of adaptation. However, the detection of genome rearrangements is often hampered by current deficiencies in data and methods: Genomes obtained from short sequence reads have generally very fragmented assemblies, and comparing multiple gene orders generally leads to computationally intractable algorithmic questions. RESULTS: We present a computational method, ADSEQ, which, by combining ancestral gene order reconstruction, comparative scaffolding and de novo scaffolding methods, overcomes these two caveats...
May 9, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29764363/gatc-a-genetic-algorithm-for-gene-tree-construction-under-the-duplication-transfer-loss-model-of-evolution
#17
Emmanuel Noutahi, Nadia El-Mabrouk
BACKGROUND: Several methods have been developed for the accurate reconstruction of gene trees. Some of them use reconciliation with a species tree to correct, a posteriori, errors in gene trees inferred from multiple sequence alignments. Unfortunately the best fit to sequence information can be lost during this process. RESULTS: We describe GATC, a new algorithm for reconstructing a binary gene tree with branch length. GATC returns optimal solutions according to a measure combining both tree likelihood (according to sequence evolution) and a reconciliation score under the Duplication-Transfer-Loss (DTL) model...
May 9, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29762663/population-genomic-data-reveal-genes-related-to-important-traits-of-quail
#18
Yan Wu, Yaolei Zhang, Zhuocheng Hou, Guangyi Fan, Jinsong Pi, Shuai Sun, Jiang Chen, Huaqiao Liu, Xiao Du, Jie Shen, Gang Hu, Wenbin Chen, Ailuan Pan, Pingping Yin, Xiaoli Chen, Yuejin Pu, He Zhang, Zhenhua Liang, Jianbo Jian, Hao Zhang, Bin Wu, Jing Sun, Jianwei Chen, Hu Tao, Ting Yang, Hongwei Xiao, Huan Yang, Chuanwei Zheng, Mingzhou Bai, Xiaodong Fang, David W Burt, Wen Wang, Qingyi Li, Xun Xu, Chengfeng Li, Huanming Yang, Jian Wang, Ning Yang, Xin Liu, Jinping Du
Background: Japanese quail (Coturnix japonica), a recently domesticated poultry species, is important not only as an agricultural product, but also as a model bird species for genetic research. However, most of the biological questions concerning genomics, phylogenetics and genetics of some important economic traits have not been answered. It is thus necessary to complete a high-quality genome sequence as well as a series of comparative genomics, evolution and functional studies. Results: Here, we present a quail genome assembly spanning 1...
May 11, 2018: GigaScience
https://www.readbyqxmd.com/read/29761593/uncovering-the-drivers-of-host-associated-microbiota-with-joint-species-distribution-modeling
#19
Johannes R Björk, Francis K C Hui, Robert B O'Hara, Jose M Montoya
In addition to the processes structuring free-living communities, host-associated microbiota are directly or indirectly shaped by the host. Therefore, microbiota data have a hierarchical structure where samples are nested under one or several variables representing host-specific factors, often spanning multiple levels of biological organization. Current statistical methods do not accommodate this hierarchical data structure, and therefore cannot explicitly account for the effect of the host in structuring the microbiota...
May 14, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29761472/cranial-morphology-in-mollisquama-sp-squaliformes-dalatiidae-and-patterns-of-cranial-evolution-in-dalatiid-sharks
#20
John S S Denton, John G Maisey, Mark Grace, Alan Pradel, Michael H Doosey, Henry L Bart, Gavin J P Naylor
Dalatiid sharks are members of a family of predominantly small, midwater meso- and bathypelagic chondrichthyans. The family is notable for both its number of monotypic genera and high morphological disparity. Three of the seven dalatiid genera are known only from holotype specimens (Mollisquama parini) or from only a handful of specimens (Euprotomicroides zantedeschia, Heteroscymnoides marleyi), with the only detailed anatomical work consistent across all taxa being studies of dentition. Here, we present detailed anatomical description of the second-ever specimen of Mollisquama (Mollisquama sp...
May 14, 2018: Journal of Anatomy
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