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Phylogenomics

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https://www.readbyqxmd.com/read/28106881/phylogenomics-of-rhodobacteraceae-reveals-evolutionary-adaptation-to-marine-and-non-marine-habitats
#1
Meinhard Simon, Carmen Scheuner, Jan P Meier-Kolthoff, Thorsten Brinkhoff, Irene Wagner-Döbler, Marcus Ulbrich, Hans-Peter Klenk, Dietmar Schomburg, Jörn Petersen, Markus Göker
Marine Rhodobacteraceae (Alphaproteobacteria) are key players of biogeochemical cycling, comprise up to 30% of bacterial communities in pelagic environments and are often mutualists of eukaryotes. As 'Roseobacter clade', these 'roseobacters' are assumed to be monophyletic, but non-marine Rhodobacteraceae have not yet been included in phylogenomic analyses. Therefore, we analysed 106 genome sequences, particularly emphasizing gene sampling and its effect on phylogenetic stability, and investigated relationships between marine versus non-marine habitat, evolutionary origin and genomic adaptations...
January 20, 2017: ISME Journal
https://www.readbyqxmd.com/read/28104589/anchored-phylogenomics-improves-the-resolution-of-evolutionary-relationships-in-the-rapid-radiation-of-protea-l
#2
Nora Mitchell, Paul O Lewis, Emily Moriarty Lemmon, Alan R Lemmon, Kent E Holsinger
PREMISE OF THE STUDY: Estimating phylogenetic relationships in relatively recent evolutionary radiations is challenging, especially if short branches associated with recent divergence result in multiple gene tree histories. We combine anchored enrichment next-generation sequencing with species tree analyses to produce a robust estimate of phylogenetic relationships in the genus Protea (Proteaceae), an iconic radiation in South Africa. METHODS: We sampled multiple individuals within 59 out of 112 species of Protea and 6 outgroup species for a total of 163 individuals, and obtained sequences for 498 low-copy, orthologous nuclear loci using anchored phylogenomics...
January 19, 2017: American Journal of Botany
https://www.readbyqxmd.com/read/28103796/phylogenomic-analysis-of-copepoda-arthropoda-crustacea-reveals-unexpected-similarities-with-earlier-proposed-morphological-phylogenies
#3
Seong-Il Eyun
BACKGROUND: Copepods play a critical role in marine ecosystems but have been poorly investigated in phylogenetic studies. Morphological evidence supports the monophyly of copepods, whereas interordinal relationships continue to be debated. In particular, the phylogenetic position of the order Harpacticoida is still ambiguous and inconsistent among studies. Until now, a small number of molecular studies have been done using only a limited number or even partial genes and thus there is so far no consensus at the order-level...
January 19, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28102365/viral-phylogenomics-using-an-alignment-free-method-a-three-step-approach-to-determine-optimal-length-of-k-mer
#4
Qian Zhang, Se-Ran Jun, Michael Leuze, David Ussery, Intawat Nookaew
The development of rapid, economical genome sequencing has shed new light on the classification of viruses. As of October 2016, the National Center for Biotechnology Information (NCBI) database contained >2 million viral genome sequences and a reference set of ~4000 viral genome sequences that cover a wide range of known viral families. Whole-genome sequences can be used to improve viral classification and provide insight into the viral "tree of life". However, due to the lack of evolutionary conservation amongst diverse viruses, it is not feasible to build a viral tree of life using traditional phylogenetic methods based on conserved proteins...
January 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28101434/an-expanded-nuclear-phylogenomic-pcr-toolkit-for-sapindales
#5
Elizabeth S Collins, Morgan R Gostel, Andrea Weeks
PREMISE OF THE STUDY: We tested PCR amplification of 91 low-copy nuclear gene loci in taxa from Sapindales using primers developed for Bursera simaruba (Burseraceae). METHODS AND RESULTS: Cross-amplification of these markers among 10 taxa tested was related to their phylogenetic distance from B. simaruba. On average, each Sapindalean taxon yielded product for 53 gene regions (range: 16-90). Arabidopsis thaliana (Brassicales), by contrast, yielded product for two...
December 2016: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28100020/independent-evolution-of-sexual-dimorphism-and-female-limited-mimicry-in-swallowtail-butterflies-papilio-dardanus-and-p-phorcas
#6
M J T N Timmermans, M J Thompson, S Collins, A P Vogler
Several species of Swallowtail butterflies (genus Papilio) are Batesian mimics that express multiple mimetic female forms, while the males are monomorphic and non-mimetic. The evolution of such sex-limited mimicry may involve sexual dimorphism arising first and mimicry subsequently. Such a stepwise scenario through a non-mimetic, sexually dimorphic stage has been proposed for two closely related sexually dimorphic species; P. phorcas, a non-mimetic species with two female forms, and P. dardanus, a female-limited polymorphic mimetic species...
January 18, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28097059/the-complete-chloroplast-genome-sequence-of-an-endemic-monotypic-genus-hagenia-rosaceae-structural-comparative-analysis-gene-content-and-microsatellite-detection
#7
Andrew W Gichira, Zhizhong Li, Josphat K Saina, Zhicheng Long, Guangwan Hu, Robert W Gituru, Qingfeng Wang, Jinming Chen
Hagenia is an endangered monotypic genus endemic to the topical mountains of Africa. The only species, Hagenia abyssinica (Bruce) J.F. Gmel, is an important medicinal plant producing bioactive compounds that have been traditionally used by African communities as a remedy for gastrointestinal ailments in both humans and animals. Complete chloroplast genomes have been applied in resolving phylogenetic relationships within plant families. We employed high-throughput sequencing technologies to determine the complete chloroplast genome sequence of H...
2017: PeerJ
https://www.readbyqxmd.com/read/28088402/historical-relationships-of-three-enigmatic-phasianid-genera-aves-galliformes-inferred-using-phylogenomic-and-mitogenomic-data
#8
Ning Wang, Peter A Hosner, Bin Liang, Edward L Braun, Rebecca T Kimball
The phylogeny of the Phasianidae (pheasants, partridges, and allies) has been studied extensively. However, these studies have largely ignored three enigmatic genera because of scarce DNA source material and limited overlapping phylogenetic data: blood pheasants (Ithaginis), snow partridges (Lerwa), and long-billed partridges (Rhizothera). Thus, phylogenetic positions of these three genera remain uncertain in what is otherwise a well-resolved phylogeny. Previous studies using different data types place Lerwa and Ithaginis in similar positions, but the absence of overlapping data means the relationship between them could not be inferred...
January 11, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28086860/nicotiana-attenuata-data-hub-nadh-an-integrative-platform-for-exploring-genomic-transcriptomic-and-metabolomic-data-in-wild-tobacco
#9
Thomas Brockmöller, Zhihao Ling, Dapeng Li, Emmanuel Gaquerel, Ian T Baldwin, Shuqing Xu
BACKGROUND: Nicotiana attenuata (coyote tobacco) is an ecological model for studying plant-environment interactions and plant gene function under real-world conditions. During the last decade, large amounts of genomic, transcriptomic and metabolomic data have been generated with this plant which has provided new insights into how native plants interact with herbivores, pollinators and microbes. However, an integrative and open access platform that allows for the efficient mining of these -omics data remained unavailable until now...
January 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28077874/asgard-archaea-illuminate-the-origin-of-eukaryotic-cellular-complexity
#10
Katarzyna Zaremba-Niedzwiedzka, Eva F Caceres, Jimmy H Saw, Disa Bäckström, Lina Juzokaite, Emmelien Vancaester, Kiley W Seitz, Karthik Anantharaman, Piotr Starnawski, Kasper U Kjeldsen, Matthew B Stott, Takuro Nunoura, Jillian F Banfield, Andreas Schramm, Brett J Baker, Anja Spang, Thijs J G Ettema
The origin and cellular complexity of eukaryotes represent a major enigma in biology. Current data support scenarios in which an archaeal host cell and an alphaproteobacterial (mitochondrial) endosymbiont merged together, resulting in the first eukaryotic cell. The host cell is related to Lokiarchaeota, an archaeal phylum with many eukaryotic features. The emergence of the structural complexity that characterizes eukaryotic cells remains unclear. Here we describe the 'Asgard' superphylum, a group of uncultivated archaea that, as well as Lokiarchaeota, includes Thor-, Odin- and Heimdallarchaeota...
January 19, 2017: Nature
https://www.readbyqxmd.com/read/28077772/phylogenomics-provides-new-insight-into-evolutionary-relationships-and-genealogical-discordance-in-the-reef-building-coral-genus-acropora
#11
Natalie L Rosser, Luke Thomas, Sean Stankowski, Zoe T Richards, W Jason Kennington, Michael S Johnson
Understanding the genetic basis of reproductive isolation is a long-standing goal of speciation research. In recently diverged populations, genealogical discordance may reveal genes and genomic regions that contribute to the speciation process. Previous work has shown that conspecific colonies of Acropora that spawn in different seasons (spring and autumn) are associated with highly diverged lineages of the phylogenetic marker PaxC Here, we used 10 034 single-nucleotide polymorphisms to generate a genome-wide phylogeny and compared it with gene genealogies from the PaxC intron and the mtDNA Control Region in 20 species of Acropora, including three species with spring- and autumn-spawning cohorts...
January 11, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28076891/comparative-genomics-of-mortierella-elongata-and-its-bacterial-endosymbiont-mycoavidus-cysteinexigens
#12
J Uehling, A Gryganskyi, K Hameed, T Tschaplinski, P K Misztal, S Wu, A Desirò, N Vande Pol, Z Du, A Zienkiewicz, K Zienkiewicz, E Morin, E Tisserant, R Splivallo, M Hainaut, B Henrissat, R Ohm, A Kuo, J Yan, A Lipzen, M Nolan, K LaButti, K Barry, A H Goldstein, J Labbé, C Schadt, G Tuskan, I Grigoriev, F Martin, R Vilgalys, G Bonito
Endosymbiosis of bacteria by eukaryotes is a defining feature of cellular evolution. In addition to well known bacterial origins for mitochondria and chloroplasts, multiple origins of bacterial endosymbiosis are known within the cells of diverse animals, plants, and fungi. Early-diverging lineages of terrestrial fungi harbor endosymbiotic bacteria belonging to the Burkholderiaceae. We sequenced the metagenome of the soil-inhabiting fungus Mortierella elongata and assembled the complete circular chromosome of its endosymbiont, Mycoavidus cysteinexigens, which we place within in a lineage of endofungal symbionts that are sister clade to Burkholderia...
January 11, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28074866/-mycobacterium-massilipolynesiensis-sp-nov-a-rapidly-growing-mycobacterium-of-medical-interest-related-to-mycobacterium-phlei
#13
M Phelippeau, S Asmar, D Aboubaker Osman, M Sassi, C Robert, C Michelle, D Musso, M Drancourt
In French Polynesia, respiratory tract clinical isolate M26, displayed unusual phenotype and contradictory phylogenetic affiliations, suggesting a hitherto unidentified rapidly-growing Mycobacterium species. The phenotype of strain M26 was further characterized and its genome sequenced. Strain M26 genome consists in a 5,732,017-bp circular chromosome with a G + C% of 67.54%, comprising 5,500 protein-coding genes and 52 RNA genes (including two copies of the 16 S rRNA gene). One region coding for a putative prophage was also predicted...
January 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28074622/-holostei-versus-halecostomi-problem-insight-from-cytogenetics-of-ancient-nonteleost-actinopterygian-fish-bowfin-amia-calva
#14
Zuzana Majtánová, Radka Symonová, Lenin Arias-Rodriguez, Lauren Sallan, Petr Ráb
Bowfin belongs to an ancient lineage of nonteleost ray-finned fishes (actinopterygians) and is the only extant survivor of a once diverged group, the Halecomorphi or Amiiformes. Owing to the scarcity of extant nonteleost ray-finned lineages, also referred as "living fossils," their phylogenetic interrelationships have been the target of multiple hypotheses concerning their sister group relationships. Molecular and morphological data sets have produced controversial results; bowfin is considered as either the sister group to genome-duplicated teleosts (together forming the group of Halecostomi) or to gars (Lepisosteiformes; together forming the group of Holostei)...
January 11, 2017: Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution
https://www.readbyqxmd.com/read/28072390/a-molecular-portrait-of-maternal-sepsis-from-byzantine-troy
#15
Alison M Devault, Tatum D Mortimer, Andrew Kitchen, Henrike Kiesewetter, Jacob M Enk, G Brian Golding, John Southon, Melanie Kuch, Ana T Duggan, William Aylward, Shea N Gardner, Jonathan E Allen, Andrew M King, Gerard Wright, Makoto Kuroda, Kengo Kato, Derek Eg Briggs, Gino Fornaciari, Edward C Holmes, Hendrik N Poinar, Caitlin S Pepperell
Pregnancy complications are poorly represented in the archeological record, despite their importance in contemporary and ancient societies. While excavating a Byzantine cemetery in Troy, we discovered calcified abscesses among a woman's remains. Scanning electron microscopy of the tissue revealed 'ghost cells', resulting from dystrophic calcification, which preserved ancient maternal, fetal and bacterial DNA of a severe infection, likely chorioamnionitis. Gardnerella vaginalis and Staphylococcus saprophyticus dominated the abscesses...
January 10, 2017: ELife
https://www.readbyqxmd.com/read/28070594/network-metamodeling-effect-of-correlation-metric-choice-on-phylogenomic-and-transcriptomic-network-topology
#16
Deborah A Weighill, Daniel Jacobson
We explore the use of a network meta-modeling approach to compare the effects of similarity metrics used to construct biological networks on the topology of the resulting networks. This work reviews various similarity metrics for the construction of networks and various topology measures for the characterization of resulting network topology, demonstrating the use of these metrics in the construction and comparison of phylogenomic and transcriptomic networks.
January 10, 2017: Advances in Biochemical Engineering/biotechnology
https://www.readbyqxmd.com/read/28061748/complete-chloroplast-genome-of-gracilaria-firma-gracilariaceae-rhodophyta-with-discussion-on-the-use-of-chloroplast-phylogenomics-in-the-subclass-rhodymeniophycidae
#17
Poh-Kheng Ng, Showe-Mei Lin, Phaik-Eem Lim, Li-Chia Liu, Chien-Ming Chen, Tun-Wen Pai
BACKGROUND: The chloroplast genome of Gracilaria firma was sequenced in view of its role as an economically important marine crop with wide industrial applications. To date, there are only 15 chloroplast genomes published for the Florideophyceae. Apart from presenting the complete chloroplast genome of G. firma, this study also assessed the utility of genome-scale data to address the phylogenetic relationships within the subclass Rhodymeniophycidae. The synteny and genome structure of the chloroplast genomes across the taxa of Eurhodophytina was also examined...
January 6, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28057682/phyloskeleton-taxon-selection-data-retrieval-and-marker-identification-for-phylogenomics
#18
Lionel Guy
: With the wealth of available genome sequences, a difficult and tedious part of inferring phylogenomic trees is now to select genomes with an appropriate taxon density in the different parts of the tree. The package described here offers tools to easily select the most representative organisms, following a set of simple rules based on taxonomy and assembly quality, to retrieve the genomes from public databases (NCBI, JGI), to annotate them if necessary, to identify given markers in these, and to prepare files for multiple sequence alignment...
January 5, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28042043/first-plastid-phylogenomic-study-reveals-potential-cyto-nuclear-discordance-in-the-evolutionary-history-of-ficus-l-moraceae
#19
Sam Bruun-Lund, Wendy L Clement, Finn Kjellberg, Nina Rønsted
Standard Sanger chloroplast markers provide limited information to resolve species level relationships within plants, in particular within large genera. Figs (Ficus L., Moraceae) compose one of the 50 largest genera of angiosperms with ∼750 species occurring in the tropics and subtropics worldwide. Figs, in addition to being a keystone food resource in rainforests, are well-known for the mutualistic interactions with their pollinating wasps. It is regarded as a model system for understanding co-evolution dating back more than 75million years...
December 29, 2016: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28039387/accounting-for-uncertainty-in-gene-tree-estimation-summary-coalescent-species-tree-inference-in-a-challenging-radiation-of-australian-lizards
#20
Mozes P K Blom, Jason G Bragg, Sally Potter, Craig Moritz
Accurate gene tree inference is an important aspect of species tree estimation in a summary-coalescent framework. Yet, in empirical studies, inferred gene trees differ in accuracy due to stochastic variation in phylogenetic signal between targeted loci. Empiricists should, therefore, examine the consistency of species tree inference, while accounting for the observed heterogeneity in gene tree resolution of phylogenomic data sets. Here, we assess the impact of gene tree estimation error on summary-coalescent species tree inference by screening [Formula: see text] exonic loci based on gene tree resolution prior to phylogenetic inference...
October 6, 2016: Systematic Biology
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