Ice-Age Climate Adaptations Trap the Alpine Marmot in a State of Low Genetic Diversity

[1]  Peter K. Joshi,et al.  Runs of homozygosity: windows into population history and trait architecture , 2018, Nature Reviews Genetics.

[2]  O. Mazet,et al.  The IICR (inverse instantaneous coalescence rate) as a summary of genomic diversity: insights into demographic inference and model choice , 2017, Heredity.

[3]  H. Nichols The causes and consequences of inbreeding avoidance and tolerance in cooperatively breeding vertebrates , 2017 .

[4]  H. Innan,et al.  varver: a database of microsatellite variation in vertebrates , 2017, Molecular ecology resources.

[5]  M. Lascoux,et al.  Genetic Diversity and the Efficacy of Purifying Selection across Plant and Animal Species , 2017, Molecular biology and evolution.

[6]  N. Bierne,et al.  Adaptive evolution and segregating load contribute to the genomic landscape of divergence in two tree species connected by episodic gene flow , 2017, Molecular ecology.

[7]  D. Allainé,et al.  Faithful or not: direct and indirect effects of climate on extra-pair paternities in a population of Alpine marmots , 2016, Proceedings of the Royal Society B: Biological Sciences.

[8]  Ming-hai Zhang,et al.  The complete mitochondrial genome of Daurian ground squirrel, Spermophilus dauricus , 2016, Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis.

[9]  Diego Ortega-Del Vecchyo,et al.  Genomic Flatlining in the Endangered Island Fox , 2016, Current Biology.

[10]  M. Russello,et al.  Low genetic diversity, restricted dispersal, and elevation-specific patterns of population decline in American pikas in an atypical environment , 2016, Journal of Mammalogy.

[11]  B. Kempenaers,et al.  Characterization of the genome and transcriptome of the blue tit Cyanistes caeruleus: polymorphisms, sex‐biased expression and selection signals , 2016, Molecular ecology resources.

[12]  Yali Xue,et al.  BCFtools/RoH: a hidden Markov model approach for detecting autozygosity from next-generation sequencing data , 2016, Bioinform..

[13]  Daniel R. Zerbino,et al.  Ensembl 2016 , 2015, Nucleic Acids Res..

[14]  Wen J. Li,et al.  Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation , 2015, Nucleic Acids Res..

[15]  Minoru Kanehisa,et al.  KEGG as a reference resource for gene and protein annotation , 2015, Nucleic Acids Res..

[16]  A. Janke,et al.  Genetic signatures of adaptation revealed from transcriptome sequencing of Arctic and red foxes , 2015, BMC Genomics.

[17]  M. Gahr,et al.  Using the canary genome to decipher the evolution of hormone-sensitive gene regulation in seasonal singing birds , 2015, Genome Biology.

[18]  María Martín,et al.  UniProt: A hub for protein information , 2015 .

[19]  R. Reinhardt,et al.  European sea bass genome and its variation provide insights into adaptation to euryhalinity and speciation , 2014, Nature Communications.

[20]  M. Bohr,et al.  Hibernation induces immune changes in the lung of 13-lined ground squirrels (Ictidomys tridecemlineatus). , 2014, Developmental and comparative immunology.

[21]  Juancarlos Chan,et al.  Gene Ontology Consortium: going forward , 2014, Nucleic Acids Res..

[22]  Davide Heller,et al.  STRING v10: protein–protein interaction networks, integrated over the tree of life , 2014, Nucleic Acids Res..

[23]  The Uniprot Consortium,et al.  UniProt: a hub for protein information , 2014, Nucleic Acids Res..

[24]  L. Duret,et al.  Comparative population genomics in animals uncovers the determinants of genetic diversity , 2014, Nature.

[25]  X. Zhang,et al.  Complete mitochondrial genome sequence of Marmota himalayana (Rodentia: Sciuridae) and phylogenetic analysis within Rodentia. , 2014, Genetics and molecular research : GMR.

[26]  X. Liu,et al.  Historical Biogeography and Body Form Evolution of Ground Squirrels (Sciuridae: Xerinae) , 2014, Evolutionary Biology.

[27]  Matthew Fraser,et al.  InterProScan 5: genome-scale protein function classification , 2014, Bioinform..

[28]  Alexandros Stamatakis,et al.  RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..

[29]  Richard M. Leggett,et al.  NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries , 2013, Bioinform..

[30]  Damian Szklarczyk,et al.  eggNOG v4.0: nested orthology inference across 3686 organisms , 2013, Nucleic Acids Res..

[31]  Mauricio O. Carneiro,et al.  From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline , 2013, Current protocols in bioinformatics.

[32]  Jing Wang,et al.  WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013 , 2013, Nucleic Acids Res..

[33]  Cole Trapnell,et al.  TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions , 2013, Genome Biology.

[34]  J. Gaillard,et al.  Decreasing litter size of marmots over time: a life history response to climate change? , 2013, Ecology.

[35]  Xiu Lin,et al.  Facing growth in the European Nucleotide Archive , 2012, Nucleic Acids Res..

[36]  Hans Lehrach,et al.  The Saccharomyces cerevisiae W303-K6001 cross-platform genome sequence: insights into ancestry and physiology of a laboratory mutt , 2012, Open Biology.

[37]  D. Dimitrov,et al.  A glimpse on the pattern of rodent diversification: a phylogenetic approach , 2012, BMC Evolutionary Biology.

[38]  M. Siol,et al.  EggLib: processing, analysis and simulation tools for population genetics and genomics , 2012, BMC Genetics.

[39]  Pablo Cingolani,et al.  © 2012 Landes Bioscience. Do not distribute. , 2022 .

[40]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[41]  David R. Kelley,et al.  Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks , 2012, Nature Protocols.

[42]  Jonathan A. Eisen,et al.  Accounting For Alignment Uncertainty in Phylogenomics , 2012, PloS one.

[43]  S. Steppan,et al.  Molecular data resolve placement of the Olympic marmot and estimate dates of trans-Beringian interchange , 2011 .

[44]  J. Griffin,et al.  The contrasting roles of PPARδ and PPARγ in regulating the metabolic switch between oxidation and storage of fats in white adipose tissue , 2011, Genome Biology.

[45]  R. Durbin,et al.  Inference of human population history from individual whole-genome sequences. , 2011, Nature.

[46]  Gonçalo R. Abecasis,et al.  The variant call format and VCFtools , 2011, Bioinform..

[47]  M. DePristo,et al.  A framework for variation discovery and genotyping using next-generation DNA sequencing data , 2011, Nature Genetics.

[48]  M. Frith,et al.  Adaptive seeds tame genomic sequence comparison. , 2011, Genome research.

[49]  Josyf Mychaleckyj,et al.  Robust relationship inference in genome-wide association studies , 2010, Bioinform..

[50]  J. Ragle,et al.  IUCN Red List of Threatened Species , 2010 .

[51]  M. DePristo,et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.

[52]  Miriah D. Meyer,et al.  Genome-wide synteny through highly sensitive sequence alignment: Satsuma , 2010, Bioinform..

[53]  Paramvir S. Dehal,et al.  FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments , 2010, PloS one.

[54]  W. Martin,et al.  Molecular Poltergeists: Mitochondrial DNA Copies (numts) in Sequenced Nuclear Genomes , 2010, PLoS genetics.

[55]  Ryan D. Hernandez,et al.  Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data , 2009, PLoS genetics.

[56]  Steven J. M. Jones,et al.  Circos: an information aesthetic for comparative genomics. , 2009, Genome research.

[57]  Kate E. Jones,et al.  PanTHERIA: a species‐level database of life history, ecology, and geography of extant and recently extinct mammals , 2009 .

[58]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[59]  F. R. Cole,et al.  Generic Revision in the Holarctic Ground Squirrel Genus Spermophilus , 2009 .

[60]  Tal Pupko,et al.  Rodent phylogeny revised: analysis of six nuclear genes from all major rodent clades , 2009, BMC Evolutionary Biology.

[61]  L. Kruckenhauser,et al.  Microsatellite variation in autochthonous and introduced populations of the Alpine marmot (Marmota marmota) along a European west–east transect , 2008 .

[62]  Joaquín Hortal,et al.  Climate Change, Humans, and the Extinction of the Woolly Mammoth , 2008, PLoS biology.

[63]  O. Gotoh,et al.  A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence , 2008, Nucleic acids research.

[64]  David Haussler,et al.  Using native and syntenically mapped cDNA alignments to improve de novo gene finding , 2008, Bioinform..

[65]  Sofia M. C. Robb,et al.  MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. , 2007, Genome research.

[66]  P. Keightley,et al.  Joint Inference of the Distribution of Fitness Effects of Deleterious Mutations and Population Demography Based on Nucleotide Polymorphism Frequencies , 2007, Genetics.

[67]  J. L. Gittleman,et al.  The Fast‐Slow Continuum in Mammalian Life History: An Empirical Reevaluation , 2007, The American Naturalist.

[68]  Peer Bork,et al.  PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments , 2006, Nucleic Acids Res..

[69]  D. Allainé,et al.  Genetic diversity-fitness correlation revealed by microsatellite analyses in European alpine marmots (Marmota marmota) , 2006, Conservation Genetics.

[70]  B. Goossens,et al.  Extra-pair paternity in the monogamous alpine marmot (Marmota marmota): the roles of social setting and female mate choice , 2006, Behavioral Ecology and Sociobiology.

[71]  Peter Schattner,et al.  The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs , 2005, Nucleic Acids Res..

[72]  Ian Korf,et al.  Gene finding in novel genomes , 2004, BMC Bioinformatics.

[73]  D. Haussler,et al.  Aligning multiple genomic sequences with the threaded blockset aligner. , 2004, Genome research.

[74]  B. L. Storz,et al.  Nuclear DNA phylogeny of the squirrels (Mammalia: Rodentia) and the evolution of arboreality from c-myc and RAG1. , 2004, Molecular phylogenetics and evolution.

[75]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[76]  V. Roth,et al.  The Effects of Cenozoic Global Change on Squirrel Phylogeny , 2003, Science.

[77]  Tom H. Pringle,et al.  The human genome browser at UCSC. , 2002, Genome research.

[78]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[79]  B. Goossens,et al.  Microsatellite analysis of genetic variation among and within Alpine marmot populations in the French Alps , 2001, Molecular ecology.

[80]  B. Charlesworth,et al.  Effects of metapopulation processes on measures of genetic diversity. , 2000, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[81]  G. Florant,et al.  White adipose tissue fatty acids of alpine marmots during their yearly cycle , 1999, Lipids.

[82]  D. V. Vuren,et al.  A 32-year demography of yellow-bellied marmots (Marmota flaviventris) , 1998 .

[83]  Ziheng Yang,et al.  PAML: a program package for phylogenetic analysis by maximum likelihood , 1997, Comput. Appl. Biosci..

[84]  L. Kruckenhauser,et al.  Alpine marmots in Austria. The present population structure as a result of the postglacial distribution history , 1995 .

[85]  Craig L. Frank,et al.  The Influence of Dietary Fatty Acids on Hibernation by Golden-Mantled Ground Squirrels (Spermophilus lateralis) , 1992, Physiological Zoology.

[86]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[87]  I. P. Gerasimov,et al.  The Periglacial Expansion of Marmots (Marmota) in Middle Europe during Late Pleistocene , 1973 .

[88]  Ira M. Hall,et al.  BEDTools: a flexible suite of utilities for comparing genomic features , 2010, Bioinform..

[89]  Claude-Alain H. Roten,et al.  Fast and accurate short read alignment with Burrows–Wheeler transform , 2009, Bioinform..

[90]  A. Walter The evolution of marmot sociality: II. Costs and benefits of joint hibernation , 2004, Behavioral Ecology and Sociobiology.

[91]  A. Walter The evolution of marmot sociality: I. Why disperse late? , 2004, Behavioral Ecology and Sociobiology.

[92]  T. Ruf,et al.  Essential Fatty Acids: Their Impact on Free-living Alpine Marmots (Marmota marmota) , 2000 .

[93]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .