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BMC Evolutionary Biology

Peter Civáň, Terence A Brown
BACKGROUND: Models for the origins of cultivated rice currently fall into two groups: ones that identify independent domestications of the indica, japonica and possibly also the aus types, and others that propose that the domestication phenotype was initially acquired by japonica, the underlying alleles then transferred by introgression to other pre-domesticated populations, giving the indica and aus varieties. Identifying the impact of past gene flow on cultivated rice genomes is therefore crucial to distinguishing between these models and understanding the domestication history of rice...
April 23, 2018: BMC Evolutionary Biology
Rosa Gabriela Beltrán-López, Omar Domínguez-Domínguez, Rodolfo Pérez-Rodríguez, Kyle Piller, Ignacio Doadrio
BACKGROUND: Volcanic and tectonic activities in conjunction with Quaternary climate are the main events that shaped the geographical distribution of genetic variation of many lineages. Poeciliopsis infans is the only poeciliid species that was able to colonize the temperate highlands of central Mexico. We inferred the phylogenetic relationships, biogeographic history, and historical demography in the widespread Neotropical species P. infans and correlated this with geological events and the Quaternary glacial-interglacial climate in the highlands of central Mexico, using the mitochondrial genes Cytochrome b and Cytochrome oxidase I and two nuclear loci, Rhodopsin and ribosomal protein S7...
April 20, 2018: BMC Evolutionary Biology
Hoi Yee Chu, Kathleen Sprouffske, Andreas Wagner
BACKGROUND: Recombination is widespread across the tree of life, because it helps purge deleterious mutations and creates novel adaptive traits. In prokaryotes, it often takes the form of horizontal gene transfer from a donor to a recipient bacterium. While such transfer is widespread in natural communities, its immediate fitness benefits are usually unknown. We asked whether any such benefits depend on the environment, and on the identity of donor and recipient strains. To this end, we adapted Escherichia coli to two novel carbon sources over several hundred generations of laboratory evolution, exposing evolving populations to various DNA donors...
April 19, 2018: BMC Evolutionary Biology
Diana Delicado, Torsten Hauffe, Thomas Wilke
BACKGROUND: Differences in species richness among phylogenetic clades are attributed to clade age and/or variation in diversification rates. Access to ecological opportunity may trigger a temporary increase in diversification rates and ecomorphological variation. In addition, lower body temperatures in poikilothermic animals may result in decreasing speciation rates as proposed by the metabolic theory of ecology. For strictly freshwater organisms, environmental gradients within a river continuum, linked to elevation and temperature, might promote access to ecological opportunity and alter metabolic rates, eventually influencing speciation and extinction processes...
April 19, 2018: BMC Evolutionary Biology
Julien Fumey, Hélène Hinaux, Céline Noirot, Claude Thermes, Sylvie Rétaux, Didier Casane
BACKGROUND: Cavefish populations belonging to the Mexican tetra species Astyanax mexicanus are outstanding models to study the tempo and mode of adaptation to a radical environmental change. They are currently assigned to two main groups, the so-called "old" and "new" lineages, which would have populated several caves independently and at different times. However, we do not have yet accurate estimations of the time frames of evolution of these populations. RESULTS: We reanalyzed the geographic distribution of mitochondrial and nuclear DNA polymorphisms and we found that these data do not support the existence of two cavefish lineages...
April 18, 2018: BMC Evolutionary Biology
Temim Deli, Evrim Kalkan, Selahattin Ünsal Karhan, Sonya Uzunova, Alireza Keikhosravi, Raşit Bilgin, Christoph D Schubart
BACKGROUND: Recently, population genetic studies of Mediterranean marine species highlighted patterns of genetic divergence and phylogeographic breaks, due to the interplay between impacts of Pleistocene climate shifts and contemporary hydrographical barriers. These factors markedly shaped the distribution of marine organisms and their genetic makeup. The present study is part of an ongoing effort to understand the phylogeography and evolutionary history of the highly dispersive Mediterranean green crab, Carcinus aestuarii (Nardo, 1847), across the Mediterranean Sea...
April 11, 2018: BMC Evolutionary Biology
A D Lokits, H Indrischek, J Meiler, H E Hamm, P F Stadler
BACKGROUND: Heterotrimeric G proteins are fundamental signaling proteins composed of three subunits, Gα and a Gβγ dimer. The role of Gα as a molecular switch is critical for transmitting and amplifying intracellular signaling cascades initiated by an activated G protein Coupled Receptor (GPCR). Despite their biochemical and therapeutic importance, the study of G protein evolution has been limited to the scope of a few model organisms. Furthermore, of the five primary Gα subfamilies, the underlying gene structure of only two families has been thoroughly investigated outside of Mammalia evolution...
April 11, 2018: BMC Evolutionary Biology
Song Yi Baek, Ji Hyoun Kang, Seo Hee Jo, Ji Eun Jang, Seo Yeon Byeon, Ju-Hyoun Wang, Hwang-Goo Lee, Jun-Kil Choi, Hyuk Je Lee
BACKGROUND: Life history characteristics are considered important factors influencing the evolutionary processes of natural populations, including the patterns of population genetic structure of a species. The sister species Cottus hangiongensis and C. koreanus are small bottom-dwelling freshwater sculpin fishes from South Korea that display marked life history divergence but are morphologically nearly indistinguishable. Cottus hangiongensis evolved an 'amphidromous' life history with a post-hatching pelagic larval phase...
April 11, 2018: BMC Evolutionary Biology
Thamayanthi Nada Raja, Ting Huey Hu, Ramlah Zainudin, Kim Sung Lee, Susan L Perkins, Balbir Singh
BACKGROUND: Non-human primates have long been identified to harbour different species of Plasmodium. Long-tailed macaques (Macaca fascicularis), in particular, are reservoirs for P. knowlesi, P. inui, P. cynomolgi, P. coatneyi and P. fieldi. A previous study conducted in Sarawak, Malaysian Borneo, however revealed that long-tailed macaques could potentially harbour novel species of Plasmodium based on sequences of small subunit ribosomal RNA and circumsporozoite genes. To further validate this finding, the mitochondrial genome and the apicoplast caseinolytic protease M genes of Plasmodium spp...
April 10, 2018: BMC Evolutionary Biology
Xue Lv, Jilong Cheng, Yang Meng, Yongbin Chang, Lin Xia, Zhixin Wen, Deyan Ge, Shaoying Liu, Qisen Yang
BACKGROUND: South China encompasses complex and diverse landforms, giving rise to high biological diversity and endemism from the Hengduan Mountains to Taiwan Island. Many species are widely distributed across South China with similar disjunct distribution patterns. To explore the causes of these disjunct distribution patterns and their genetic consequences, we investigated the endemic species Père David's Chinese Vole (Eothenomys melanogaster) by integrating geological and ecological factors...
April 10, 2018: BMC Evolutionary Biology
Nadia Tahiri, Matthieu Willems, Vladimir Makarenkov
BACKGROUND: Gene trees carry important information about specific evolutionary patterns which characterize the evolution of the corresponding gene families. However, a reliable species consensus tree cannot be inferred from a multiple sequence alignment of a single gene family or from the concatenation of alignments corresponding to gene families having different evolutionary histories. These evolutionary histories can be quite different due to horizontal transfer events or to ancient gene duplications which cause the emergence of paralogs within a genome...
April 5, 2018: BMC Evolutionary Biology
Georg Brenneis, Gerhard Scholtz, Barbara S Beltz
BACKGROUND: Comparative studies of neuroanatomy and neurodevelopment provide valuable information for phylogenetic inference. Beyond that, they reveal transformations of neuroanatomical structures during animal evolution and modifications in the developmental processes that have shaped these structures. In the extremely diverse Arthropoda, such comparative studies contribute with ever-increasing structural resolution and taxon coverage to our understanding of nervous system evolution...
April 5, 2018: BMC Evolutionary Biology
Barbara H Dobrin, Derrick J Zwickl, Michael J Sanderson
BACKGROUND: The pattern of data availability in a phylogenetic data set may lead to the formation of terraces, collections of equally optimal trees. Terraces can arise in tree space if trees are scored with parsimony or with partitioned, edge-unlinked maximum likelihood. Theory predicts that terraces can be large, but their prevalence in contemporary data sets has never been surveyed. We selected 26 data sets and phylogenetic trees reported in recent literature and investigated the terraces to which the trees would belong, under a common set of inference assumptions...
April 4, 2018: BMC Evolutionary Biology
Lin Zhang, Kun Guo, Guang-Zheng Zhang, Long-Hui Lin, Xiang Ji
BACKGROUND: Energy (resources) acquired by animals should be allocated towards competing demands, maintenance, growth, reproduction and fat storage. Reproduction has the second lowest priority in energy allocation and only is allowed after meeting the energetic demands for maintenance and growth. This hierarchical allocation of energy suggests the hypothesis that species or taxa with high maintenance costs would be less likely to invest more energy in reproduction or to evolve an energetically more expensive mode of reproduction...
April 3, 2018: BMC Evolutionary Biology
V Manzanilla, A Kool, L Nguyen Nhat, H Nong Van, H Le Thi Thu, H J de Boer
BACKGROUND: The economic value of ginseng in the global medicinal plant trade is estimated to be in excess of US$2.1 billion. At the same time, the evolutionary placement of ginseng (Panax ginseng) and the complex evolutionary history of the genus is poorly understood despite several molecular phylogenetic studies. In this study, we use a full plastome phylogenomic framework to resolve relationships in Panax and to identify molecular markers for species discrimination. RESULTS: We used high-throughput sequencing of MBD2-Fc fractionated Panax DNA to supplement publicly available plastid genomes to create a phylogeny based on fully assembled and annotated plastid genomes from 60 accessions of 8 species...
April 3, 2018: BMC Evolutionary Biology
Zhiliang Zhang, Leonid E Popov, Lars E Holmer, Zhifei Zhang
BACKGROUND: Our understanding of the ontogeny of Palaeozoic brachiopods has changed significantly during the last two decades. However, the micromorphic acrotretoids have received relatively little attention, resulting in a poor knowledge of their ontogeny, origin and earliest evolution. The uniquely well preserved early Cambrian fossil records in South China provide a great new opportunity to investigate the phylogenetically important ontogeny of the earliest acrotretoid brachiopods, and give new details of the dramatic changes in anatomy of acrotretoid brachiopods during the transition from planktotrophic larvae to filter feeding sedentary juveniles...
April 2, 2018: BMC Evolutionary Biology
Huan Qiu, Alessandro W Rossoni, Andreas P M Weber, Hwan Su Yoon, Debashish Bhattacharya
BACKGROUND: Genome reduction in intracellular pathogens and endosymbionts is usually compensated by reliance on the host for energy and nutrients. Free-living taxa with reduced genomes must however evolve strategies for generating functional diversity to support their independent lifestyles. An emerging model for the latter case is the Rhodophyta (red algae) that comprises an ecologically widely distributed, species-rich phylum. Red algae have undergone multiple phases of significant genome reduction, including extremophilic unicellular taxa with limited nuclear gene inventories that must cope with hot, highly acidic environments...
April 2, 2018: BMC Evolutionary Biology
E Quéméré, J M Gaillard, M Galan, C Vanpé, I David, M Pellerin, P Kjellander, A J M Hewison, J M Pemberton
BACKGROUND: Understanding the genetic and environmental mechanisms governing variation in morphology or phenology in wild populations is currently an important challenge. While there is a general consensus that selection is stronger under stressful conditions, it remains unclear whether the evolutionary potential of traits should increase or decrease with increasingly stressful conditions. Here, we investigate how contrasting environmental conditions during growth may affect the maternal and genetic components of body mass in roe deer, the most abundant and widespread wild ungulate in Western Europe...
March 28, 2018: BMC Evolutionary Biology
Jonathan Romiguier, Jonathan Rolland, Claire Morandin, Laurent Keller
BACKGROUND: The ants of the Formica genus are classical model species in evolutionary biology. In particular, Darwin used Formica as model species to better understand the evolution of slave-making, a parasitic behaviour where workers of another species are stolen to exploit their workforce. In his book "On the Origin of Species" (1859), Darwin first hypothesized that slave-making behaviour in Formica evolved in incremental steps from a free-living ancestor. METHODS: The absence of a well-resolved phylogenetic tree of the genus prevent an assessment of whether relationships among Formica subgenera are compatible with this scenario...
March 28, 2018: BMC Evolutionary Biology
Madlen Stange, Gabriel Aguirre-Fernández, Walter Salzburger, Marcelo R Sánchez-Villagra
BACKGROUND: Morphological convergence triggered by trophic adaptations is a common pattern in adaptive radiations. The study of shape variation in an evolutionary context is usually restricted to well-studied fish models. We take advantage of the recently revised systematics of New World Ariidae and investigate skull shape evolution in six genera of northern Neotropical Ariidae. They constitute a lineage that diversified in the marine habitat but repeatedly adapted to freshwater habitats...
March 27, 2018: BMC Evolutionary Biology
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