Climate Change Impacts on Southern Ross Sea Phytoplankton Composition, Productivity, and Export

The Ross Sea, a highly productive region of the Southern Ocean, is expected to experience warming during the next century along with reduced summer sea ice concentrations and shallower mixed layers. This study investigates how these climatic changes may alter phytoplankton assemblage composition, primary productivity, and export. Glider measurements are used to force a one-dimensional biogeochemical model, which includes diatoms and both solitary and colonial forms of Phaeocystis antarctica. Model performance is evaluated with glider observations, and experiments are conducted using projections of physical drivers for mid-21st and late-21st century. These scenarios reveal a 5% increase in primary productivity by midcentury and 14% by late-century and a proportional increase in carbon export, which remains approximately 18% of primary production. In addition, scenario results indicate diatom biomass increases while P. antarctica biomass decreases in the first half of the 21st century. In the second half of the century, diatom biomass remains relatively constant and P. antarctica biomass increases. Additional scenarios examining the independent contributions of expected future changes (temperature, mixed layer depth, irradiance, and surface iron inputs from melting ice) demonstrate that earlier availability of low light due to reduction of sea ice early in the growing season is the primary driver of productivity increases over the next century; shallower mixed layer depths additionally contribute to changes of assemblage composition and export. This study further demonstrates how glider data can be effectively used to facilitate model development and simulation, and inform interpretation of biogeochemical observations in the context of climate change

A search for human Y-chromosomes specific minisatellites and microsatellites.

This thesis describes an attempt to isolate polymorphic minisatellite and microsatellite loci from the male-specific region of the human Y chromosome. Y chromosome polymorphisms are useful in the study of human evolution, since the majority of the chromosome is exempt from meiotic recombination and is passed down intact in paternal lineages. Y-specific polymorphisms can be used to identify males that are related by descent. Base substitutions and sequence insertions are ideal for such analysis, because they represent very rare events and are unlikely to recur. However, these mutations are often highly population-specific, making them of little use in the investigation of inter-population relationships, or of intra-population studies in many cases. Minisatellite and microsatellite loci, on the other hand, show variability in all populations and complement the 'unique event' markers. A systematic search of a human Y-specific cosmid library for G+C-rich minisatellites identified many repetitive sequences, including 14 minisatellites from the Yp pseudoautosomal region. However no Y-specific minisatellites were found. Such sequences must be very rare, and may not be present at all in the Y-specific euchromatin, perhaps because inter-allelic exchange events are precluded in this region. Six novel Y-specific microsatellites were cloned using hybridisation selection from a degenerate PCR library. One multi-locus and two single-locus trinucleotide microsatellites were shown to be polymorphic and were used with two other microsatellites in a survey of diversity in 340 males, and to investigate the relationships between males in different haplotypic groups. No evidence for increased African diversity of Y chromosomes was found in an intercontinental comparison. These markers were also used to classify deletion and duplication events at the 50f2/C locus in 66 males from various populations. This analysis allowed the identification of novel deletion events that had not been distinguished by previous haplotyping analysis with base substitution and other polymorphisms

Population Structure and Inbreeding From Pedigree Analysis of Purebred Dogs

Dogs are of increasing interest as models for human diseases, and many canine population-association studies are beginning to emerge. The choice of breeds for such studies should be informed by a knowledge of factors such as inbreeding, genetic diversity, and population structure, which are likely to depend on breed-specific selective breeding patterns. To address the lack of such studies we have exploited one of the world's most extensive resources for canine population-genetics studies: the United Kingdom (UK) Kennel Club registration database. We chose 10 representative breeds and analyzed their pedigrees since electronic records were established around 1970, corresponding to about eight generations before present. We find extremely inbred dogs in each breed except the greyhound and estimate an inbreeding effective population size between 40 and 80 for all but 2 breeds. For all but 3 breeds, >90% of unique genetic variants are lost over six generations, indicating a dramatic effect of breeding patterns on genetic diversity. We introduce a novel index Ψ for measuring population structure directly from the pedigree and use it to identify subpopulations in several breeds. As well as informing the design of canine population genetics studies, our results have implications for breeding practices to enhance canine welfare

A web resource on DNA tests for canine and feline hereditary diseases

a b s t r a c t Following the first identification of a disease-causing mutation in dogs in 1989 and the more recent completion of canine and feline genome sequences, much progress has been made in the molecular characterization of hereditary diseases in dogs and cats. To increase access to information on diagnosing hereditary diseases in dogs and cats, a web application has been developed to collect, organize and display information on available DNA tests and other supporting information, including gene and chromosomal locations, mutations, primary research citations and disease descriptions. The DNA testing information can be accessed at the URL: http://research.vet.upenn.edu/WSAVA-LabSearch. There are currently 131 molecular genetic tests available for hereditary diseases in dogs and cats offered by 43 laboratories worldwide. This tool should provide clinicians, researchers, breeders and companion animal owners with a single comprehensive, up-to-date and readily searchable webpage for information on hereditary disease testing

Frequency of five disease-causing genetic mutations in a large mixed-breed dog population (2011–2012)

<div><p>Background</p><p>A large and growing number of inherited genetic disease mutations are now known in the dog. Frequencies of these mutations are typically examined within the breed of discovery, possibly in related breeds, but nearly always in purebred dogs. No report to date has examined the frequencies of specific genetic disease mutations in a large population of mixed-breed dogs. Further, veterinarians and dog owners typically dismiss inherited/genetic diseases as possibilities for health problems in mixed-breed dogs, assuming hybrid vigor will guarantee that single-gene disease mutations are not a cause for concern. Therefore, the objective of this study was to screen a large mixed-breed canine population for the presence of mutant alleles associated with five autosomal recessive disorders: hyperuricosuria and hyperuricemia (HUU), cystinuria (CYST), factor VII deficiency (FVIID), myotonia congenita (MYC) and phosphofructokinase deficiency (PKFD). Genetic testing was performed in conjunction with breed determination via the commercially-available Wisdom Panel^TM test.</p><p>Results</p><p>From a population of nearly 35,000 dogs, homozygous mutant dogs were identified for HUU (n = 57) and FVIID (n = 65). Homozygotes for HUU and FVIID were identified even among dogs with highly mixed breed ancestry. Carriers were identified for all disorders except MYC. HUU and FVIID were of high enough frequency to merit consideration in any mixed-breed dog, while CYST, MYC, and PKFD are vanishingly rare.</p><p>Conclusions</p><p>The assumption that mixed-breed dogs do not suffer from single-gene genetic disorders is shown here to be false. Within the diseases examined, HUU and FVIID should remain on any practitioner’s rule-out list, when clinically appropriate, for all mixed-breed dogs, and judicious genetic testing should be performed for diagnosis or screening. Future testing of large mixed-breed dog populations that include additional known canine genetic mutations will refine our knowledge of which genetic diseases can strike mixed-breed dogs.</p></div

Observed frequencies of alternate/mutated alleles by disorder in a large, mixed-breed canine population.

<p>Observed frequencies of alternate/mutated alleles by disorder in a large, mixed-breed canine population.</p

Frequency and distribution of 152 genetic disease variants in over 100,000 mixed breed and purebred dogs

Knowledge on the genetic epidemiology of disorders in the dog population has implications for both veterinary medicine and sustainable breeding. Limited data on frequencies of genetic disease variants across breeds exists, and the disease heritage of mixed breed dogs remains poorly explored to date. Advances in genetic screening technologies now enable comprehensive investigations of the canine disease heritage, and generate health-related big data that can be turned into action. We pursued population screening of genetic variants implicated in Mendelian disorders in the largest canine study sample examined to date by examining over 83,000 mixed breed and 18,000 purebred dogs representing 330 breeds for 152 known variants using a custom-designed beadchip microarray. We further announce the creation of MyBreedData (www.mybreeddata.com), an online updated inherited disorder prevalence resource with its foundation in the generated data. We identified the most prevalent, and rare, disease susceptibility variants across the general dog population while providing the first extensive snapshot of the mixed breed disease heritage. Approximately two in five dogs carried at least one copy of a tested disease variant. Most disease variants are shared by both mixed breeds and purebreds, while breed-or line-specificity of others is strongly suggested. Mixed breed dogs were more likely to carry a common recessive disease, whereas purebreds were more likely to be genetically affected with one, providing DNA-based evidence for hybrid vigor. We discovered genetic presence of 22 disease variants in at least one additional breed in which they were previously undescribed. Some mutations likely manifest similarly independently of breed background; however, we emphasize the need for follow up investigations in each case and provide a suggested validation protocol for broader consideration. In conclusion, our study provides unique insight into genetic epidemiology of canine disease risk variants, and their relevance for veterinary medicine, breeding programs and animal welfare.Peer reviewe

Data from: Frequency and distribution of 152 genetic disease variants in over 100,000 mixed breed and purebred dogs

Knowledge on the genetic epidemiology of disorders in the dog population has implications for both veterinary medicine and sustainable breeding. Limited data on frequencies of genetic disease variants across breeds exists, and the disease heritage of mixed breed dogs remains poorly explored to date. Advances in genetic screening technologies now enable comprehensive investigations of the canine disease heritage, and generate health-related big data that can be turned into action. We pursued population screening of genetic variants implicated in Mendelian disorders in the largest canine study sample examined to date by examining around 83,000 mixed breed and 18,000 purebred dogs representing 330 breeds for 152 known variants using a custom-designed beadchip microarray. We further announce the creation of MyBreedData (www.mybreeddata.com), an online updated inherited disorder prevalence resource with its foundation in the generated data. We identified the most prevalent, and rare, disease susceptibility variants across the general dog population while providing the first extensive snapshot of the mixed breed disease heritage. Around 2 in 5 dogs carried at least one copy of a tested disease variant. Most disease variants are shared by both mixed breeds and purebreds, while breed- or line-specificity of others is strongly suggested. Mixed breed dogs were more likely to carry a common recessive disease, whereas purebreds were more likely to be genetically affected with one, providing DNA-based evidence for hybrid vigor. We discovered genetic presence of 22 disease variants in at least one additional breed in which they were previously undescribed. Some mutations likely manifest similarly independently of breed background; however, we emphasize the need for follow up investigations in each case and provide a suggested validation protocol for broader consideration. In conclusion, our study provides unique insight into genetic epidemiology of canine disease risk variants, and their relevance for veterinary medicine, breeding programs and animal welfare