Assessing the realized effect of dispersal in the genetic makeup of a species has significant evolutionary, ecological, and economical consequences. Here, we investigate the genetic diversity and population differentiation in the aquilopelagic golden cownose ray Rhinoptera steindachneri from the Gulf of California (GC) and the Pacific coast of Baja California (PCBC) using the mitochondrial NADH2 gene. Low levels of genetic diversity were found with only 4 polymerase chain reaction-restriction fragment length polymorphism haplotypes among 76...

BACKGROUND: Most of our knowledge about the ancient evolutionary history of organisms has been derived from data associated with specific known organisms (i.e., organisms that we can study directly such as plants, metazoans, and culturable microbes). Recently, however, a new source of data for such studies has arrived: DNA sequence data generated directly from environmental samples. Such metagenomic data has enormous potential in a variety of areas including, as we argue here, in studies of...

Data from the seedling experiment.

SUPPLEMENTARY FIGURE S3. Net diversification rates (r = lineages/million years) in Lupinus estimated under the MEDUSA birth–death likelihood model, including relative extinction (ε = birth/death) as a free parameter. MEDUSA analyses were conducted using 1000 trees randomly selected from the posterior distribution of constrained pure–birth Bayesian MCMC tree searches in BEAST, pruned to the infrageneric skeleton topology in Figure 3 of the main text. Surface plots show the frequency (ƒ) of estimates from replicate MEDUSA...

Morphometric data for Callosobruchus maculatus beetles from 16 replicate artificial evolution lines.

When resources are limited, there is a tradeoff between growth/reproduction and stress defense in plants. Most temperate plant species, including Arabidopsis thaliana, can enhance freezing tolerance through cold acclimation at low but non-freezing temperatures. Induction of the cold acclimation pathway should be beneficial in environments where plants frequently encounter freezing stress, but might represent a cost in environments where freezing events are rare. In A. thaliana, induction of the cold acclimation pathway critically involves a...

The evolutionary trajectories of trade-offs are ultimately governed by the evolution of the underlying physiological processes of the acquisition and subsequent allocation of resources. In this study, we focused directly on acquisition and allocation as traits and estimated their genetic architecture in the trade-off between flight capability and reproduction in the cricket, Gryllus firmus. To determine the evolutionary genetics of acquisition and allocation both within and between resource environments we performed a large-scale quantitative genetic...

Sulfide tolerance in Poecilia mexicana and P. sulphuraria from sulfidic and non-sulfidic habitats.

full list of descriptive statistics for the seven microsatellite loci

Trawl survey data for Rockall plateau and west coast of scotland between depths of 90-250 m. See 'read me' sheet in file for further details.

Next-generation sequencing provides a powerful new approach for developing functional genomic tools for nonmodel species, helping to narrow the gap between studies of model organisms and those of natural populations. Consequently, massively parallel 454 sequencing was used to characterize a normalized cDNA library derived from skin biopsy samples of twelve Antarctic fur seal (Arctocephalus gazella) individuals. Over 412 Mb of sequence data were generated, comprising 1.4 million reads of average length 286 bp. De novo...

Brownie rag1 input file for males

DNA sequences of the entire coding region of the Toll-like receptor 2 (TLR2) gene of Myodes glareolus, Myodes rutilus, Myodes smithii, Myodes andersoni, Myodes rufocanus, Myodes rex, Chionomys nivalis, Microtus agrestis, Microtus arvalis, Microtus oeconomus, Arvicola amphibius, Apodemus alpicola, Apodemus flavicollis, Apodemus sylvaticus, Micromys minutus, Mus musculus, Rattus norvegicus

Consensus topology recovered from MrBayes analysis of RAG1 sequences

Rag1 nexus file used for MrBayes

Brownie mtDNA input file for females

OUCH mtDNA input file for males

Plants stably transformed to manipulate the expression of genes mediating ecological performance have profoundly altered research in plant ecology. Agrobacterium-mediated transformation remains the most effective method of creating plants harboring a limited number of transgene integrations of low complexity. For ecological/physiological research, the following requirements must be met: 1) the regenerated plants should have the same ploidy level as the corresponding wild type plant and 2) contain a single transgene copy in a homozygous state;...

Locality information for genetic samples in this study

see README file for key to mtDNA unique sequences; each unique sequence corresponds to one or more field codes, each of which corresponds to an individual frog.

Philippine limnonectes male morphological distances for partial mantel test

Philippine limnonectes mitochondrial DNA genetic distances for partial mantel test

Philippine limnonectes rag1 genetic distances for partial mantel test

The ignita species group within the genus Chrysis includes over 100 cuckoo wasp species, which all lead a parasitic lifestyle and exhibit very similar morphology. The lack of robust, diagnostic morphological characters has hindered phylogenetic reconstructions and contributed to frequent misidentification and inconsistent interpretations of species in this group. Therefore, molecular phylogenetic analysis is the most suitable approach for resolving the phylogeny and taxonomy of this group. We present a well-resolved phylogeny of the Chrysisignita...