Biomedical subjects

John K Colbourne

Publications and source records attributed to John K Colbourne.

6 recordsLinked to original sources

PubMed2006

A microsatellite-based genetic linkage map of the waterflea, Daphnia pulex: On the prospect of crustacean genomics.

We describe the first genetic linkage map for Daphnia pulex using 185 microsatellite markers, including 115 new markers reported in this study. Our approach was to study the segregation of polymorphisms in 129 F2 progeny of one F1 hybrid obtained by crossing two genetically divergent lineages of Daphnia isolated from two Oregon populations. The map spanned 1206 Kosambi cM and had an average intermarker distance of 7 cM. Linkage groups ranged in size from 7 to 185 cM and contained 4 to 27 markers. The map revealed 12 linkage groups corresponding to the expected number of chromosomes and covers approximately 87% of the genome. Tests for random segregation of alleles at individual loci revealed that 21% of the markers showed significant transmission ratio distortion (primarily homozygote deficiency) likely due to markers being linked to deleterious recessive alleles. This map will become the anchor for the physical map of the Daphnia genome and will serve as a starting point for mapping single and quantitative trait loci affecting ecologically important phenotypes. By mapping 342 tentative orthologous gene pairs (Daphnia/Drosophila) into the Daphnia linkage map, we facilitate future comparative projects.

Animals↗

PubMed2005

wFleaBase: the Daphnia genome database.

BACKGROUND: wFleaBase is a database with the necessary infrastructure to curate, archive and share genetic, molecular and functional genomic data and protocols for an emerging model organism, the microcrustacean Daphnia. Commonly known as the water-flea, Daphnia's ecological merit is unequaled among metazoans, largely because of its sentinel role within freshwater ecosystems and over 200 years of biological investigations. By consequence, the Daphnia Genomics Consortium (DGC) has launched an interdisciplinary research program to create the resources needed to study genes that affect ecological and evolutionary success in natural environments. DISCUSSION: These tools include the genome database wFleaBase, which currently contains functions to search and extract information from expressed sequenced tags, genome survey sequences and full genome sequencing projects. This new database is built primarily from core components of the Generic Model Organism Database project, and related bioinformatics tools. SUMMARY: Over the coming year, preliminary genetic maps and the nearly complete genomic sequence of Daphnia pulex will be integrated into wFleaBase, including gene predictions and ortholog assignments based on sequence similarities with eukaryote genes of known function. wFleaBase aims to serve a large ecological and evolutionary research community. Our challenge is to rapidly expand its content and to ultimately integrate genetic and functional genomic information with population-level responses to environmental challenges. URL: http://wfleabase.org/.

Animals↗

PubMed2005

Evolutionary history of contagious asexuality in Daphnia pulex.

Asexual taxa are short-lived, suggesting that transitions to asexuality represent evolutionary dead-ends. However, with high rates of clonal origin and coexistence of asexuals and sexuals via selective asymmetries, asexuality may persist in the long term as a result of a dynamic equilibrium between clonal origin and extinction. Few such systems have been studied in detail. Here, we investigate the evolutionary history of asexual lineages of Daphnia pulex, which are derived from sexual relatives via the inheritance of a dominant female-limited meiosis-suppressing locus and inhabit ponds throughout northeastern North America (NA). Our extensive sampling and subsequent phylogenetic analysis using mitochondrial sequence data reveals a young and genetically diverse asexual assemblage, reflecting high rates of clonal origin due to the contagious nature of asexuality. Yet, asexuality is restricted to two phylogroups (B and C) with historical and/or present associations with northeastern NA and is absent from a northwestern phylogroup (A), supporting a recent northeastern origin of asexuality in this species. Furthermore, macrogeographic patterns of genetic variability indicate that phylogroups B and C recolonized northeastern NA from opposite directions, yet their presently overlapping geographic distributions are similarly divided into an eastern asexual and a western sexual region. We attribute these patterns to a recent contagious spread of asexuality from a northeastern source. If environment-mediated selective asymmetries play no significant role in determining the outcome of competitive interactions between sexuals and asexuals, regions of contact may be setting the stage for continued asexual conquests.

Adaptation, Physiological↗

PubMed2004

Molecular evolution of daphnia immunity genes: polymorphism in a gram-negative binding protein gene and an alpha-2-macroglobulin gene.

Studies of DNA polymorphism have shown that some immune system genes of mammals and plants are exceptionally diverse, indicating that coevolution between these taxa and their parasites mediates positive selective sweeps and/or balancing selection. The genes of the arthropod immune system remain comparatively unstudied. We isolated two putative immune system genes from the cladoceran crustacean Daphnia and examined DNA sequence diversity. For one gene, encoding a putative gram-negative binding protein, we found evidence of only purifying selection, indicating that this gene is under strong functional constraint and that selection acts to eliminate amino acid variation. For another gene, encoding a putative alpha-2-macroglobulin, we found evidence of positive selection, indicating the possible involvement of this gene in a host-parasite arms race. We discuss the assumed function of these genes and offer speculation regarding which components of the arthropod immune system might experience diversifying adaptive evolution.

Amino Acid Sequence↗

PubMed2003

Reconstruction of centuries-old Daphnia communities in a lake recovering from acidification and metal contamination.

Paleolimnological and molecular genetic techniques were combined to reconstruct the long-term patterns in Daphnia community composition in Hannah Lake--a lake recovering from industrial acidification, metal contamination and faunal extirpation. Like many zooplankters, Daphnia produce diapausing eggs that can remain viable for decades and even over a century. Yet, the appearance of D. mendotae in Hannah Lake during the last two decades is likely the outcome of dispersal from other nearby lakes, not by colonization from the sediment egg-bank. Our genetic tests using PCR, SSCP and sequencing indicate that D. mendotae diapausing eggs are absent within the sediment record of the previous 250 years and that, prior to metal smelting operations in the region, the community was dominated by D. pulicaria. This species shift following the lake's chemical restoration is consistent with earlier historical changes in lake acidity. Environmental fluctuations may have governed community composition throughout Hannah Lake's more ancient past. Extending this molecular-paleolimnological approach to other lakes should help develop more accurate formulations of the biological recovery process.

Acid Rain↗

PubMed2002

Accelerated molecular evolution in halophilic crustaceans.

In contrast to the stable ionic composition of the oceans, inland waters show striking diversity, possessing salt concentrations varying from I mM to 5 M. Although species diversity is highest in fresh water, some lineages have colonized hypersaline environments where they encounter elevated levels of both ultraviolet (UV) radiation and osmotic stress. This study compares rates of evolution in halophilic and freshwater taxa for two groups of microcrustaceans, anostracans and daphniids, from Australia and North America. The results establish that halophilic species show consistent rate acceleration, involving elevated levels of both insertion/deletion events and of nucleotide substitutions. The elevated pace of molecular evolution does not appear to be linked to selection or to other agents that are known to influence the supply rate of mutations, such as UV exposure, generation length, or shifts in metabolic rate. However, variance in ionic strength, which is known to have potent effects on DNA-protein interactions as well as on the structural properties of DNA and proteins, might account for the lowered fidelity of DNA replication in life from hypersaline settings. Regardless of its cause, the consistent rate acceleration in halophiles suggests that past efforts to employ sequence divergences to date events, such as the age of asexual lineages in Artemia, have resulted in serious overestimates. More generally, the results indicate that coordinated shifts in rates of molecular evolution may occur in lineages exposed to extreme environmental conditions.

Animals↗