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Schumer M, Rosenthal GG, Andolfatto P. What do we mean when we talk about hybrid speciation? Heredity (Edinb) 2018; 120:379-382. [PMID: 29302049 PMCID: PMC5842215 DOI: 10.1038/s41437-017-0036-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 11/10/2017] [Accepted: 11/11/2017] [Indexed: 01/01/2023] Open
Affiliation(s)
- Molly Schumer
- Hanna Gray Fellow, Howard Hughes Medical Institute, Cambridge, MA, USA.
- Harvard Society of Fellows, Harvard University, Boston, MA, USA.
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA.
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", Calnali, Hidalgo, Mexico.
| | - Gil G Rosenthal
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", Calnali, Hidalgo, Mexico
- Department of Biology and Interdisciplinary Faculty of Ecology & Evolutionary Biology, Texas A&M University, College Station, TX, USA
| | - Peter Andolfatto
- Department of Ecology and Evolutionary Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
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52
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Janzen T, Nolte AW, Traulsen A. The breakdown of genomic ancestry blocks in hybrid lineages given a finite number of recombination sites. Evolution 2018; 72:735-750. [PMID: 29411878 PMCID: PMC5947311 DOI: 10.1111/evo.13436] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Accepted: 01/16/2018] [Indexed: 01/03/2023]
Abstract
When a lineage originates from hybridization genomic blocks of contiguous ancestry from different ancestors are fragmented through genetic recombination. The resulting blocks are delineated by so called junctions, which accumulate with every generation that passes. Modeling the accumulation of ancestry block junctions can elucidate processes and timeframes of genomic admixture. Previous models have not addressed ancestry block dynamics for chromosomes that consist of a finite number of recombination sites. However, genomic data typically consist of informative markers that are interspersed with fragments for which no ancestry information is available. Hence, repeated recombination events may occur between markers, effectively removing existing junctions. Here, we present an analytical treatment of the dynamics of the mean number of junctions over time, taking into account the number of recombination sites per chromosome, population size, genetic map length, and the frequency of the ancestral species in the founding hybrid swarm. We describe the expected number of junctions using equidistant molecular markers and estimate the number of junctions using random markers. This extended theory of junctions thus reflects properties of empirical data and can serve to study the genomic patterns following admixture.
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Affiliation(s)
- Thijs Janzen
- Carl von Ossietzky UniversityCarl‐von‐Ossietzky‐Str. 9‐1126111OldenburgGermany
- Max‐Planck‐Institute for Evolutionary BiologyAugust‐Thienemann‐Straße 224306PlönGermany
| | - Arne W. Nolte
- Carl von Ossietzky UniversityCarl‐von‐Ossietzky‐Str. 9‐1126111OldenburgGermany
| | - Arne Traulsen
- Max‐Planck‐Institute for Evolutionary BiologyAugust‐Thienemann‐Straße 224306PlönGermany
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53
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Sousa F, Bertrand YJK, Doyle JJ, Oxelman B, Pfeil BE. Using Genomic Location and Coalescent Simulation to Investigate Gene Tree Discordance in Medicago L. Syst Biol 2018; 66:934-949. [PMID: 28177088 DOI: 10.1093/sysbio/syx035] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 02/01/2017] [Indexed: 12/28/2022] Open
Abstract
Several well-documented evolutionary processes are known to cause conflict between species-level phylogenies and gene-level phylogenies. Three of the most challenging processes for species tree inference are incomplete lineage sorting, hybridization and gene duplication, which may result in unwarranted comparisons of paralogous genes. Several existing methods have dealt with these processes but none has yet been able to untangle all three at once. Here, we propose a stepwise method by which these processes can be discerned using information on genomic location coupled with coalescent simulations. In the first step, highly discordant genes within genomic blocks (putative paralogs) are identified and excluded from the data set and, in the second step, blocks of linked genes are grouped according to their hybrid history. Existing multispecies coalescent software can then be applied to recover the principal tree(s) that make up the species tree/network without violating the underlying model. The potential of the approach is evaluated on simulated data derived from a species network composed of nine species, of which one is of hybrid origin, and displaying a single-gene duplication that leads to paralogous comparisons. We apply our method to an empirical set of 12 genes from 7 species sampled in the plant genus Medicago that display phylogenetic discordance. We identify the causes of the discordance and demonstrate that the Medicago orbicularis lineage experienced an episode of ancient hybridization. Our results show promise as a new way to explore phylogenetic sequence data that can significantly improve species tree inference in presence of hybridization and undetected paralogy or other causes leading to extremely discordant gene trees. [Coalescent simulation; gene tree; genomic location; hybridization; incomplete lineage sorting; paralogy; phylogenetic incongruence; principal tree; species tree.].
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Affiliation(s)
- F Sousa
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 40530 Gothenburg, Sweden
| | - Y J K Bertrand
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 40530 Gothenburg, Sweden
| | - J J Doyle
- Department of Plant Biology, Cornell University, 404 Mann Library Building, Ithaca, NY 14853, USA
| | - B Oxelman
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 40530 Gothenburg, Sweden
| | - B E Pfeil
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 40530 Gothenburg, Sweden
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54
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Runemark A, Trier CN, Eroukhmanoff F, Hermansen JS, Matschiner M, Ravinet M, Elgvin TO, Sætre GP. Variation and constraints in hybrid genome formation. Nat Ecol Evol 2018; 2:549-556. [DOI: 10.1038/s41559-017-0437-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 12/04/2017] [Indexed: 11/09/2022]
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55
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56
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Hybrid speciation leads to novel male secondary sexual ornamentation of an Amazonian bird. Proc Natl Acad Sci U S A 2017; 115:E218-E225. [PMID: 29279398 DOI: 10.1073/pnas.1717319115] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Hybrid speciation is rare in vertebrates, and reproductive isolation arising from hybridization is infrequently demonstrated. Here, we present evidence supporting a hybrid-speciation event involving the genetic admixture of the snow-capped (Lepidothrix nattereri) and opal-crowned (Lepidothrix iris) manakins of the Amazon basin, leading to the formation of the hybrid species, the golden-crowned manakin (Lepidothrix vilasboasi). We used a genome-wide SNP dataset together with analysis of admixture, population structure, and coalescent modeling to demonstrate that the golden-crowned manakin is genetically an admixture of these species and does not represent a hybrid zone but instead formed through ancient genetic admixture. We used spectrophotometry to quantify the coloration of the species-specific male crown patches. Crown patches are highly reflective white (snow-capped manakin) or iridescent whitish-blue to pink (opal-crowned manakin) in parental species but are a much less reflective yellow in the hybrid species. The brilliant coloration of the parental species results from nanostructural organization of the keratin matrix feather barbs of the crown. However, using electron microscopy, we demonstrate that the structural organization of this matrix is different in the two parental species and that the hybrid species is intermediate. The intermediate nature of the crown barbs, resulting from past admixture appears to have rendered a duller structural coloration. To compensate for reduced brightness, selection apparently resulted in extensive thickening of the carotenoid-laden barb cortex, producing the yellow crown coloration. The evolution of this unique crown-color signal likely culminated in premating isolation of the hybrid species from both parental species.
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57
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Dennenmoser S, Sedlazeck FJ, Iwaszkiewicz E, Li X, Altmüller J, Nolte AW. Copy number increases of transposable elements and protein-coding genes in an invasive fish of hybrid origin. Mol Ecol 2017; 26:4712-4724. [PMID: 28390096 PMCID: PMC5638112 DOI: 10.1111/mec.14134] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 03/23/2017] [Accepted: 03/27/2017] [Indexed: 12/25/2022]
Abstract
Evolutionary dynamics of structural genetic variation in lineages of hybrid origin is not well explored, although structural mutations may increase in controlled hybrid crosses. We therefore tested whether structural variants accumulate in a fish of recent hybrid origin, invasive Cottus, relative to both parental species Cottus rhenanus and Cottus perifretum. Copy-number variation in exons of 10,979 genes was assessed using comparative genome hybridization arrays. Twelve genes showed significantly higher copy numbers in invasive Cottus compared to both parents. This coincided with increased expression for three genes related to vision, detoxification and muscle development, suggesting possible gene dosage effects. Copy number increases of putative transposons were assessed by comparative mapping of genomic DNA reads against a de novo assembly of 1,005 repetitive elements. In contrast to exons, copy number increases of repetitive elements were common (20.7%) in invasive Cottus, whereas decrease was very rare (0.01%). Among the increased repetitive elements, 53.8% occurred at higher numbers in C. perifretum compared to C. rhenanus, while only 1.4% were more abundant in C. rhenanus. This implies a biased mutational process that amplifies genetic material from one ancestor. To assess the frequency of de novo mutations through hybridization, we screened 64 laboratory-bred F2 offspring between the parental species for copy-number changes at five candidate loci. We found no evidence for new structural variants, indicating that they are too rare to be detected given our sampling scheme. Instead, they must have accumulated over more generations than we observed in a controlled cross.
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Affiliation(s)
- Stefan Dennenmoser
- Department for Evolutionary GeneticsMax‐Planck Institute for Evolutionary BiologyPlönGermany
- Institute for BiologyCarl von Ossietzky University OldenburgOldenburgGermany
| | | | - Elzbieta Iwaszkiewicz
- Department for Evolutionary GeneticsMax‐Planck Institute for Evolutionary BiologyPlönGermany
| | - Xiang‐Yi Li
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
| | - Janine Altmüller
- Cologne Center for Genomics, and Institute of Human GeneticsUniversity of CologneCologneGermany
| | - Arne W. Nolte
- Department for Evolutionary GeneticsMax‐Planck Institute for Evolutionary BiologyPlönGermany
- Institute for BiologyCarl von Ossietzky University OldenburgOldenburgGermany
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58
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Galaverni M, Caniglia R, Pagani L, Fabbri E, Boattini A, Randi E. Disentangling Timing of Admixture, Patterns of Introgression, and Phenotypic Indicators in a Hybridizing Wolf Population. Mol Biol Evol 2017; 34:2324-2339. [PMID: 28549194 PMCID: PMC5850710 DOI: 10.1093/molbev/msx169] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Hybridization is a natural or anthropogenic process that can deeply affect the genetic make-up of populations, possibly decreasing individual fitness but sometimes favoring local adaptations. The population of Italian wolves (Canis lupus), after protracted demographic declines and isolation, is currently expanding in anthropic areas, with documented cases of hybridization with stray domestic dogs. However, identifying admixture patterns in deeply introgressed populations is far from trivial. In this study, we used a panel of 170,000 SNPs analyzed with multivariate, Bayesian and local ancestry reconstruction methods to identify hybrids, estimate their ancestry proportions and timing since admixture. Moreover, we carried out preliminary genotype-phenotype association analyses to identify the genetic bases of three phenotypic traits (black coat, white claws, and spur on the hind legs) putative indicators of hybridization. Results showed no sharp subdivisions between nonadmixed wolves and hybrids, indicating that recurrent hybridization and deep introgression might have started mostly at the beginning of the population reexpansion. In hybrids, we identified a number of genomic regions with excess of ancestry in one of the parental populations, and regions with excess or resistance to introgression compared with neutral expectations. The three morphological traits showed significant genotype-phenotype associations, with a single genomic region for black coats and white claws, and with multiple genomic regions for the spur. In all cases the associated haplotypes were likely derived from dogs. In conclusion, we show that the use of multiple genome-wide ancestry reconstructions allows clarifying the admixture dynamics even in highly introgressed populations, and supports their conservation management.
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Affiliation(s)
- Marco Galaverni
- Area per la Genetica della Conservazione, ISPRA, Ozzano dell'Emilia Bologna, Italy
- Area Conservazione, WWF Italia, Rome, Italy
| | - Romolo Caniglia
- Area per la Genetica della Conservazione, ISPRA, Ozzano dell'Emilia Bologna, Italy
| | - Luca Pagani
- Dipartimento di Biologia, Universita degli Studi di Padova, Padua, Italy
- Estonian Biocentre, Tartu, Estonia
| | - Elena Fabbri
- Area per la Genetica della Conservazione, ISPRA, Ozzano dell'Emilia Bologna, Italy
| | - Alessio Boattini
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Ettore Randi
- Area per la Genetica della Conservazione, ISPRA, Ozzano dell'Emilia Bologna, Italy
- Department 18/Section of Environmental Engineering, Aalborg Universitet, Aalborg, Denmark
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59
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Ravinet M, Faria R, Butlin RK, Galindo J, Bierne N, Rafajlović M, Noor MAF, Mehlig B, Westram AM. Interpreting the genomic landscape of speciation: a road map for finding barriers to gene flow. J Evol Biol 2017; 30:1450-1477. [DOI: 10.1111/jeb.13047] [Citation(s) in RCA: 306] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 01/31/2017] [Accepted: 02/01/2017] [Indexed: 12/14/2022]
Affiliation(s)
- M. Ravinet
- Centre for Ecological and Evolutionary Synthesis; University of Oslo; Oslo Norway
- National Institute of Genetics; Mishima Shizuoka Japan
| | - R. Faria
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos; InBIO, Laboratório Associado; Universidade do Porto; Vairão Portugal
- Department of Experimental and Health Sciences; IBE, Institute of Evolutionary Biology (CSIC-UPF); Pompeu Fabra University; Barcelona Spain
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield UK
| | - R. K. Butlin
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield UK
- Department of Marine Sciences; Centre for Marine Evolutionary Biology; University of Gothenburg; Gothenburg Sweden
| | - J. Galindo
- Department of Biochemistry, Genetics and Immunology; University of Vigo; Vigo Spain
| | - N. Bierne
- CNRS; Université Montpellier; ISEM; Station Marine Sète France
| | - M. Rafajlović
- Department of Physics; University of Gothenburg; Gothenburg Sweden
| | | | - B. Mehlig
- Department of Physics; University of Gothenburg; Gothenburg Sweden
| | - A. M. Westram
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield UK
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60
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Caicedo A, Aponte PM, Cabrera F, Hidalgo C, Khoury M. Artificial Mitochondria Transfer: Current Challenges, Advances, and Future Applications. Stem Cells Int 2017; 2017:7610414. [PMID: 28751917 PMCID: PMC5511681 DOI: 10.1155/2017/7610414] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 04/30/2017] [Accepted: 05/15/2017] [Indexed: 12/18/2022] Open
Abstract
The objective of this review is to outline existing artificial mitochondria transfer techniques and to describe the future steps necessary to develop new therapeutic applications in medicine. Inspired by the symbiotic origin of mitochondria and by the cell's capacity to transfer these organelles to damaged neighbors, many researchers have developed procedures to artificially transfer mitochondria from one cell to another. The techniques currently in use today range from simple coincubations of isolated mitochondria and recipient cells to the use of physical approaches to induce integration. These methods mimic natural mitochondria transfer. In order to use mitochondrial transfer in medicine, we must answer key questions about how to replicate aspects of natural transport processes to improve current artificial transfer methods. Another priority is to determine the optimum quantity and cell/tissue source of the mitochondria in order to induce cell reprogramming or tissue repair, in both in vitro and in vivo applications. Additionally, it is important that the field explores how artificial mitochondria transfer techniques can be used to treat different diseases and how to navigate the ethical issues in such procedures. Without a doubt, mitochondria are more than mere cell power plants, as we continue to discover their potential to be used in medicine.
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Affiliation(s)
- Andrés Caicedo
- Colegio de Ciencias de la Salud, Escuela de Medicina, Universidad San Francisco de Quito (USFQ), 170901 Quito, Ecuador
- Colegio de Ciencias Biológicas y Ambientales, Instituto de Microbiología, Universidad San Francisco de Quito (USFQ), 170901 Quito, Ecuador
- Mito-Act Research Consortium, Quito, Ecuador
| | - Pedro M. Aponte
- Mito-Act Research Consortium, Quito, Ecuador
- Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), 170901 Quito, Ecuador
| | - Francisco Cabrera
- Mito-Act Research Consortium, Quito, Ecuador
- Colegio de Ciencias de la Salud, Escuela de Medicina Veterinaria, Universidad San Francisco de Quito (USFQ), 170901 Quito, Ecuador
- Institute for Regenerative Medicine and Biotherapy (IRMB), INSERM U1183, 2 Montpellier University, Montpellier, France
| | - Carmen Hidalgo
- Mito-Act Research Consortium, Quito, Ecuador
- Laboratory of Nano-Regenerative Medicine, Faculty of Medicine, Universidad de Los Andes, Santiago, Chile
| | - Maroun Khoury
- Mito-Act Research Consortium, Quito, Ecuador
- Laboratory of Nano-Regenerative Medicine, Faculty of Medicine, Universidad de Los Andes, Santiago, Chile
- Consorcio Regenero, Chilean Consortium for Regenerative Medicine, Santiago, Chile
- Cells for Cells, Santiago, Chile
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61
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Elgvin TO, Trier CN, Tørresen OK, Hagen IJ, Lien S, Nederbragt AJ, Ravinet M, Jensen H, Sætre GP. The genomic mosaicism of hybrid speciation. SCIENCE ADVANCES 2017; 3:e1602996. [PMID: 28630911 PMCID: PMC5470830 DOI: 10.1126/sciadv.1602996] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 04/26/2017] [Indexed: 05/21/2023]
Abstract
Hybridization is widespread in nature and, in some instances, can result in the formation of a new hybrid species. We investigate the genetic foundation of this poorly understood process through whole-genome analysis of the hybrid Italian sparrow and its progenitors. We find overall balanced yet heterogeneous levels of contribution from each parent species throughout the hybrid genome and identify areas of novel divergence in the hybrid species exhibiting signals consistent with balancing selection. High-divergence areas are disproportionately located on the Z chromosome and overrepresented in gene networks relating to key traits separating the focal species, which are likely involved in reproductive barriers and/or species-specific adaptations. Of special interest are genes and functional groups known to affect body patterning, beak morphology, and the immune system, which are important features of diversification and fitness. We show that a combination of mosaic parental inheritance and novel divergence within the hybrid lineage has facilitated the origin and maintenance of an avian hybrid species.
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Affiliation(s)
- Tore O. Elgvin
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, P.O. Box 1066, N-0316 Oslo, Norway
| | - Cassandra N. Trier
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, P.O. Box 1066, N-0316 Oslo, Norway
| | - Ole K. Tørresen
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, P.O. Box 1066, N-0316 Oslo, Norway
| | - Ingerid J. Hagen
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | - Sigbjørn Lien
- Department of Animal and Aquacultural Sciences, Faculty for Biosciences, Centre for Integrative Genetics, Norwegian University of Life Sciences, P.O. Box 5003, Ås, Norway
| | - Alexander J. Nederbragt
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, P.O. Box 1066, N-0316 Oslo, Norway
| | - Mark Ravinet
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, P.O. Box 1066, N-0316 Oslo, Norway
| | - Henrik Jensen
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | - Glenn-Peter Sætre
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, P.O. Box 1066, N-0316 Oslo, Norway
- Corresponding author.
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62
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Sætre GP, Cuevas A, Hermansen JS, Elgvin TO, Fernández LP, Sæther SA, Cascio Sætre CL, Eroukhmanoff F. Rapid polygenic response to secondary contact in a hybrid species. Proc Biol Sci 2017; 284:20170365. [PMID: 28446700 PMCID: PMC5413929 DOI: 10.1098/rspb.2017.0365] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 03/22/2017] [Indexed: 12/26/2022] Open
Abstract
Secondary contact between closely related species can have genetic consequences. Competition for essential resources may lead to divergence in heritable traits that reduces interspecific competition leading to increased rate of genetic divergence. Conversely, hybridization and backcrossing can lead to genetic convergence. Here, we study a population of a hybrid species, the Italian sparrow (Passer italiae), before and after it came into secondary contact with one of its parent species, the Spanish sparrow (P. hispaniolensis), in 2013. We demonstrate strong consequences of interspecific competition: Italian sparrows were kept away from a popular feeding site by its parent species, resulting in poorer body condition and a significant drop in population size. Although no significant morphological change could be detected, after only 3 years of sympatry, the Italian sparrows had diverged significantly from the Spanish sparrows across a set of 81 protein-coding genes. These temporal genetic changes are mirrored by genetic divergence observed in older sympatric Italian sparrow populations within the same area of contact. Compared with microallopatric birds, sympatric ones are genetically more diverged from Spanish sparrows. Six significant outlier genes in the temporal and spatial comparison (i.e. showing the greatest displacement) have all been found to be associated with learning and neural development in other bird species.
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Affiliation(s)
- Glenn-Peter Sætre
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, 0316 Oslo, Norway
| | - Angélica Cuevas
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, 0316 Oslo, Norway
| | - Jo S Hermansen
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, 0316 Oslo, Norway
| | - Tore O Elgvin
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, 0316 Oslo, Norway
| | - Laura Piñeiro Fernández
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, 0316 Oslo, Norway
| | - Stein A Sæther
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, 0316 Oslo, Norway
- Norwegian Institute for Nature Research (NINA), PO Box 5685, Sluppen, 7485 Trondheim, Norway
| | - Camilla Lo Cascio Sætre
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, 0316 Oslo, Norway
| | - Fabrice Eroukhmanoff
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, 0316 Oslo, Norway
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63
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Schield DR, Adams RH, Card DC, Perry BW, Pasquesi GM, Jezkova T, Portik DM, Andrew AL, Spencer CL, Sanchez EE, Fujita MK, Mackessy SP, Castoe TA. Insight into the roles of selection in speciation from genomic patterns of divergence and introgression in secondary contact in venomous rattlesnakes. Ecol Evol 2017; 7:3951-3966. [PMID: 28616190 PMCID: PMC5468163 DOI: 10.1002/ece3.2996] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 03/21/2017] [Indexed: 01/03/2023] Open
Abstract
Investigating secondary contact of historically isolated lineages can provide insight into how selection and drift influence genomic divergence and admixture. Here, we studied the genomic landscape of divergence and introgression following secondary contact between lineages of the Western Diamondback Rattlesnake (Crotalus atrox) to determine whether genomic regions under selection in allopatry also contribute to reproductive isolation during introgression. We used thousands of nuclear loci to study genomic differentiation between two lineages that have experienced recent secondary contact following isolation, and incorporated sampling from a zone of secondary contact to identify loci that are resistant to gene flow in hybrids. Comparisons of patterns of divergence and introgression revealed a positive relationship between allelic differentiation and resistance to introgression across the genome, and greater‐than‐expected overlap between genes linked to lineage‐specific divergence and loci that resist introgression. Genes linked to putatively selected markers were related to prominent aspects of rattlesnake biology that differ between populations of Western Diamondback rattlesnakes (i.e., venom and reproductive phenotypes). We also found evidence for selection against introgression of genes that may contribute to cytonuclear incompatibility, consistent with previously observed biased patterns of nuclear and mitochondrial alleles suggestive of partial reproductive isolation due to cytonuclear incompatibilities. Our results provide a genome‐scale perspective on the relationships between divergence and introgression in secondary contact that is relevant for understanding the roles of selection in maintaining partial isolation of lineages, causing admixing lineages to not completely homogenize.
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Affiliation(s)
- Drew R Schield
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Richard H Adams
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Daren C Card
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Blair W Perry
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Giulia M Pasquesi
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Tereza Jezkova
- Department of Ecology and Evolutionary Biology University of Arizona Tucson AZ USA
| | - Daniel M Portik
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Audra L Andrew
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Carol L Spencer
- Museum of Vertebrate Zoology University of California Berkeley CA USA
| | - Elda E Sanchez
- National Natural Toxins Research Center and Department of Chemistry Texas A&M University Kingsville Kingsville TX USA
| | - Matthew K Fujita
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Stephen P Mackessy
- School of Biological Sciences University of Northern Colorado Greeley CO USA
| | - Todd A Castoe
- Department of Biology The University of Texas at Arlington Arlington TX USA
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64
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Sloan DB, Havird JC, Sharbrough J. The on-again, off-again relationship between mitochondrial genomes and species boundaries. Mol Ecol 2017; 26:2212-2236. [PMID: 27997046 PMCID: PMC6534505 DOI: 10.1111/mec.13959] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 11/16/2016] [Accepted: 11/18/2016] [Indexed: 12/12/2022]
Abstract
The study of reproductive isolation and species barriers frequently focuses on mitochondrial genomes and has produced two alternative and almost diametrically opposed narratives. On one hand, mtDNA may be at the forefront of speciation events, with co-evolved mitonuclear interactions responsible for some of the earliest genetic incompatibilities arising among isolated populations. On the other hand, there are numerous cases of introgression of mtDNA across species boundaries even when nuclear gene flow is restricted. We argue that these seemingly contradictory patterns can result from a single underlying cause. Specifically, the accumulation of deleterious mutations in mtDNA creates a problem with two alternative evolutionary solutions. In some cases, compensatory or epistatic changes in the nuclear genome may ameliorate the effects of mitochondrial mutations, thereby establishing coadapted mitonuclear genotypes within populations and forming the basis of reproductive incompatibilities between populations. Alternatively, populations with high mitochondrial mutation loads may be rescued by replacement with a more fit, foreign mitochondrial haplotype. Coupled with many nonadaptive mechanisms of introgression that can preferentially affect cytoplasmic genomes, this form of adaptive introgression may contribute to the widespread discordance between mitochondrial and nuclear genealogies. Here, we review recent advances related to mitochondrial introgression and mitonuclear incompatibilities, including the potential for cointrogression of mtDNA and interacting nuclear genes. We also address an emerging controversy over the classic assumption that selection on mitochondrial genomes is inefficient and discuss the mechanisms that lead lineages down alternative evolutionary paths in response to mitochondrial mutation accumulation.
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Affiliation(s)
- Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Justin C Havird
- Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Joel Sharbrough
- Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA
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65
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Stojković B, Sayadi A, Đorđević M, Jović J, Savković U, Arnqvist G. Divergent evolution of life span associated with mitochondrial DNA evolution. Evolution 2016; 71:160-166. [PMID: 27778315 DOI: 10.1111/evo.13102] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 10/18/2016] [Accepted: 10/20/2016] [Indexed: 01/03/2023]
Abstract
Mitochondria play a key role in ageing. The pursuit of genes that regulate variation in life span and ageing have shown that several nuclear-encoded mitochondrial genes are important. However, the role of mitochondrial encoded genes (mtDNA) is more controversial and our appreciation of the role of mtDNA for the evolution of life span is limited. We use replicated lines of seed beetles that have been artificially selected for long or short life for >190 generations, now showing dramatic phenotypic differences, to test for a possible role of mtDNA in the divergent evolution of ageing and life span. We show that these divergent selection regimes led to the evolution of significantly different mtDNA haplotype frequencies. Selection for a long life and late reproduction generated positive selection for one specific haplotype, which was fixed in most such lines. In contrast, selection for reproduction early in life led to both positive selection as well as negative frequency-dependent selection on two different haplotypes, which were both present in all such lines. Our findings suggest that the evolution of life span was in part mediated by mtDNA, providing support for the emerging general tenet that adaptive evolution of life-history syndromes may involve mtDNA.
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Affiliation(s)
- Biljana Stojković
- Institute of Zoology, Faculty of Biology, University of Belgrade, Studentski trg 16, 11000, Belgrade, Serbia.,Department of Evolutionary Biology, Institute for Biological Research "Siniša Stanković, University of Belgrade, Despota Stefana Boulevard 142, 11060, Belgrade, Serbia
| | - Ahmed Sayadi
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden
| | - Mirko Đorđević
- Department of Evolutionary Biology, Institute for Biological Research "Siniša Stanković, University of Belgrade, Despota Stefana Boulevard 142, 11060, Belgrade, Serbia
| | - Jelena Jović
- Department of Plant Pests, Institute for Plant Protection and Environment, Banatska 33, 11080, Zemun, Serbia
| | - Uroš Savković
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden
| | - Göran Arnqvist
- Department of Evolutionary Biology, Institute for Biological Research "Siniša Stanković, University of Belgrade, Despota Stefana Boulevard 142, 11060, Belgrade, Serbia
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66
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McFarlane SE, Sirkiä PM, Ålund M, Qvarnström A. Hybrid Dysfunction Expressed as Elevated Metabolic Rate in Male Ficedula Flycatchers. PLoS One 2016; 11:e0161547. [PMID: 27583553 PMCID: PMC5008804 DOI: 10.1371/journal.pone.0161547] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 08/08/2016] [Indexed: 02/06/2023] Open
Abstract
Studies of ecological speciation are often biased towards extrinsic sources of selection against hybrids, resulting from intermediate hybrid morphology, but the knowledge of how genetic incompatibilities accumulate over time under natural conditions is limited. Here we focus on a physiological trait, metabolic rate, which is central to life history strategies and thermoregulation but is also likely to be sensitive to mismatched mitonuclear interactions. We measured the resting metabolic rate of male collared, and pied flycatchers as well as of naturally occurring F1 hybrid males, in a recent hybrid zone. We found that hybrid males had a higher rather than intermediate metabolic rate, which is indicative of hybrid physiological dysfunction. Fitness costs associated with elevated metabolic rate are typically environmentally dependent and exaggerated under harsh conditions. By focusing on male hybrid dysfunction in an eco-physiological trait, our results contribute to the general understanding of how combined extrinsic and intrinsic sources of hybrid dysfunction build up under natural conditions.
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Affiliation(s)
- S. Eryn McFarlane
- Animal Ecology/ Department of Ecology and Genetics, Norbyvägen 18D, SE-752 36, Uppsala, Sweden
| | - Päivi M. Sirkiä
- Finnish Museum of Natural History, Zoology Unit, University of Helsinki, Helsinki, Finland
- Section of Ecology, Department of Biology, University of Turku, Turku, Finland
| | - Murielle Ålund
- Animal Ecology/ Department of Ecology and Genetics, Norbyvägen 18D, SE-752 36, Uppsala, Sweden
| | - Anna Qvarnström
- Animal Ecology/ Department of Ecology and Genetics, Norbyvägen 18D, SE-752 36, Uppsala, Sweden
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67
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Gante HF, Matschiner M, Malmstrøm M, Jakobsen KS, Jentoft S, Salzburger W. Genomics of speciation and introgression in Princess cichlid fishes from Lake Tanganyika. Mol Ecol 2016; 25:6143-6161. [DOI: 10.1111/mec.13767] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 05/30/2016] [Accepted: 07/11/2016] [Indexed: 01/02/2023]
Affiliation(s)
- Hugo F. Gante
- Zoological Institute University of Basel Vesalgasse 1 4051 Basel Switzerland
| | - Michael Matschiner
- Department of Biosciences CEES (Centre for Ecological and Evolutionary Synthesis) University of Oslo 0316 Oslo Norway
| | - Martin Malmstrøm
- Department of Biosciences CEES (Centre for Ecological and Evolutionary Synthesis) University of Oslo 0316 Oslo Norway
| | - Kjetill S. Jakobsen
- Department of Biosciences CEES (Centre for Ecological and Evolutionary Synthesis) University of Oslo 0316 Oslo Norway
| | - Sissel Jentoft
- Department of Biosciences CEES (Centre for Ecological and Evolutionary Synthesis) University of Oslo 0316 Oslo Norway
- Department of Natural Sciences University of Agder 4604 Kristiansand Norway
| | - Walter Salzburger
- Zoological Institute University of Basel Vesalgasse 1 4051 Basel Switzerland
- Department of Biosciences CEES (Centre for Ecological and Evolutionary Synthesis) University of Oslo 0316 Oslo Norway
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68
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Grossen C, Seneviratne SS, Croll D, Irwin DE. Strong reproductive isolation and narrow genomic tracts of differentiation among three woodpecker species in secondary contact. Mol Ecol 2016; 25:4247-66. [DOI: 10.1111/mec.13751] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Revised: 06/25/2016] [Accepted: 06/27/2016] [Indexed: 12/29/2022]
Affiliation(s)
- Christine Grossen
- Department of Zoology and Biodiversity Research Centre; University of British Columbia; 6270 University Blvd. Vancouver BC V6T 1Z4 Canada
- Institute of Evolutionary Biology and Environmental Studies; University of Zürich; Winterthurerstrasse 190 CH-8057 Zürich Switzerland
| | - Sampath S. Seneviratne
- Department of Zoology and Biodiversity Research Centre; University of British Columbia; 6270 University Blvd. Vancouver BC V6T 1Z4 Canada
- Avian Evolution Node; Department of Zoology; University of Colombo; PO Box 1490 Colombo 03 Sri Lanka
| | - Daniel Croll
- Integrative Biology; ETH Zürich; Universitätstrasse 2 CH-8092 Zürich Switzerland
| | - Darren E. Irwin
- Department of Zoology and Biodiversity Research Centre; University of British Columbia; 6270 University Blvd. Vancouver BC V6T 1Z4 Canada
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69
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Ait Belkacem A, Gast O, Stuckas H, Canal D, LoValvo M, Giacalone G, Päckert M. North African hybrid sparrows (Passer domesticus, P. hispaniolensis) back from oblivion - ecological segregation and asymmetric mitochondrial introgression between parental species. Ecol Evol 2016; 6:5190-206. [PMID: 27551376 PMCID: PMC4984497 DOI: 10.1002/ece3.2274] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 05/31/2016] [Accepted: 06/03/2016] [Indexed: 01/23/2023] Open
Abstract
A stabilized hybrid form of the house sparrow (Passer domesticus) and the Spanish sparrow (P. hispaniolensis) is known as Passer italiae from the Italian Peninsula and a few Mediterranean islands. The growing attention for the Italian hybrid sparrow and increasing knowledge on its biology and genetic constitution greatly contrast the complete lack of knowledge of the long‐known phenotypical hybrid sparrow populations from North Africa. Our study provides new data on the breeding biology and variation of mitochondrial DNA in three Algerian populations of house sparrows, Spanish sparrows, and phenotypical hybrids. In two field seasons, the two species occupied different breeding habitats: Spanish sparrows were only found in rural areas outside the cities and bred in open‐cup nests built in large jujube bushes. In contrast, house sparrows bred only in the town centers and occupied nesting holes in walls of buildings. Phenotypical hybrids were always associated with house sparrow populations. House sparrows and phenotypical hybrids started breeding mid of March, and most pairs had three successive clutches, whereas Spanish sparrows started breeding almost one month later and had only two successive clutches. Mitochondrial introgression is strongly asymmetric because about 75% of the rural Spanish sparrow population carried house sparrow haplotypes. In contrast, populations of the Italian hybrid form, P. italiae, were genetically least diverse among all study populations and showed a near‐fixation of house sparrow haplotypes that elsewhere were extremely rare or that were even unique for the Italian Peninsula. Such differences between mitochondrial gene pools of Italian and North African hybrid sparrow populations provide first evidence that different demographic histories have shaped the extant genetic diversity observed on both continents.
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Affiliation(s)
- Abdelkrim Ait Belkacem
- Faculty of Sciences of nature and lifes Department of Agropastoralism University of Djelfa BP. 3117 17000 Djelfa Algeria
| | - Oliver Gast
- Senckenberg Naturhistorische Sammlungen Königsbrücker Landstraße 159D-01109 Dresden Germany; Institute of Vertebrate Biology Czech Academy of Sciences External Research Facility Studenec Studenec 122675 02 Koněšín Czech Republic
| | - Heiko Stuckas
- Senckenberg Naturhistorische Sammlungen Königsbrücker Landstraße 159 D-01109 Dresden Germany
| | - David Canal
- Department of Evolutionary Ecology Estación Biológica de Doñana - CSIC Avda. Américo Vespucio s/n 41092 Seville Spain
| | - Mario LoValvo
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche Via Archirafi 18 I-90123 Palermo Italy
| | | | - Martin Päckert
- Senckenberg Naturhistorische Sammlungen Königsbrücker Landstraße 159 D-01109 Dresden Germany
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70
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Sloan DB, Fields PD, Havird JC. Mitonuclear linkage disequilibrium in human populations. Proc Biol Sci 2016; 282:rspb.2015.1704. [PMID: 26378221 DOI: 10.1098/rspb.2015.1704] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
There is extensive evidence from model systems that disrupting associations between co-adapted mitochondrial and nuclear genotypes can lead to deleterious and even lethal consequences. While it is tempting to extrapolate from these observations and make inferences about the human-health effects of altering mitonuclear associations, the importance of such associations may vary greatly among species, depending on population genetics, demographic history and other factors. Remarkably, despite the extensive study of human population genetics, the statistical associations between nuclear and mitochondrial alleles remain largely uninvestigated. We analysed published population genomic data to test for signatures of historical selection to maintain mitonuclear associations, particularly those involving nuclear genes that encode mitochondrial-localized proteins (N-mt genes). We found that significant mitonuclear linkage disequilibrium (LD) exists throughout the human genome, but these associations were generally weak, which is consistent with the paucity of population genetic structure in humans. Although mitonuclear LD varied among genomic regions (with especially high levels on the X chromosome), N-mt genes were statistically indistinguishable from background levels, suggesting that selection on mitonuclear epistasis has not preferentially maintained associations involving this set of loci at a species-wide level. We discuss these findings in the context of the ongoing debate over mitochondrial replacement therapy.
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Affiliation(s)
- Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Peter D Fields
- Zoological Institute, University of Basel, Vesalgasse 1, Basel, 4051, Switzerland
| | - Justin C Havird
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
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71
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Hwang AS, Pritchard VL, Edmands S. Recovery from hybrid breakdown in a marine invertebrate is faster, stronger and more repeatable under environmental stress. J Evol Biol 2016; 29:1793-803. [DOI: 10.1111/jeb.12913] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 05/30/2016] [Indexed: 11/26/2022]
Affiliation(s)
- A. S. Hwang
- Department of Biological Sciences University of Southern California Los Angeles CA USA
| | - V. L. Pritchard
- Department of Biological Sciences University of Southern California Los Angeles CA USA
| | - S. Edmands
- Department of Biological Sciences University of Southern California Los Angeles CA USA
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72
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Sardell JM, Uy JAC. Hybridization following recent secondary contact results in asymmetric genotypic and phenotypic introgression between island species ofMyzomelahoneyeaters. Evolution 2016; 70:257-69. [DOI: 10.1111/evo.12864] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 12/22/2015] [Indexed: 01/21/2023]
Affiliation(s)
- Jason M. Sardell
- Department of Biology; University of Miami; Coral Gables Florida 33146
| | - J. Albert C. Uy
- Department of Biology; University of Miami; Coral Gables Florida 33146
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73
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Immonen E, Rönn J, Watson C, Berger D, Arnqvist G. Complex mitonuclear interactions and metabolic costs of mating in male seed beetles. J Evol Biol 2015; 29:360-70. [PMID: 26548644 DOI: 10.1111/jeb.12789] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 11/03/2015] [Indexed: 02/02/2023]
Abstract
The lack of evolutionary response to selection on mitochondrial genes through males predicts the evolution of nuclear genetic influence on male-specific mitochondrial function, for example by gene duplication and evolution of sex-specific expression of paralogs involved in metabolic pathways. Intergenomic epistasis may therefore be a prevalent feature of the genetic architecture of male-specific organismal function. Here, we assess the role of mitonuclear genetic variation for male metabolic phenotypes [metabolic rate and respiratory quotient (RQ)] associated with ejaculate renewal, in the seed beetle Callosobruchus maculatus, by assaying lines with crossed combinations of distinct mitochondrial haplotypes and nuclear lineages. We found a significant increase in metabolic rate following mating relative to virgin males. Moreover, processes associated with ejaculate renewal showed variation in metabolic rate that was affected by mitonuclear interactions. Mitochondrial haplotype influenced mating-related changes in RQ, but this pattern varied over time. Mitonuclear genotype and the energy spent during ejaculate production affected the weight of the ejaculate, but the strength of this effect varied across mitochondrial haplotypes showing that the genetic architecture of male-specific reproductive function is complex. Our findings unveil hitherto underappreciated metabolic costs of mating and ejaculate renewal, and provide the first empirical demonstration of mitonuclear epistasis on male reproductive metabolic processes.
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Affiliation(s)
- E Immonen
- Evolutionary Biology Centre, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - J Rönn
- Evolutionary Biology Centre, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - C Watson
- Evolutionary Biology Centre, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - D Berger
- Evolutionary Biology Centre, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - G Arnqvist
- Evolutionary Biology Centre, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
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74
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Levin L, Bar-Yaacov D, Bouskila A, Chorev M, Carmel L, Mishmar D. LEMONS - A Tool for the Identification of Splice Junctions in Transcriptomes of Organisms Lacking Reference Genomes. PLoS One 2015; 10:e0143329. [PMID: 26606265 PMCID: PMC4659627 DOI: 10.1371/journal.pone.0143329] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 11/03/2015] [Indexed: 11/18/2022] Open
Abstract
RNA-seq is becoming a preferred tool for genomics studies of model and non-model organisms. However, DNA-based analysis of organisms lacking sequenced genomes cannot rely on RNA-seq data alone to isolate most genes of interest, as DNA codes both exons and introns. With this in mind, we designed a novel tool, LEMONS, that exploits the evolutionary conservation of both exon/intron boundary positions and splice junction recognition signals to produce high throughput splice-junction predictions in the absence of a reference genome. When tested on multiple annotated vertebrate mRNA data, LEMONS accurately identified 87% (average) of the splice-junctions. LEMONS was then applied to our updated Mediterranean chameleon transcriptome, which lacks a reference genome, and predicted a total of 90,820 exon-exon junctions. We experimentally verified these splice-junction predictions by amplifying and sequencing twenty randomly selected genes from chameleon DNA templates. Exons and introns were detected in 19 of 20 of the positions predicted by LEMONS. To the best of our knowledge, LEMONS is currently the only experimentally verified tool that can accurately predict splice-junctions in organisms that lack a reference genome.
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Affiliation(s)
- Liron Levin
- Department of Life Sciences, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel
| | - Dan Bar-Yaacov
- Department of Life Sciences, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel
| | - Amos Bouskila
- Department of Life Sciences, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel
| | - Michal Chorev
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Liran Carmel
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Dan Mishmar
- Department of Life Sciences, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel
- * E-mail:
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75
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Bar-Yaacov D, Hadjivasiliou Z, Levin L, Barshad G, Zarivach R, Bouskila A, Mishmar D. Mitochondrial Involvement in Vertebrate Speciation? The Case of Mito-nuclear Genetic Divergence in Chameleons. Genome Biol Evol 2015; 7:3322-36. [PMID: 26590214 PMCID: PMC4700957 DOI: 10.1093/gbe/evv226] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Compatibility between the nuclear (nDNA) and mitochondrial (mtDNA) genomes is important for organismal health. However, its significance for major evolutionary processes such as speciation is unclear, especially in vertebrates. We previously identified a sharp mtDNA-specific sequence divergence between morphologically indistinguishable chameleon populations (Chamaeleo chamaeleon recticrista) across an ancient Israeli marine barrier (Jezreel Valley). Because mtDNA introgression and gender-based dispersal were ruled out, we hypothesized that mtDNA spatial division was maintained by mito-nuclear functional compensation. Here, we studied RNA-seq generated from each of ten chameleons representing the north and south populations and identified candidate nonsynonymous substitutions (NSSs) matching the mtDNA spatial distribution. The most prominent NSS occurred in 14 nDNA-encoded mitochondrial proteins. Increased chameleon sample size (N = 70) confirmed the geographic differentiation in POLRMT, NDUFA5, ACO1, LYRM4, MARS2, and ACAD9. Structural and functionality evaluation of these NSSs revealed high functionality. Mathematical modeling suggested that this mito-nuclear spatial divergence is consistent with hybrid breakdown. We conclude that our presented evidence and mathematical model underline mito-nuclear interactions as a likely role player in incipient speciation in vertebrates.
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Affiliation(s)
- Dan Bar-Yaacov
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Zena Hadjivasiliou
- Centre for Mathematics, Physics and Engineering in the Life Sciences and Experimental Biology, UCL, London, United Kingdom Department of Genetics, Evolution and Environment, UCL, London, United Kingdom
| | - Liron Levin
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Gilad Barshad
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Raz Zarivach
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Amos Bouskila
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Dan Mishmar
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
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76
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Mounier A, Caparros M. The phylogenetic status of Homo heidelbergensis – a cladistic study of Middle Pleistocene hominins. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/s13219-015-0127-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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77
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Bailey RI, Tesaker MR, Trier CN, Saetre GP. Strong selection on male plumage in a hybrid zone between a hybrid bird species and one of its parents. J Evol Biol 2015; 28:1257-69. [PMID: 25940369 DOI: 10.1111/jeb.12652] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Revised: 04/08/2015] [Accepted: 04/29/2015] [Indexed: 01/28/2023]
Abstract
Homoploid hybrid speciation (HHS) requires reproductive barriers between hybrid and parent species, despite incomplete reproductive isolation (RI) between the parents. Novel secondary sexual trait values in hybrids may cause prezygotic isolation from both parents, whereas signals inherited by the hybrid from one parent species may cause prezygotic isolation with the other. Here we investigate whether differences in male plumage function as a premating barrier between the hybrid Italian sparrow and one of its parent species, the house sparrow, in a narrow Alpine hybrid zone. Italian sparrow male plumage is a composite mosaic of the parental traits, with its head plumage most similar to its other parent, the Spanish sparrow. We use geographical cline analysis to examine selection on three plumage traits, 75 nuclear single nucleotide polymorphisms (SNPs) and hybrid indices based on these SNPs. Several SNPs showed evidence of restricted introgression in the Alps, supporting earlier findings. Crown colour exhibited the narrowest plumage cline, representing a 37% (range 4-65%) drop in fitness. The cline was too narrow to be due to neutral introgression. Only crown colour was significantly bimodal in the hybrid zone. Bimodality may be due to RI or a major QTL, although fitness estimates suggest that selection contributes to the pattern. We discuss the implications with respect to HHS and the species status of the Italian sparrow.
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Affiliation(s)
- R I Bailey
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway
| | - M R Tesaker
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway
| | - C N Trier
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway
| | - G-P Saetre
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway
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78
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Morales HE, Pavlova A, Joseph L, Sunnucks P. Positive and purifying selection in mitochondrial genomes of a bird with mitonuclear discordance. Mol Ecol 2015; 24:2820-37. [DOI: 10.1111/mec.13203] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 04/02/2015] [Accepted: 04/08/2015] [Indexed: 12/21/2022]
Affiliation(s)
- Hernán E. Morales
- School of Biological Sciences Monash University; Clayton Campus Melbourne Vic. 3800 Australia
| | - Alexandra Pavlova
- School of Biological Sciences Monash University; Clayton Campus Melbourne Vic. 3800 Australia
| | - Leo Joseph
- Australian National Wildlife Collection; CSIRO National Facilities and Collections; GPO Box 1700 Canberra ACT 2601 Australia
| | - Paul Sunnucks
- School of Biological Sciences Monash University; Clayton Campus Melbourne Vic. 3800 Australia
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79
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Taylor SA, Larson EL, Harrison RG. Hybrid zones: windows on climate change. Trends Ecol Evol 2015; 30:398-406. [PMID: 25982153 DOI: 10.1016/j.tree.2015.04.010] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 04/16/2015] [Accepted: 04/17/2015] [Indexed: 12/16/2022]
Abstract
Defining the impacts of anthropogenic climate change on biodiversity and species distributions is currently a high priority. Niche models focus primarily on predicted changes in abiotic factors; however, species interactions and adaptive evolution will impact the ability of species to persist in the face of changing climate. Our review focuses on the use of hybrid zones to monitor responses of species to contemporary climate change. Monitoring hybrid zones provides insight into how range boundaries shift in response to climate change by illuminating the combined effects of species interactions and physiological sensitivity. At the same time, the semipermeable nature of species boundaries allows us to document adaptive introgression of alleles associated with response to climate change.
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Affiliation(s)
- Scott A Taylor
- Cornell Lab of Ornithology, Fuller Evolutionary Biology Program, Ithaca, NY 14850, USA; Cornell University, Department of Ecology and Evolutionary Biology, Ithaca, NY 14853, USA.
| | - Erica L Larson
- University of Montana, Division of Biological Sciences, Missoula, MT 59812, USA
| | - Richard G Harrison
- Cornell University, Department of Ecology and Evolutionary Biology, Ithaca, NY 14853, USA
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80
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Abstract
Eukaryotes were born of a chimeric union between two prokaryotes--the progenitors of the mitochondrial and nuclear genomes. Early in eukaryote evolution, most mitochondrial genes were lost or transferred to the nucleus, but a core set of genes that code exclusively for products associated with the electron transport system remained in the mitochondrion. The products of these mitochondrial genes work in intimate association with the products of nuclear genes to enable oxidative phosphorylation and core energy production. The need for coadaptation, the challenge of cotransmission, and the possibility of genomic conflict between mitochondrial and nuclear genes have profound consequences for the ecology and evolution of eukaryotic life. An emerging interdisciplinary field that I call "mitonuclear ecology" is reassessing core concepts in evolutionary ecology including sexual reproduction, two sexes, sexual selection, adaptation, and speciation in light of the interactions of mitochondrial and nuclear genomes.
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81
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Schumer M, Cui R, Rosenthal GG, Andolfatto P. Reproductive isolation of hybrid populations driven by genetic incompatibilities. PLoS Genet 2015; 11:e1005041. [PMID: 25768654 PMCID: PMC4359097 DOI: 10.1371/journal.pgen.1005041] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 01/29/2015] [Indexed: 12/25/2022] Open
Abstract
Despite its role in homogenizing populations, hybridization has also been proposed as a means to generate new species. The conceptual basis for this idea is that hybridization can result in novel phenotypes through recombination between the parental genomes, allowing a hybrid population to occupy ecological niches unavailable to parental species. Here we present an alternative model of the evolution of reproductive isolation in hybrid populations that occurs as a simple consequence of selection against genetic incompatibilities. Unlike previous models of hybrid speciation, our model does not incorporate inbreeding, or assume that hybrids have an ecological or reproductive fitness advantage relative to parental populations. We show that reproductive isolation between hybrids and parental species can evolve frequently and rapidly under this model, even in the presence of substantial ongoing immigration from parental species and strong selection against hybrids. An interesting prediction of our model is that replicate hybrid populations formed from the same pair of parental species can evolve reproductive isolation from each other. This non-adaptive process can therefore generate patterns of species diversity and relatedness that resemble an adaptive radiation. Intriguingly, several known hybrid species exhibit patterns of reproductive isolation consistent with the predictions of our model.
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Affiliation(s)
- Molly Schumer
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Rongfeng Cui
- Department of Biology, Texas A&M University, College Station, Texas, United States of America
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, Calnali, Hidalgo, Mexico
- Max Planck Institute for the Biology of Ageing, Cologne, Germany
| | - Gil G. Rosenthal
- Department of Biology, Texas A&M University, College Station, Texas, United States of America
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, Calnali, Hidalgo, Mexico
| | - Peter Andolfatto
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
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82
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Differential introgression and effective size of marker type influence phylogenetic inference of a recently divergent avian group (Phasianidae: Tympanuchus). Mol Phylogenet Evol 2014; 84:1-13. [PMID: 25554526 DOI: 10.1016/j.ympev.2014.12.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 12/12/2014] [Accepted: 12/18/2014] [Indexed: 11/20/2022]
Abstract
Life history strategies can influence the effective population size (Ne) of loci differently based on their mode of inheritance. Recognizing how this may affect the rate of lineage sorting among marker types is important for studies focused on resolving phylogenetic relationships among recently divergent taxa. In this study, we use gene tree, coalescent-based species tree, and isolation-with-migration analyses to explore the differences between marker types (autosomal, Z-linked, and mitochondrial) in resolving phylogenetic relationships among North American prairie grouse (Tympanuchus). We found that Z-linked loci were more likely to identify monophyletic relationships among prairie grouse species compared to autosomal and mtDNA loci in both species and gene tree analyses, with species tree analyses outperforming gene trees. These results were further supported with isolation-with-migration analyses, where Z-linked loci largely followed a strict isolation model while autosomal loci were more likely to fit a model with gene flow between species following population divergence. While accounting for differences in inheritance pattern (or Ne) for marker type, results suggest that additional factors, such as strong sexual selection and sex-biased introgression (i.e., male-biased postzygotic hybrid behavioral isolation or "unsexy son"), may further explain the decreased diversity levels and increased rate of lineage sorting observed with the Z-linked loci relative to autosomal and mtDNA loci. In fact, to our knowledge no hybrid male prairie grouse have been observed breeding in the wild, yet hybrid females along with backcross females are known to produce viable offspring. Overall, this study highlights that more work is needed to determine how complex models of gene flow (i.e., sex biased introgression) and differences in the effective size among marker types based on differing life history strategies influence divergence date estimation and species delimitation.
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83
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Levin L, Blumberg A, Barshad G, Mishmar D. Mito-nuclear co-evolution: the positive and negative sides of functional ancient mutations. Front Genet 2014; 5:448. [PMID: 25566330 PMCID: PMC4274989 DOI: 10.3389/fgene.2014.00448] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 12/08/2014] [Indexed: 12/31/2022] Open
Abstract
Most cell functions are carried out by interacting factors, thus underlying the functional importance of genetic interactions between genes, termed epistasis. Epistasis could be under strong selective pressures especially in conditions where the mutation rate of one of the interacting partners notably differs from the other. Accordingly, the order of magnitude higher mitochondrial DNA (mtDNA) mutation rate as compared to the nuclear DNA (nDNA) of all tested animals, should influence systems involving mitochondrial-nuclear (mito-nuclear) interactions. Such is the case of the energy producing oxidative phosphorylation (OXPHOS) and mitochondrial translational machineries which are comprised of factors encoded by both the mtDNA and the nDNA. Additionally, the mitochondrial RNA transcription and mtDNA replication systems are operated by nDNA-encoded proteins that bind mtDNA regulatory elements. As these systems are central to cell life there is strong selection toward mito-nuclear co-evolution to maintain their function. However, it is unclear whether (A) mito-nuclear co-evolution befalls only to retain mitochondrial functions during evolution or, also, (B) serves as an adaptive tool to adjust for the evolving energetic demands as species' complexity increases. As the first step to answer these questions we discuss evidence of both negative and adaptive (positive) selection acting on the mtDNA and nDNA-encoded genes and the effect of both types of selection on mito-nuclear interacting factors. Emphasis is given to the crucial role of recurrent ancient (nodal) mutations in such selective events. We apply this point-of-view to the three available types of mito-nuclear co-evolution: protein-protein (within the OXPHOS system), protein-RNA (mainly within the mitochondrial ribosome), and protein-DNA (at the mitochondrial replication and transcription machineries).
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Affiliation(s)
- Liron Levin
- Department of Life Sciences, Ben-Gurion University of the Negev Beersheba, Israel
| | - Amit Blumberg
- Department of Life Sciences, Ben-Gurion University of the Negev Beersheba, Israel
| | - Gilad Barshad
- Department of Life Sciences, Ben-Gurion University of the Negev Beersheba, Israel
| | - Dan Mishmar
- Department of Life Sciences, Ben-Gurion University of the Negev Beersheba, Israel
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84
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Hermansen JS, Haas F, Trier CN, Bailey RI, Nederbragt AJ, Marzal A, Saetre GP. Hybrid speciation through sorting of parental incompatibilities in Italian sparrows. Mol Ecol 2014; 23:5831-42. [DOI: 10.1111/mec.12910] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 08/29/2014] [Accepted: 09/01/2014] [Indexed: 01/17/2023]
Affiliation(s)
- Jo S. Hermansen
- Department of Biosciences; Centre for Ecological and Evolutionary Synthesis; University of Oslo; PO Box 1066, Blindern N-0316 Oslo Norway
| | - Fredrik Haas
- Department of Biosciences; Centre for Ecological and Evolutionary Synthesis; University of Oslo; PO Box 1066, Blindern N-0316 Oslo Norway
| | - Cassandra N. Trier
- Department of Biosciences; Centre for Ecological and Evolutionary Synthesis; University of Oslo; PO Box 1066, Blindern N-0316 Oslo Norway
| | - Richard I. Bailey
- Department of Biosciences; Centre for Ecological and Evolutionary Synthesis; University of Oslo; PO Box 1066, Blindern N-0316 Oslo Norway
| | - Alexander J. Nederbragt
- Department of Biosciences; Centre for Ecological and Evolutionary Synthesis; University of Oslo; PO Box 1066, Blindern N-0316 Oslo Norway
| | - Alfonso Marzal
- Department of Zoology; University of Extremadura; ES-06071 Badajoz Spain
| | - Glenn-Peter Saetre
- Department of Biosciences; Centre for Ecological and Evolutionary Synthesis; University of Oslo; PO Box 1066, Blindern N-0316 Oslo Norway
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85
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Stelkens RB, Brockhurst MA, Hurst GDD, Miller EL, Greig D. The effect of hybrid transgression on environmental tolerance in experimental yeast crosses. J Evol Biol 2014; 27:2507-19. [PMID: 25262771 DOI: 10.1111/jeb.12494] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 08/22/2014] [Accepted: 09/01/2014] [Indexed: 01/29/2023]
Abstract
Evidence is rapidly accumulating that hybridization generates adaptive variation. Transgressive segregation in hybrids could promote the colonization of new environments. Here, we use an assay to select hybrid genotypes that can proliferate in environmental conditions beyond the conditions tolerated by their parents, and we directly compete them against parental genotypes in habitats across environmental clines. We made 45 different hybrid swarms by crossing yeast strains (both Saccharomyces cerevisiae and S. paradoxus) with different genetic and phenotypic divergence. We compared the ability of hybrids and parents to colonize seven types of increasingly extreme environmental clines, representing both natural and novel challenges (mimicking pollution events). We found that a significant majority of hybrids had greater environmental ranges compared to the average of both their parents' ranges (mid-parent transgression), but only a minority of hybrids had ranges exceeding their best parent (best-parent transgression). Transgression was affected by the specific strains involved in the cross and by the test environment. Genetic and phenotypic crossing distance predicted the extent of transgression in only two of the seven environments. We isolated a set of potentially transgressive hybrids selected at the extreme ends of the clines and found that many could directly outcompete their parents across whole clines and were between 1.5- and 3-fold fitter on average. Saccharomyces yeast is a good model for quantitative and replicable experimental speciation studies, which may be useful in a world where hybridization is becoming increasingly common due to the relocation of plants and animals by humans.
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Affiliation(s)
- R B Stelkens
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
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86
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Taylor SA, Curry RL, White TA, Ferretti V, Lovette I. Spatiotemporally consistent genomic signatures of reproductive isolation in a moving hybrid zone. Evolution 2014; 68:3066-81. [DOI: 10.1111/evo.12510] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 07/28/2014] [Indexed: 01/19/2023]
Affiliation(s)
- Scott A. Taylor
- Fuller Evolutionary Biology Program; Cornell Lab of Ornithology; 159 Sapsucker Woods Road Ithaca New York 14850
- Department of Ecology and Evolutionary Biology; Cornell University; Ithaca New York 14850
| | - Robert L. Curry
- Department of Biology; Villanova University; 800 Lancaster Avenue Villanova Pennsylvania 19085
| | - Thomas A. White
- Department of Ecology and Evolutionary Biology; Cornell University; Ithaca New York 14850
- Ecology Research Group; Department of Geographical and Life Sciences; Canterbury Christ Church University; North Holmes Campus; Canterbury CT1 1QU United Kingdom
| | - Valentina Ferretti
- Fuller Evolutionary Biology Program; Cornell Lab of Ornithology; 159 Sapsucker Woods Road Ithaca New York 14850
- Department of Biology; Villanova University; 800 Lancaster Avenue Villanova Pennsylvania 19085
| | - Irby Lovette
- Fuller Evolutionary Biology Program; Cornell Lab of Ornithology; 159 Sapsucker Woods Road Ithaca New York 14850
- Department of Ecology and Evolutionary Biology; Cornell University; Ithaca New York 14850
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87
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Das R, Hergenrother SD, Soto-Calderón ID, Dew JL, Anthony NM, Jensen-Seaman MI. Complete mitochondrial genome sequence of the Eastern gorilla (Gorilla beringei) and implications for african ape biogeography. J Hered 2014; 105:752-61. [PMID: 25189777 DOI: 10.1093/jhered/esu056] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The Western and Eastern species of gorillas (Gorilla gorilla and Gorilla beringei) began diverging in the mid-Pleistocene, but in a complex pattern with ongoing gene flow following their initial split. We sequenced the complete mitochondrial genomes of 1 Eastern and 1 Western gorilla to provide the most accurate date for their mitochondrial divergence, and to analyze patterns of nucleotide substitutions. The most recent common ancestor of these genomes existed about 1.9 million years ago, slightly more recent than that of chimpanzee and bonobo. We in turn use this date as a calibration to reanalyze sequences from the Eastern lowland and mountain gorilla subspecies to estimate their mitochondrial divergence at approximately 380000 years ago. These dates help frame a hypothesis whereby populations became isolated nearly 2 million years ago with restricted maternal gene flow, followed by ongoing male migration until the recent past. This process of divergence with prolonged hybridization occurred against the backdrop of the African Pleistocene, characterized by intense fluctuations in temperature and aridity, while at the same time experiencing tectonic uplifting and consequent shifts in the drainage of major river systems. Interestingly, this same pattern of introgression following divergence and discrepancies between mitochondrial and nuclear loci is seen in fossil hominins from Eurasia, suggesting that such processes may be common in hominids and that living gorillas may provide a useful model for understanding isolation and migration in our extinct relatives.
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Affiliation(s)
- Ranajit Das
- From the Department of Biological Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, PA 15282 (Das, Hergenrother, and Jensen-Seaman); Department of Biological Sciences, University of New Orleans, 2000 Lakeshore Drive, New Orleans, LA 70148 (Soto-Calderón, Dew, and Anthony); and Biology Institute, University of Antioquia, AA.1226, Medellín, Colombia (Soto-Calderón)
| | - Scott D Hergenrother
- From the Department of Biological Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, PA 15282 (Das, Hergenrother, and Jensen-Seaman); Department of Biological Sciences, University of New Orleans, 2000 Lakeshore Drive, New Orleans, LA 70148 (Soto-Calderón, Dew, and Anthony); and Biology Institute, University of Antioquia, AA.1226, Medellín, Colombia (Soto-Calderón)
| | - Iván D Soto-Calderón
- From the Department of Biological Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, PA 15282 (Das, Hergenrother, and Jensen-Seaman); Department of Biological Sciences, University of New Orleans, 2000 Lakeshore Drive, New Orleans, LA 70148 (Soto-Calderón, Dew, and Anthony); and Biology Institute, University of Antioquia, AA.1226, Medellín, Colombia (Soto-Calderón)
| | - J Larry Dew
- From the Department of Biological Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, PA 15282 (Das, Hergenrother, and Jensen-Seaman); Department of Biological Sciences, University of New Orleans, 2000 Lakeshore Drive, New Orleans, LA 70148 (Soto-Calderón, Dew, and Anthony); and Biology Institute, University of Antioquia, AA.1226, Medellín, Colombia (Soto-Calderón)
| | - Nicola M Anthony
- From the Department of Biological Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, PA 15282 (Das, Hergenrother, and Jensen-Seaman); Department of Biological Sciences, University of New Orleans, 2000 Lakeshore Drive, New Orleans, LA 70148 (Soto-Calderón, Dew, and Anthony); and Biology Institute, University of Antioquia, AA.1226, Medellín, Colombia (Soto-Calderón)
| | - Michael I Jensen-Seaman
- From the Department of Biological Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, PA 15282 (Das, Hergenrother, and Jensen-Seaman); Department of Biological Sciences, University of New Orleans, 2000 Lakeshore Drive, New Orleans, LA 70148 (Soto-Calderón, Dew, and Anthony); and Biology Institute, University of Antioquia, AA.1226, Medellín, Colombia (Soto-Calderón).
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88
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Mitochondrial-nuclear epistasis contributes to phenotypic variation and coadaptation in natural isolates of Saccharomyces cerevisiae. Genetics 2014; 198:1251-65. [PMID: 25164882 DOI: 10.1534/genetics.114.168575] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Mitochondria are essential multifunctional organelles whose metabolic functions, biogenesis, and maintenance are controlled through genetic interactions between mitochondrial and nuclear genomes. In natural populations, mitochondrial efficiencies may be impacted by epistatic interactions between naturally segregating genome variants. The extent that mitochondrial-nuclear epistasis contributes to the phenotypic variation present in nature is unknown. We have systematically replaced mitochondrial DNAs in a collection of divergent Saccharomyces cerevisiae yeast isolates and quantified the effects on growth rates in a variety of environments. We found that mitochondrial-nuclear interactions significantly affected growth rates and explained a substantial proportion of the phenotypic variances under some environmental conditions. Naturally occurring mitochondrial-nuclear genome combinations were more likely to provide growth advantages, but genetic distance could not predict the effects of epistasis. Interruption of naturally occurring mitochondrial-nuclear genome combinations increased endogenous reactive oxygen species in several strains to levels that were not always proportional to growth rate differences. Our results demonstrate that interactions between mitochondrial and nuclear genomes generate phenotypic diversity in natural populations of yeasts and that coadaptation of intergenomic interactions likely occurs quickly within the specific niches that yeast occupy. This study reveals the importance of considering allelic interactions between mitochondrial and nuclear genomes when investigating evolutionary relationships and mapping the genetic basis underlying complex traits.
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89
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Lee-Yaw JA, Jacobs CGC, Irwin DE. Individual performance in relation to cytonuclear discordance in a northern contact zone between long-toed salamander (Ambystoma macrodactylum) lineages. Mol Ecol 2014; 23:4590-602. [DOI: 10.1111/mec.12878] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2014] [Revised: 07/01/2014] [Accepted: 07/10/2014] [Indexed: 01/29/2023]
Affiliation(s)
- Julie A. Lee-Yaw
- Department of Zoology; University of British Columbia; 6270 University Blvd. Vancouver British Columbia Canada V6T 1Z4
| | - Chris G. C. Jacobs
- Institute of Biology Leiden; Leiden University; Sylviusweg 72 2333 BE Leiden The Netherlands
| | - Darren E. Irwin
- Department of Zoology; University of British Columbia; 6270 University Blvd. Vancouver British Columbia Canada V6T 1Z4
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90
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Seehausen O, Butlin RK, Keller I, Wagner CE, Boughman JW, Hohenlohe PA, Peichel CL, Saetre GP, Bank C, Brännström A, Brelsford A, Clarkson CS, Eroukhmanoff F, Feder JL, Fischer MC, Foote AD, Franchini P, Jiggins CD, Jones FC, Lindholm AK, Lucek K, Maan ME, Marques DA, Martin SH, Matthews B, Meier JI, Möst M, Nachman MW, Nonaka E, Rennison DJ, Schwarzer J, Watson ET, Westram AM, Widmer A. Genomics and the origin of species. Nat Rev Genet 2014; 15:176-92. [PMID: 24535286 DOI: 10.1038/nrg3644] [Citation(s) in RCA: 591] [Impact Index Per Article: 59.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Speciation is a fundamental evolutionary process, the knowledge of which is crucial for understanding the origins of biodiversity. Genomic approaches are an increasingly important aspect of this research field. We review current understanding of genome-wide effects of accumulating reproductive isolation and of genomic properties that influence the process of speciation. Building on this work, we identify emergent trends and gaps in our understanding, propose new approaches to more fully integrate genomics into speciation research, translate speciation theory into hypotheses that are testable using genomic tools and provide an integrative definition of the field of speciation genomics.
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Affiliation(s)
- Ole Seehausen
- Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland; and Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Roger K Butlin
- Department of Animal and Plant Sciences, the University of Sheffield, Sheffield S10 2TN, UK; and the Sven Lovén Centre - Tjärnö, University of Gothenburg, S-452 96 Strömstad, Sweden
| | - Irene Keller
- Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland; the Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland; and the Institute of Integrative Biology, ETH Zürich, ETH Zentrum CHN, 8092 Zürich, Switzerland
| | - Catherine E Wagner
- Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland; and the Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Janette W Boughman
- Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland; and the Department of Zoology; Ecology, Evolutionary Biology and Behavior Program; BEACON Center, Michigan State University, 203 Natural Sciences, East Lansing, Michigan 48824, USA
| | - Paul A Hohenlohe
- Department of Biological Sciences, Institute of Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho 83844-3051, USA
| | - Catherine L Peichel
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Glenn-Peter Saetre
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, PO BOX 1066, Blindern, N-0316 Oslo, Norway
| | - Claudia Bank
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Ake Brännström
- Integrated Science Laboratory and the Department of Mathematics and Mathematical Statistics, Umeå University, 90187 Umeå, Sweden
| | - Alan Brelsford
- Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland
| | | | - Fabrice Eroukhmanoff
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, PO BOX 1066, Blindern, N-0316 Oslo, Norway
| | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556-0369 USA
| | - Martin C Fischer
- Institute of Integrative Biology, ETH Zürich, ETH Zentrum CHN, 8092 Zürich, Switzerland
| | - Andrew D Foote
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark. Present address: the Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Paolo Franchini
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Felicity C Jones
- Friedrich Miescher Laboratory of the Max Planck Society, 72076 Tübingen, Germany
| | - Anna K Lindholm
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, CH-8057 Zurich, Switzerland
| | - Kay Lucek
- Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland; and the Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Martine E Maan
- Behavioural Biology Group, Centre for Behaviour and Neurosciences, University of Groningen, PO BOX 11103, 9700 CC Groningen, The Netherlands
| | - David A Marques
- Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland; the Division of Aquatic Ecology and Evolution, and the Computational and Molecular Population Genetics Laboratory, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Simon H Martin
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Blake Matthews
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland
| | - Joana I Meier
- Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland; the Division of Aquatic Ecology and Evolution, and the Computational and Molecular Population Genetics Laboratory, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Markus Möst
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK; and the Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Michael W Nachman
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, California 94720-3160, USA
| | - Etsuko Nonaka
- Integrated Science Laboratory and Department of Ecology and Environmental Science, Umeå University, 90187 Umeå, Sweden
| | - Diana J Rennison
- Department of Zoology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Julia Schwarzer
- Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland; the Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland; and Zoologisches Forschungsmuseum Alexander Koenig, 53113 Bonn, Germany
| | - Eric T Watson
- Department of Biology, The University of Texas at Arlington, 76010-0498 Texas, USA
| | - Anja M Westram
- Department of Animal and Plant Sciences, the University of Sheffield, Sheffield S10 2TN, UK
| | - Alex Widmer
- Institute of Integrative Biology, ETH Zürich, ETH Zentrum CHN, 8092 Zürich, Switzerland
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91
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Eroukhmanoff F, Elgvin TO, Gonzàlez Rojas MF, Haas F, Hermansen JS, Sætre GP. Effect of Species Interaction on Beak Integration in an Avian Hybrid Species Complex. Evol Biol 2014. [DOI: 10.1007/s11692-014-9278-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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