1
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St John ME, Dunker JC, Richards EJ, Romero S, Martin CH. Parallel evolution of integrated craniofacial traits in trophic specialist pupfishes. Ecol Evol 2024; 14:e11640. [PMID: 38979003 PMCID: PMC11228360 DOI: 10.1002/ece3.11640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 05/14/2024] [Accepted: 06/13/2024] [Indexed: 07/10/2024] Open
Abstract
Populations may adapt to similar environments via parallel or non-parallel genetic changes, but the frequency of these alternative mechanisms and underlying contributing factors are still poorly understood outside model systems. We used QTL mapping to investigate the genetic basis of highly divergent craniofacial traits between the scale-eater (Cyprinodon desquamator) and molluscivore (C. brontotheroides) pupfish adapting to two different hypersaline lake environments on San Salvador Island, Bahamas. We lab-reared F2 scale-eater x molluscivore intercrosses from two different lake populations, estimated linkage maps, scanned for significant QTL for 29 skeletal and craniofacial traits, female mate preference, and sex. We compared the location of QTL between lakes to quantify parallel and non-parallel genetic changes. We detected significant QTL for six craniofacial traits in at least one lake. However, nearly all shared QTL loci were associated with a different craniofacial trait within each lake. Therefore, our estimate of parallel evolution of craniofacial genetic architecture could range from one out of six identical trait QTL (low parallelism) to five out of six integrated trait QTL (high parallelism). We suggest that pleiotropy and trait integration can affect estimates of parallel evolution, particularly within rapid radiations. We also observed increased adaptive introgression in shared QTL regions, suggesting that gene flow contributed to parallel evolution. Overall, our results suggest that the same genomic regions may contribute to parallel adaptation across integrated suites of craniofacial traits, rather than specific traits, and highlight the need for a more expansive definition of parallel evolution.
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Affiliation(s)
| | - Julia C Dunker
- Department of Integrative Biology University of California Berkeley California USA
| | - Emilie J Richards
- Department of Ecology, Evolution and Behavior University of Minnesota Minneapolis Minnesota USA
| | - Stephanie Romero
- Department of Evolution and Ecology University of California Davis California USA
| | - Christopher H Martin
- Department of Integrative Biology University of California Berkeley California USA
- Museum of Vertebrate Zoology University of California Berkeley California USA
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2
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Runemark A, Moore EC, Larson EL. Hybridization and gene expression: Beyond differentially expressed genes. Mol Ecol 2024:e17303. [PMID: 38411307 DOI: 10.1111/mec.17303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 02/06/2024] [Accepted: 02/15/2024] [Indexed: 02/28/2024]
Abstract
Gene expression has a key role in reproductive isolation, and studies of hybrid gene expression have identified mechanisms causing hybrid sterility. Here, we review the evidence for altered gene expression following hybridization and outline the mechanisms shown to contribute to altered gene expression in hybrids. Transgressive gene expression, transcending that of both parental species, is pervasive in early generation sterile hybrids, but also frequently observed in viable, fertile hybrids. We highlight studies showing that hybridization can result in transgressive gene expression, also in established hybrid lineages or species. Such extreme patterns of gene expression in stabilized hybrid taxa suggest that altered hybrid gene expression may result in hybridization-derived evolutionary novelty. We also conclude that while patterns of misexpression in hybrids are well documented, the understanding of the mechanisms causing misexpression is lagging. We argue that jointly assessing differences in cell composition and cell-specific changes in gene expression in hybrids, in addition to assessing changes in chromatin and methylation, will significantly advance our understanding of the basis of altered gene expression. Moreover, uncovering to what extent evolution of gene expression results in altered expression for individual genes, or entire networks of genes, will advance our understanding of how selection moulds gene expression. Finally, we argue that jointly studying the dual roles of altered hybrid gene expression, serving both as a mechanism for reproductive isolation and as a substrate for hybrid ecological adaptation, will lead to significant advances in our understanding of the evolution of gene expression.
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Affiliation(s)
- Anna Runemark
- Department of Biology, Lund University, Lund, Sweden
| | - Emily C Moore
- Department of Biological Sciences, University of Denver, Denver, Colorado, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Erica L Larson
- Department of Biological Sciences, University of Denver, Denver, Colorado, USA
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3
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Kautt AF, Chen J, Lewarch CL, Hu C, Turner K, Lassance JM, Baier F, Bedford NL, Bendesky A, Hoekstra HE. Evolution of gene expression across brain regions in behaviourally divergent deer mice. Mol Ecol 2024:e17270. [PMID: 38263608 DOI: 10.1111/mec.17270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 01/03/2024] [Accepted: 01/08/2024] [Indexed: 01/25/2024]
Abstract
The evolution of innate behaviours is ultimately due to genetic variation likely acting in the nervous system. Gene regulation may be particularly important because it can evolve in a modular brain-region specific fashion through the concerted action of cis- and trans-regulatory changes. Here, to investigate transcriptional variation and its regulatory basis across the brain, we perform RNA sequencing (RNA-Seq) on ten brain subregions in two sister species of deer mice (Peromyscus maniculatus and P. polionotus)-which differ in a range of innate behaviours, including their social system-and their F1 hybrids. We find that most of the variation in gene expression distinguishes subregions, followed by species. Interspecific differential expression (DE) is pervasive (52-59% of expressed genes), whereas the number of DE genes between sexes is modest overall (~3%). Interestingly, the identity of DE genes varies considerably across brain regions. Much of this modularity is due to cis-regulatory divergence, and while 43% of genes were consistently assigned to the same gene regulatory class across subregions (e.g. conserved, cis- or trans-regulatory divergence), a similar number were assigned to two or more different gene regulatory classes. Together, these results highlight the modularity of gene expression differences and divergence in the brain, which may be key to explain how the evolution of brain gene expression can contribute to the astonishing diversity of animal behaviours.
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Affiliation(s)
- Andreas F Kautt
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Center for Brain Science, Harvard University, Cambridge, Massachusetts, USA
| | - Jenny Chen
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Center for Brain Science, Harvard University, Cambridge, Massachusetts, USA
| | - Caitlin L Lewarch
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Center for Brain Science, Harvard University, Cambridge, Massachusetts, USA
| | - Caroline Hu
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Center for Brain Science, Harvard University, Cambridge, Massachusetts, USA
| | - Kyle Turner
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Center for Brain Science, Harvard University, Cambridge, Massachusetts, USA
| | - Jean-Marc Lassance
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Center for Brain Science, Harvard University, Cambridge, Massachusetts, USA
| | - Felix Baier
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Center for Brain Science, Harvard University, Cambridge, Massachusetts, USA
| | - Nicole L Bedford
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Center for Brain Science, Harvard University, Cambridge, Massachusetts, USA
| | - Andres Bendesky
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Center for Brain Science, Harvard University, Cambridge, Massachusetts, USA
| | - Hopi E Hoekstra
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Center for Brain Science, Harvard University, Cambridge, Massachusetts, USA
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4
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Palominos MF, Muhl V, Richards EJ, Miller CT, Martin CH. Jaw size variation is associated with a novel craniofacial function for galanin receptor 2 in an adaptive radiation of pupfishes. Proc Biol Sci 2023; 290:20231686. [PMID: 37876194 PMCID: PMC10598438 DOI: 10.1098/rspb.2023.1686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/02/2023] [Indexed: 10/26/2023] Open
Abstract
Understanding the genetic basis of novel adaptations in new species is a fundamental question in biology. Here we demonstrate a new role for galr2 in vertebrate craniofacial development using an adaptive radiation of trophic specialist pupfishes endemic to San Salvador Island, Bahamas. We confirmed the loss of a putative Sry transcription factor binding site upstream of galr2 in scale-eating pupfish and found significant spatial differences in galr2 expression among pupfish species in Meckel's cartilage using in situ hybridization chain reaction (HCR). We then experimentally demonstrated a novel role for Galr2 in craniofacial development by exposing embryos to Garl2-inhibiting drugs. Galr2-inhibition reduced Meckel's cartilage length and increased chondrocyte density in both trophic specialists but not in the generalist genetic background. We propose a mechanism for jaw elongation in scale-eaters based on the reduced expression of galr2 due to the loss of a putative Sry binding site. Fewer Galr2 receptors in the scale-eater Meckel's cartilage may result in their enlarged jaw lengths as adults by limiting opportunities for a circulating Galr2 agonist to bind to these receptors during development. Our findings illustrate the growing utility of linking candidate adaptive SNPs in non-model systems with highly divergent phenotypes to novel vertebrate gene functions.
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Affiliation(s)
- M. Fernanda Palominos
- Department of Integrative Biology, University of California, 3101 Valley Life Sciences Building, Berkeley, CA 94720, USA
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
| | - Vanessa Muhl
- Department of Integrative Biology, University of California, 3101 Valley Life Sciences Building, Berkeley, CA 94720, USA
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
| | - Emilie J. Richards
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN, USA
| | - Craig T. Miller
- Department of Molecular & Cell Biology, University of California, Berkeley, CA, USA
| | - Christopher H. Martin
- Department of Integrative Biology, University of California, 3101 Valley Life Sciences Building, Berkeley, CA 94720, USA
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
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5
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Horta-Lacueva QJB, Jónsson ZO, Thorholludottir DAV, Hallgrímsson B, Kapralova KH. Rapid and biased evolution of canalization during adaptive divergence revealed by dominance in gene expression variability during Arctic charr early development. Commun Biol 2023; 6:897. [PMID: 37652977 PMCID: PMC10471602 DOI: 10.1038/s42003-023-05264-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 08/21/2023] [Indexed: 09/02/2023] Open
Abstract
Adaptive evolution may be influenced by canalization, the buffering of developmental processes from environmental and genetic perturbations, but how this occurs is poorly understood. Here, we explore how gene expression variability evolves in diverging and hybridizing populations, by focusing on the Arctic charr (Salvelinus alpinus) of Thingvallavatn, a classic case of divergence between feeding habitats. We report distinct profiles of gene expression variance for both coding RNAs and microRNAs between the offspring of two contrasting morphs (benthic/limnetic) and their hybrids reared in common conditions and sampled at two key points of cranial development. Gene expression variance in the hybrids is substantially affected by maternal effects, and many genes show biased expression variance toward the limnetic morph. This suggests that canalization, as inferred by gene expression variance, can rapidly diverge in sympatry through multiple gene pathways, which are associated with dominance patterns possibly biasing evolutionary trajectories and mitigating the effects of hybridization on adaptive evolution.
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Affiliation(s)
- Quentin Jean-Baptiste Horta-Lacueva
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland.
- Department of Biology, Lund University, Lund, Sweden.
| | | | - Dagny A V Thorholludottir
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
- University of Veterinary Medicine Vienna, Institute of Population Genetics, Vienna, Austria
| | - Benedikt Hallgrímsson
- Department of Cell Biology and Anatomy, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - Kalina Hristova Kapralova
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland.
- The Institute for Experimental Pathology at Keldur, University of Iceland, Reykjavík, Iceland.
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6
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Berbel-Filho WM, Pacheco G, Lira MG, Garcia de Leaniz C, Lima SMQ, Rodríguez-López CM, Zhou J, Consuegra S. Additive and non-additive epigenetic signatures of natural hybridisation between fish species with different mating systems. Epigenetics 2022; 17:2356-2365. [PMID: 36082413 PMCID: PMC9665120 DOI: 10.1080/15592294.2022.2123014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Hybridization is a major source of evolutionary innovation. In plants, epigenetic mechanisms can help to stabilize hybrid genomes and contribute to reproductive isolation, but the relationship between genetic and epigenetic changes in animal hybrids is unclear. We analysed the relationship between genetic background and methylation patterns in natural hybrids of two genetically divergent fish species with different mating systems, Kryptolebias hermaphroditus (self-fertilizing) and K. ocellatus (outcrossing). Co-existing parental species displayed highly distinct genetic (SNPs) and methylation patterns (37,000 differentially methylated cytosines). Hybrids had predominantly intermediate methylation patterns (88.5% of the sites) suggesting additive effects, as expected from hybridization between genetically distant species. The large number of differentially methylated cytosines between hybrids and parental species (n = 5,800) suggests that hybridization may play a role in increasing genetic and epigenetic variation. Although most of the observed epigenetic variation was additive and had a strong genetic component, we also found a small percentage of non-additive, potentially stochastic, methylation differences that might act as an evolutionary bet-hedging strategy and increase fitness under environmental instability.
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Affiliation(s)
- Waldir M Berbel-Filho
- Centre for Sustainable Aquatic Research, Department of Biosciences, College of Science, Swansea University, Swansea, UK
| | - George Pacheco
- Section for Evolutionary Genomics, The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Mateus G Lira
- Laboratório de Ictiologia Sistemática e Evolutiva, Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande, Natal, Brazil
| | - Carlos Garcia de Leaniz
- Centre for Sustainable Aquatic Research, Department of Biosciences, College of Science, Swansea University, Swansea, UK
| | - Sergio M Q Lima
- Laboratório de Ictiologia Sistemática e Evolutiva, Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande, Natal, Brazil
| | - Carlos M Rodríguez-López
- Environmental Epigenetics and Genetics Group, Department of Horticulture, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, USA
| | - Jia Zhou
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Sofia Consuegra
- Centre for Sustainable Aquatic Research, Department of Biosciences, College of Science, Swansea University, Swansea, UK
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7
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Payne C, Bovio R, Powell DL, Gunn TR, Banerjee SM, Grant V, Rosenthal GG, Schumer M. Genomic insights into variation in thermotolerance between hybridizing swordtail fishes. Mol Ecol 2022. [PMID: 35510780 DOI: 10.1111/mec.16489] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 02/22/2022] [Accepted: 04/19/2022] [Indexed: 11/30/2022]
Abstract
Understanding how organisms adapt to changing environments is a core focus of research in evolutionary biology. One common mechanism is adaptive introgression, which has received increasing attention as a potential route to rapid adaptation in populations struggling in the face of ecological change, particularly global climate change. However, hybridization can also result in deleterious genetic interactions that may limit the benefits of adaptive introgression. Here, we used a combination of genome-wide quantitative trait locus mapping and differential gene expression analyses between the swordtail fish species Xiphophorus malinche and X. birchmanni to study the consequences of hybridization on thermotolerance. While these two species are adapted to different thermal environments, we document a complicated architecture of thermotolerance in hybrids. We identify a region of the genome that contributes to reduced thermotolerance in individuals heterozygous for X. malinche and X. birchmanni ancestry, as well as widespread misexpression in hybrids of genes that respond to thermal stress in the parental species, particularly in the circadian clock pathway. We also show that a previously mapped hybrid incompatibility between X. malinche and X. birchmanni contributes to reduced thermotolerance in hybrids. Together, our results highlight the challenges of understanding the impact of hybridization on complex ecological traits and its potential impact on adaptive introgression.
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Affiliation(s)
- Cheyenne Payne
- Department of Biology, Stanford University, Stanford, California, USA
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, México
| | - Richard Bovio
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, México
- Department of Biology, Texas A&M University, College Station, Texas, USA
| | - Daniel L Powell
- Department of Biology, Stanford University, Stanford, California, USA
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, México
| | - Theresa R Gunn
- Department of Biology, Stanford University, Stanford, California, USA
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, México
| | - Shreya M Banerjee
- Department of Biology, Stanford University, Stanford, California, USA
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, México
| | - Victoria Grant
- Department of Biology, Stanford University, Stanford, California, USA
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, México
| | - Gil G Rosenthal
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, México
- Department of Biology, Texas A&M University, College Station, Texas, USA
- Department of Biology, University of Padua, Italy
| | - Molly Schumer
- Department of Biology, Stanford University, Stanford, California, USA
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", A.C., Calnali, Hidalgo, México
- Department of Biology, University of Padua, Italy
- Hanna H. Gray Fellow, Howard Hughes Medical Institute, Stanford, California, USA
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8
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Horta-Lacueva QJB, Snorrason SS, Morrissey MB, Leblanc CAL, Kapralova KH. Multivariate analysis of morphology, behaviour, growth and developmental timing in hybrids brings new insights into the divergence of sympatric Arctic charr morphs. BMC Ecol Evol 2021; 21:170. [PMID: 34493202 PMCID: PMC8422654 DOI: 10.1186/s12862-021-01904-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/18/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Studying the development of fitness related traits in hybrids from populations diverging in sympatry is a fundamental approach to understand the processes of speciation. However, such traits are often affected by covariance structures that complicate the comprehension of these processes, especially because the interactive relationships between traits of different nature (e.g. morphology, behaviour, life-history) remain largely unknown in this context. In a common garden setup, we conducted an extensive examination of a large suit of traits putatively involved in the divergence of two morphs of Arctic charr (Salvelinus alpinus), and investigated the consequences of potential patterns of trait covariance on the phenotype of their hybrids. These traits were measured along ontogeny and involved growth, yolk sac resorption, developmental timing (hatching and the onset of exogeneous feeding), head morphology and feeding behaviour. RESULTS Growth trajectories provided the strongest signal of phenotypic divergence between the two charr. Strikingly, the first-generation hybrids did not show intermediate nor delayed growth but were similar to the smallest morph, suggesting parental biases in the inheritance of growth patterns. However, we did not observe extensive multivariate trait differences between the two morphs and their hybrids. Growth was linked to head morphology (suggesting that morphological variations in early juveniles relate to simple allometric effects) but this was the only strong signal of covariance observed between all the measured traits. Furthermore, we did not report evidence for differences in overall phenotypic variance between morphs, nor for enhanced phenotypic variability in their hybrids. CONCLUSION Our study shed light on the multivariate aspect of development in a context of adaptive divergence. The lack of evidence for the integration of most traits into a single covariance structure suggested that phenotypic constraints may not always favour nor impede divergence toward ecological niches differing in numerous physical and ecological variables, as observed in the respective habitats of the two charr. Likewise, the role of hybridization as a disruptive agent of trait covariance may not necessarily be significant in the evolution of populations undergoing resource polymorphism.
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Affiliation(s)
- Quentin J-B Horta-Lacueva
- Institute of Life and Environmental Sciences, University of Iceland, Askja - Náttúrufræðihús, Sturlugötu 7, 102, Reykjavík, Iceland.
| | - Sigurður S Snorrason
- Institute of Life and Environmental Sciences, University of Iceland, Askja - Náttúrufræðihús, Sturlugötu 7, 102, Reykjavík, Iceland
| | - Michael B Morrissey
- School of Biology, University of St Andrews, Sir Harold Mitchell Building, Greenside Place, St Andrews, UK
| | - Camille A-L Leblanc
- Department of Aquaculture and Fish Biology, Hólar University, Háeyri 1, 550, Sauðárkrókur, Iceland
| | - Kalina H Kapralova
- Institute of Life and Environmental Sciences, University of Iceland, Askja - Náttúrufræðihús, Sturlugötu 7, 102, Reykjavík, Iceland
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9
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Oppenheimer J, Rosen BD, Heaton MP, Vander Ley BL, Shafer WR, Schuetze FT, Stroud B, Kuehn LA, McClure JC, Barfield JP, Blackburn HD, Kalbfleisch TS, Bickhart DM, Davenport KM, Kuhn KL, Green RE, Shapiro B, Smith TPL. A Reference Genome Assembly of American Bison, Bison bison bison. J Hered 2021; 112:174-183. [PMID: 33595645 PMCID: PMC8006816 DOI: 10.1093/jhered/esab003] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 01/13/2021] [Indexed: 11/14/2022] Open
Abstract
Bison are an icon of the American West and an ecologically, commercially, and culturally important species. Despite numbering in the hundreds of thousands today, conservation concerns remain for the species, including the impact on genetic diversity of a severe bottleneck around the turn of the 20th century and genetic introgression from domestic cattle. Genetic diversity and admixture are best evaluated at genome-wide scale, for which a high-quality reference is necessary. Here, we use trio binning of long reads from a bison-Simmental cattle (Bos taurus taurus) male F1 hybrid to sequence and assemble the genome of the American plains bison (Bison bison bison). The male haplotype genome is chromosome-scale, with a total length of 2.65 Gb across 775 scaffolds (839 contigs) and a scaffold N50 of 87.8 Mb. Our bison genome is ~13× more contiguous overall and ~3400× more contiguous at the contig level than the current bison reference genome. The bison genome sequence presented here (ARS-UCSC_bison1.0) will enable new research into the evolutionary history of this iconic megafauna species and provide a new tool for the management of bison populations in federal and commercial herds.
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Affiliation(s)
- Jonas Oppenheimer
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Benjamin D Rosen
- USDA, ARS, Animal Genomics and Improvement Laboratory, Beltsville, MD, USA
| | - Michael P Heaton
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, USA
| | - Brian L Vander Ley
- Great Plains Veterinary Educational Center, University of Nebraska-Lincoln, Lincoln, NE, USA
| | | | | | - Brad Stroud
- Stroud Veterinary Embryo Services, Weatherford, TE, USA
| | - Larry A Kuehn
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, USA
| | | | - Jennifer P Barfield
- College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | | | | | | | - Kimberly M Davenport
- Department of Animal, Veterinary, and Food Science, University of Idaho, Moscow, ID, USA
| | - Kristen L Kuhn
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, USA
| | - Richard E Green
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA.,Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA
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10
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Swamy KBS, Schuyler SC, Leu JY. Protein Complexes Form a Basis for Complex Hybrid Incompatibility. Front Genet 2021; 12:609766. [PMID: 33633780 PMCID: PMC7900514 DOI: 10.3389/fgene.2021.609766] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 01/20/2021] [Indexed: 12/20/2022] Open
Abstract
Proteins are the workhorses of the cell and execute many of their functions by interacting with other proteins forming protein complexes. Multi-protein complexes are an admixture of subunits, change their interaction partners, and modulate their functions and cellular physiology in response to environmental changes. When two species mate, the hybrid offspring are usually inviable or sterile because of large-scale differences in the genetic makeup between the two parents causing incompatible genetic interactions. Such reciprocal-sign epistasis between inter-specific alleles is not limited to incompatible interactions between just one gene pair; and, usually involves multiple genes. Many of these multi-locus incompatibilities show visible defects, only in the presence of all the interactions, making it hard to characterize. Understanding the dynamics of protein-protein interactions (PPIs) leading to multi-protein complexes is better suited to characterize multi-locus incompatibilities, compared to studying them with traditional approaches of genetics and molecular biology. The advances in omics technologies, which includes genomics, transcriptomics, and proteomics can help achieve this end. This is especially relevant when studying non-model organisms. Here, we discuss the recent progress in the understanding of hybrid genetic incompatibility; omics technologies, and how together they have helped in characterizing protein complexes and in turn multi-locus incompatibilities. We also review advances in bioinformatic techniques suitable for this purpose and propose directions for leveraging the knowledge gained from model-organisms to identify genetic incompatibilities in non-model organisms.
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Affiliation(s)
- Krishna B. S. Swamy
- Division of Biological and Life Sciences, School of Arts and Sciences, Ahmedabad University, Ahmedabad, India
| | - Scott C. Schuyler
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Division of Head and Neck Surgery, Department of Otolaryngology, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Jun-Yi Leu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
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11
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Martin CH, Gould KJ. Surprising spatiotemporal stability of a multi-peak fitness landscape revealed by independent field experiments measuring hybrid fitness. Evol Lett 2020; 4:530-544. [PMID: 33312688 PMCID: PMC7719547 DOI: 10.1002/evl3.195] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 07/23/2020] [Accepted: 09/14/2020] [Indexed: 12/14/2022] Open
Abstract
The effect of the environment on fitness in natural populations is a fundamental question in evolutionary biology. However, experimental manipulations of both environment and phenotype at the same time are rare. Thus, the relative importance of the competitive environment versus intrinsic organismal performance in shaping the location, height, and fluidity of fitness peaks and valleys remains largely unknown. Here, we experimentally tested the effect of competitor frequency on the complex fitness landscape driving adaptive radiation of a generalist and two trophic specialist pupfishes, a scale-eater and molluscivore, endemic to hypersaline lakes on San Salvador Island (SSI), Bahamas. We manipulated phenotypes, by generating 3407 F4/F5 lab-reared hybrids, and competitive environment, by altering the frequency of rare transgressive hybrids between field enclosures in two independent lake populations. We then tracked hybrid survival and growth rates across these four field enclosures for 3-11 months. In contrast to competitive speciation theory, we found no evidence that the frequency of hybrid phenotypes affected their survival. Instead, we observed a strikingly similar fitness landscape to a previous independent field experiment, each supporting multiple fitness peaks for generalist and molluscivore phenotypes and a large fitness valley isolating the divergent scale-eater phenotype. These features of the fitness landscape were stable across manipulated competitive environments, multivariate trait axes, and spatiotemporal heterogeneity. We suggest that absolute performance constraints and divergent gene regulatory networks shape macroevolutionary (interspecific) fitness landscapes in addition to microevolutionary (intraspecific) competitive dynamics. This interplay between organism and environment underlies static and dynamic features of the adaptive landscape.
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Affiliation(s)
- Christopher H. Martin
- Department of Integrative BiologyUniversity of California, BerkeleyBerkeleyCalifornia94720
- Museum of Vertebrate ZoologyUniversity of California, BerkeleyBerkeleyCalifornia94720
| | - Katelyn J. Gould
- Department of BiologyUniversity of North Carolina at Chapel HillChapel HillNorth Carolina27515
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12
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Satokangas I, Martin SH, Helanterä H, Saramäki J, Kulmuni J. Multi-locus interactions and the build-up of reproductive isolation. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190543. [PMID: 32654649 PMCID: PMC7423273 DOI: 10.1098/rstb.2019.0543] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2020] [Indexed: 12/15/2022] Open
Abstract
All genes interact with other genes, and their additive effects and epistatic interactions affect an organism's phenotype and fitness. Recent theoretical and empirical work has advanced our understanding of the role of multi-locus interactions in speciation. However, relating different models to one another and to empirical observations is challenging. This review focuses on multi-locus interactions that lead to reproductive isolation (RI) through reduced hybrid fitness. We first review theoretical approaches and show how recent work incorporating a mechanistic understanding of multi-locus interactions recapitulates earlier models, but also makes novel predictions concerning the build-up of RI. These include high variance in the build-up rate of RI among taxa, the emergence of strong incompatibilities producing localized barriers to introgression, and an effect of population size on the build-up of RI. We then review recent experimental approaches to detect multi-locus interactions underlying RI using genomic data. We argue that future studies would benefit from overlapping methods like ancestry disequilibrium scans, genome scans of differentiation and analyses of hybrid gene expression. Finally, we highlight a need for further overlap between theoretical and empirical work, and approaches that predict what kind of patterns multi-locus interactions resulting in incompatibilities will leave in genome-wide polymorphism data. This article is part of the theme issue 'Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.
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Affiliation(s)
- I. Satokangas
- Organismal & Evolutionary Biology Research Programme, University of Helsinki, Viikinkaari 1, PO Box 65, 00014 Helsinki, Finland
| | - S. H. Martin
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh EH9 3FL, UK
| | - H. Helanterä
- Ecology and Genetics research unit, University of Oulu, PO Box 3000, 90014 Oulu, Finland
| | - J. Saramäki
- Department of Computer Science, Aalto University, PO Box 11000, 00076 Aalto, Espoo, Finland
| | - J. Kulmuni
- Organismal & Evolutionary Biology Research Programme, University of Helsinki, Viikinkaari 1, PO Box 65, 00014 Helsinki, Finland
- Tvärminne Zoological Station, University of Helsinki, J. A. Palménin tie 260, 10900 Hanko, Finland
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13
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McGirr JA, Martin CH. Ecological divergence in sympatry causes gene misexpression in hybrids. Mol Ecol 2020; 29:2707-2721. [PMID: 32557903 PMCID: PMC8209238 DOI: 10.1111/mec.15512] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 05/21/2020] [Accepted: 06/01/2020] [Indexed: 12/17/2022]
Abstract
Ecological speciation occurs when reproductive isolation evolves as a byproduct of adaptive divergence between populations. Selection favouring gene regulatory divergence between species could result in transgressive levels of gene expression in F1 hybrids that may lower hybrid fitness. We combined 58 resequenced genomes with 124 transcriptomes to identify patterns of hybrid gene misexpression that may be driven by adaptive regulatory divergence within a young radiation of Cyprinodon pupfishes, which consists of a dietary generalist and two trophic specialists-a molluscivore and a scale-eater. We found more differential gene expression between closely related sympatric specialists than between allopatric generalist populations separated by 1,000 km. Intriguingly, 9.6% of genes that were differentially expressed between sympatric species were also misexpressed in F1 hybrids. A subset of these genes were in highly differentiated genomic regions and enriched for functions important for trophic specialization, including head, muscle and brain development. These regions also included genes that showed evidence of hard selective sweeps and were significantly associated with oral jaw length-the most rapidly diversifying skeletal trait in this radiation. Our results indicate that divergent ecological selection in sympatry can contribute to hybrid gene misexpression which may act as a reproductive barrier between nascent species.
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Affiliation(s)
- Joseph A. McGirr
- Department of Biology, University of North Carolina, Chapel
Hill, NC 27514
| | - Christopher H. Martin
- Department of Biology, University of North Carolina, Chapel
Hill, NC 27514
- Department of Integrative Biology and Museum of Vertebrate
Zoology, University of California, Berkeley, CA 94720
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14
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Compensatory Evolution of Gene Expression. Trends Genet 2019; 35:890-891. [PMID: 31645272 DOI: 10.1016/j.tig.2019.09.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 09/18/2019] [Indexed: 11/21/2022]
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15
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Martin CH, McGirr JA, Richards EJ, St. John ME. How to Investigate the Origins of Novelty: Insights Gained from Genetic, Behavioral, and Fitness Perspectives. Integr Org Biol 2019; 1:obz018. [PMID: 33791533 PMCID: PMC7671130 DOI: 10.1093/iob/obz018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Biologists are drawn to the most extraordinary adaptations in the natural world, often referred to as evolutionary novelties, yet rarely do we understand the microevolutionary context underlying the origins of novel traits, behaviors, or ecological niches. Here we discuss insights gained into the origins of novelty from a research program spanning biological levels of organization from genotype to fitness in Caribbean pupfishes. We focus on a case study of the origins of novel trophic specialists on San Salvador Island, Bahamas and place this radiation in the context of other rapid radiations. We highlight questions that can be addressed about the origins of novelty at different biological levels, such as measuring the isolation of novel phenotypes on the fitness landscape, locating the spatial and temporal origins of adaptive variation contributing to novelty, detecting dysfunctional gene regulation due to adaptive divergence, and connecting behaviors with novel traits. Evolutionary novelties are rare, almost by definition, and we conclude that integrative case studies can provide insights into this rarity relative to the dynamics of adaptation to more common ecological niches and repeated parallel speciation, such as the relative isolation of novel phenotypes on fitness landscapes and the transient availability of ecological, genetic, and behavioral opportunities.
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Affiliation(s)
- C H Martin
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
| | - J A McGirr
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - E J Richards
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
| | - M E St. John
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
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