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536 results on '"BAKER, ALLAN J."'

6. Feather Development Genes and Associated Regulatory Innovation Predate the Origin of Dinosauria

Author

Lowe, Craig B, Clarke, Julia A, Baker, Allan J, Haussler, David, and Edwards, Scott V

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Evolutionary Biology, Genetics, Human Genome, Generic health relevance, Animals, Biological Evolution, Birds, Body Size, Dinosaurs, Evolution, Molecular, Feathers, Genomics, Insulin-Like Growth Factor Binding Protein 2, Insulin-Like Growth Factor Binding Protein 5, Keratins, Mutation Rate, Phylogeny, Regulatory Elements, Transcriptional, enhancer, gene regulation, comparative genomics, integument, body size, dinosaur, Biochemistry and Cell Biology, Biochemistry and cell biology, Evolutionary biology
Abstract

The evolution of avian feathers has recently been illuminated by fossils and the identification of genes involved in feather patterning and morphogenesis. However, molecular studies have focused mainly on protein-coding genes. Using comparative genomics and more than 600,000 conserved regulatory elements, we show that patterns of genome evolution in the vicinity of feather genes are consistent with a major role for regulatory innovation in the evolution of feathers. Rates of innovation at feather regulatory elements exhibit an extended period of innovation with peaks in the ancestors of amniotes and archosaurs. We estimate that 86% of such regulatory elements and 100% of the nonkeratin feather gene set were present prior to the origin of Dinosauria. On the branch leading to modern birds, we detect a strong signal of regulatory innovation near insulin-like growth factor binding protein (IGFBP) 2 and IGFBP5, which have roles in body size reduction, and may represent a genomic signature for the miniaturization of dinosaurian body size preceding the origin of flight.

Published
2015

7. Natural selection shaped the rise and fall of passenger pigeon genomic diversity

Author

Murray, Gemma G. R., Soares, André E. R., Novak, Ben J., Schaefer, Nathan K., Cahill, James A., Baker, Allan J., Demboski, John R., Doll, Andrew, Da Fonseca, Rute R., Fulton, Tara L., Gilbert, M. Thomas P., Heintzman, Peter D., Letts, Brandon, McIntosh, George, O’Connell, Brendan L., Peck, Mark, Pipes, Marie-Lorraine, Rice, Edward S., Santos, Kathryn M., Sohrweide, A. Gregory, Vohr, Samuel H., Corbett-Detig, Russell B., Green, Richard E., and Shapiro, Beth

Published
2017

12. Effects of Horseshoe Crab Harvest in Delaware Bay on Red Knots: Are Harvest Restrictions Working?

Author

Niles, Lawrence J., Bart, Jonathan, Sitters, Humphrey P., Dey, Amanda D., Clark, Kathleen E., Atkinson, Phillip W., Baker, Allan J., Bennett, Karen A., Kalasz, Kevin S., Clark, Nigel A., Clark, Jacquie, Gillings, Simon, Gates, Albert S., González, Patricia M., Hernandez, Daniel E., Minton, Clive D. T., Morrison, R. I. Guy, Porter, Ronald R., Ross, R. Ken, and Veitch, C. Richard

Published
2009
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39. Molecular evidence for introgressive hybridization in New Zealand masked gulls.

Author

Given, Andrew D., Mills, James A., Momigliano, Paolo, and Baker, Allan J.

Subjects
SPECIES hybridization, INTROGRESSION (Genetics), REPRODUCTIVE isolation, GULLS, NUCLEAR DNA, MITOCHONDRIAL DNA, GENE flow
Abstract

We used mitochondrial DNA (mtDNA) gene sequences and nuclear microsatellite loci to investigate the extent and outcome of hybridization between the Black‐billed Gull Chroicocephalus bulleri and the Red‐billed Gull Chroicocephalus novaehollandiae scopulinus in New Zealand. Six of 26 sampled Black‐billed Gulls possessed mtDNA typical of Red‐billed Gulls, but allele frequencies at six polymorphic microsatellites provided little evidence of mixed ancestry expected in very recent hybrids. None of the Red‐billed Gulls sampled from different colonies possessed Black‐billed Gull mtDNA expected in the reciprocal cross, suggesting that hybridization in the two species typically occurs between female Red‐billed Gulls and Black‐billed Gull males. The lack of any hybrid signal in the nuclear loci indicates that there has been extensive backcrossing with Black‐billed Gulls, effectively diluting the Red‐billed Gull nuclear DNA contribution. Divergence of Red‐billed Gulls and Black‐billed Gulls occurred approximately 250 000 years ago, indicating that unsorted ancestral polymorphism is an unlikely alternative to hybridization. Comparing demographic models within an approximate Bayesian computation (ABC) framework, we confirm that the observed patterns cannot result from incomplete lineage sorting. Using an ABC random forest approach, we determined that the most likely model explaining the data is a recent introgression scenario, whereby unidirectional gene flow is re‐established following a period of strict isolation. The ability of Black‐billed and Red‐billed Gulls to successfully interbreed shows that despite significant differentiation (FST > 0.3), there has been insufficient time for the two species to develop complete reproductive isolation. The apparent one‐way transfer of Red‐billed Gull mtDNA into Black‐billed Gulls and extensive backcrossing argues against cytoplasmic–nuclear genome incompatibilities between the two species. We hypothesize that the specific mate recognition system cued on colours of soft parts normally functions to prevent hybridization, but that it can break down under demographic conditions where there is a shortage of available mates and a surplus of females in the Red‐billed Gull population. The high incidence of introgression in Black‐billed Gulls conflicts with field observations that interbreeding is extremely rare. [ABSTRACT FROM AUTHOR]

Published
2023
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