Thomas R. Famula

Bio: Thomas R. Famula is an academic researcher from University of California, Davis. The author has contributed to research in topics: Population & Heritability. The author has an hindex of 35, co-authored 148 publications receiving 3963 citations. Previous affiliations of Thomas R. Famula include University of California, Berkeley.

And the beak shall inherit – evolution in response to invasion

Abstract: The increased demographic performance of biological invaders may often depend on their escape from specifically adapted enemies. Here we report that native taxa in colonized regions may swiftly evolve to exploit such emancipated exotic species because of selection caused by invaders. A native Australian true bug has expanded it host range to include a vine imported from tropical America that has become a serious environmental weed. Based on field comparisons and historical museum specimens, we show that over the past 30-40 years, seed feeding soapberry bugs have evolved 5-10% longer mouthparts, better suited to attack the forest-invading balloon vines, which have large fruits. Laboratory experiments show that these differences are genetically based, and result in a near-doubling of the rate at which seeds are attacked. Thus a native biota that initially permits invasion may rapidly respond in ways that ultimately facilitate control.

Growth, development, and gene expression by in vivo- and in vitro-produced day 7 and 16 bovine embryos.

Abstract: The effects of the embryo production system on growth and transcription rate of day 7 and 16 bovine embryos were investigated. In vivo- (controls) and in vitro-produced (IVP) embryos were transferred to female recipients on day 7 of development, and were allowed to develop in a synchronous uterine environment to day 16. Embryonic transcripts for insulin-like growth factors-1 and -2 (IGF-1 and -2), their receptors (IGF-1r and -2r), facilitative glucose transporters-1 and -3 (Glut-1 and -3), and interferon-τ (IFN-τ) were determined by real-time quantitative PCR (TaqMan®); gender diagnosis was performed on day 16 concepti only. On day 7, IVP embryos presented lower mRNA levels than controls (P < 0.05), but these differences were generally reduced on day 16. No IGF-1 transcripts were detected on day 7, but a low IGF-1 mRNA level was observed in day 16 embryos. In the IVP group, IFN-τ mRNA levels were lower on day 7 (P < 0.05), but higher than controls on day 16 (P < 0.05). Control embryos showed a temporal decrease in the relative transcription from day 7 to 16 (P < 0.05), except IGF-1 mRNA. On day 16, IVP concepti were shorter and displayed smaller embryonic discs (P < 0.05). Female concepti were generally smaller than males, and IGF-2r mRNA and growth were negatively correlated. The in vitro production of bovine embryos negatively affected the amount of gene expression on day 7 and the rate of development on day 16. Physical traits and transcriptional activity on day 16 were associated with one another, which appeared to be significant for growth and development. Mol. Reprod. Dev. 63: 318–328, 2002. © 2002 Wiley-Liss, Inc.

Analysis of Genetic Variation in 28 Dog Breed Populations With 100 Microsatellite Markers

Abstract: Dog breeds were created by man choosing for select phenotypic traits such as size, shape, coat color, conformation, and behavior. Rigorous phenotypic selection likely resulted in a loss of genetic information. The present study extends previous dog population observations by assessing the genotypic variation within and across 28 breeds representing the seven recognized breed groups of the American Kennel Club (AKC). One hundred autosomal microsatellite markers distributed across the canine genome were used to examine variation within breeds. Resulting breed-specific allele frequencies were then used in an attempt to elucidate phylogeny and genetic distances between breeds. While the set of autosomal microsatellites was useful in describing genetic variation within breeds, establishing the genetic relatedness between breeds was less conclusive. A more accurate determination of breed phylogeny will likely require the use of single-nucleotide polymorphisms (SNPs).

Long-term observations on the dynamics of bovine digital dermatitis lesions on a California dairy after topical treatment with lincomycin HCl

Abstract: The objective of this study was to observe the dynamics of clinical cure and recurrence of the lesions of bovine digital dermatitis for 11 months after treatment with topical lincomycin HCl The study was a clinical follow-up of 39 active bovine digital dermatitis lesions (from 29 cows) Cows with active, painful bovine digital dermatitis (BDD) lesions on the interdigital commissure of the rear feet were identified on day 0 On day 1, lesions in all cows were photographed and full-skin thickness 6 mm punch biopsies were obtained for histological evaluation All lesions on all cows were treated with topical lincomycin paste under a light bandage On days 12 and 23, a subsample of 10 lesions was randomly selected, photographed, and biopsied On day 37, all lesions on all cows were photographed and biopsied After day 37, lesions were evaluated on a monthly basis All lesions were photographed at each observation until day 341 (end of study) but only cows that had macroscopically active lesions were biopsied Of the 39 lesions treated on day 1, 21 (54%) required re-treatment on at least one occasion before day 341 Macroscopic classification agreed well with histological classification when lesions were small, focal and active (M1 lesions) or large, ulcerative and active (M2), but agreement was variable for lesions that had healed macroscopically (M5) or that were chronic (M4) A transition model showed that M1 and M2 lesions were 27 times more likely to be an M2 lesion on the next observation than to be a healed (M5) lesion

Human biochemical genetics

Abstract: So far in this course we have dealt entirely with the evolution of characters that are controlled by simple Mendelian inheritance at a single locus. There are notes on the course website about gametic disequilibrium and how allele frequencies change at two loci simultaneously, but we didn’t discuss them. In every example we’ve considered we’ve imagined that we could understand something about evolution by examining the evolution of a single gene. That’s the domain of classical population genetics. For the next few weeks we’re going to be exploring a field that’s actually older than classical population genetics, although the approach we’ll be taking to it involves the use of population genetic machinery. If you know a little about the history of evolutionary biology, you may know that after the rediscovery of Mendel’s work in 1900 there was a heated debate between the “biometricians” (e.g., Galton and Pearson) and the “Mendelians” (e.g., de Vries, Correns, Bateson, and Morgan). Biometricians asserted that the really important variation in evolution didn’t follow Mendelian rules. Height, weight, skin color, and similar traits seemed to

Modern Applied Statistics With S

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Integrative Genomics Viewer

Abstract: Rapid improvements in sequencing and array-based platforms are resulting in a flood of diverse genome-wide data, including data from exome and whole-genome sequencing, epigenetic surveys, expression profiling of coding and noncoding RNAs, single nucleotide polymorphism (SNP) and copy number profiling, and functional assays. Analysis of these large, diverse data sets holds the promise of a more comprehensive understanding of the genome and its relation to human disease. Experienced and knowledgeable human review is an essential component of this process, complementing computational approaches. This calls for efficient and intuitive visualization tools able to scale to very large data sets and to flexibly integrate multiple data types, including clinical data. However, the sheer volume and scope of data pose a significant challenge to the development of such tools.