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BMC Evolutionary Biology

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https://www.readbyqxmd.com/read/29439676/evolution-of-cyp2j19-a-gene-involved-in-colour-vision-and-red-coloration-in-birds-positive-selection-in-the-face-of-conservation-and-pleiotropy
#1
Hanlu Twyman, Staffan Andersson, Nicholas I Mundy
BACKGROUND: Exaggerated signals, such as brilliant colours, are usually assumed to evolve through antagonistic coevolution between senders and receivers, but the underlying genetic mechanisms are rarely known. Here we explore a recently identified "redness gene", CYP2J19, that is highly interesting in this context since it encodes a carotenoid-modifying enzyme (a C4 ketolase involved in both colour signalling and colour discrimination in the red (long wavelength) spectral region.) RESULTS: A single full-length CYP2J19 was retrieved from 43 species out of 70 avian genomes examined, representing all major avian clades...
February 13, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29433448/the-role-of-facial-pattern-variation-for-species-recognition-in-red-fronted-lemurs-eulemur-rufifrons
#2
Hanitriniaina Rakotonirina, Peter M Kappeler, Claudia Fichtel
BACKGROUND: Species recognition, i.e., the ability to distinguish conspecifics from heterospecifics, plays an essential role in reproduction. The role of facial cues for species recognition has been investigated in several non-human primate species except for lemurs. We therefore investigated the role of facial cues for species recognition in wild red-fronted lemurs (Eulemur rufifrons) at Kirindy Forest. We presented adult red-fronted lemurs pictures of male faces from five species including red-fronted lemurs, three closely related species, white-fronted lemurs (E...
February 13, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29433444/a-novel-short-l-arginine-responsive-protein-coding-gene-laob-antiparallel-overlapping-to-a-cadc-like-transcriptional-regulator-in-escherichia-coli-o157-h7-sakai-originated-by-overprinting
#3
Sarah M Hücker, Sonja Vanderhaeghen, Isabel Abellan-Schneyder, Romy Wecko, Svenja Simon, Siegfried Scherer, Klaus Neuhaus
BACKGROUND: Due to the DNA triplet code, it is possible that the sequences of two or more protein-coding genes overlap to a large degree. However, such non-trivial overlaps are usually excluded by genome annotation pipelines and, thus, only a few overlapping gene pairs have been described in bacteria. In contrast, transcriptome and translatome sequencing reveals many signals originated from the antisense strand of annotated genes, of which we analyzed an example gene pair in more detail...
February 12, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29426277/phylogeography-of-eomecon-chionantha-in-subtropical-china-the-dual-roles-of-the-nanling-mountains-as-a-glacial-refugium-and-a-dispersal-corridor
#4
Shuang Tian, Yixuan Kou, Zhirong Zhang, Lin Yuan, Derong Li, Jordi López-Pujol, Dengmei Fan, Zhiyong Zhang
BACKGROUND: Mountains have not only provided refuge for species, but also offered dispersal corridors during the Neogene and Quaternary global climate changes. Compared with a plethora of studies on the refuge role of China's mountain ranges, their dispersal corridor role has received little attention in plant phylogeographic studies. Using phylogeographic data of Eomecon chionantha Hance (Papaveraceae), this study explicitly tested whether the Nanling Mountains, which spans from west to east for more than 1000 km in subtropical China, could have functioned as a dispersal corridor during the late Quaternary in addition to a glacial refugium...
February 9, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29422028/the-curious-case-of-peroxiredoxin-5-what-its-absence-in-aves-can-tell-us-and-how-it-can-be-used
#5
Marc Pirson, André Clippe, Bernard Knoops
BACKGROUND: Peroxiredoxins are ubiquitous thiol-dependent peroxidases that represent a major antioxidant defense in both prokaryotic cells and eukaryotic organisms. Among the six vertebrate peroxiredoxin isoforms, peroxiredoxin-5 (PRDX5) appears to be a particular peroxiredoxin, displaying a different catalytic mechanism, as well as a wider substrate specificity and subcellular distribution. In addition, several evolutionary peculiarities, such as loss of subcellular targeting in certain species, have been reported for this enzyme...
February 8, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29422024/protein-evolution-depends-on-multiple-distinct-population-size-parameters
#6
REVIEW
Alexander Platt, Claudia C Weber, David A Liberles
That population size affects the fate of new mutations arising in genomes, modulating both how frequently they arise and how efficiently natural selection is able to filter them, is well established. It is therefore clear that these distinct roles for population size that characterize different processes should affect the evolution of proteins and need to be carefully defined. Empirical evidence is consistent with a role for demography in influencing protein evolution, supporting the idea that functional constraints alone do not determine the composition of coding sequences...
February 8, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29409440/macroevolutionary-diversification-with-limited-niche-disparity-in-a-species-rich-lineage-of-cold-climate-lizards
#7
Ashley M Reaney, Mónica Saldarriaga-Córdoba, Daniel Pincheira-Donoso
BACKGROUND: Life diversifies via adaptive radiation when natural selection drives the evolution of ecologically distinct species mediated by their access to novel niche space, or via non-adaptive radiation when new species diversify while retaining ancestral niches. However, while cases of adaptive radiation are widely documented, examples of non-adaptively radiating lineages remain rarely observed. A prolific cold-climate lizard radiation from South America (Phymaturus), sister to a hyper-diverse adaptive radiation (Liolaemus), has extensively diversified phylogenetically and geographically, but with exceptionally minimal ecological and life-history diversification...
February 6, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29402230/ongoing-niche-differentiation-under-high-gene-flow-in-a-polymorphic-brackish-water-threespine-stickleback-gasterosteus-aculeatus-population
#8
Kjartan Østbye, Annette Taugbøl, Mark Ravinet, Chris Harrod, Ruben Alexander Pettersen, Louis Bernatchez, Leif Asbjørn Vøllestad
BACKGROUND: Marine threespine sticklebacks colonized and adapted to brackish and freshwater environments since the last Pleistocene glacial. Throughout the Holarctic, three lateral plate morphs are observed; the low, partial and completely plated morph. We test if the three plate morphs in the brackish water Lake Engervann, Norway, differ in body size, trophic morphology (gill raker number and length), niche (stable isotopes; δ15N, δ13C, and parasites (Theristina gasterostei, Trematoda spp...
February 5, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29402211/phylogenomics-of-a-rapid-radiation-the-australian-rainbow-skinks
#9
Jason G Bragg, Sally Potter, Ana C Afonso Silva, Conrad J Hoskin, Benjamin Y H Bai, Craig Moritz
BACKGROUND: The application of target capture with next-generation sequencing now enables phylogenomic analyses of rapidly radiating clades of species. But such analyses are complicated by extensive incomplete lineage sorting, demanding the use of methods that consider this process explicitly, such as the multispecies coalescent (MSC) model. However, the MSC makes strong assumptions about divergence history and population structure, and when using the full Bayesian implementation, current computational limits mean that relatively few loci and samples can be analysed for even modest sized radiations...
February 5, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29402209/breeding-consequences-of-flavivirus-infection-in-the-collared-flycatcher
#10
Tanja M Strand, Åke Lundkvist, Björn Olsen, Lars Gustafsson
BACKGROUND: The breeding consequences of virus infections have rarely been studied in avian natural breeding populations. In this paper we investigated the links between humoral immunity following a natural flavivirus infection and reproduction in a wild bird population of collared flycatcher (Ficedula albicollis). We analyzed plasma from 744 birds for antibodies and correlated these results to a number of reproductive components. RESULTS: Nearly one third (27.8%) of the sampled collared flycatchers were found seropositive for flavivirus...
February 5, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29394881/wnt-signaling-and-polarity-in-freshwater-sponges
#11
Pamela J Windsor Reid, Eugueni Matveev, Alexandra McClymont, Dora Posfai, April L Hill, Sally P Leys
BACKGROUND: The Wnt signaling pathway is uniquely metazoan and used in many processes during development, including the formation of polarity and body axes. In sponges, one of the earliest diverging animal groups, Wnt pathway genes have diverse expression patterns in different groups including along the anterior-posterior axis of two sponge larvae, and in the osculum and ostia of others. We studied the function of Wnt signaling and body polarity formation through expression, knockdown, and larval manipulation in several freshwater sponge species...
February 2, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29390973/mpboot-fast-phylogenetic-maximum-parsimony-tree-inference-and-bootstrap-approximation
#12
Diep Thi Hoang, Le Sy Vinh, Tomáš Flouri, Alexandros Stamatakis, Arndt von Haeseler, Bui Quang Minh
BACKGROUND: The nonparametric bootstrap is widely used to measure the branch support of phylogenetic trees. However, bootstrapping is computationally expensive and remains a bottleneck in phylogenetic analyses. Recently, an ultrafast bootstrap approximation (UFBoot) approach was proposed for maximum likelihood analyses. However, such an approach is still missing for maximum parsimony. RESULTS: To close this gap we present MPBoot, an adaptation and extension of UFBoot to compute branch supports under the maximum parsimony principle...
February 2, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29390964/evolutionary-fates-of-universal-stress-protein-paralogs-in-platyhelminthes
#13
Sergio Martin Espinola, Martin Pablo Cancela, Lauís Brisolara Corrêa, Arnaldo Zaha
BACKGROUND: Universal stress proteins (USPs) are present in all domains of life. Their expression is upregulated in response to a large variety of stress conditions. The functional diversity found in this protein family, paired with the sequence degeneration of the characteristic ATP-binding motif, suggests a complex evolutionary pattern for the paralogous USP-encoding genes. In this work, we investigated the origin, genomic organization, expression patterns and evolutionary history of the USP gene family in species of the phylum Platyhelminthes...
February 1, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29374461/allele-phasing-is-critical-to-revealing-a-shared-allopolyploid-origin-of-medicago-arborea-and-m-strasseri-fabaceae
#14
Jonna S Eriksson, Filipe de Sousa, Yann J K Bertrand, Alexandre Antonelli, Bengt Oxelman, Bernard E Pfeil
BACKGROUND: Whole genome duplication plays a central role in plant evolution. There are two main classes of polyploid formation: autopolyploids which arise within one species by doubling of similar homologous genomes; in contrast, allopolyploidy (hybrid polyploidy) arise via hybridization and subsequent doubling of nonhomologous (homoeologous) genomes. The distinction between polyploid origins can be made using gene phylogenies, if alleles from each genome can be correctly retrieved. We examined whether two closely related tetraploid Mediterranean shrubs (Medicago arborea and M...
January 27, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29370752/the-pivotal-role-of-aristaless-in-development-and-evolution-of-diverse-antennal-morphologies-in-moths-and-butterflies
#15
Toshiya Ando, Haruhiko Fujiwara, Tetsuya Kojima
BACKGROUND: Antennae are multi-segmented appendages and main odor-sensing organs in insects. In Lepidoptera (moths and butterflies), antennal morphologies have diversified according to their ecological requirements. While diurnal butterflies have simple, rod-shaped antennae, nocturnal moths have antennae with protrusions or lateral branches on each antennal segment for high-sensitive pheromone detection. A previous study on the Bombyx mori (silk moth) antenna, forming two lateral branches per segment, during metamorphosis has revealed the dramatic change in expression of antennal patterning genes to segmentally reiterated, branch-associated pattern and abundant proliferation of cells contributing almost all the dorsal half of the lateral branch...
January 25, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29368587/widespread-signatures-of-selection-for-secreted-peptidases-in-a-fungal-plant-pathogen
#16
Parvathy Krishnan, Xin Ma, Bruce A McDonald, Patrick C Brunner
BACKGROUND: Fungal plant pathogens secrete a large arsenal of hydrolytic enzymes during the course of infection, including peptidases. Secreted peptidases have been extensively studied for their role as effectors. In this study, we combined transcriptomics, comparative genomics and evolutionary analyses to investigate all 39 secreted peptidases in the fungal wheat pathogen Zymoseptoria tritici and its close relatives Z. pseudotritici and Z. ardabiliae. RESULTS: RNA-seq data revealed that a majority of the secreted peptidases displayed differential transcription during the course of Z...
January 24, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29351742/herv-w-group-evolutionary-history-in-non-human-primates-characterization-of-erv-w-orthologs-in-catarrhini-and-related-erv-groups-in-platyrrhini
#17
Nicole Grandi, Marta Cadeddu, Jonas Blomberg, Jens Mayer, Enzo Tramontano
BACKGROUND: The genomes of all vertebrates harbor remnants of ancient retroviral infections, having affected the germ line cells during the last 100 million years. These sequences, named Endogenous Retroviruses (ERVs), have been transmitted to the offspring in a Mendelian way, being relatively stable components of the host genome even long after their exogenous counterparts went extinct. Among human ERVs (HERVs), the HERV-W group is of particular interest for our physiology and pathology...
January 19, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29351740/population-size-may-shape-the-accumulation-of-functional-mutations-following-domestication
#18
Jianhai Chen, Pan Ni, Xinyun Li, Jianlin Han, Ivan Jakovlić, Chengjun Zhang, Shuhong Zhao
BACKGROUND: Population genetics theory predicts an important role of differences in the effective population size (N e ) among species on shaping the accumulation of functional mutations by regulating the selection efficiency. However, this correlation has never been tested in domesticated animals. RESULTS: Here, we synthesized 62 whole genome data in eight domesticated species (cat, dog, pig, goat, sheep, chicken, cattle and horse) and compared domesticates with their wild (or ancient) relatives...
January 19, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29351730/population-structure-of-venturia-inaequalis-a-causal-agent-of-apple-scab-in-response-to-heterogeneous-apple-tree-cultivation
#19
Monika Michalecka, Sylwester Masny, Thibault Leroy, Joanna Puławska
BACKGROUND: Tracking newly emergent virulent populations in agroecosystems provides an opportunity to increase our understanding of the co-evolution dynamics of pathogens and their hosts. On the one hand host plants exert selective pressure on pathogen populations, thus dividing them into subpopulations of different virulence, while on the other hand they create an opportunity for secondary contact between the two divergent populations on one tree. The main objectives of the study were to explore whether the previously reported structure between two Venturia inaequalis population types, virulent or avirulent towards Malus x domestica cultivars carrying Rvi6 gene, is maintained or broken several years after the first emergence of new virulent strains in Poland, and to investigate the relationship between 'new' and 'native' populations derived from the same commercial orchards...
January 19, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29338681/the-evolutionary-process-of-mammalian-sex-determination-genes-focusing-on-marsupial-srys
#20
Yukako Katsura, Hiroko X Kondo, Janelle Ryan, Vincent Harley, Yoko Satta
BACKGROUND: Maleness in mammals is genetically determined by the Y chromosome. On the Y chromosome SRY is known as the mammalian male-determining gene. Both placental mammals (Eutheria) and marsupial mammals (Metatheria) have SRY genes. However, only eutherian SRY genes have been empirically examined by functional analyses, and the involvement of marsupial SRY in male gonad development remains speculative. RESULTS: In order to demonstrate that the marsupial SRY gene is similar to the eutherian SRY gene in function, we first examined the sequence differences between marsupial and eutherian SRY genes...
January 16, 2018: BMC Evolutionary Biology
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