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"Evolutionary biology"

V M Lourenço, P C Rodrigues, A M Pires, H-P Piepho
Motivation: In genetic association studies, linear mixed models (LMMs) are used to test for associations between phenotypes and candidate single nucleotide polymorphisms (SNPs). These same models are also used to estimate heritability, which is central not only to evolutionary biology but also to the prediction of the response to selection in plant and animal breeding, as well as the prediction of disease risk in humans. However, when one or more of the underlying assumptions are violated, the estimation of variance components may be compromised and therefore so may the estimates of heritability and any other functions of these...
July 14, 2017: Bioinformatics
Alexey Markin, Oliver Eulenstein
Synthesizing large-scale phylogenetic trees is a fundamental problem in evolutionary biology. Median tree problems have evolved as a powerful tool to reconstruct such trees. Such problems seek a median tree for a given collection of input trees under some problem-specific tree distance. There has been an increased interest in the median tree problem for the classical path-difference distance between trees. While this problem is NP-hard, standard local search heuristics have been described that are based on solving a local search problem exactly...
October 16, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
Marie-Agnès Coutellec
Mollusc shells, beyond the treasure of information inherently conveyed through their morphology and chemical composition also have the capacity to preserve DNA sequences over the long term in their inner structure. This has been clearly demonstrated for the first time in the study published in this issue of Molecular Ecology Resources by Der Sarkissian et al. (). With a methodology specifically dedicated to ancient DNA and solid matrices, the authors were able to successfully extract and amplify DNA from marine shells spanning the last 7,000 years...
September 2017: Molecular Ecology Resources
Michel Morange, Ute Deichmann
Between November 30th and December 2nd, 2015, the Jacques Loeb Centre for the History and Philosophy of the Life Sciences at Ben-Gurion University of the Negev in Beer Sheva (Israel) held its Eighth International Workshop under the title "From Genome to Gene: Causality, Synthesis and Evolution". Eric Davidson, the founder of the concept of developmental Gene Regulatory Networks, had regularly attended the previous meetings, and his participation in this one was expected, but he suddenly passed away 3 months before...
October 13, 2017: History and Philosophy of the Life Sciences
Charles Perrier, Anne-Laure Ferchaud, Pascal Sirois, Isabel Thibault, Louis Bernatchez
Understanding genomic signatures of divergent selection underlying long-term adaptation in populations located in heterogeneous environments is a key goal in evolutionary biology. In this study, we investigated neutral, adaptive and deleterious genetic variation using 7,192 SNPs in 31 Lake Trout (Salvelinus namaycush) populations (n = 673) from Québec, Canada. Average genetic diversity was low, weakly shared among lakes, and positively correlated to lake size, indicating a major role for genetic drift subsequent to lake isolation...
October 12, 2017: Molecular Ecology
Matthew J Zdilla, Michelle L Russell, Kaitlyn N Bliss, Kelsey R Mangus, Aaron W Koons
BACKGROUND: The foramen magnum (FM) has garnered broad interest across the disciplines of anthropology, comparative anatomy, evolutionary biology, and clinical sciences. Most studies regarding the structure of the FM in humans have been intrapopulation morphometric studies rather than interpopulation morphologic studies. The few studies assessing the morphology of the foramen have utilized ambiguous and subjective descriptors to describe foraminal shape and are, consequently, difficult to reproduce...
July 2017: Journal of Craniovertebral Junction and Spine
Fernanda Gonçalves Arcanjo, Edson Pereira Silva
In 1868, Darwin published his book The variation of animals and plants under domestication, which laid out his theory of heredity. This included the assumption that development was essential to understanding the evolutionary process. This present article reassesses the Darwinian theory of pangenesis in order to revisit its historical value. The conclusion is that the theory of pangenesis was well-suited to its time, and additionally, reflections of this assumption can be found in work in new areas known as evolutionary biology of development (evo-devo) and epigenetics...
July 2017: História, Ciências, Saúde—Manguinhos
Jérémy Tissier, Jean-Claude Rage, Michel Laurin
Fossils are almost always represented by hard tissues but we present here the exceptional case of a three-dimensionally preserved specimen that was 'mummified' (likely between 40 and 34 million years ago) in a terrestrial karstic environment. This fossil is the incomplete body of a salamander, Phosphotriton sigei, whose skeleton and external morphology are well preserved, as revealed by phase-contrast synchrotron X-ray microtomography. In addition, internal structures composed of soft tissues preserved in three dimensions are now identified: a lung, the spinal cord, a lumbosacral plexus, the digestive tract, muscles and urogenital organs that may be cloacal glands...
2017: PeerJ
Kristyn E Sylvia, Gregory E Demas
Sickness is typically characterized by fever, anorexia, cachexia, and reductions in social, pleasurable, and sexual behaviors. These responses can be displayed at varying intensities both within and among individuals, and the adaptive nature of sickness responses can be demonstrated by the context-dependent nature of their expression. The study of sickness has become an important area of investigation for researchers in a wide range of areas, including psychoneuroimmunology (PNI) and ecoimmunology (EI). The general goal of PNI is to identify key interactions among the nervous, endocrine and immune systems and behavior, and how disruptions in these processes might contribute to disease states...
August 25, 2017: Integrative and Comparative Biology
Clare Andrews, Daniel Nettle, Maria Larriva, Robert Gillespie, Sophie Reichert, Ben O Brilot, Thomas Bedford, Pat Monaghan, Karen A Spencer, Melissa Bateson
The acute stress response functions to prioritize behavioural and physiological processes that maximize survival in the face of immediate threat. There is variation between individuals in the strength of the adult stress response that is of interest in both evolutionary biology and medicine. Age is an established source of this variation-stress responsiveness diminishes with increasing age in a range of species-but unexplained variation remains. Since individuals of the same chronological age may differ markedly in their pace of biological ageing, we asked whether biological age-measured here via erythrocyte telomere length-predicts variation in stress responsiveness in adult animals of the same chronological age...
September 2017: Royal Society Open Science
Mats Olsson, Erik Wapstra, Christopher R Friesen
Telomere-induced selection could take place if telomere-associated disease risk shortens reproductive life span and differently reduces relative fitness among individuals. Some of these diseases first appear before reproductive senescence and could thus influence ongoing selection. We ask whether we can estimate the components of the breeder's equation for telomeres, in which the response to selection (R, by definition "evolution") is the product of ongoing selection (S) and heritability (h(2) ). However, telomere inheritance is a conundrum: in quantitative genetics, traits can usually be allocated to categories with relatively high or low heritability, depending on their association with relative fitness...
October 6, 2017: Annals of the New York Academy of Sciences
Jiaxin Zhang, Zhenguo Liu, Yawen Zou, Nanxiangzi Zhang, Dongliang Wang, Di Tu, Linchen Yang, Zhibang Deng, Yi Yang, Ping Jiang, Naidong Wang
Porcine circovirus type 3 (PCV3) has recently been isolated from diseased pigs within the USA. The objective was to detect the presence of PCV3 in dogs. Nested polymerase chain reactions (PCR) with PCV3-specific primers for the capsid gene were used to detect PCV3 genomic DNA in serum samples from dogs (n = 44) in China. There was PCV3 DNA detected in 4 of 44 dogs [all were negative for PCV2 and canine circovirus (CanineCV)]. Based on sequence analysis, positive sequences were grouped into PCV3 genotypes...
October 5, 2017: Virus Genes
Pablo G Cámara
Topological methods are emerging as a new set of tools for the analysis of large genomic datasets. They are mathematically grounded methods that extract information from the geometric structure of data. In the last few years, applications to evolutionary biology, cancer genomics, and the analysis of complex diseases have uncovered significant biological results, highlighting their utility for fulfilling some of the current analytic needs of genomics. In this review, the state of the art in the application of topological methods to genomics is summarized, and some of the present limitations and possible future developments are reviewed...
February 2017: Current opinion in systems biology
Venkat Talla, Alexander Suh, Faheema Kalsoom, Vlad Dinca, Roger Vila, Magne Friberg, Christer Wiklund, Niclas Backström
Characterizing and quantifying genome size variation among organisms and understanding if genome size evolves as a consequence of adaptive or stochastic processes have been long-standing goals in evolutionary biology. Here, we investigate genome size variation and association with transposable elements (TEs) across lepidopteran lineages using a novel genome assembly of the common wood-white (Leptidea sinapis) and population re-sequencing data from both L. sinapis and the closely related L. reali and L. juvernica together with 12 previously available lepidopteran genome assemblies...
October 1, 2017: Genome Biology and Evolution
Maureen A O'Malley
Since the 1940s, microbiologists, biochemists and population geneticists have experimented with the genetic mechanisms of microorganisms in order to investigate evolutionary processes. These evolutionary studies of bacteria and other microorganisms gained some recognition from the standard-bearers of the modern synthesis of evolutionary biology, especially Theodosius Dobzhansky and Ledyard Stebbins. A further period of post-synthesis bacterial evolutionary research occurred between the 1950s and 1980s. These experimental analyses focused on the evolution of population and genetic structure, the adaptive gain of new functions, and the evolutionary consequences of competition dynamics...
October 4, 2017: Journal of the History of Biology
Arlin Stoltzfus
High-level debates in evolutionary biology often treat the Modern Synthesis as a framework of population genetics, or as an intellectual lineage with a changing distribution of beliefs. Unfortunately, these flexible notions, used to negotiate decades of innovations, are now thoroughly detached from their historical roots in the original Modern Synthesis (OMS), a falsifiable scientific theory. The OMS held that evolution can be adequately understood as a process of smooth adaptive change by shifting the frequencies of small-effect alleles at many loci simultaneously, without the direct involvement of new mutations...
October 2, 2017: Biology Direct
Jeremy Van Cleve
One of the triumphs of evolutionary biology is the discovery of robust mechanisms that promote the evolution of cooperative behaviors even when cooperation reduces the fertility or survival of cooperators. These mechanisms include, kin selection, reciprocity, and direct benefits to cooperation that are often nonlinear. Though they have been extensively studied separately, investigating the joint action of these mechanisms has been more difficult. Moreover, how these mechanisms shape variation in cooperation is not well known...
September 1, 2017: Integrative and Comparative Biology
Rimjhim Roy Choudhury, Christian Parisod
Studying hybridization has the potential to elucidate challenging questions in evolutionary biology such as the nature of adaptive genetic variation and reproductive isolation. A growing body of work highlights that the merging of divergent genomes goes beyond the reshuffling of standing variation from related species and promotes mutations (Abbott et al., ). However, to what extent such genome instability generates evolutionary significant variation remains largely elusive. In this issue of Molecular Ecology, Dennenmoser et al...
September 2017: Molecular Ecology
Joseph W Brown, Stephen A Smith
Divergence time estimation-the calibration of a phylogeny to geological time-is an integral first step in modelling the tempo of biological evolution (traits and lineages). However, despite increasingly sophisticated methods to infer divergence times from molecular genetic sequences, the estimated age of many nodes across the tree of life contrast significantly and consistently with timeframes conveyed by the fossil record. This is perhaps best exemplified by crown angiosperms, where molecular clock (Triassic) estimates predate the oldest (Early Cretaceous) undisputed angiosperm fossils by tens of millions of years or more...
September 7, 2017: Systematic Biology
Hákon Jónsson, Patrick Sulem, Birte Kehr, Snaedis Kristmundsdottir, Florian Zink, Eirikur Hjartarson, Marteinn T Hardarson, Kristjan E Hjorleifsson, Hannes P Eggertsson, Sigurjon Axel Gudjonsson, Lucas D Ward, Gudny A Arnadottir, Einar A Helgason, Hannes Helgason, Arnaldur Gylfason, Adalbjorg Jonasdottir, Aslaug Jonasdottir, Thorunn Rafnar, Soren Besenbacher, Michael L Frigge, Simon N Stacey, Olafur Th Magnusson, Unnur Thorsteinsdottir, Gisli Masson, Augustine Kong, Bjarni V Halldorsson, Agnar Helgason, Daniel F Gudbjartsson, Kari Stefansson
Understanding of sequence diversity is the cornerstone of analysis of genetic disorders, population genetics, and evolutionary biology. Here, we present an update of our sequencing set to 15,220 Icelanders who we sequenced to an average genome-wide coverage of 34X. We identified 39,020,168 autosomal variants passing GATK filters: 31,079,378 SNPs and 7,940,790 indels. Calling de novo mutations (DNMs) is a formidable challenge given the high false positive rate in sequencing datasets relative to the mutation rate...
September 21, 2017: Scientific Data
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