1,414 Works

Data from: Genetic differentiation of Alaska Chinook salmon: the missing link for migratory studies

William D. Templin, James E. Seeb, Andrew W. Barclay, James R. Jasper & Lisa W. Seeb
Most information about Chinook salmon genetic diversity and life history originates from studies from the west coast USA, western Canada, and Southeast Alaska; less is known about Chinook salmon from western and southcentral Alaska drainages. Populations in this large area are genetically distinct from populations to the south and represent an evolutionary legacy of unique genetic, phenotypic, and life history diversity. More genetic information is necessary to advance mixed stock analysis applications for studies involving...

Data from: Genealogical lineage sorting leads to significant, but incorrect Bayesian multilocus inference of population structure

Pablo Orozco-TerWengel, Jukka Corander & Christian Schlötterer
Over the past decades the use of molecular markers has revolutionized biology and led to the foundation of a new research discipline -- phylogeography. Of particular interest has been the inference of population structure and biogeography. While initial studies focused on mtDNA as a molecular marker, it has become apparent that selection and genealogical lineage sorting could lead to erroneous inferences. As it is not clear to what extent these forces affect a given marker,...

Data from: Development of 54 novel SNP assays for sockeye and coho salmon and assessment of available SNPs to differentiate stocks within the Columbia River

Nathan R. Campbell & Shawn R. Narum
Single nucleotide polymorphisms (SNPs) have potential for broad application in population and conservation genetics, but availability of these markers are limited in many non-model species. In this study, genomic and expressed sequence tagged (EST) sequences from closely related salmonids (Chinook salmon, and rainbow trout) were used to design primers for amplification and sequencing of sockeye (Oncorhynchus nerka) and coho (O. kisutch) salmon DNA for SNP discovery. One-hundred and six primer sets were designed and tested...

Data from: Multiplex preamplification PCR and microsatellite validation allows accurate single nucleotide polymorphism (SNP) genotyping of historical fish scales

Matt J. Smith, Carita E. Pascal, Zac Grauvogel, Christopher Habicht, James E. Seeb & Lisa W. Seeb
Incorporating historical tissues into the study of ecological, conservation, and management questions can broaden the scope of population genetic research by enhancing our understanding of evolutionary processes and anthropogenic influences on natural populations. Genotyping historical and low-quality samples has been plagued by challenges associated with low amounts of template DNA and the potential for preexisting DNA contamination among samples. We describe a two-step process designed to (i) accurately genotype large numbers of historical low-quality scale...

Data from: Delimiting Species Using DNA and Morphological Variation and Discordant Species Limits in Spiny Lizards (Sceloporus)

John J. Wiens & Tonya A. Penkrot
Haplotype phylogenies based on DNA sequence data are increasingly being used to test traditional species-level taxonomies based on morphology. However, few studies have critically compared species limits based on morphological and DNA data, and the methods used to delimit species using either type of data are only rarely explained. In this paper, we review three approaches for species delimitation (tree-based with DNA data and tree-based and character-based with morphological data) and propose explicit protocols for...

Data from: Phenotypic selection in natural populations: what limits directional selection?

Joel G Kingsolver & Sarah E Diamond
Studies of phenotypic selection document directional selection in many natural populations. What factors reduce total directional selection, and the cumulative evolutionary responses to selection? We combine two datasets for phenotypic selection, representing more than 4600 distinct estimates of selection from 143 studies, to evaluate the potential roles of fitness trade-offs, indirect (correlated) selection, temporally varying selection, and stabilizing selection for reducing net directional selection and cumulative responses to selection. We detected little evidence that trade-offs...

Data from: Comparison of SNPs and microsatellites for fine-scale application of genetic stock identification of Chinook salmon in the Columbia River Basin

Jon E. Hess, Andrew P. Matala & Shawn R. Narum
Genetic stock identification (GSI) is an important tool in fisheries management. Microsatellites (µSATs) have been the dominant genetic marker for GSI, however increasing availability and numerous advantages of single nucleotide polymorphism (SNP) markers make them an appealing alternative. We tested performance of 13 µSAT versus 92 SNP loci in a fine-scale application of GSI, using a new baseline for Chinook salmon consisting of 49 collections (n=4014) distributed across the Columbia River Basin. In GSI, baseline...

Data from: Where do monomorphic sexual systems fit in the evolution of dioecy? Insights from the largest family of angiosperms

Rubén Torices, Marcos Méndez & José María Gómez
A range of hypothesized evolutionary pathways has been proposed for describing the evolution of dioecy. However, the evolutionary links between other sexual systems not directly involved in dioecy evolution remain largely unexplored, and hence, a comprehensive picture of evolutionary transitions between sexual systems is still lacking. We explored the diversity and evolution of sexual systems in Asteraceae, the largest family of flowering plants, where almost all sexual systems are present. We used a phylogenetic approach...

Data from: Molecular analysis of parasitoid linkages (MAPL): gut contents of adult parasitoid wasps reveal larval host

Rodolphe Rougerie, M Alex Smith, Jose Fernandez-Triana, Carlos Lopez-Vaamonde, Sujeevan Ratnasingham & Paul D N Hebert
Metamorphosing insects often have complex and poorly known life-histories. In particular, what they feed on during their larval stages remains unknown for the vast majority of species and its documentation only results from difficult and time-intensive field observations, rearing or dissections. Through the application of a DNA analysis of gut contents in adult parasitoid wasps, we were able to selectively sequence a diagnostic DNA marker that permitted the identification of the host used by these...

Data from: A tale of two genomes: contrasting patterns of phylogeographic structure in a widely distributed bat

Amy S. Turmelle, Thomas H. Kunz & Michael D. Sorenson
One of the most widely distributed bats in the New World, the big brown bat (Eptesicus fuscus) exhibits well-documented geographic variation in morphology and life history traits, suggesting the potential for significant phylogeographic structure as well as adaptive differentiation among populations. In a pattern broadly consistent with morphologically defined subspecies, we found deeply divergent mitochondrial lineages restricted to different geographic regions. In contrast, sequence data from two nuclear loci suggest a general lack of regional...

Data from: Post-Pleistocene demographic history of the North Atlantic endemic Irish moss Chondrus crispus: glacial survival, spatial expansion and gene flow

Zi Min Hu, Wei Li, Jing Jing Li & De Lin Duan
Range expansions and gene flow as micro-evolutionary processes played a leading role in the population demographic history of marine organisms. Herein, we sequenced partial mtDNA Cox1 gene from 26 assigned geographic populations in order to understand how Irish moss (Chondrus crispus) responded to severe climatic oscillations during the Pleistocene glaciations and contemporary forces such as gene flow. Phylogeographic patterns indicated that haplotype frequency distributions were strongly skewed, with nearly half found only in single samples...

Data from: Time-dependent speciation and extinction from phylogenies: a least squares approach

Emmanuel Paradis
Molecular phylogenies contribute to the study of the patterns and processes of macroevolution even though past events (fossils) are not recorded in these data. In this paper, I consider the general time-dependent birth–death model in order to fit any model of temporal variation in speciation and extinction to phylogenies. I establish formulae to compute the expected cumulative distribution function of branching times for any model, and, building on previous published works, I derive maximum likelihood...

Data from: Genome-scale phylogenetics: inferring the plant tree of life from 18,896 gene trees

J. Gordon Burleigh, Mukul S. Bansal, Oliver Eulenstein, Stefanie Hartmann, André Wehe & Todd J. Vision
Phylogenetic analyses using genome-scale data sets must confront incongruence among gene trees, which in plants is exacerbated by frequent gene duplications and losses. Gene tree parsimony is a phylogenetic optimization criterion in which a species tree is selected that minimizes the number of gene duplications induced among a set of gene trees. The run time performance of previous implementations has limited its use on large-scale data sets. We used new software that incorporates recent algorithmic...

Data from: Influence of alignment on the mtDNA phylogeny of Cetacea: questionable support for a Mysticeti/Physeteroidea clade

Salvatore Cerchio & Priscilla Tucker
Cerchio and Tucker Data Matrix: MALIGN.124.08MALIGN.124.08Cerchio and Tucker Data Matrix: MilinkovitchMilinkovitch.htmCerchio and Tucker Data Matrix: MALIGN.124.07MALIGN.124.07Cerchio and Tucker Data Matrix: MALIGN.124.10MALIGN.124.10Cerchio and Tucker Data Matrix: ClustalClustal.htmCerchio and Tucker Data Matrix: MALIGN.136.02MALIGN.136.02Cerchio and Tucker Data Matrix: MALIGN.124.09MALIGN.124.09Cerchio and Tucker Data Matrix: Conservative-1Conservative-1.htmCerchio and Tucker Data Matrix: Conservative-2Conservative-2.htmCerchio and Tucker Data Matrix: MALIGN.111.02MALIGN.111.02Cerchio and Tucker Data Matrix: MALIGN.111.01MALIGN.111.01Cerchio and Tucker Data Matrix: MALIGN.124.03MALIGN.124.03Cerchio and Tucker Data Matrix: MALIGN.136.06MALIGN.124.06Cerchio and Tucker Data Matrix: MALIGN.136.03MALIGN.136.03Cerchio and Tucker Data Matrix:...

Data from: Phylogeny of Trichoptera (caddisflies): characterization of signal and noise within multiple datasets

Karl M. Kjer, Roger J. Blahnik & Ralph W. Holzenthal
Trichoptera are holometabolous insects with aquatic larvae that, together with the Lepidoptera, comprise the Amphiesmenoptera. Despite extensive previous morphological work, there has been little phylogenetic agreement over the relationship among the three suborders: Annulipalpia, Spicipalpia, and Integripalpia, and conflict over the monophyly of Spicipalpia. In an effort to resolve this conflict, we sequenced fragments of the large and small subunit nuclear ribosomal RNAs (1078 nts; D1, D3, V4-5), the nuclear Elongation factor 1α gene (1098...

Data from: Phylogenetics of flowering plants based on combined analysis of plastid atpB and rbcL gene sequences

Vincent Savolainen, Mark W. Chase, Sara B. Hoot, Cynthia M. Morton, Douglas E. Soltis, Clemens Bayer, Michael F. Fay, Anette Y. De Bruijn, Stuart Sullivan & Yin-Long Qiu
Following (1) the large scale molecular phylogeny of seed plants based on plastid rbcL gene sequences (published in 1993 by Chase et al., Ann. Missouri Bot. Gard. 80: 528-580) and (2) the 18S nuclear phylogeny of flowering plants (published in 1997 by Soltis et al., Ann. Missouri Bot. Gard. 84: 1-49), we present a phylogenetic analysis of flowering plants based upon a second plastid gene, atpB, analyzed separately and in combination with rbcL sequences for...

Data from: Effects of population structure and sex on association between serotonin receptors and Drosophila heart rate

Naruo Nikoh, April Duty & Greg Gibson
As a first step toward population and quantitative genetic analysis of neurotransmitter receptors in Drosophila melanogaster, we describe the parameters of nucleotide variation in three serotonin receptors and their association with pupal heart rate. Thirteen kilobases of DNA including the complete coding regions of 5-HT1A, 5-HT1B, and 5-HT2 were sequenced in 216 highly inbred lines extracted from two North American populations in California and North Carolina. Nucleotide and amino acid polymorphism is in the normal...

Data from: Complex phylogeographic patterns in the freshwater alga Synura provide new insights on ubiquity versus endemism in microbial eukaryotes

Sung Min Boo, Han Soon Kim, Woongghi Shin, Ga Hun Boo, Sung Mi Cho, Bok Yeon Cho, Jee-Hwan Kim, Jin Hee Kim, Eun Chan Yang, Peter A Siver, Alexander P Wolfe, Debashish Bhattacharya, Robert A Andersen & Hwan Su Yoon
The global distribution, abundance, and diversity of microscopic freshwater algae demonstrate an ability to overcome significant barriers such as dry land and oceans by exploiting a range of biotic and abiotic colonization vectors. If these vectors are considered unlimited and colonization occurs in proportion to population size, then globally ubiquitous distributions are predicted to arise. This model contrasts with observations that many freshwater microalgal taxa possess true biogeographies. Here, using a concatenated multi-gene dataset, we...

Data from: The transcriptomics of sympatric dwarf and normal lake whitefish (Coregonus clupeaformis spp., Salmonidae) divergence as revealed by next-generation sequencing

Julie Jeukens, Sébastien Renaut, Jérôme St-Cyr, Arne W. Nolte & Louis Bernatchez
Gene expression divergence is one of the mechanisms thought to be involved in the emergence of incipient species. Next-generation sequencing has become an extremely valuable tool for the study of this process by allowing whole transcriptome sequencing, or RNA-Seq. We have conducted a 454 GS-FLX pyrosequencing experiment in order to refine our understanding of adaptive divergence between dwarf and normal lake whitefish species (Coregonus clupeaformis spp.). The objectives were to: (1) investigate transcriptomic divergence as...

Data from: Multielement stoichiometry in aquatic invertebrates: when growth dilution matters

Roxanne Karimi, Nicholas S Fisher & Carol L Folt
Element concentrations in organisms can be variable, often causing deviations from otherwise consistent, taxon-specific multielement stoichiometries. Such variation can have considerable ecological consequences, yet physiological mechanisms remain unclear. We tested the influence of somatic growth dilution (SGD) on multiple element concentrations under different bioenergetic conditions. SGD occurs when rapid individual growth causes a disproportional gain in biomass relative to gain of a specific element. SGD can strongly affect elements in various organisms, but we lack...

Data from: Behavioral and biomaterial coevolution in spider orb webs

Andrew Sensenig, Todd Blackledge & Ingi Agnarsson
Mechanical performance of biological structures, such as tendons, byssal threads, muscles, and spider webs, is determined by a complex interplay between material quality (intrinsic material properties, larger scale morphology) and proximate behavior. Spider orb webs are a system in which fibrous biomaterials―silks―are arranged in a complex design resulting from stereotypical behavioral patterns, to produce effective energy absorbing traps for flying prey. Orb webs show an impressive range of designs, some effective at capturing tiny and...

Data from: Adaptive differences in gene expression associated with heavy metal tolerance in the soil arthropod Orchesella cincta

Dick Roelofs, Thierry K. S. Janssens, Martijn J. T. N. Timmermans, Benjamin Nota, Janine Mariën, Zoltán Bochdanovits, Bauke Ylstra & Nico M. Van Straalen
Field-selected tolerance to heavy metals has been reported for Orchesella cincta (Arthropoda: Collembola) populations occurring at metal-contaminated mining sites. This tolerance is correlated with heritable increase of metal excretion efficiency; less pronounced cadmium (Cd) induced growth reduction and, over-expression of the metallothionein gene. We applied transcriptomics to determine differential gene expression caused by this abiotic stress in reference and Cd tolerant populations. Many cDNAs responded to Cd exposure in the reference population. Significantly fewer clones...

Data from: Life history determines biogeographical patterns of soil bacterial communities over multiple spatial scales

Andrew Bissett, Alan E. Richardson, Geoff Baker, Steven Wakelin & Peter H. Thrall
The extent to which the distribution of soil bacteria is controlled by local environment versus spatial factors (e.g., dispersal, colonisation limitation, evolutionary events) is poorly understood and widely debated. Our understanding of biogeographic controls in microbial communities is likely hampered by the enormous environmental variability encountered across spatial scales and the broad diversity of microbial life histories. Here we constrained environmental factors (soil chemistry, climate, above-ground plant community) to investigate the specific influence of space,...

Data from: The role of pleiotropy in the maintenance of sex in yeast

Jessica A. Hill & Sarah P. Otto
In facultatively sexual species, lineages that reproduce asexually for a period of time can accumulate mutations that reduce their ability to undergo sexual reproduction when sex is favorable. We propagated Saccharomyces cerevisiae asexually for ~800 generations, after which we measured the change in sexual fitness, measured as the proportion of asci observed in sporulation medium. The sporulation rate in cultures propagated asexually at small population size declined by 8%, on average, over this time period,...

Data from: Genetics of incipient speciation in Drosophila mojavensis. III. Life history divergence in allopatry and reproductive isolation

William J. Etges, Cássia Cardoso De Oliveira, Mohamed A. F. Noor & Michael G. Ritchie
We carried out a three-tiered genetic analysis of egg-to-adult development time and viability in ancestral and derived populations of cactophilic D. mojavensis to test the hypothesis that evolution of these life history characters has shaped premating reproductive isolation in this species. First, a common garden experiment with 11 populations from Baja California and mainland Mexico and Arizona reared on two host cacti revealed significant host plant X region and population interactions for viability and development...

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  • 2010
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  • North Carolina State University
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  • Dalian Maritime University
    1