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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
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
Sajad Mirzaei, Yufeng Wu
MOTIVATION: Haplotypes from one or multiple related populations share a common genealogical history. If this shared genealogy can be inferred from haplotypes, it can be very useful for many population genetics problems. However, with the presence of recombination, the genealogical history of haplotypes is complex and cannot be represented by a single genealogical tree. Therefore, inference of genealogical history with recombination is much more challenging than the case of no recombination...
January 8, 2017: Bioinformatics
Tine Huyse, Merel Oeyen, Maarten H D Larmuseau, Filip A M Volckaert
We performed a comparative phylogeographic study on the monogenean flatworm Gyrodactylus gondae Huyse, Malmberg & Volckaert 2005 (Gyrodactylidae) and its sand goby host Pomatoschistus minutus (Pallas, 1770) (Gobiidae). G. gondae is a host-specific parasite with a direct life cycle and a very short generation time. These properties are expected to increase the chance to track the genealogical history of the host with genetic data of the parasite ('magnifying glass principle'). To investigate this hypothesis we screened nine sand goby populations (n=326) along the Atlantic coasts of Europe for Gyrodactylus specimens...
December 24, 2016: Parasitology International
Jonathan Terhorst, John A Kamm, Yun S Song
It has recently been demonstrated that inference methods based on genealogical processes with recombination can uncover past population history in unprecedented detail. However, these methods scale poorly with sample size, limiting resolution in the recent past, and they require phased genomes, which contain switch errors that can catastrophically distort the inferred history. Here we present SMC++, a new statistical tool capable of analyzing orders of magnitude more samples than existing methods while requiring only unphased genomes (its results are independent of phasing)...
December 26, 2016: Nature Genetics
Bradly Alicea
To examine the role of natural selection in fecundity in a variety of Caenorhabditis elegans genetic backgrounds, we used an experimental evolution protocol to evolve 14 distinct genetic strains over 15-20 generations. We were able to generate 790 distinct genealogies, which provided information on both the effects of natural selection and the evolvability of each strain. Among these genotypes are a wild-type (N2) and a collection of mutants with targeted mutations in the daf-c, daf-d and AMPK pathways. Differences are observed in reproductive fitness along with related changes in reproductive timing...
November 2016: Royal Society Open Science
Bertis B Little, Maria Eugenia Peña Reyes, Robert M Malina
OBJECTIVE: This study tests the hypothesis that natural selection is associated with type 2 diabetes (T2D)-associated mortality and fertility in a rural isolated Zapotec community in the Valley of Oaxaca, southern Mexico. PARTICIPANTS AND METHODS: Mortality data and related demographic and genealogic information were linked with data for fertility, prereproductive mortality and family history of mortality attributed to T2D. Physician verified T2D mortality (n = 27) between 1980 and 2009 and imputed T2D (n = 70) from cardiovascular mortality (68% random sample) and renal failure (44% random sample)...
December 23, 2016: American Journal of Physical Anthropology
Alaitz Poveda, Yan Chen, Anders Brändström, Elisabeth Engberg, Göran Hallmans, Ingegerd Johansson, Frida Renström, Azra Kurbasic, Paul W Franks
AIMS/HYPOTHESIS: Little is known about the heritable basis of gene-environment interactions in humans. We therefore screened multiple cardiometabolic traits to assess the probability that they are influenced by genotype-environment interactions. METHODS: Fourteen established environmental risk exposures and 11 cardiometabolic traits were analysed in the VIKING study, a cohort of 16,430 Swedish adults from 1682 extended pedigrees with available detailed genealogical, phenotypic and demographic information, using a maximum likelihood variance decomposition method in Sequential Oligogenic Linkage Analysis Routines software...
December 21, 2016: Diabetologia
Nathan D Jackson, Bryan C Carstens, Ariadna E Morales, Brian C O'Meara
Species are commonly thought to be evolutionarily independent in a way that populations within a species are not. In recent years, studies that seek to identify evolutionarily independent lineages (i.e., to delimit species) using genetic data have typically adopted multispecies coalescent approaches that assume that evolutionary independence is formed by the differential sorting of ancestral alleles due to genetic drift. However, gene flow appears to be common among populations and nascent species, and while this process may inhibit lineage divergence (and thus independence), it is usually not explicitly considered when delimiting species...
December 20, 2016: Systematic Biology
Noemi Kurt, Mathias Rafler
For the seedbank coalescent with mutation under the infinite alleles assumption, which describes the gene genealogy of a population with a strong seedbank effect subject to mutations, we study the distribution of the final partition with mutation. This generalizes the coalescent with freeze by Dong et al. (2007) to coalescents where ancestral lineages are blocked from coalescing. We derive an implicit recursion which we show to have a unique solution and give an interpretation in terms of absorption problems of a random walk...
December 18, 2016: Theoretical Population Biology
Daniel B Sloan, Justin C Havird, Joel Sharbrough
The study of reproductive isolation and species barriers frequently focuses on mitochondrial genomes and has produced two alternative and almost diametrically opposed narratives. On one hand, mtDNA may be at the forefront of speciation events, with coevolved mitonuclear interactions responsible for some of the earliest genetic incompatibilities arising among isolated populations. On the other hand, there are numerous cases of introgression of mtDNA across species boundaries even when nuclear gene flow is restricted...
December 20, 2016: Molecular Ecology
Zhiyong Yuan, Yunke Wu, Jiajun Zhou, Jing Che
New amphibian species have been constantly discovered throughout southern China, including from areas close to heavily populated cities that remain poorly surveyed for amphibian diversity. We describe a new species of the newt genus Paramesotriton from Fujian, a developed province on the southeastern coast of mainland China. The mitochondrial genealogy suggests that the new species is the sister taxon to Paramesotriton hongkongensis, separated by an uncorrected pairwise distances of 5.8% at the ND2 gene fragment analyzed...
December 12, 2016: Zootaxa
Amparo Martínez, Arianna Manunza, Juan Vicente Delgado, Vincenzo Landi, Ayotunde Adebambo, Muritala Ismaila, Juan Capote, Mabrouk El Ouni, Ahmed Elbeltagy, Asmaa M Abushady, Salah Galal, Ainhoa Ferrando, Mariano Gómez, Agueda Pons, Bouabid Badaoui, Jordi Jordana, Oriol Vidal, Marcel Amills
Human-driven migrations are one of the main processes shaping the genetic diversity and population structure of domestic species. However, their magnitude and direction have been rarely analysed in a statistical framework. We aimed to estimate the impact of migration on the population structure of Spanish and African goats. To achieve this goal, we analysed a dataset of 1,472 individuals typed with 23 microsatellites. Population structure of African and Spanish goats was moderate (mean FST = 0.07), with the exception of the Canarian and South African breeds that displayed a significant differentiation when compared to goats from North Africa and Nigeria...
December 14, 2016: Scientific Reports
Christopher M Crittenden, Lucas D Akin, Lindsay J Morrison, M Stephen Trent, Jennifer S Brodbelt
Lipid A molecules consist of a diglucosamine sugar core with a number of appended acyl chains that vary in their length and connectivity. Because of the challenging nature of characterizing these molecules and differentiating between isomeric species, an energy-resolved MS/MS strategy was undertaken to track the fragmentation trends and map genealogies of product ions originating from consecutive cleavages of acyl chains. Generalizations were developed based on the number and locations of the primary and secondary acyl chains as well as variations in preferential cleavages arising from the location of the phosphate groups...
December 13, 2016: Journal of the American Society for Mass Spectrometry
John Robert Warren, Carolina Milesi, Karen Grigorian, Melissa Humphries, Chandra Muller, Eric Grodsky
PURPOSE: Researchers who study mortality among survey participants have multiple options for obtaining information about which participants died (and when and how they died). Some use public record and commercial databases; others use the National Death Index; some use the Social Security Death Master File; and still others triangulate sources and use Internet searches and genealogic methods. We ask how inferences about mortality rates and disparities depend on the choice of source of mortality information...
November 22, 2016: Annals of Epidemiology
Elaine Françoso, Alexandre Rizzo Zuntini, Ana Carolina Carnaval, Maria Cristina Arias
BACKGROUND: Bombus morio and B. pauloensis are sympatric widespread bumblebee species that occupy two major Brazilian biomes, the Atlantic forest and the savannas of the Cerrado. Differences in dispersion capacity, which is greater in B. morio, likely influence their phylogeographic patterns. This study asks which processes best explain the patterns of genetic variation observed in B. morio and B. pauloensis, shedding light on the phenomena that shaped the range of local populations and the spatial distribution of intra-specific lineages...
December 7, 2016: BMC Evolutionary Biology
Maria Raquel Gomes Maia Pires, Rosa Maria Godoy Serpa da Fonseca, Beatriz Padilla
Objectives: analyze gender inequalities among Brazilian women in Portugal and in contemporary nursing based on care politicity in the light of gender; disclose oppression of the female produced by the stereotypes that look upon women as natural caregivers; point out politicity to deconstruct gender stereotypes. Method: theoretical reflection with narrative review of literature to analyze classic references in the feminist epistemology combined with the care politicity thesis...
November 2016: Revista Brasileira de Enfermagem
E Peripolli, D P Munari, M V G B Silva, A L F Lima, R Irgang, F Baldi
This review presents a broader approach to the implementation and study of runs of homozygosity (ROH) in animal populations, focusing on identifying and characterizing ROH and their practical implications. ROH are continuous homozygous segments that are common in individuals and populations. The ability of these homozygous segments to give insight into a population's genetic events makes them a useful tool that can provide information about the demographic evolution of a population over time. Furthermore, ROH provide useful information about the genetic relatedness among individuals, helping to minimize the inbreeding rate and also helping to expose deleterious variants in the genome...
December 1, 2016: Animal Genetics
Tokurou Shimizu, Akira Kitajima, Keisuke Nonaka, Terutaka Yoshioka, Satoshi Ohta, Shingo Goto, Atsushi Toyoda, Asao Fujiyama, Takako Mochizuki, Hideki Nagasaki, Eli Kaminuma, Yasukazu Nakamura
Most indigenous citrus varieties are assumed to be natural hybrids, but their parentage has so far been determined in only a few cases because of their wide genetic diversity and the low transferability of DNA markers. Here we infer the parentage of indigenous citrus varieties using simple sequence repeat and indel markers developed from various citrus genome sequence resources. Parentage tests with 122 known hybrids using the selected DNA markers certify their transferability among those hybrids. Identity tests confirm that most variant strains are selected mutants, but we find four types of kunenbo (Citrus nobilis) and three types of tachibana (Citrus tachibana) for which we suggest different origins...
2016: PloS One
Ezgi Dursun, Max Endele, Andrea Musumeci, Henrik Failmezger, Shu-Hung Wang, Achim Tresch, Timm Schroeder, Anne B Krug
Functionally distinct plasmacytoid and conventional dendritic cells (pDC and cDC) shape innate and adaptive immunity. They are derived from common dendritic cell progenitors (CDPs) in the murine bone marrow, which give rise to CD11c(+) MHCII(-) precursors with early commitment to DC subpopulations. In this study, we dissect pDC development from CDP into an ordered sequence of differentiation events by monitoring the expression of CD11c, MHC class II, Siglec H and CCR9 in CDP cultures by continuous single cell imaging and tracking...
November 28, 2016: Scientific Reports
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