Author
James R. Walters
Other affiliations: Kyoto Institute of Technology, Bowdoin College, University of Cambridge ...read more
Bio: James R. Walters is an academic researcher from University of Kansas. The author has contributed to research in topics: Heliconius & Autosome. The author has an hindex of 23, co-authored 51 publications receiving 2997 citations. Previous affiliations of James R. Walters include Kyoto Institute of Technology & Bowdoin College.
Topics: Heliconius, Autosome, Sperm, Z chromosome, Danaus
Papers published on a yearly basis
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University College London1, University of Cambridge2, University of California, Irvine3, University of Maryland, College Park4, University of Oxford5, Smithsonian Institution6, University of Greifswald7, Max Planck Society8, Imperial College London9, Harvard University10, University of East Anglia11, Mississippi State University12, University of Texas at Austin13, Commonwealth Scientific and Industrial Research Organisation14, University of Paris15, University of Hawaii16, California Academy of Sciences17, Williams College18, Yale University19, University of Puerto Rico20, Johns Hopkins University21, North Carolina State University22, University of Bristol23, University of Edinburgh24, Baylor College of Medicine25, Del Rosario University26, University of Exeter27, Boston University28
TL;DR: It is inferred that closely related Heliconius species exchange protective colour-pattern genes promiscuously, implying that hybridization has an important role in adaptive radiation.
Abstract: Sequencing of the genome of the butterfly Heliconius melpomene shows that closely related Heliconius species exchange protective colour-pattern genes promiscuously.
1,103 citations
TL;DR: Overall these results show that species divergence can occur in the face of persistent and genome-wide admixture over long periods of time.
Abstract: Most speciation events probably occur gradually, without complete and immediate reproductive isolation, but the full extent of gene flow between diverging species has rarely been characterized on a genome-wide scale. Documenting the extent and timing of admixture between diverging species can clarify the role of geographic isolation in speciation. Here we use new methodology to quantify admixture at different stages of divergence in Heliconius butterflies, based on whole-genome sequences of 31 individuals. Comparisons between sympatric and allopatric populations of H. melpomene, H. cydno, and H. timareta revealed a genome-wide trend of increased shared variation in sympatry, indicative of pervasive interspecific gene flow. Up to 40% of 100-kb genomic windows clustered by geography rather than by species, demonstrating that a very substantial fraction of the genome has been shared between sympatric species. Analyses of genetic variation shared over different time intervals suggested that admixture between these species has continued since early in speciation. Alleles shared between species during recent time intervals displayed higher levels of linkage disequilibrium than those shared over longer time intervals, suggesting that this admixture took place at multiple points during divergence and is probably ongoing. The signal of admixture was significantly reduced around loci controlling divergent wing patterns, as well as throughout the Z chromosome, consistent with strong selection for Mullerian mimicry and with known Z-linked hybrid incompatibility. Overall these results show that species divergence can occur in the face of persistent and genome-wide admixture over long periods of time.
604 citations
University of Bristol1, Great Western Hospital2, Staffordshire University3, North Tees and Hartlepool NHS Foundation Trust4, South Tees Hospitals NHS Trust5, Guy's and St Thomas' NHS Foundation Trust6, University of Manchester7, Lancashire Teaching Hospitals NHS Foundation Trust8, Cambridge University Hospitals NHS Foundation Trust9, Northumbria Healthcare NHS Foundation Trust10, Sherwood Forest Hospitals NHS Foundation Trust11, NHS Ayrshire and Arran12, Worcestershire Acute Hospitals NHS Trust13, United Hospitals14, Aintree University Hospitals NHS Foundation Trust15, Hampshire Hospitals NHS Foundation Trust16, University of Oxford17, North Bristol NHS Trust18, Sir Charles Gairdner Hospital19, University College London20
TL;DR: Among patients without substantial lung entrapment, the outpatient administration of talc through an indwelling pleural catheter for the treatment of malignant pleural effusion resulted in a significantly higher chance of pleurodesis at 35 days than an ind welling catheter alone, with no deleterious effects.
Abstract: Background Malignant pleural effusion affects more than 750,000 persons each year across Europe and the United States. Pleurodesis with the administration of talc in hospitalized patients is the most common treatment, but indwelling pleural catheters placed for drainage offer an ambulatory alternative. We examined whether talc administered through an indwelling pleural catheter was more effective at inducing pleurodesis than the use of an indwelling pleural catheter alone. Methods Over a period of 4 years, we recruited patients with malignant pleural effusion at 18 centers in the United Kingdom. After the insertion of an indwelling pleural catheter, patients underwent drainage regularly on an outpatient basis. If there was no evidence of substantial lung entrapment (nonexpandable lung, in which lung expansion and pleural apposition are not possible because of visceral fibrosis or bronchial obstruction) at 10 days, patients were randomly assigned to receive either 4 g of talc slurry or placebo thr...
166 citations
Kansas State University1, Oklahoma State University–Stillwater2, Boyce Thompson Institute for Plant Research3, University of Rhode Island4, Max Planck Society5, University of Sydney6, Human Genome Sequencing Center7, University of Kansas8, Massachusetts Institute of Technology9, University of Barcelona10, China Agricultural University11, François Rabelais University12, Commonwealth Scientific and Industrial Research Organisation13, University of Oxford14, Academy of Athens15, University of Copenhagen16, Columbia University17, Southwest University18, Reed College19, Fraunhofer Society20, Donghua University21, Northwest A&F University22, University of Texas Southwestern Medical Center23, University of Southern Maine24, University of California, Irvine25, Anhui Agricultural University26, University of Rochester27, Northeastern University28, Cornell University29, Chinese Academy of Sciences30, Hamilton College31, University of Hamburg32, Ghent University33, National and Kapodistrian University of Athens34, University of Wisconsin-Madison35, North Carolina State University36, University of Siegen37, Oregon Health & Science University38, University of Cambridge39, University of Massachusetts Amherst40, College of Charleston41, University of Giessen42, University of South Carolina43, University of Missouri–Kansas City44, Rothamsted Research45
TL;DR: The sequence and annotation of the M. sexta genome, and a survey of gene expression in various tissues and developmental stages, provide an important new resource from a well-studied model insect species and will facilitate further biochemical and mechanistic experimental studies of many biological systems in insects.
154 citations
TL;DR: It is argued that either population bottlenecks or the repeated action of natural selection, coupled with high levels of selfing, are likely to explain the observed reductions in species-wide genetic diversity.
Abstract: Self-fertilizing species often harbor less genetic variation than cross-fertilizing species, and at least four different models have been proposed to explain this trend. To investigate further the relationship between mating system and genetic variation, levels of DNA sequence polymorphism were compared among three closely related species in the genus Caenorhabditis: two self-fertilizing species, Caenorhabditis elegans and C. briggsae, and one cross-fertilizing species, C. remanei. As expected, estimates of silent site nucleotide diversity were lower in the two self-fertilizing species. For the mitochondrial genome, diversity in the selfing species averaged 42% of diversity in C. remanei. Interestingly, the reduction in genetic variation was much greater for the nuclear than for the mitochondrial genome. For two nuclear genes, diversity in the selfing species averaged 6 and 13% of diversity in C. remanei. We argue that either population bottlenecks or the repeated action of natural selection, coupled with high levels of selfing, are likely to explain the observed reductions in species-wide genetic diversity.
153 citations
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TL;DR: It is suggested that the natural selection against large insertion/deletion is so weak that a large amount of variation is maintained in a population.
11,521 citations
Journal Article•
TL;DR: In this paper, a test based on two conserved CHD (chromo-helicase-DNA-binding) genes that are located on the avian sex chromosomes of all birds, with the possible exception of the ratites (ostriches, etc.).
2,554 citations
TL;DR: Both BlastKOALA and GhostKOalA are automatic annotation servers for genome and metagenome sequences, which perform KO (KEGG Orthology) assignments to characterize individual gene functions and reconstruct KEGG pathways, BRITE hierarchies and K EGG modules to infer high-level functions of the organism or the ecosystem.
2,247 citations
TL;DR: A suite of methods for learning about population mixtures are presented, implemented in a software package called ADMIXTOOLS, that support formal tests for whether mixture occurred and make it possible to infer proportions and dates of mixture.
Abstract: Population mixture is an important process in biology. We present a suite of methods for learning about population mixtures, implemented in a software package called ADMIXTOOLS, that support formal tests for whether mixture occurred and make it possible to infer proportions and dates of mixture. We also describe the development of a new single nucleotide polymorphism (SNP) array consisting of 629,433 sites with clearly documented ascertainment that was specifically designed for population genetic analyses and that we genotyped in 934 individuals from 53 diverse populations. To illustrate the methods, we give a number of examples that provide new insights about the history of human admixture. The most striking finding is a clear signal of admixture into northern Europe, with one ancestral population related to present-day Basques and Sardinians and the other related to present-day populations of northeast Asia and the Americas. This likely reflects a history of admixture between Neolithic migrants and the indigenous Mesolithic population of Europe, consistent with recent analyses of ancient bones from Sweden and the sequencing of the genome of the Tyrolean "Iceman."
1,877 citations
University of St Andrews1, University of Oldenburg2, Natural History Museum3, Naturalis4, Centre national de la recherche scientifique5, Michigan State University6, University of Lausanne7, University of Wyoming8, Queen Mary University of London9, University of Sheffield10, International Institute for Applied Systems Analysis11, University of Oslo12, University of Vienna13, University of Vermont14, University of East Anglia15, Spanish National Research Council16, University of Cambridge17, University of Konstanz18, University of Zurich19, Royal Botanic Garden Edinburgh20, Harvard University21, Autonomous University of Madrid22, Swiss Federal Institute of Aquatic Science and Technology23, Boston University24, Max Planck Society25, University of Neuchâtel26, University of North Carolina at Chapel Hill27, Lehigh University28, American Museum of Natural History29, University of Montpellier30, University of Liverpool31, Jagiellonian University32, Uppsala University33, German Primate Center34
TL;DR: A perspective on the context and evolutionary significance of hybridization during speciation is offered, highlighting issues of current interest and debate and suggesting that the Dobzhansky–Muller model of hybrid incompatibilities requires a broader interpretation.
Abstract: Hybridization has many and varied impacts on the process of speciation. Hybridization may slow or reverse differentiation by allowing gene flow and recombination. It may accelerate speciation via adaptive introgression or cause near-instantaneous speciation by allopolyploidization. It may have multiple effects at different stages and in different spatial contexts within a single speciation event. We offer a perspective on the context and evolutionary significance of hybridization during speciation, highlighting issues of current interest and debate. In secondary contact zones, it is uncertain if barriers to gene flow will be strengthened or broken down due to recombination and gene flow. Theory and empirical evidence suggest the latter is more likely, except within and around strongly selected genomic regions. Hybridization may contribute to speciation through the formation of new hybrid taxa, whereas introgression of a few loci may promote adaptive divergence and so facilitate speciation. Gene regulatory networks, epigenetic effects and the evolution of selfish genetic material in the genome suggest that the Dobzhansky-Muller model of hybrid incompatibilities requires a broader interpretation. Finally, although the incidence of reinforcement remains uncertain, this and other interactions in areas of sympatry may have knock-on effects on speciation both within and outside regions of hybridization.
1,715 citations