10 Works

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: 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: 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: 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: 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: 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: 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: 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: 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...

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