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BMC Evolutionary Biology

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https://www.readbyqxmd.com/read/28212607/a-case-of-modular-phenotypic-plasticity-in-the-depth-gradient-for-the-gorgonian-coral-antillogorgia-bipinnata-cnidaria-octocorallia
#1
Iván Calixto-Botía, Juan A Sánchez
BACKGROUND: Phenotypic plasticity, as a phenotypic response induced by the environment, has been proposed as a key factor in the evolutionary history of corals. A significant number of octocoral species show high phenotypic variation, exhibiting a strong overlap in intra- and inter-specific morphologic variation. This is the case of the gorgonian octocoral Antillogorgia bipinnata (Verrill 1864), which shows three polyphyletic morphotypes along a bathymetric gradient. This research tested the phenotypic plasticity of modular traits in A...
February 17, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28209121/evolution-of-toll-like-receptors-in-the-context-of-terrestrial-ungulates-and-cetaceans-diversification
#2
Edson Ishengoma, Morris Agaba
BACKGROUND: Toll-like receptors (TLRs) are the frontline actors in the innate immune response to various pathogens and are expected to be targets of natural selection in species adapted to habitats with contrasting pathogen burdens. The recent publication of genome sequences of giraffe and okapi together afforded the opportunity to examine the evolution of selected TLRs in broad range of terrestrial ungulates and cetaceans during their complex habitat diversification. Through direct sequence comparisons and standard evolutionary approaches, the extent of nucleotide and protein sequence diversity in seven Toll-like receptors (TLR2, TLR3, TLR4, TLR5, TLR7, TLR9 and TLR10) between giraffe and closely related species was determined...
February 16, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28201989/revisiting-phylogenetic-signal-strong-or-negligible-impacts-of-polytomies-and-branch-length-information
#3
Rafael Molina-Venegas, Miguel Á Rodríguez
BACKGROUND: Inaccurate estimates of phylogenetic signal may mislead interpretations of many ecological and evolutionary processes, and hence understanding where potential sources of uncertainty may lay has become a priority for comparative studies. Importantly, the sensitivity of phylogenetic signal indices and their associated statistical tests to incompletely resolved phylogenies and suboptimal branch-length information has been only partially investigated. METHODS: Here, we use simulations of trait evolution along phylogenetic trees to assess whether incompletely resolved phylogenies (polytomic chronograms) and phylogenies with suboptimal branch-length information (pseudo-chronograms) could produce directional biases in significance tests (p-values) associated with Blomberg et al...
February 15, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28196465/metabolite-toxicity-determines-the-pace-of-molecular-evolution-within-microbial-populations
#4
Elin E Lilja, David R Johnson
BACKGROUND: The production of toxic metabolites has shaped the spatial and temporal arrangement of metabolic processes within microbial cells. While diverse solutions to mitigate metabolite toxicity have evolved, less is known about how evolution itself is affected by metabolite toxicity. We hypothesized that the pace of molecular evolution should increase as metabolite toxicity increases. At least two mechanisms could cause this. First, metabolite toxicity could increase the mutation rate...
February 14, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28193159/erratum-to-phylogenomics-of-strongylocentrotid-sea-urchins
#5
Kord M Kober, Giacomo Bernardi
No abstract text is available yet for this article.
February 13, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28193153/molecular-evolution-of-globin-genes-in-gymnotiform-electric-fishes-relation-to-hypoxia-tolerance
#6
Ran Tian, Mauricio Losilla, Ying Lu, Guang Yang, Harold Zakon
BACKGROUND: Nocturnally active gymnotiform weakly electric fish generate electric signals for communication and navigation, which can be energetically taxing. These fish mainly inhabit the Amazon basin, where some species prefer well-oxygenated waters and others live in oxygen-poor, stagnant habitats. The latter species show morphological, physiological, and behavioral adaptations for hypoxia-tolerance. However, there have been no studies of hypoxia tolerance on the molecular level. Globins are classic respiratory proteins...
February 13, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28187706/genome-data-on-the-extinct-bison-schoetensacki-establish-it-as-a-sister-species-of-the-extant-european-bison-bison-bonasus
#7
Pauline Palacio, Véronique Berthonaud, Claude Guérin, Josie Lambourdière, Frédéric Maksud, Michel Philippe, Delphine Plaire, Thomas Stafford, Marie-Claude Marsolier-Kergoat, Jean-Marc Elalouf
BACKGROUND: The European bison (Bison bonasus), now found in Europe and the Caucasus, has been proposed to originate either from the extinct steppe/extant American bison lineage or from the extinct Bison schoetensacki lineage. Bison schoetensacki remains are documented in Eurasian Middle Pleistocene sites, but their presence in Upper Pleistocene sites has been questioned. Despite extensive genetic studies carried out on the steppe and European bison, no remains from the fossil record morphologically identified as Bison schoetensacki has been analyzed up to now...
February 10, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28187705/the-evolution-of-social-learning-mechanisms-and-cultural-phenomena-in-group-foragers
#8
Daniel J van der Post, Mathias Franz, Kevin N Laland
BACKGROUND: Advanced cognitive abilities are widely thought to underpin cultural traditions and cumulative cultural change. In contrast, recent simulation models have found that basic social influences on learning suffice to support both cultural phenomena. In the present study we test the predictions of these models in the context of skill learning, in a model with stochastic demographics, variable group sizes, and evolved parameter values, exploring the cultural ramifications of three different social learning mechanisms...
February 10, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28173765/selection-on-the-mitochondrial-atp-synthase-6-and-the-nadh-dehydrogenase-2-genes-in-hares-lepus-capensis-l-1758-from-a-steep-ecological-gradient-in-north-africa
#9
Hichem Ben Slimen, Helmut Schaschl, Felix Knauer, Franz Suchentrunk
BACKGROUND: Recent studies of selection on mitochondrial (mt) OXPHOS genes suggest adaptation due mainly to environmental variation. In this context, Tunisian hares that display several external phenotypes with phylogenetically rather homogenous gene pool and shallow population structure provide a good precondition to detect positive selection on mt genes related to environmental/climatic variation, specifically ambient temperature and precipitation. RESULTS: We used codon-based methods along with population genetic data to test for positive selection on ATPase synthase 6 (ATP6) and NADH dehydrogenase 2 (ND2) of cape hares (Lepus capensis) collected along a steep ecological gradient in Tunisia...
February 7, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28173760/grandparental-immune-priming-in-the-pipefish-syngnathus-typhle
#10
Anne Beemelmanns, Olivia Roth
BACKGROUND: Phenotypic changes in response to environmental influences can persist from one generation into the next. In many systems parental parasite experience influences offspring immune responses, known as transgenerational immune priming (TGIP). TGIP in vertebrates is mainly maternal and short-term, supporting the adaptive immune system of the offspring during its maturation. However, if fathers and offspring have a close physical connection, evolution of additional paternal immune priming can be adaptive...
February 7, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28173751/the-importance-of-selection-in-the-evolution-of-blindness-in-cavefish
#11
Reed A Cartwright, Rachel S Schwartz, Alexandra L Merry, Megan M Howell
BACKGROUND: Blindness has evolved repeatedly in cave-dwelling organisms, and many hypotheses have been proposed to explain this observation, including both accumulation of neutral loss-of-function mutations and adaptation to darkness. Investigating the loss of sight in cave dwellers presents an opportunity to understand the operation of fundamental evolutionary processes, including drift, selection, mutation, and migration. RESULTS: Here we model the evolution of blindness in caves...
February 7, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28173748/susceptibility-to-type-2-diabetes-may-be-modulated-by-haplotypes-in-g6pc2-a-target-of-positive-selection
#12
Nasser M Al-Daghri, Chiara Pontremoli, Rachele Cagliani, Diego Forni, Majed S Alokail, Omar S Al-Attas, Shaun Sabico, Stefania Riva, Mario Clerici, Manuela Sironi
BACKGROUND: The endoplasmic reticulum enzyme glucose-6-phosphatase catalyzes the common terminal reaction in the gluconeogenic/glycogenolytic pathways and plays a central role in glucose homeostasis. In most mammals, different G6PC subunits are encoded by three paralogous genes (G6PC, G6PC2, and G6PC3). Mutations in G6PC and G6PC3 are responsible for human mendelian diseases, whereas variants in G6PC2 are associated with fasting glucose (FG) levels. RESULTS: We analyzed the evolutionary history of G6Pase genes...
February 7, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28173747/origin-and-diversification-of-leucine-rich-repeat-receptor-like-protein-kinase-lrr-rlk-genes-in-plants
#13
Ping-Li Liu, Liang Du, Yuan Huang, Shu-Min Gao, Meng Yu
BACKGROUND: Leucine-rich repeat receptor-like protein kinases (LRR-RLKs) are the largest group of receptor-like kinases in plants and play crucial roles in development and stress responses. The evolutionary relationships among LRR-RLK genes have been investigated in flowering plants; however, no comprehensive studies have been performed for these genes in more ancestral groups. The subfamily classification of LRR-RLK genes in plants, the evolutionary history and driving force for the evolution of each LRR-RLK subfamily remain to be understood...
February 7, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28166720/increased-rates-of-protein-evolution-and-asymmetric-deceleration-after-the-whole-genome-duplication-in-yeasts
#14
Diana Ascencio, Soledad Ochoa, Luis Delaye, Alexander DeLuna
BACKGROUND: Whole-genome duplication (WGD) events have shaped the genomes of eukaryotic organisms. Relaxed selection after duplication along with inherent functional constraints are thought to determine the fate of the paralogs and, ultimately, the evolution of gene function. Here, we investigated the rate of protein evolution (as measured by dN/dS ratios) before and after the WGD in the hemiascomycete yeasts, and the way in which changes in such rates relate to molecular and biological function...
February 6, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28166715/bmodeltest-bayesian-phylogenetic-site-model-averaging-and-model-comparison
#15
Remco R Bouckaert, Alexei J Drummond
BACKGROUND: Reconstructing phylogenies through Bayesian methods has many benefits, which include providing a mathematically sound framework, providing realistic estimates of uncertainty and being able to incorporate different sources of information based on formal principles. Bayesian phylogenetic analyses are popular for interpreting nucleotide sequence data, however for such studies one needs to specify a site model and associated substitution model. Often, the parameters of the site model is of no interest and an ad-hoc or additional likelihood based analysis is used to select a single site model...
February 6, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28166714/cross-generational-comparison-of-reproductive-success-in-recently-caught-strains-of-drosophila-melanogaster
#16
Trinh T X Nguyen, Amanda J Moehring
BACKGROUND: Males and females often have opposing strategies for increasing fitness. Males that out-compete others will acquire more mating opportunities and thus have higher lifetime reproductive success. Females that mate with a high quality male receive either direct benefits through productivity or acquisition of additional resources or indirect benefits through the increased fitness of offspring. These components may be in conflict: factors that increase offspring fitness may decrease a female's productivity, and alleles that are beneficial in one sex may be detrimental in the opposite sex...
February 6, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28143390/analysis-of-a-mechanistic-markov-model-for-gene-duplicates-evolving-under-subfunctionalization
#17
Tristan L Stark, David A Liberles, Barbara R Holland, Małgorzata M O'Reilly
BACKGROUND: Gene duplication has been identified as a key process driving functional change in many genomes. Several biological models exist for the evolution of a pair of duplicates after a duplication event, and it is believed that gene duplicates can evolve in different ways, according to one process, or a mix of processes. Subfunctionalization is one such process, under which the two duplicates can be preserved by dividing up the function of the original gene between them. Analysis of genomic data using subfunctionalization and related processes has thus far been relatively coarse-grained, with mathematical treatments usually focusing on the phenomenological features of gene duplicate evolution...
January 31, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28137244/cambrian-suspension-feeding-lobopodians-and-the-early-radiation-of-panarthropods
#18
Jean-Bernard Caron, Cédric Aria
BACKGROUND: Arthropoda, Tardigrada and Onychophora evolved from lobopodians, a paraphyletic group of disparate Palaeozoic vermiform animals with soft legs. Although the morphological diversity that this group encompasses likely illustrates the importance of niche diversification in the early radiation of panarthropods, the ecology of lobopodians remains poorly characterized. RESULTS: Here we describe a new luolishaniid taxon from the middle Cambrian Burgess Shale (Walcott Quarry) in British Columbia, Canada, whose specialized morphology epitomizes the suspension-feeding ecology of this clade, and is convergent with some modern marine animals, such as caprellid crustaceans...
January 31, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28125973/habitat-structure-is-linked-to-the-evolution-of-plumage-colour-in-female-but-not-male-fairy-wrens
#19
Iliana Medina, Kaspar Delhey, Anne Peters, Kristal E Cain, Michelle L Hall, Raoul A Mulder, Naomi E Langmore
BACKGROUND: Both natural and sexual selection may drive the evolution of plumage colouration in birds. This can lead to great variation in plumage not only across species, but also between sexes within species. Australasian fairy-wrens are famous for their brightly coloured males, which exhibit colours ranging from bright blue to red and black. Female plumage in fairy wrens (and in general) has been rarely studied, but it can also be highly variable, including both bright and cryptic plumages...
January 26, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28125959/assessing-in-silico-the-recruitment-and-functional-spectrum-of-bacterial-enzymes-from-secondary-metabolism
#20
Valery Veprinskiy, Leonhard Heizinger, Maximilian G Plach, Rainer Merkl
BACKGROUND: Microbes, plants, and fungi synthesize an enormous number of metabolites exhibiting rich chemical diversity. For a high-level classification, metabolism is subdivided into primary (PM) and secondary (SM) metabolism. SM products are often not essential for survival of the organism and it is generally assumed that SM enzymes stem from PM homologs. RESULTS: We wanted to assess evolutionary relationships and function of bona fide bacterial PM and SM enzymes...
January 26, 2017: BMC Evolutionary Biology
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