15 Works

Data from: Estimation of effective population size in continuously distributed populations: there goes the neighborhood

Maile C. Neel, Kevin McKelvey, Robin S. Waples, Nils Ryman, Michael W. Lloyd, Ruth Short Bull, Fred W. Allendorf & Michael K. Schwartz
Use of genetic methods to estimate effective population size (N^e) is rapidly increasing, but all approaches make simplifying assumptions unlikely to be met in real populations. In particular, all assume a single, unstructured population, and none has been evaluated for use with continuously distributed species. We simulated continuous populations with local mating structure, as envisioned by Wright's concept of neighborhood size (NS), and evaluated performance of a single-sample estimator based on linkage disequilibrium (LD), which...

Data from: Genetic consequences of a century of protection: serial founder events and survival of the little spotted kiwi (Apteryx owenii)

Kristina M. Ramstad, Rogan M. Colbourne, Hugh A. Robertson, Fred W. Allendorf & Charles H. Daugherty
We present the outcome of a century of post-bottleneck isolation of a long-lived species, the little spotted kiwi (Apteryx owenii, LSK) and demonstrate that profound genetic consequences can result from protecting few individuals in isolation. LSK were saved from extinction by translocation of five birds from South Island, New Zealand to Kapiti Island 100 years ago. The Kapiti population now numbers some 1200 birds and provides founders for new populations. We used 15 microsatellite loci...

Data from: Not so old Archaea - the antiquity of biogeochemical processes in the archaeal domain of life

Carrine E. Blank
Since the archaeal domain of life was first recognized, it has often been assumed that Archaea are ancient, and harbor primitive traits. In fact, the names of the major archaeal lineages reflect our assumptions regarding the antiquity of their traits. Ancestral state reconstruction and relaxed molecular clock analyses using newly articulated oxygen age constraints show that although the archaeal domain itself is old, tracing back to the Archean eon, many clades and traits within the...

Data from: Differential introgression in a mosaic hybrid zone reveals candidate barrier genes

Erica L. Larson, Jose A. Andres, Steven M. Bogdanowicz & Richard G. Harrison
Hybrid zones act as genomic sieves; although globally advantageous alleles will spread throughout the zone and neutral alleles can be freely exchanged between species, introgression will be restricted for genes that contribute to reproductive barriers or local adaptation. Seminal fluid proteins (SFPs) are known to contribute to reproductive barriers in insects and have been proposed as candidate barrier genes in the hybridizing field crickets G. pennsylvanicus and G. firmus. Here, we have used 125 SNPs...

Data from: Comparative linkage maps suggest that fission, not polyploidy, underlies near-doubling of chromosome number within monkeyflowers (Mimulus; Phrymaceae)

Lila Fishman, John H. Willis, Carrie A. Wu & Young-Wha Lee
Changes in chromosome number and structure are important contributors to adaptation, speciation, and macroevolution. In flowering plants, polyploidy and subsequent reductions in chromosome number by fusion are major sources of chromosomal evolution, but chromosome number increase by fission has been relatively unexplored. Here, we use comparative linkage mapping with gene-based markers to reconstruct chromosomal synteny within the model flowering plant genus Mimulus (monkeyflowers). Two sections of the genus with haploid numbers {greater than or equal...

Data from: Population genomics of a symbiont in the early stages of a pest invasion

Amanda M. V. Brown, Lynn Y. Huynh, Caitlin M. Bolender, Kelly G. Nelson & John P. McCutcheon
Invasive species often depend on microbial symbionts, but few studies have examined the evolutionary dynamics of symbionts during the early stages of an invasion. The insect Megacopta cribraria and its bacterial nutritional symbiont Candidatus Ishikawaella capsulata invaded the southeastern US in 2009. While M. cribraria was initially discovered on wild kudzu plants, it was found as a pest on soybeans within 1 year of infestation. Because prior research suggests Ishikawaella confers the pest status—that is,...

Data from: Plasticity of parental care under the risk of predation: how much should parents reduce care?

Cameron K. Ghalambor, Susana I. Peluc & Thomas E. Martin
Predation can be an important agent of natural selection shaping parental care behaviours, and can also favor behavioural plasticity. Parent birds often decrease the rate that they visit the nest to provision offspring when perceived risk is high. Yet the plasticity of such responses may differ among species as a function of either their relative risk of predation, or the mean rate of provisioning. Here, we report parental provisioning responses to experimental increases in the...

Data from: Low rates of lateral gene transfer among metabolic genes define the evolving biogeochemical niches of archaea through deep time

Carrine E. Blank
Phylogenomic analyses of archaeal genome sequences are providing windows into the group's evolutionary past, even though most archaeal taxa lack a conventional fossil record. Here, phylogenetic analyses were performed using key metabolic genes that define the metabolic niche of microorganisms. Such genes are generally considered to have undergone high rates of lateral gene transfer. Many gene sequences formed clades that were identical, or similar, to the tree constructed using large numbers of genes from the...

Data from: Chromosomal rearrangements and the genetics of reproductive barriers in Mimulus (monkeyflowers)

Lila Fishman, Angela Stathos, Paul M. Beardsley, Charles F. Williams & Jeffrey P. Hill
Chromosomal rearrangements may directly cause hybrid sterility and can facilitate speciation by preserving local adaptation in the face of gene flow. We used comparative linkage mapping with shared gene-based markers to identify potential chromosomal rearrangements between the sister monkeyflowers Mimulus lewisii and M. cardinalis, which are textbook examples of ecological speciation. We then re-mapped quantitative trait loci (QTLs) for floral traits and flowering time (pre-mating isolation) and hybrid sterility (post-zygotic isolation). We identified three major...

Data from: Unlocking the vault: next generation museum population genomics

Ke Bi, Tyler Linderoth, Dan Vanderpool, Jeffrey M. Good, Rasmus Nielsen & Craig Moritz
Natural history museum collections provide unique resources for understanding how species respond to environmental change, including the abrupt, anthropogenic climate change of the past century. Ideally, researchers would conduct genome-scale screening of museum specimens to explore the evolutionary consequences of environmental changes, but to date such analyses have been severely limited by the numerous challenges of working with the highly degraded DNA typical of historic samples. Here we circumvent these challenges by using custom, multiplexed,...

Data from: Ontogenetic changes in the body temperature of an insect herbivore

H. Arthur Woods
1. Over ontogeny, many insect larvae grow substantially, through at least several orders of magnitude in body size. Increasing size can profoundly change how individuals interact with their environments, by altering the opportunities for, and constraints on, feeding, changing the relative risk and sources of predation, and shifting the relative importance of physical factors in the environment. 2. Here I use eggs and larvae of Manduca sexta, which are herbivores on solanaceous plants in the...

Data from: Timing of morphological and ecological innovations in the cyanobacteria – a key to understanding the rise in atmospheric oxygen

Carrine E. Blank & P. Sánchez-Baracaldo
When cyanobacteria originated and diversified, and what their ancient traits were, remain critical unresolved problems. Here, we used a phylogenomic approach to construct a well-resolved 'core' cyanobacterial tree. The branching positions of four lineages (Thermosynechococcus elongatus, Synechococcus elongatus, Synechococcus PCC 7335 and Acaryochloris marina) were problematic, probably due to long branch attraction artifacts. A consensus genomic tree was used to study trait evolution using ancestral state reconstruction (ASR). The early cyanobacteria were probably unicellular, freshwater,...

Data from: Gene flow and the maintenance of species boundaries

Erica L. Larson, Thomas A. White, Charles L. Ross & Richard G. Harrison
Hybrid zones are regions where individuals from genetically differentiated populations meet and mate, resulting in at least some offspring of mixed ancestry. Patterns of gene flow (introgression) in hybrid zones vary across the genome, allowing assessment of the role of individual genes or genome regions in reproductive isolation. Here, we document patterns of introgression between two recently diverged species of field crickets. We sample at a very fine spatial scale and genotype crickets for 110...

Data from: Genomic patterns of introgression in rainbow and westslope cutthroat trout illuminated by overlapping paired-end RAD sequencing

Paul A. Hohenlohe, Mitch D. Day, Stephen J. Amish, Michael R. Miller, Nicholas Kamps-Hughes, Matthew C. Boyer, Clint C. Muhlfeld, Fred W. Allendorf, Eric A. Johnson, Gordon Luikart & Nick Kamps-Hughes
Rapid and inexpensive methods for genomewide single nucleotide polymorphism (SNP) discovery and genotyping are urgently needed for population management and conservation. In hybridized populations, genomic techniques that can identify and genotype thousands of species-diagnostic markers would allow precise estimates of population- and individual-level admixture as well as identification of ‘super invasive’ alleles, which show elevated rates of introgression above the genomewide background (likely due to natural selection). Techniques like restriction-site-associated DNA (RAD) sequencing can discover...

Data from: An expansion of age constraints for microbial clades that lack a conventional fossil record using phylogenomic dating

Carrine E. Blank
Most microbial taxa lack a conventional microfossil or biomarker record, and so we currently have little information regarding how old most microbial clades and their associated traits are. Building on the previously published oxygen age constraint, two new age constraints are proposed based on the ability of microbial clades to metabolize chitin and aromatic compounds derived from lignin. Using the archaeal domain of life as a test case, phylogenetic analyses, along with published metabolic and...

Registration Year

  • 2013

Resource Types

  • Dataset


  • University of Montana
  • Cornell University
  • Victoria University of Wellington
  • University of California System
  • Duke University
  • University of Saskatchewan
  • Idaho State University
  • Australian National University
  • University of California, Berkeley
  • University of Oregon