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Tapanes E, Rennison DJ. The genetic basis of divergent melanic pigmentation in benthic and limnetic threespine stickleback. Heredity (Edinb) 2024:10.1038/s41437-024-00706-0. [PMID: 39048622 DOI: 10.1038/s41437-024-00706-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/02/2024] [Accepted: 07/12/2024] [Indexed: 07/27/2024] Open
Abstract
Pigmentation is an excellent trait to examine patterns of evolutionary change because it is often under natural selection. Benthic and limnetic threespine stickleback (Gasterosteus aculeatus) exhibit distinct pigmentation phenotypes, likely an adaptation to occupation of divergent niches. The genetic architecture of pigmentation in vertebrates appears to be complex. Prior QTL mapping of threespine stickleback pigmentation phenotypes has identified several candidate loci. However-relative to other morphological phenotypes (e.g., spines or lateral plates)-the genetic architecture of threespine stickleback pigmentation remains understudied. Here, we performed QTL mapping for two melanic pigmentation traits (melanophore density and lateral barring) using benthic-limnetic F2 crosses. The two traits mapped to different chromosomes, suggesting a distinct genetic basis. The resulting QTLs were additive, but explained a relatively small fraction of the total variance (~6%). QTLs maps differed by F1 family, suggesting variation in genetic architecture or ability to detect loci of small effect. Functional analysis identified enriched pathways for candidate loci. Several of the resulting candidate loci for pigmentation, including three loci in enriched pathways (bco1, sulf1, and tyms) have been previously indicated to affect pigmentation in other vertebrates. These findings add to a growing body of evidence suggesting pigmentation is often polygenic.
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Affiliation(s)
- Elizabeth Tapanes
- School of Biological Sciences, Section of Ecology, Behavior and Evolution, University of California San Diego, La Jolla, CA, USA
| | - Diana J Rennison
- School of Biological Sciences, Section of Ecology, Behavior and Evolution, University of California San Diego, La Jolla, CA, USA.
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Shpak M, Lawrence KN, Pool JE. The Precision and Power of Population Branch Statistics in Identifying the Genomic Signatures of Local Adaptation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.14.594139. [PMID: 38798330 PMCID: PMC11118325 DOI: 10.1101/2024.05.14.594139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Population branch statistics, which estimate the branch lengths of focal populations with respect to two outgroups, have been used as an alternative to FST-based genome-wide scans for identifying loci associated with local selective sweeps. In addition to the original population branch statistic (PBS), there are subsequently proposed branch rescalings: normalized population branch statistic (PBSn1), which adjusts focal branch length with respect to outgroup branch lengths at the same locus, and population branch excess (PBE), which also incorporates median branch lengths at other loci. PBSn1 and PBE have been proposed to be less sensitive to allele frequency divergence generated by background selection or geographically ubiquitous positive selection rather than local selective sweeps. However, the accuracy and statistical power of branch statistics have not been systematically assessed. To do so, we simulate genomes in representative large and small populations with varying proportions of sites evolving under genetic drift or background selection (approximated using variable Ne), local selective sweeps, and geographically parallel selective sweeps. We then assess the probability that local selective sweep loci are correctly identified as outliers by FST and by each of the branch statistics. We find that branch statistics consistently outperform FST at identifying local sweeps. When background selection and/or parallel sweeps are introduced, PBSn1 and especially PBE correctly identify local sweeps among their top outliers at a higher frequency than PBS. These results validate the greater specificity of rescaled branch statistics such as PBE to detect population-specific positive selection, supporting their use in genomic studies focused on local adaptation.
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Affiliation(s)
- Max Shpak
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, WI, USA
| | - Kadee N. Lawrence
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, WI, USA
| | - John E. Pool
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, WI, USA
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McKinnon JS, Newsome WB, Balakrishnan CN. Gene expression in male and female stickleback from populations with convergent and divergent throat coloration. Ecol Evol 2022; 12:e8860. [PMID: 35509607 PMCID: PMC9055290 DOI: 10.1002/ece3.8860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/01/2022] [Accepted: 04/01/2022] [Indexed: 11/06/2022] Open
Affiliation(s)
- Jeffrey S. McKinnon
- Department of Biology East Carolina University Greenville North Carolina USA
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Frommen JG, Thünken T, Santostefano F, Balzarini V, Hettyey A. Effects of chronic and acute predation risk on sexual ornamentation and mating preferences. Behav Ecol 2021. [DOI: 10.1093/beheco/arab116] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Phenotypic plasticity is widespread in animals. Still, how plastic responses to predator presence affect traits under sexual selection and influence mating preferences is not well understood. Here, we examined how simulated chronic predator presence during development and acute predator presence during mate choice affect the expression of male secondary sexual traits and female mating preference in the three-spined stickleback, Gasterosteus aculeatus. Males reared under chronic predator presence developed less intense red breeding coloration but showed higher courtship activity than males that grew up in a predator-free environment. Acute predator presence during mate choice trials did not influence male behavior or ornamentation. Predator presence experienced during development did not affect female mating preferences, whereas acute predator presence altered preferences for male courtship activity. Male body size and eye coloration influenced the intensity of female mating preferences, while the trait changing most in response to predator presence during development (red coloration) had no significant impact. The observed interplay between developmental plasticity in male ornamental traits and environment-dependent female mating preferences may lead to dynamic processes altering the strength and direction of sexual selection depending on both the chronic and acute risk of predation. These processes may contribute to the maintenance of within- and among-population variation in secondary sexual traits, and may, ultimately, facilitate speciation.
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Affiliation(s)
- Joachim G Frommen
- Konrad Lorenz Institute of Ethology, Department of Integrative Biology and Evolution, University of Veterinary Medicine Vienna, Savoyenstr. 1a, 1160 Vienna, Austria
- Division of Behavioural Ecology, Institute of Ecology and Evolution, University of Bern, Wohlenstr. 50a, 3032 Hinterkappelen, Switzerland
- Conservation, Ecology, Evolution and Behaviour Research Group, Ecology and Environment Research Centre, Manchester Metropolitan University, Manchester, UK
| | - Timo Thünken
- Division of Behavioural Ecology, Institute of Ecology and Evolution, University of Bern, Wohlenstr. 50a, 3032 Hinterkappelen, Switzerland
| | - Francesca Santostefano
- Konrad Lorenz Institute of Ethology, Department of Integrative Biology and Evolution, University of Veterinary Medicine Vienna, Savoyenstr. 1a, 1160 Vienna, Austria
- Département des Sciences Biologiques, Université du Québec à Montréal, C.P. 8888, Succ. Centre-ville Montréal, QC, Canada
| | - Valentina Balzarini
- Konrad Lorenz Institute of Ethology, Department of Integrative Biology and Evolution, University of Veterinary Medicine Vienna, Savoyenstr. 1a, 1160 Vienna, Austria
- Division of Behavioural Ecology, Institute of Ecology and Evolution, University of Bern, Wohlenstr. 50a, 3032 Hinterkappelen, Switzerland
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall, UK
| | - Attila Hettyey
- Konrad Lorenz Institute of Ethology, Department of Integrative Biology and Evolution, University of Veterinary Medicine Vienna, Savoyenstr. 1a, 1160 Vienna, Austria
- Lendület Evolutionary Ecology Research Group, Plant Protection Institute, Centre for Agricultural Research, Eötvös Loránd Research Network, Herman Ottó út 15, Budapest 1022, Hungary
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Hudson CM, Lucek K, Marques DA, Alexander TJ, Moosmann M, Spaak P, Seehausen O, Matthews B. Threespine Stickleback in Lake Constance: The Ecology and Genomic Substrate of a Recent Invasion. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2020.611672] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Invasive species can be powerful models for studying contemporary evolution in natural environments. As invading organisms often encounter new habitats during colonization, they will experience novel selection pressures. Threespine stickleback (Gasterosteus aculeatus complex) have recently colonized large parts of Switzerland and are invasive in Lake Constance. Introduced to several watersheds roughly 150 years ago, they spread across the Swiss Plateau (400–800 m a.s.l.), bringing three divergent hitherto allopatric lineages into secondary contact. As stickleback have colonized a variety of different habitat types during this recent range expansion, the Swiss system is a useful model for studying contemporary evolution with and without secondary contact. For example, in the Lake Constance region there has been rapid phenotypic and genetic divergence between a lake population and some stream populations. There is considerable phenotypic variation within the lake population, with individuals foraging in and occupying littoral, offshore pelagic, and profundal waters, the latter of which is a very unusual habitat for stickleback. Furthermore, adults from the lake population can reach up to three times the size of adults from the surrounding stream populations, and are large by comparison to populations globally. Here, we review the historical origins of the threespine stickleback in Switzerland, and the ecomorphological variation and genomic basis of its invasion in Lake Constance. We also outline the potential ecological impacts of this invasion, and highlight the interest for contemporary evolution studies.
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