Search

Your search keyword '"Geneva, Anthony J"' showing total 159 results
Start Over Author "Geneva, Anthony J"
159 results on '"Geneva, Anthony J"'

5. Evolutionary genomics of oceanic island radiations

Author

Cerca, José, Cotoras, Darko D., Bieker, Vanessa C., De-Kayne, Rishi, Vargas, Pablo, Fernández-Mazuecos, Mario, López-Delgado, Julia, White, Oliver, Stervander, Martin, Geneva, Anthony J., Guevara Andino, Juan Ernesto, Meier, Joana Isabel, Roeble, Lizzie, Brée, Baptiste, Patiño, Jairo, Guayasamin, Juan M., Torres, María de Lourdes, Valdebenito, Hugo, Castañeda, María del Rosario, Chaves, Jaime A., Díaz, Patricia Jaramillo, Valente, Luis, Knope, Matthew L., Price, Jonathan P., Rieseberg, Loren H., Baldwin, Bruce G., Emerson, Brent C., Rivas-Torres, Gonzalo, Gillespie, Rosemary, and Martin, Michael D.

Published
2023
Full Text
View/download PDF

13. A new method to scan genomes for introgression in a secondary contact model

Author

Geneva, Anthony J., Kingan, Sarah B., and Garrigan, Daniel

Subjects
Quantitative Biology - Populations and Evolution
Abstract

Secondary contact between divergent populations or incipient species may result in the exchange and introgression of genomic material. We develop a simple DNA sequence measure, called Gmin, which is designed to identify genomic regions experiencing introgression in a secondary contact model. Gmin is defined as the ratio of the minimum between-population number of nucleotide differences to the average number of between-population differences. One advantage of Gmin is that it is computationally inexpensive relative to model-based methods for detecting gene flow and it scales easily to the level of whole-genome analysis. We compare the sensitivity and specificity of Gmin to those of the widely used index of population differentiation, Fst, and suggest a simple statistical test for identifying genomic outliers. Extensive computer simulations demonstrate that Gmin has both greater sensitivity and specificity for detecting recent introgression than does Fst. Furthermore, we find that the sensitivity of Gmin is robust with respect to both the population mutation and recombination rates. Finally, a scan of Gmin across the X chromosome of Drosophila melanogaster identifies candidate regions of introgression between sub-Saharan African and cosmopolitan populations that were previously missed by other methods. These results show that Gmin is a biologically straightforward, yet powerful, alternative to Fst, as well as to more computationally intensive model-based methods for detecting gene flow., Comment: 34 pages, 4 figures, 1 table (10 supplementary figures, 4 supplementary tables)

Published
2014
Full Text
View/download PDF

24. Chromosome-scale genome assembly of the brown anole (Anolis sagrei), a model species for evolution and ecology

Author

Geneva, Anthony J., primary, Park, Sungdae, additional, Bock, Dan, additional, de Mello, Pietro, additional, Sarigol, Fatih, additional, Tollis, Marc, additional, Donihue, Colin, additional, Reynolds, R. Graham, additional, Feiner, Nathalie, additional, Rasys, Ashley M., additional, Lauderdale, James D., additional, Minchey, Sergio G., additional, Alcala, Aaron J., additional, Infante, Carlos R., additional, Kolbe, Jason J., additional, Schluter, Dolph, additional, Menke, Douglas B., additional, and Losos, Jonathan B., additional

Published
2021
Full Text
View/download PDF

30. Author response: Gene flow mediates the role of sex chromosome meiotic drive during complex speciation

Author

Meiklejohn, Colin D, primary, Landeen, Emily L, additional, Gordon, Kathleen E, additional, Rzatkiewicz, Thomas, additional, Kingan, Sarah B, additional, Geneva, Anthony J, additional, Vedanayagam, Jeffrey P, additional, Muirhead, Christina A, additional, Garrigan, Daniel, additional, Stern, David L, additional, and Presgraves, Daven C, additional

Published
2018
Full Text
View/download PDF

37. A method to scan genomes for introgression in a secondary contact model

Author

Geneva, Anthony J, Kingan, Sarah B., Machado, Carlos A, and Garrigan, Daniel

Abstract

This poster was presented at the 2014 meeting of the Society for Molecular Biology & Evolution, in San Juan, PR. Abstract: Secondary contact between divergent populations, or incipient species, may result in the exchange and introgression of genomic material. We develop a simple DNA sequence measure, called Gmin, that is designed to identify genomic regions experiencing introgression in a secondary contact model. Gmin is simply defined as the ratio of the minimum between-population number of nucleotide differences to the average number of between-population differences. The utility of Gmin is that it is computationally inexpensive relative to likelihood-based methods for detecting gene flow and it has better sensitivity and specificity than traditional measures, such as Fst. We present extensive evaluations of the sensitivity and specificity of Gmin and suggest a simple statistical testing procedure for identifying genomic outliers. Finally, we present genome-level scans of Gmin for three different data sets. The first data set evaluates cosmopolitan and African populations of Drosophila melanogaster. In this case, Gmin is able to identify all of the regions of the X chromosome that were identified by a previous, more computationally intense method, in addition to one region that was not previously identified. Second, we perform genome scans of Gmin for two species of the Drosophila simulans clade. In this case, we identify large tracts of introgression between species whose hybrid males are sterile. Lastly, we apply the Gmin statistic to an analysis of African and non-African populations of domesticated rice. In this case, it was previously shown that that these populations have a history of recent genetic exchange, however, scans of Gmin show no evidence introgression of domestication genes between these two populations. Gmin is a biologically straightforward, yet powerful, alternative to Fst, as well as to more computationally intensive model-based methods for detecting gene flow.

Published
2014
Full Text
View/download PDF

38. Anolis sex chromosomes are derived from a single ancestral pair

Author

Gamble, Tony, Geneva, Anthony J., Glor, Richard E., and Zarkower, David

Subjects
Evolution, Molecular, Male, X Chromosome, Y Chromosome, Cytogenetic Analysis, Animals, Female, Lizards, Polymerase Chain Reaction, Article, In Situ Hybridization, Fluorescence, Phylogeny
Abstract

To explain the frequency and distribution of heteromorphic sex chromosomes in the lizard genus Anolis, we compared the relative roles of sex chromosome conservation versus turnover of sex-determining mechanisms. We used model-based comparative methods to reconstruct karyotype evolution and the presence of heteromorphic sex chromosomes onto a newly generated Anolis phylogeny. We found that heteromorphic sex chromosomes evolved multiple times in the genus. Fluorescent in situ hybridization (FISH) of repetitive DNA showed variable rates of Y chromosome degeneration among Anolis species and identified previously undetected, homomorphic sex chromosomes in two species. We confirmed homology of sex chromosomes in the genus by performing FISH of an X-linked bacterial artificial chromosome (BAC) and quantitative PCR of X-linked genes in multiple Anolis species sampled across the phylogeny. Taken together, these results are consistent with long-term conservation of sex chromosomes in the group. Our results pave the way to address additional questions related to Anolis sex chromosome evolution and describe a conceptual framework that can be used to evaluate the origins and evolution of heteromorphic sex chromosomes in other clades.

Published
2013

40. Nucleotide sequence data confirm diagnosis and local endemism of variable morphospecies of Andean astroblepid catfishes (Siluriformes: Astroblepidae)

Author

Schaefer, Scott A., Chakrabarty, Prosanta, Geneva, Anthony J., and Sabaj Pérez, Mark H.

Subjects
Biodiversity, Taxonomy
Abstract

Schaefer, Scott A., Chakrabarty, Prosanta, Geneva, Anthony J., Sabaj Pérez, Mark H. (2011): Nucleotide sequence data confirm diagnosis and local endemism of variable morphospecies of Andean astroblepid catfishes (Siluriformes: Astroblepidae). Zoological Journal of the Linnean Society 162 (1): 90-102, DOI: 10.1111/j.1096-3642.2010.00673.x, URL: http://dx.doi.org/10.1111/j.1096-3642.2010.00673.x

Published
2011

Catalog

Books, media, physical & digital resources
See catalog results