15 Works

Data from: Disruption of gene expression in hybrids of the fire ants Solenopsis invicta and Solenopsis richteri

Lino Ometto, Kenneth G. Ross, D. DeWayne Shoemaker & Laurent Keller
Transcriptome analysis is a powerful tool for unveiling the distribution and magnitude of genetic incompatibilities between hybridizing taxa. The nature of such incompatibilities is closely associated with the evolutionary histories of the parental species and may differ across tissues and between the sexes. In eusocial insects, the presence of castes that experience divergent selection regimes may result in additional distinct patterns of caste-specific hybrid incompatibilities. We analyzed levels of expression of >14,000 genes in two...

Data from: Differential effects of landscape-level environmental features on genetic structure in three co-distributed tree species in Central America

Monica F. Poelchau, Jim L. Hamrick & J. L. Hamrick
Landscape genetic studies use spatially explicit population genetic information to determine the physical and environmental causes of population genetic structure on regional scales. Comparative studies that identify common barriers to gene flow across multiple species within a community are important to both understand the evolutionary trajectories of populations and to prioritize habitat conservation. Here, we use a comparative landscape genetic approach to ask whether gradients in temperature or precipitation seasonality structure genetic variation across three...

Data from: Discordant introgression in a rapidly expanding hybrid swarm

Jessica L. Ward, Mike J. Blum, David M. Walters, Brady A. Porter, Noel Burkhead & Byron Freeman
The erosion of species boundaries can involve rapid evolutionary change. Consequently, many aspects of the process remain poorly understood, including the formation, expansion and evolution of hybrid swarms. Biological invasions involving hybridization present exceptional opportunities to study the erosion of species boundaries because timelines of interactions and outcomes are frequently well known. Here, we examined clinal variation across codominant and maternally inherited genetic markers as well as phenotypic traits to characterize the expansion and evolution...

Data from: Phylogeography of Asian wild rice, Oryza rufipogon: a genome-wide view

Pu Huang, Jeanmaire Molina, Jonathan M. Flowers, Samara Rubinstein, Scott A. Jackson, Michael D. Purugganan & Barbara A. Schaal
Asian wild rice (Oryza rufipogon) that ranges widely across the eastern and southern part of Asia is recognized as the direct ancestor of cultivated Asian rice (O. sativa). Studies of the geographic structure of O. rufipogon, based on chloroplast and low-copy nuclear markers, reveal a possible phylogeographic signal of subdivision in O. rufipogon. However, this signal of geographic differentiation is not consistently observed among different markers and studies, with often conflicting results. To more precisely...

Data from: More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs

Nicholas G. Crawford, Brant C. Faircloth, John E. McCormack, Robb T. Brumfield, Kevin Winker, Travis C. Glenn, B. C. Faircloth, R. T. Brumfield, J. E. McCormack, T. C. Glenn & N. G. Crawford
We present the first genomic-scale analysis addressing the phylogenetic position of turtles, using over 1,000 loci from representatives of all major reptile lineages including tuatara. Previously, studies of morphological traits positioned turtles either at the base of the reptile tree or with lizards, snakes, and tuatara (lepidosaurs), whereas molecular analyses typically allied turtles with crocodiles and birds (archosaurs). A recent analysis of shared microRNA families found that turtles are more closely related to lepidosaurs. To...

Data from: Genomic conflict drives patterns of X-linked population structure in Drosophila neotestacea

Kelly A. Dyer, Michael J. Bray, Simon Lopez & S. Jeese Lopez
Intra-genomic conflict has the potential to cause widespread changes in patterns of genetic diversity and genome evolution. In this study, we investigate the consequences of sex-ratio (SR) drive on the population genetic patterns of the X-chromosome in Drosophila neotestacea. An SR X-chromosome prevents the maturation of Y-bearing sperm during male spermatogenesis, and thus is transmitted to ~100% of the offspring, nearly all of which are daughters. Selection on the rest of the genome to suppress...

Data from: Consequences of a poecilogonous life history for genetic structure in coastal populations of the polychaete Streblospio benedicti

Christina Zakas & John P. Wares
In many species, alternative developmental pathways lead to the production of two distinct phenotypes, promoting the evolution of morphological novelty and diversification. Offspring type in marine invertebrates influences transport time by ocean currents, which dictate dispersal potential and gene flow, and thus has sweeping evolutionary effects on the potential for local adaptation and on rates of speciation, extinction, and molecular evolution. Here we use the polychaete Streblospio benedicti to investigate the effects of dimorphic offspring...

Data from: Phylogeny, classification and evolution of ladybird beetles (Coleoptera: Coccinellidae) based on simultaneous analysis of molecular and morphological data

Ainsley E. Seago, Jose Adriano Giorgi, Jiahui Li & Adam Ślipiński
Ladybird beetles (family Coccinellidae) are a species-rich, ecologically diverse group of substantial agricultural significance, yet have been consistently problematic to classify, with evolutionary relationships poorly understood. In order to identify major clades within Coccinellidae, evaluate the current classification system, and identify likely drivers of diversification in this polyphagous group, we conducted the first simultaneous Bayesian analysis of morphological and multi-locus molecular data for any beetle family. Addition of morphological data significantly improved phylogenetic resolution and...

Data from: Not all sequence tags are created equal: designing and validating sequence identification tags robust to indels

Brant C. Faircloth & Travis C. Glenn
Ligating adapters with unique synthetic oligonucleotide sequences (sequence tags) onto individual DNA samples before massively parallel sequencing is a popular and efficient way to obtain sequence data from many individual samples. Tag sequences should be numerous and sufficiently different to ensure sequencing, replication, and oligonucleotide synthesis errors do not cause tags to be unrecoverable or confused. However, many design approaches only protect against substitution errors during sequencing and extant tag sets contain too few tag...

Data from: Development of an ultra-dense genetic map of the sunflower genome

John E. Bowers, Savithri Nambeesan, Jonathan Corbi, John M. Burke, Michael S. Barker, Loren H. Rieseberg & Steven J. Knapp
The development of ultra-dense genetic maps has the potential to facilitate detailed comparative genomic analyses and whole genome sequence assemblies. Here we describe the use of a custom Affymetrix GeneChip containing nearly 2.4 million features (25 bp sequences) targeting 86,023 unigenes from sunflower (Helianthus annuus L.) and related species to test for single-feature polymorphisms (SFPs) in a recombinant inbred line (RIL) mapping population derived from a cross between confectionery and oilseed sunflower lines (RHA280 x...

Data from: Characterization of 42 polymorphic microsatellite loci in Mimulus ringens (Phrymaceae) using Illumina sequencing

Schyler O. Nunziata, Jeffrey D. Karron, Randall J. Mitchell, Stacey L. Lance, Kenneth L. Jones & Dorset W. Trapnell
Premise of the study: Microsatellite markers were isolated and characterized in Mimulus ringens (Phrymaceae), a herbaceous wetland perennial, to facilitate studies of mating patterns and population genetic structure. Methods and Results: A total of 42 polymorphic loci were identified from a sample of 24 individuals from a single popula- tion in Ohio, USA. The number of alleles per locus ranged from two to nine, and median observed heterozygosity was 0.435. Conclusions: This large number of...

Data from: Phage loss and the breakdown of a defensive symbiosis in aphids

Stephanie R. Weldon, Kerry M. Oliver, Michael R. Strand, K. M. Oliver, M. R. Strand & S. R. Weldon
Terrestrial arthropods are often infected with heritable bacterial symbionts which may themselves be infected by bacteriophages. However, what role, if any, bacteriophages play in the regulation and maintenance of insect-bacteria symbioses is largely unknown. Infection of the aphid Acyrthosiphon pisum by the bacterial symbiont Hamiltonella defensa confers protection against parasitoid wasps, but only when H. defensa is itself infected by the phage APSE. Here we use a controlled genetic background and correlation-based assays to show...

Data from: A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing

John E. McCormack, Michael G. Harvey, Brant C. Faircloth, Nicholas G. Crawford, Travis C. Glenn & Robb T. Brumfield
Evolutionary relationships among birds in Neoaves, the clade comprising the vast majority of avian diversity, have vexed systematists due to the ancient, rapid radiation of numerous lineages. We applied a new phylogenomic approach to resolve relationships in Neoaves using target enrichment (sequence capture) and high-throughput sequencing of ultraconserved elements (UCEs) in avian genomes. We collected sequence data from UCE loci for 32 members of Neoaves and one outgroup (chicken) and analyzed data sets that differed...

Data from: The banana (Musa acuminata) genome and the evolution of monocotyledonous plants

Angelique D'Hont, France Denoeud, Jean-Marc Aury, Franc-Christophe Baurens, Françoise Carreel, Olivier Garsmeur, Benjamin Noel, Stéphanie Bocs, Gaëtan Droc, Mathieu Rouard, Corinne Da Silva, Jabbari Kamel, Céline Cardi, Julie Poulain, Marlène Souquet, Karine Labadie, Cyril Jourda, Juliette Lengellé, Marguerite Rodier-Goud, Adriana Alberti, Maria Bernard, Margot Correa, Saravanaraj Ayyampalayam, Michael R. McKain, Jim Leebens-Mack … & Patrick Wincker
Bananas (Musa spp.), including dessert and cooking types, are giant perennial monocotyledonous herbs of the order Zingiberales, a sister group to the well-studied Poales, which include cereals. Bananas are vital for food security in many tropical and subtropical countries and the most popular fruit in industrialized countries1. The Musa domestication process started some 7,000 years ago in Southeast Asia. It involved hybridizations between diverse species and subspecies, fostered by human migrations2, and selection of diploid...

Data from: Genetic estimates of population age in the water flea, Daphnia magna

John D. Robinson, Christoph R. Haag, David W. Hall, V. Pajunen & John P. Wares
Genetic datasets can be used to date evolutionary events, even on recent time scales if sufficient data are available. We used statistics calculated from multilocus microsatellite datasets to estimate population ages in data generated through coalescent simulations and in samples from populations of known age in a metapopulation of Daphnia magna in Finland. Our simulation results show that age estimates improve with additional loci and define a time frame over which these statistics are most...

Registration Year

  • 2012

Resource Types

  • Dataset


  • University of Georgia
  • University of California Los Angeles
  • University of Arizona
  • Louisiana State University of Alexandria
  • Boston University
  • University of Évry Val d'Essonne
  • University of Minnesota
  • New York University
  • University of Lausanne
  • University of California, Berkeley