1
|
Schneemann H, De Sanctis B, Welch JJ. Fisher's Geometric Model as a Tool to Study Speciation. Cold Spring Harb Perspect Biol 2024; 16:a041442. [PMID: 38253415 PMCID: PMC11216183 DOI: 10.1101/cshperspect.a041442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Interactions between alleles and across environments play an important role in the fitness of hybrids and are at the heart of the speciation process. Fitness landscapes capture these interactions and can be used to model hybrid fitness, helping us to interpret empirical observations and clarify verbal models. Here, we review recent progress in understanding hybridization outcomes through Fisher's geometric model, an intuitive and analytically tractable fitness landscape that captures many fitness patterns observed across taxa. We use case studies to show how the model parameters can be estimated from different types of data and discuss how these estimates can be used to make inferences about the divergence history and genetic architecture. We also highlight some areas where the model's predictions differ from alternative incompatibility-based models, such as the snowball effect and outlier patterns in genome scans.
Collapse
Affiliation(s)
- Hilde Schneemann
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Bianca De Sanctis
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom
| | - John J Welch
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| |
Collapse
|
2
|
Terasaki Hart DE, Wang IJ. Genomic architecture controls multivariate adaptation to climate change. GLOBAL CHANGE BIOLOGY 2024; 30:e17179. [PMID: 38403891 DOI: 10.1111/gcb.17179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 12/11/2023] [Accepted: 01/12/2024] [Indexed: 02/27/2024]
Abstract
As climate change advances, environmental gradients may decouple, generating novel multivariate environments that stress wild populations. A commonly invoked mechanism of evolutionary rescue is adaptive gene flow tracking climate shifts, but gene flow from populations inhabiting similar conditions on one environmental axis could cause maladaptive introgression when populations are adapted to different environmental variables that do not shift together. Genomic architecture can play an important role in determining the effectiveness and relative magnitudes of adaptive gene flow and in situ adaptation. This may have direct consequences for how species respond to climate change but is often overlooked. Here, we simulated microevolutionary responses to environmental change under scenarios defined by variation in the polygenicity, linkage, and genetic redundancy of two independent traits, one of which is adapted to a gradient that shifts under climate change. We used these simulations to examine how genomic architecture influences evolutionary outcomes under climate change. We found that climate-tracking (up-gradient) gene flow, though present in all scenarios, was strongly constrained under scenarios of lower linkage and higher polygenicity and redundancy, suggesting in situ adaptation as the predominant mechanism of evolutionary rescue under these conditions. We also found that high polygenicity caused increased maladaptation and demographic decline, a concerning result given that many climate-adapted traits may be polygenic. Finally, in scenarios with high redundancy, we observed increased adaptive capacity. This finding adds to the growing recognition of the importance of redundancy in mediating in situ adaptive capacity and suggests opportunities for better understanding the climatic vulnerability of real populations.
Collapse
Affiliation(s)
- Drew E Terasaki Hart
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, California, USA
- The Nature Conservancy, Arlington, Virginia, USA
- CSIRO Environment, Brisbane, Queensland, Australia
| | - Ian J Wang
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, California, USA
| |
Collapse
|
3
|
Langdon QK, Powell DL, Kim B, Banerjee SM, Payne C, Dodge TO, Moran B, Fascinetto-Zago P, Schumer M. Predictability and parallelism in the contemporary evolution of hybrid genomes. PLoS Genet 2022; 18:e1009914. [PMID: 35085234 PMCID: PMC8794199 DOI: 10.1371/journal.pgen.1009914] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 10/28/2021] [Indexed: 12/28/2022] Open
Abstract
Hybridization between species is widespread across the tree of life. As a result, many species, including our own, harbor regions of their genome derived from hybridization. Despite the recognition that this process is widespread, we understand little about how the genome stabilizes following hybridization, and whether the mechanisms driving this stabilization tend to be shared across species. Here, we dissect the drivers of variation in local ancestry across the genome in replicated hybridization events between two species pairs of swordtail fish: Xiphophorus birchmanni × X. cortezi and X. birchmanni × X. malinche. We find unexpectedly high levels of repeatability in local ancestry across the two types of hybrid populations. This repeatability is attributable in part to the fact that the recombination landscape and locations of functionally important elements play a major role in driving variation in local ancestry in both types of hybrid populations. Beyond these broad scale patterns, we identify dozens of regions of the genome where minor parent ancestry is unusually low or high across species pairs. Analysis of these regions points to shared sites under selection across species pairs, and in some cases, shared mechanisms of selection. We show that one such region is a previously unknown hybrid incompatibility that is shared across X. birchmanni × X. cortezi and X. birchmanni × X. malinche hybrid populations.
Collapse
Affiliation(s)
- Quinn K. Langdon
- Department of Biology, Stanford University, Stanford, California, United States of America
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C., Calnali, Mexico
| | - Daniel L. Powell
- Department of Biology, Stanford University, Stanford, California, United States of America
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C., Calnali, Mexico
| | - Bernard Kim
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Shreya M. Banerjee
- Department of Biology, Stanford University, Stanford, California, United States of America
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C., Calnali, Mexico
| | - Cheyenne Payne
- Department of Biology, Stanford University, Stanford, California, United States of America
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C., Calnali, Mexico
| | - Tristram O. Dodge
- Department of Biology, Stanford University, Stanford, California, United States of America
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C., Calnali, Mexico
| | - Ben Moran
- Department of Biology, Stanford University, Stanford, California, United States of America
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C., Calnali, Mexico
| | - Paola Fascinetto-Zago
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C., Calnali, Mexico
- Department of Biology, Texas A&M University, College Station, Texas, United States of America
| | - Molly Schumer
- Department of Biology, Stanford University, Stanford, California, United States of America
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C., Calnali, Mexico
- Hanna H. Gray Fellow, Howard Hughes Medical Institutes, Chevy Chase, Maryland, United States of America
| |
Collapse
|
4
|
Thompson KA, Peichel CL, Rennison DJ, McGee MD, Albert AYK, Vines TH, Greenwood AK, Wark AR, Brandvain Y, Schumer M, Schluter D. Analysis of ancestry heterozygosity suggests that hybrid incompatibilities in threespine stickleback are environment dependent. PLoS Biol 2022; 20:e3001469. [PMID: 35007278 PMCID: PMC8746713 DOI: 10.1371/journal.pbio.3001469] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 11/04/2021] [Indexed: 12/25/2022] Open
Abstract
Hybrid incompatibilities occur when interactions between opposite ancestry alleles at different loci reduce the fitness of hybrids. Most work on incompatibilities has focused on those that are "intrinsic," meaning they affect viability and sterility in the laboratory. Theory predicts that ecological selection can also underlie hybrid incompatibilities, but tests of this hypothesis using sequence data are scarce. In this article, we compiled genetic data for F2 hybrid crosses between divergent populations of threespine stickleback fish (Gasterosteus aculeatus L.) that were born and raised in either the field (seminatural experimental ponds) or the laboratory (aquaria). Because selection against incompatibilities results in elevated ancestry heterozygosity, we tested the prediction that ancestry heterozygosity will be higher in pond-raised fish compared to those raised in aquaria. We found that ancestry heterozygosity was elevated by approximately 3% in crosses raised in ponds compared to those raised in aquaria. Additional analyses support a phenotypic basis for incompatibility and suggest that environment-specific single-locus heterozygote advantage is not the cause of selection on ancestry heterozygosity. Our study provides evidence that, in stickleback, a coarse-albeit indirect-signal of environment-dependent hybrid incompatibility is reliably detectable and suggests that extrinsic incompatibilities can evolve before intrinsic incompatibilities.
Collapse
Affiliation(s)
- Ken A. Thompson
- Department of Zoology & Biodiversity Research Centre, University of British Columbia, Canada
| | - Catherine L. Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Diana J. Rennison
- Division of Biological Sciences, University of California San Diego, San Diego, California, United States of America
| | - Matthew D. McGee
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | | | - Timothy H. Vines
- DataSeer Research Data Services, Vancouver, British Columbia, Canada
| | | | - Abigail R. Wark
- Harvard Medical School, Cambridge, Massachusetts, United States of America
| | - Yaniv Brandvain
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Molly Schumer
- Department of Biology, Stanford University, Stanford, California, United States of America
- Howard Hughes Medical Institute, Maryland, United States of America
| | - Dolph Schluter
- Department of Zoology & Biodiversity Research Centre, University of British Columbia, Canada
| |
Collapse
|
5
|
Moran BM, Payne C, Langdon Q, Powell DL, Brandvain Y, Schumer M. The genomic consequences of hybridization. eLife 2021; 10:e69016. [PMID: 34346866 PMCID: PMC8337078 DOI: 10.7554/elife.69016] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 07/09/2021] [Indexed: 12/29/2022] Open
Abstract
In the past decade, advances in genome sequencing have allowed researchers to uncover the history of hybridization in diverse groups of species, including our own. Although the field has made impressive progress in documenting the extent of natural hybridization, both historical and recent, there are still many unanswered questions about its genetic and evolutionary consequences. Recent work has suggested that the outcomes of hybridization in the genome may be in part predictable, but many open questions about the nature of selection on hybrids and the biological variables that shape such selection have hampered progress in this area. We synthesize what is known about the mechanisms that drive changes in ancestry in the genome after hybridization, highlight major unresolved questions, and discuss their implications for the predictability of genome evolution after hybridization.
Collapse
Affiliation(s)
- Benjamin M Moran
- Department of Biology, Stanford UniversityStanfordUnited States
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”HidalgoMexico
| | - Cheyenne Payne
- Department of Biology, Stanford UniversityStanfordUnited States
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”HidalgoMexico
| | - Quinn Langdon
- Department of Biology, Stanford UniversityStanfordUnited States
| | - Daniel L Powell
- Department of Biology, Stanford UniversityStanfordUnited States
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”HidalgoMexico
| | - Yaniv Brandvain
- Department of Ecology, Evolution & Behavior and Plant and Microbial Biology, University of MinnesotaMinneapolisUnited States
| | - Molly Schumer
- Department of Biology, Stanford UniversityStanfordUnited States
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”HidalgoMexico
- Hanna H. Gray Fellow, Howard Hughes Medical InstituteStanfordUnited States
| |
Collapse
|
6
|
Brice C, Zhang Z, Bendixsen D, Stelkens R. Hybridization Outcomes Have Strong Genomic and Environmental Contingencies. Am Nat 2021; 198:E53-E67. [PMID: 34403309 DOI: 10.1086/715356] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractExtreme F2 phenotypes known as transgressive segregants can cause increased or decreased fitness in hybrids beyond the ranges seen in parental populations. Despite the usefulness of transgression for plant and animal breeding and its potential role in hybrid speciation, the genetic mechanisms and predictors of transgressive segregation remain largely untested. We generated seven hybrid crosses between five widely divergent Saccharomyces yeast species and measured the fitness of the parents and their viable F1 and F2 hybrids in seven stressful environments. We found that on average 16.6% of all replicate F2 hybrids had higher fitness than both parents. Against our predictions, transgression frequency was not a function of parental genetic and phenotypic distances across test environments. Within environments, some relationships were significant, but not in the predicted direction; for example, genetic distance was negatively related to transgression in ethanol and hydrogen peroxide. Significant effects of hybrid cross, test environment, and cross × environment interactions suggest that the amount of transgression produced in a hybrid cross is highly context specific and that outcomes of hybridization differ even among crosses made from the same two parents. If the goal is to reliably predict hybrid fitness and forecast the evolutionary potential of admixed populations, we need more efforts to identify patterns beyond the idiosyncrasies caused by specific genomic or environmental contexts.
Collapse
|
7
|
Thompson KA, Urquhart-Cronish M, Whitney KD, Rieseberg LH, Schluter D. Patterns, Predictors, and Consequences of Dominance in Hybrids. Am Nat 2021; 197:E72-E88. [PMID: 33625966 DOI: 10.1086/712603] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractCompared to those of their parents, are the traits of first-generation (F1) hybrids typically intermediate, biased toward one parent, or mismatched for alternative parental phenotypes? To address this empirical gap, we compiled data from 233 crosses in which traits were measured in a common environment for two parent taxa and their F1 hybrids. We find that individual traits in F1s are halfway between the parental midpoint and one parental value. Considering pairs of traits together, a hybrid's bivariate phenotype tends to resemble one parent (parent bias) about 50% more than the other, while also exhibiting a similar magnitude of mismatch due to different traits having dominance in conflicting directions. Using data from an experimental field planting of recombinant hybrid sunflowers, we illustrate that parent bias improves fitness, whereas mismatch reduces fitness. Our study has three major conclusions. First, hybrids are not phenotypically intermediate but rather exhibit substantial mismatch. Second, dominance is likely determined by the idiosyncratic evolutionary trajectories of individual traits and populations. Finally, selection against hybrids likely results from selection against both intermediate and mismatched phenotypes.
Collapse
|