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BMC Evolutionary Biology

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https://www.readbyqxmd.com/read/28821229/mechanisms-of-peripheral-phylogeographic-divergence-in-the-indo-pacific-lessons-from-the-spiny-lobster-panulirus-homarus
#1
Ahmad Farhadi, Andrew G Jeffs, Hamid Farahmand, Thankappan Sarasam Rejiniemon, Greg Smith, Shane D Lavery
BACKGROUND: There is increasing recognition of the concordance between marine biogeographic and phylogeographic boundaries. However, it is still unclear how population-level divergence translates into species-level divergence, and what are the principal factors that first initiate that divergence, and then maintain reproductive isolation. This study examines the likely forces driving population and lineage divergences in the broadly-distributed Indo-Pacific spiny lobster Panulirus homarus, which has peripheral divergent lineages in the west and east...
August 18, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28814277/phenotypes-antioxidant-responses-and-gene-expression-changes-accompanying-a-sugar-only-diet-in-bactrocera-dorsalis-hendel-diptera-tephritidae
#2
Er-Hu Chen, Qiu-Li Hou, Dan-Dan Wei, Hong-Bo Jiang, Jin-Jun Wang
BACKGROUND: Diet composition (yeast:carbohydrate ratio) is an important determinant of growth, development, and reproduction. Recent studies have shown that decreased yeast intake elicits numerous transcriptomic changes and enhances somatic maintenance and lifespan, which in turn reduces reproduction in various insects. However, our understanding of the responses leading to a decrease in yeast ratio to 0% is limited. RESULTS: In the present study, we investigated the effects of a sugar-only diet (SD) on the gene expression patterns of the oriental fruit fly, Bactrocera dorsalis (Hendel), one of the most economically important pests in the family Tephritidae...
August 17, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28814266/lack-of-satellite-dna-species-specific-homogenization-and-relationship-to-chromosomal-rearrangements-in-monitor-lizards-varanidae-squamata
#3
Ornjira Prakhongcheep, Watcharaporn Thapana, Aorarat Suntronpong, Worapong Singchat, Khampee Pattanatanang, Rattanin Phatcharakullawarawat, Narongrit Muangmai, Surin Peyachoknagul, Kazumi Matsubara, Tariq Ezaz, Kornsorn Srikulnath
BACKGROUND: Satellite DNAs (stDNAs) are highly repeated sequences that constitute large portions of any genome. The evolutionary dynamics of stDNA (e.g. copy number, nucleotide sequence, location) can, therefore, provide an insight into genome organization and evolution. We investigated the evolutionary origin of VSAREP stDNA in 17 monitor lizards (seven Asian, five Australian, and five African) at molecular and cytogenetic level. RESULTS: Results revealed that VSAREP is conserved in the genome of Asian and Australian varanids, but not in African varanids, suggesting that these sequences are either differentiated or lost in the African varanids...
August 16, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28810830/annotating-long-intergenic-non-coding-rnas-under-artificial-selection-during-chicken-domestication
#4
Yun-Mei Wang, Hai-Bo Xu, Ming-Shan Wang, Newton Otieno Otecko, Ling-Qun Ye, Dong-Dong Wu, Ya-Ping Zhang
BACKGROUND: Numerous biological functions of long intergenic non-coding RNAs (lincRNAs) have been identified. However, the contribution of lincRNAs to the domestication process has remained elusive. Following domestication from their wild ancestors, animals display substantial changes in many phenotypic traits. Therefore, it is possible that diverse molecular drivers play important roles in this process. RESULTS: We analyzed 821 transcriptomes in this study and annotated 4754 lincRNA genes in the chicken genome...
August 15, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28806933/the-evolutionary-and-coevolutionary-consequences-of-defensive-microbes-for-host-parasite-interactions
#5
Kayla C King, Michael B Bonsall
BACKGROUND: Animal and plant species can harbour microbes that provide them with protection against enemies. These beneficial microbes can be a significant component of host defence that complement or replaces a repertoire of immunity, but they can also be costly. Given their impact on host and parasite fitness, defensive microbes have the potential to influence host-parasite interactions on an evolutionary timescale. RESULTS: Using a phenotypic framework, we explore the evolutionary and coevolutionary dynamics of a host-parasite interaction in the presence of defensive microbes...
August 14, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28806928/colour-polymorphic-lures-exploit-innate-preferences-for-spectral-versus-luminance-cues-in-dipteran-prey
#6
Thomas E White, Darrell J Kemp
BACKGROUND: Theory predicts that colour polymorphism may be favored by variation in the visual context under which signals are perceived. The context encompasses all environmental determinants of light availability and propagation, but also the dynamics of perception in receivers. Color vision involves the neural separation of information into spectral versus luminance channels, which often differentially guide specific tasks. Here we explicitly tested whether this discrete perceptual basis contributes to the maintenance of polymorphism in a prey-luring system...
August 14, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28806923/historical-biogeography-and-ecological-niche-modelling-of-the-asimina-disepalum-clade-annonaceae-role-of-ecological-differentiation-in-neotropical-asian-disjunctions-and-diversification-in-asia
#7
Pui-Sze Li, Daniel C Thomas, Richard M K Saunders
BACKGROUND: The Asimina-Disepalum clade (Annonaceae subfam. Annonoideae tribe Annoneae) includes a major Neotropical-Asian biogeographical disjunction. We evaluate whether this disjunction can be explained by the Eocene boreotropics hypothesis, which relies on the existence of extensive boreotropical forests during the Late Palaeocene-Early Eocene thermal maximum (52-50 Ma), followed by disruption of boreotropical vegetation during post-Eocene cooling. Molecular dating using an uncorrelated relaxed molecular clock (UCLD) model with two fossil calibrations, ancestral range estimation, and ecological niche modelling across evolutionary time were performed...
August 14, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28806915/evaluating-the-maintenance-of-disease-associated-variation-at-the-blood-group-related-gene-b4galnt2-in-house-mice
#8
Marie Vallier, Maria Abou Chakra, Laura Hindersin, Miriam Linnenbrink, Arne Traulsen, John F Baines
BACKGROUND: B4galnt2 is a blood group-related glycosyltransferase that displays cis-regulatory variation for its tissue-specific expression patterns in house mice. The wild type allele, found e.g. in the C57BL/6 J strain, directs intestinal expression of B4galnt2, which is the pattern observed among vertebrates, including humans. An alternative allele class found in the RIIIS/J strain and other mice instead drives expression in blood vessels, which leads to a phenotype similar to type 1 von Willebrand disease (VWD), a common human bleeding disorder...
August 14, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28806900/drift-selection-or-migration-processes-affecting-genetic-differentiation-and-variation-along-a-latitudinal-gradient-in-an-amphibian
#9
Maria Cortázar-Chinarro, Ella Z Lattenkamp, Yvonne Meyer-Lucht, Emilien Luquet, Anssi Laurila, Jacob Höglund
BACKGROUND: Past events like fluctuations in population size and post-glacial colonization processes may influence the relative importance of genetic drift, migration and selection when determining the present day patterns of genetic variation. We disentangle how drift, selection and migration shape neutral and adaptive genetic variation in 12 moor frog populations along a 1700 km latitudinal gradient. We studied genetic differentiation and variation at a MHC exon II locus and a set of 18 microsatellites...
August 14, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28797242/going-deeper-in-the-automated-identification-of-herbarium-specimens
#10
Jose Carranza-Rojas, Herve Goeau, Pierre Bonnet, Erick Mata-Montero, Alexis Joly
BACKGROUND: Hundreds of herbarium collections have accumulated a valuable heritage and knowledge of plants over several centuries. Recent initiatives started ambitious preservation plans to digitize this information and make it available to botanists and the general public through web portals. However, thousands of sheets are still unidentified at the species level while numerous sheets should be reviewed and updated following more recent taxonomic knowledge. These annotations and revisions require an unrealistic amount of work for botanists to carry out in a reasonable time...
August 11, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28797243/polymorphism-and-structure-of-style-specific-arabinogalactan-proteins-as-determinants-of-pollen-tube-growth-in-nicotiana
#11
Andrzej K Noyszewski, Yi-Cheng Liu, Koichiro Tamura, Alan G Smith
BACKGROUND: Pollen tube growth and fertilization are key processes in angiosperm sexual reproduction. The transmitting tract (TT) of Nicotiana tabacum controls pollen tube growth in part by secreting pistil extensin-like protein III (PELPIII), transmitting-tract-specific (TTS) protein and 120 kDa glycoprotein (120 K) into the stylar extracellular matrix. The three arabinogalactan proteins (AGP) are referred to as stylar AGPs and are the focus of this research. The transmitting tract regulates pollen tube growth, promoting fertilization or rejecting pollen tubes...
August 10, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28793858/mtdna-structure-the-women-who-formed-the-brazilian-northeast
#12
Ana Paula Schaan, Lorenna Costa, Diego Santos, Antonio Modesto, Marcos Amador, Camile Lopes, Sílvia Helena Rabenhorst, Raquel Montenegro, Bruno D A Souza, Thayson Lopes, France Keiko Yoshioka, Giovanny Pinto, Vivian Silbiger, Ândrea Ribeiro-Dos-Santos
BACKGROUND: The distribution of mitochondrial DNA (mtDNA) lineages in Brazil is heterogeneous due to different regional colonization dynamics. Northeastern Brazil, although being an important region in terms of human imigration and ethnic admixture, has little information regarding its population mtDNA composition. Here, we determine which mitochondrial lineages contributed to the formation of the Northeastern Brazilian population. Our sample consisted of 767 individuals distributed as follows i) 550 individuals from eight Northeastern states (Piauí, Ceará, Rio Grande do Norte, Paraíba, Pernambuco, Alagoas, Sergipe, and Bahia) which were sequenced for mtDNA hypervariable segments I, II, and III; ii) 217 individuals from Alagoas and Pernambuco (previously published data)...
August 9, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28793855/contrasting-morphology-with-molecular-data-an-approach-to-revision-of-species-complexes-based-on-the-example-of-european-phoxinus-cyprinidae
#13
Anja Palandačić, Alexander Naseka, David Ramler, Harald Ahnelt
BACKGROUND: Molecular taxonomy studies and barcoding projects can provide rapid means of detecting cryptic diversity. Nevertheless, the use of molecular data for species delimitation should be undertaken with caution. Especially the single-gene approaches are linked with certain pitfalls for taxonomical inference. In the present study, recent and historical species descriptions based upon morphology were used as primary species hypotheses, which were then evaluated with molecular data (including in type and historical museum material) to form secondary species hypotheses...
August 9, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28784114/phylogenetic-analysis-of-the-sina-siah-ubiquitin-e3-ligase-family-in-metazoa
#14
Ian J Pepper, Robert E Van Sciver, Amy H Tang
BACKGROUND: The RAS signaling pathway is a pivotal developmental pathway that controls many fundamental biological processes including cell proliferation, differentiation, movement and apoptosis. Drosophila Seven-IN-Absentia (SINA) is a ubiquitin E3 ligase that is the most downstream signaling "gatekeeper" whose biological activity is essential for proper RAS signal transduction. Vertebrate SINA homologs (SIAHs) share a high degree of amino acid identity with that of Drosophila SINA. SINA/SIAH is the most conserved signaling component in the canonical EGFR/RAS/RAF/MAPK signal transduction pathway...
August 7, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28778150/using-the-neandertal-genome-to-study-the-evolution-of-small-insertions-and-deletions-in-modern-humans
#15
Manjusha Chintalapati, Michael Dannemann, Kay Prüfer
BACKGROUND: Small insertions and deletions occur in humans at a lower rate compared to nucleotide changes, but evolve under more constraint than nucleotide changes. While the evolution of insertions and deletions have been investigated using ape outgroups, the now available genome of a Neandertal can shed light on the evolution of indels in more recent times. RESULTS: We used the Neandertal genome together with several primate outgroup genomes to differentiate between human insertion/deletion changes that likely occurred before the split from Neandertals and those that likely arose later...
August 4, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28778145/evaluating-allopolyploid-origins-in-strawberries-fragaria-using-haplotypes-generated-from-target-capture-sequencing
#16
Olga K Kamneva, John Syring, Aaron Liston, Noah A Rosenberg
BACKGROUND: Hybridization is observed in many eukaryotic lineages and can lead to the formation of polyploid species. The study of hybridization and polyploidization faces challenges both in data generation and in accounting for population-level phenomena such as coalescence processes in phylogenetic analysis. Genus Fragaria is one example of a set of plant taxa in which a range of ploidy levels is observed across species, but phylogenetic origins are unknown. RESULTS: Here, using 20 diploid and polyploid Fragaria species, we combine approaches from NGS data analysis and phylogenetics to infer evolutionary origins of polyploid strawberries, taking into account coalescence processes...
August 4, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28774284/transcriptional-activity-of-pif-and-pong-like-class-ii-transposable-elements-in-triticeae
#17
Dragomira N Markova, Roberta J Mason-Gamer
BACKGROUND: Transposable elements are major contributors to genome size and variability, accounting for approximately 70-80% of the maize, barley, and wheat genomes. PIF and Pong-like elements belong to two closely-related element families within the PIF/Harbinger superfamily of Class II (DNA) transposons. Both elements contain two open reading frames; one encodes a transposase (ORF2) that catalyzes transposition of the functional elements and their related non-autonomous elements, while the function of the second is still debated...
August 3, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28774266/evolution-of-the-p53-mdm2-pathway
#18
Emma Åberg, Fulvio Saccoccia, Manfred Grabherr, Wai Ying Josefin Ore, Per Jemth, Greta Hultqvist
BACKGROUND: The p53 signalling pathway, which controls cell fate, has been extensively studied due to its prominent role in tumor development. The pathway includes the tumor supressor protein p53, its vertebrate paralogs p63 and p73, and their negative regulators MDM2 and MDM4. The p53/p63/p73-MDM system is ancient and can be traced in all extant animal phyla. Despite this, correct phylogenetic trees including both vertebrate and invertebrate species of the p53/p63/p73 and MDM families have not been published...
August 3, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28768477/hostplant-change-and-paleoclimatic-events-explain-diversification-shifts-in-skipper-butterflies-family-hesperiidae
#19
Ranjit Kumar Sahoo, Andrew D Warren, Steve C Collins, Ullasa Kodandaramaiah
BACKGROUND: Skippers (Family: Hesperiidae) are a large group of butterflies with ca. 4000 species under 567 genera. The lack of a time-calibrated higher-level phylogeny of the group has precluded understanding of its evolutionary past. We here use a 10-gene dataset to reconstruct the most comprehensive time-calibrated phylogeny of the group, and explore factors that affected the diversification of these butterflies. RESULTS: Ancestral state reconstructions show that the early hesperiid lineages utilized dicots as larval hostplants...
August 2, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28768476/pan-genome-and-phylogeny-of-bacillus-cereus-sensu-lato
#20
Adam L Bazinet
BACKGROUND: Bacillus cereus sensu lato (s. l.) is an ecologically diverse bacterial group of medical and agricultural significance. In this study, I use publicly available genomes and novel bioinformatic workflows to characterize the B. cereus s. l. pan-genome and perform the largest phylogenetic and population genetic analyses of this group to date in terms of the number of genes and taxa included. With these fundamental data in hand, I identify genes associated with particular phenotypic traits (i...
August 2, 2017: BMC Evolutionary Biology
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