Parentage

One of the major goals of the Jones lab has been to use modern molecular techniques to learn more about evolutionary processes in natural populations of organisms. One particularly fruitful area of research has been in the assessment of parentage in nature, with a particular emphasis on the important evolutionary process of sexual selection. Several taxa of fishes and amphibians have been the focus of this research.

For more information on parentage analysis techniques and their applications, see these recent reviews by Jones and colleagues:

Avise, J. C., A. G. Jones, D. Walker, J. A. DeWoody, and collaborators. 2002. Genetic mating systems and reproductive natural histories of fishes: Lessons for ecology and evolution. Annual Review of Genetics 36:19-45.

Jones, A. G. and W. R. Ardren. 2003. Methods of parentage analysis in natural populations. Molecular Ecology 12:2511-2523.

Mating Systems in Male-Pregnant Pipefishes and Seahorses
Our studies of parentage in pipefishes and seahorses have shown that these fishes, all of which are characterized by male pregnancy, enjoy complete confidence of paternity. Comparative evidence supports the notion that the form of the mating system is related to the intensity of sexual selection, with the more polyandrous species experiencing relatively more intense sexual selection than the less polyandrous or monogamous species.

For more details, see Pipefish and Seahorse Evolution.

Alternative Mating Strategies in Natural Fish Populations
In many species of fishes, males engage in multiple reproductive strategies. A common manifestation of this phenomenon is for a population to contain one set of males that build nests or defend territories and another set of males that attempt to parasatize the reproductive efforts of these territorial males. Molecular markers have been instrumental in documenting the fertilization success of the parasitic male tactics. We have studied these topics in fifteenspine sticklebacks and sand gobies.

Jones, A. G., S. Östlund-Nilsson and J. C. Avise. 1998. A microsatellite assessment of sneaked fertilizations and egg thievery in the fifteenspine stickleback. Evolution 52: 848-858.

Jones, A. G., D. Walker, C. Kvarnemo, K. Lindström, and J. C. Avise. 2001. How cuckoldry can decrease the opportunity for sexual selection: data and theory from a genetic parentage analysis of the sand goby, Pomatoschistus minutus. Proceedings of the National Academy of Sciences USA 98: 9151-9156.

Jones, A.G., D. Walker, K. Lindström, C. Kvarnemo, and J.C. Avise. 2001. Surprising similarity of sneaking rates and genetic mating patterns in two populations of the sand goby experiencing disparate sexual selection regimes. Molecular Ecology 10: 461-469.

Bateman's Principles and the Measurement of Sexual Selection
The major recent focus of parentage studies in the lab has been on techniques for the characterization of mating systems in natural populations. Our results suggest that one promising approaches may be to use measures based on Bateman's principles. Bateman's three principles have been formalized into quantitative measures of mating patterns in natural populations. The three measures are the opportunity for sexual selection (based on variance in mating success), the opportunity for selection (based on variance in reproductive success) and the sexual selection gradient or Bateman gradient (based on the relationship between mating success and reproductive success). Studies of newts and pipefish support the assertion that the combined use of these measures provides a useful way of characterizing mating patterns with respect to sexual selection.

Jones, A. G., G. Rosenqvist, A. Berglund, S. J. Arnold, and J. C. Avise. 2000. The Bateman gradient and the cause of sexual selection in a sex-role-reversed pipefish. Proceedings of the Royal Society of London B: Biological Sciences 267:677-680.

Jones, A. G., J. R. Arguello, and S. J. Arnold. 2002. Validation of Bateman's principles: a genetic study of mating patterns and sexual selection in newts. Proceedings of the Royal Society of London B: Biological Sciences 269:2533-2539.

Jones, A. G., J. R. Arguello, and S. J. Arnold. 2004. Molecular parentage analysis in experimental newt populations: the response of mating system measures to variation in the operational sex ratio. The American Naturalist 164:444-456.

Jones, A. G., G. Rosenqvist, A. Berglund, and J. C. Avise.  2005.  The measurement of sexual selection using Bateman’s principles: an experimental test in the sex-role-reversed pipefish Syngnathus typhle.  Integrative and Comparative Biology 45:874-884.

Reconstructing Parental Genotypes from Progeny Arrays with GERUD1.0
GERUD1.0 is a windows-based computer program that reconstructs parental genotypes from molecular data on progeny arrays. The current version requires a progeny array with one known parent. It also requires data from multiple co-dominant loci for the parent and the offspring. Given these data, GERUD1.0 uses an exhaustive algorithm to determine the minimum number of unknown parents necessary to explain the progeny array. GERUD1.0 also reconstructs all possible combinations of parental genotypes that are consistent with the progeny array. A second program, GERUDsim1.0, can be used to assess the power of GERUD1.0 to reconstruct genotypes for a particular biological system.

Click here to download a zip archive of GERUD1.0 and its documentation

See the following reference for additional details:

Jones, A. G. 2001. GERUD1.0: A computer program for the reconstruction of parental genotypes from progeny arrays using multi-locus DNA data. Molecular Ecology Notes 1: 215-218.

NEW:  Reconstructing Parental Genotypes when Neither Parent is Known with GERUD2.0
GERUD2.0 is an update of GERUD1.0 that permits the analysis of progeny arrays without knowing the genotypes of any of the parents.  This program is useful for analyzing field-collected egg masses, for example.  It does require that the progeny array comprises only full or half-siblings, however, so each progeny array must have a single mother (and one or more fathers) or a single father (and one or more mothers).  This assumption is probably fulfilled in many organisms that lay eggs in masses, however, so the program should help with the analysis of parentage in a large number of species in which parents cannot be collected with the egg masses.

Click here to download a zip archive of GERUD2.0 and its documentation

See the following reference for additional details:

Jones, A. G. 2005. GERUD2.0: A computer program for the reconstruction of parental genotypes from progeny arrays with known or unknown parents. Molecular Ecology Notes 5:708-711.