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Wang S. Divergent island hybrids mixed waves of ancient gene flow. Mol Ecol 2024; 33:e17279. [PMID: 38308460 DOI: 10.1111/mec.17279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 12/27/2023] [Accepted: 01/12/2024] [Indexed: 02/04/2024]
Abstract
In this issue of Molecular Ecology, Salter et al. (2023) discovered that the Cuban Northern Bobwhite subspecies, Colinus virginianus cubanensis (Gould, 1850), is an ancient hybrid population formed due to historical hybridization potentially brought by waves of historical human migration. This study revealed a complex mixture of gene flow from distinct spatiotemporal origins underlying a seemingly semi-independent evolutionary trajectory. Hybridization can be more common and complex than we thought.
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Affiliation(s)
- Silu Wang
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York, USA
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Cauceglia JW, Nelson AC, Rubinstein ND, Kukreja S, Sasso LN, Beaufort JA, Rando OJ, Potts WK. Transitions in paternal social status predict patterns of offspring growth and metabolic transcription. Mol Ecol 2020; 29:624-638. [PMID: 31885115 DOI: 10.1111/mec.15346] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 11/27/2019] [Accepted: 12/16/2019] [Indexed: 12/17/2022]
Abstract
One type of parental effect occurs when changes in parental phenotype or environment trigger changes to offspring phenotype. Such nongenetic parental effects can be precisely triggered in response to an environmental cue in time-locked fashion, or in other cases, persist for multiple generations after the cue has been removed, suggesting multiple timescales of action. For parental effects to serve as reliable signals of current environmental conditions, they should be reversible, such that when cues change, offspring phenotypes change in accordance. Social hierarchy is a prevalent feature of the environment, and current parental social status could signal the environment in which offspring will be born. Here, we sought to address parental effects of social status and their timescale of action in mice. We show that territorial competition in seminatural environments affects offspring growth. Although dominant males are not heavier than nondominant or control males, they produce faster growing offspring, particularly sons. The timing, effect-size, and sex-specificity of this association are modulated by maternal social experience. We show that a change in paternal social status is sufficient to modulate offspring weight: from one breeding cycle to the next, status-ascending males produce heavier sons than before, and status-descending males produce lighter sons than before. Current paternal status is also highly predictive of liver transcription in sons, including molecular pathways controlling oxidative phosphorylation and iron metabolism. These results are consistent with a parental effect of social experience, although alternative explanations are considered. In summary, changes in paternal social status are associated with changes in offspring growth and metabolism.
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Affiliation(s)
- Joseph W Cauceglia
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Adam C Nelson
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, MA, USA
| | | | - Shweta Kukreja
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Lynsey N Sasso
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - John A Beaufort
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Oliver J Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Wayne K Potts
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
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López-Cortegano E, Pérez-Figueroa A, Caballero A. metapop2: Re-implementation of software for the analysis and management of subdivided populations using gene and allelic diversity. Mol Ecol Resour 2019; 19:1095-1100. [PMID: 30938911 DOI: 10.1111/1755-0998.13015] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 03/07/2019] [Accepted: 03/19/2019] [Indexed: 01/06/2023]
Abstract
Management programmes often have to make decisions based on the analysis of the genetic properties and diversity of populations. Expected heterozygosity (or gene diversity) and population structure parameters are often used to make recommendations for conservation, such as avoidance of inbreeding or migration across subpopulations. Allelic diversity, however, can also provide complementary and useful information for conservation programmes, as it is highly sensitive to population bottlenecks, and is more related to long-term selection response than heterozygosity. Here we present a completely revised and updated re-implementation of the software metapop for the analysis of diversity in subdivided populations, as well as a tool for the management and dynamic estimation of optimal contributions in conservation programmes. This new update includes computation of allelic diversity for population analysis and management, as well as a simulation mode to forecast the consequences of taking different management strategies over time. Furthermore, the new implementation in C++ includes code optimization and improved memory usage, allowing for fast analysis of large data sets including single nucleotide polymorphism markers, as well as enhanced cross-software and cross-platform compatibility.
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Affiliation(s)
- Eugenio López-Cortegano
- Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, Vigo, Spain.,Centro de Investigación Marina (CIM-UVIGO), Universidade de Vigo, Vigo, Spain
| | - Andrés Pérez-Figueroa
- Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, Vigo, Spain.,Centro de Investigaciones Biomédicas (CINBIO), Universidade de Vigo, Vigo, Spain
| | - Armando Caballero
- Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, Vigo, Spain.,Centro de Investigación Marina (CIM-UVIGO), Universidade de Vigo, Vigo, Spain
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Abstract
The concept of kinship permeates many domains of fundamental and applied biology ranging from social evolution to conservation science to quantitative and human genetics. Until recently, pedigrees were the gold standard to infer kinship, but the advent of next‐generation sequencing and the availability of dense genetic markers in many species make it a good time to (re)evaluate the usefulness of genetic markers in this context. Using three published data sets where both pedigrees and markers are available, we evaluate two common and a new genetic estimator of kinship. We show discrepancies between pedigree values and marker estimates of kinship and explore via simulations the possible reasons for these. We find these discrepancies are attributable to two main sources: pedigree errors and heterogeneity in the origin of founders. We also show that our new marker‐based kinship estimator has very good statistical properties and behaviour and is particularly well suited for situations where the source population is of small size, as will often be the case in conservation biology, and where high levels of kinship are expected, as is typical in social evolution studies.
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Affiliation(s)
- Jérôme Goudet
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Tomas Kay
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Bruce S Weir
- Department of Biostatistics, University of Washington, Seattle, Washington
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Tibayrenc M, Ayala F. Hybridization in Trypanosoma congolense does not challenge the predominant clonal evolution model. A comment on Tihon et al., 2017, Mol. Ecol. Mol Ecol 2018; 27:3421-3424. [PMID: 30146716 DOI: 10.1111/mec.14714] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 04/17/2018] [Accepted: 04/19/2018] [Indexed: 11/28/2022]
Abstract
Tihon et al. have just published in Mol. Ecol. a fine genomic study on Trypanosoma congolense, agent of Animal African Trypanosomiasis. They present very convincing evidence that T. congolense underwent several hybridization events between distinct genetic lines in Zambia. They claim that their data challenge our predominant clonal evolution model (PCE) of micropathogens. We point out the main tenets of our model and show that Tihon et al.'s claim is based on a misinterpretation of the PCE model. Actually, their data strongly support PCE in T. congolense at a microevolutionary level.
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Affiliation(s)
- Michel Tibayrenc
- Maladies Infectieuses et Vecteurs Ecologie, Génétique, Evolution et Contrôle, MIVEGEC (IRD 224-CNRS 5290-UM1-UM2), Institut de recherché pour le développement, Montpellier, France
| | - Francisco Ayala
- Department of Ecology and Evolutionary Biology, University of California at Irvine, Irvine, California
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Young BW, Dean MD. To be, or not to be, related: how female guppies bias sperm usage. Mol Ecol 2015; 24:4039-41. [PMID: 26255978 DOI: 10.1111/mec.13272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 06/11/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Brent W Young
- Molecular and Computational Biology, University of Southern California, 1050 Childs Way, Los Angeles, 90089, CA, USA
| | - Matthew D Dean
- Molecular and Computational Biology, University of Southern California, 1050 Childs Way, Los Angeles, 90089, CA, USA
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Hess JE, Campbell NR, Docker MF, Baker C, Jackson A, Lampman R, McIlraith B, Moser ML, Statler DP, Young WP, Wildbill AJ, Narum SR. Use of genotyping by sequencing data to develop a high-throughput and multifunctional SNP panel for conservation applications in Pacific lamprey. Mol Ecol Resour 2014; 15:187-202. [PMID: 24842551 DOI: 10.1111/1755-0998.12283] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 05/13/2014] [Accepted: 05/14/2014] [Indexed: 11/29/2022]
Abstract
Next-generation sequencing data can be mined for highly informative single nucleotide polymorphisms (SNPs) to develop high-throughput genomic assays for nonmodel organisms. However, choosing a set of SNPs to address a variety of objectives can be difficult because SNPs are often not equally informative. We developed an optimal combination of 96 high-throughput SNP assays from a total of 4439 SNPs identified in a previous study of Pacific lamprey (Entosphenus tridentatus) and used them to address four disparate objectives: parentage analysis, species identification and characterization of neutral and adaptive variation. Nine of these SNPs are FST outliers, and five of these outliers are localized within genes and significantly associated with geography, run-timing and dwarf life history. Two of the 96 SNPs were diagnostic for two other lamprey species that were morphologically indistinguishable at early larval stages and were sympatric in the Pacific Northwest. The majority (85) of SNPs in the panel were highly informative for parentage analysis, that is, putatively neutral with high minor allele frequency across the species' range. Results from three case studies are presented to demonstrate the broad utility of this panel of SNP markers in this species. As Pacific lamprey populations are undergoing rapid decline, these SNPs provide an important resource to address critical uncertainties associated with the conservation and recovery of this imperiled species.
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Affiliation(s)
- Jon E Hess
- Columbia River Inter-Tribal Fish Commission, 3059-F National Fish Hatchery Rd, Hagerman, ID, 83332, USA
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Serbezov D, Jorde PE, Bernatchez L, Olsen EM, Vøllestad LA. Life history and demographic determinants of effective/census size ratios as exemplified by brown trout (Salmo trutta). Evol Appl 2012; 5:607-18. [PMID: 23028401 PMCID: PMC3461143 DOI: 10.1111/j.1752-4571.2012.00239.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Accepted: 12/19/2011] [Indexed: 11/30/2022] Open
Abstract
A number of demographic factors, many of which related to human-driven encroachments, are predicted to decrease the effective population size (N(e)) relative to the census population size (N), but these have been little investigated. Yet, it is necessary to know which factors most strongly impact N(e), and how to mitigate these effects through sound management actions. In this study, we use parentage analysis of a stream-living brown trout (Salmo trutta) population to quantify the effect of between-individual variance in reproductive success on the effective number of breeders (N(b)) relative to the census number of breeders (N(i)). Comprehensive estimates of the N(b)/N ratio were reduced to 0.16-0.28, almost entirely due to larger than binomial variance in family size. We used computer simulations, based on empirical estimates of age-specific survival and fecundity rates, to assess the effect of repeat spawning (iteroparity) on N(e) and found that the variance in lifetime reproductive success was substantially higher for repeat spawners. Random family-specific survival, on the other hand, acts to buffer these effects. We discuss the implications of these findings for the management of small populations, where maintaining high and stable levels of N(e) is crucial to extenuate inbreeding and protect genetic variability.
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Affiliation(s)
- Dimitar Serbezov
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biology, University of OsloBlindern, Oslo, Norway
| | - Per Erik Jorde
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biology, University of OsloBlindern, Oslo, Norway
- Institute of Marine ResearchFlødevigen, Norway
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène Marchand, Université LavalQuébec, QC, Canada
| | - Esben Moland Olsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biology, University of OsloBlindern, Oslo, Norway
- Institute of Marine ResearchFlødevigen, Norway
| | - Leif Asbjørn Vøllestad
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biology, University of OsloBlindern, Oslo, Norway
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