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Alale TY, Sormunen JJ, Vesterinen EJ, Klemola T, Knott KE, Baltazar‐Soares M. Genomic signatures of hybridization between Ixodes ricinus and Ixodes persulcatus in natural populations. Ecol Evol 2024; 14:e11415. [PMID: 38770117 PMCID: PMC11103643 DOI: 10.1002/ece3.11415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 04/03/2024] [Accepted: 04/29/2024] [Indexed: 05/22/2024] Open
Abstract
Identifying hybridization between common pathogen vectors is essential due to the major public health implications through risks associated with hybrid's enhanced pathogen transmission potential. The hard-ticks Ixodes ricinus and Ixodes persulcatus are the two most common vectors of tick-borne pathogens that affect human and animal health in Europe. Ixodes ricinus is a known native species in Finland with a well-known distribution, whereas I. persulcatus has expanded in range and abundance over the past 60 years, and currently it appears the most common tick species in certain areas in Finland. Here we used double-digest restriction site-associated DNA (ddRAD) sequencing on 186 ticks (morphologically identified as 92 I. ricinus, and 94 I. persulcatus) collected across Finland to investigate whether RAD generated single nucleotide polymorphisms (SNPs) can discriminate tick species and identify potential hybridization events. Two different clustering methods were used to assign specific species based on how they clustered and identified hybrids among them. We were able to discriminate between the two tick species and identified 11 putative hybrids with admixed genomic proportions ranging from approximately 24 to 76 percent. Four of these hybrids were morphologically identified as I. ricinus while the remaining seven were identified as I. persulcatus. Our results thus indicate that RAD SNPs are robust in identifying both species of the ticks as well as putative hybrids. These results further suggest ongoing hybridization between I. ricinus and I. persulcatus in their natural populations in Finland. The unique ability of RAD markers to discriminate between tick species and hybrids adds a useful aspect to tick evolutionary studies. Our findings align with previous studies and suggest a shared evolutionary history between the species, with instances of individuals possessing a considerable proportion of the other species' genome. This study is a significant step in understanding the formation of hybridization zones due to range expansion potentially associated with climate change.
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Affiliation(s)
- Theophilus Yaw Alale
- Department of BiologyUniversity of TurkuTurkuFinland
- Biodiversity UnitUniversity of TurkuTurkuFinland
| | - Jani J. Sormunen
- Department of BiologyUniversity of TurkuTurkuFinland
- Biodiversity UnitUniversity of TurkuTurkuFinland
| | | | - Tero Klemola
- Department of BiologyUniversity of TurkuTurkuFinland
| | - K. Emily Knott
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
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Schmid M, Rueffler C, Lehmann L, Mullon C. Resource Variation Within and Between Patches: Where Exploitation Competition, Local Adaptation, and Kin Selection Meet. Am Nat 2024; 203:E19-E34. [PMID: 38207145 DOI: 10.1086/727483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
AbstractIn patch- or habitat-structured populations, different processes can favor adaptive polymorphism at different scales. While spatial heterogeneity can generate spatially disruptive selection favoring variation between patches, local competition can lead to locally disruptive selection promoting variation within patches. So far, almost all theory has studied these two processes in isolation. Here, we use mathematical modeling to investigate how resource variation within and between habitats influences the evolution of variation in a consumer population where individuals compete in finite patches connected by dispersal. We find that locally and spatially disruptive selection typically act in concert, favoring polymorphism under a wider range of conditions than when in isolation. But when patches are small and dispersal between them is low, kin competition inhibits the emergence of polymorphism, especially when the latter is driven by local competition for resources. We further use our model to clarify what comparisons between trait and neutral genetic differentiation (Q ST / F ST comparisons) can tell about the nature of selection. Overall, our results help us understand the interaction between two major drivers of polymorphism: locally and spatially disruptive selection, and how this interaction is modulated by the unavoidable effects of kin selection under limited dispersal.
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Estandía A, Sendell-Price AT, Oatley G, Robertson F, Potvin D, Massaro M, Robertson BC, Clegg SM. Candidate gene polymorphisms are linked to dispersive and migratory behaviour: Searching for a mechanism behind the "paradox of the great speciators". J Evol Biol 2023; 36:1503-1516. [PMID: 37750610 DOI: 10.1111/jeb.14222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 07/22/2023] [Indexed: 09/27/2023]
Abstract
The "paradox of the great speciators" has puzzled evolutionary biologists for over half a century. A great speciator requires excellent dispersal propensity to explain its occurrence on multiple islands, but reduced dispersal ability to explain its high number of subspecies. A rapid reduction in dispersal ability is often invoked to solve this apparent paradox, but a proximate mechanism has not been identified yet. Here, we explored the role of six genes linked to migration and animal personality differences (CREB1, CLOCK, ADCYAP1, NPAS2, DRD4, and SERT) in 20 South Pacific populations of silvereye (Zosterops lateralis) that range from highly sedentary to partially migratory, to determine if genetic variation is associated with dispersal propensity and migration. We detected genetic associations in three of the six genes: (i) in a partial migrant population, migrant individuals had longer microsatellite alleles at the CLOCK gene compared to resident individuals from the same population; (ii) CREB1 displayed longer average microsatellite allele lengths in recently colonized island populations (<200 years), compared to evolutionarily older populations. Bayesian broken stick regression models supported a reduction in CREB1 length with time since colonization; and (iii) like CREB1, DRD4 showed differences in polymorphisms between recent and old colonizations but a larger sample is needed to confirm. ADCYAP1, SERT, and NPAS2 were variable but that variation was not associated with dispersal propensity. The association of genetic variants at three genes with migration and dispersal ability in silvereyes provides the impetus for further exploration of genetic mechanisms underlying dispersal shifts, and the prospect of resolving a long-running evolutionary paradox through a genetic lens.
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Affiliation(s)
- Andrea Estandía
- Edward Grey Institute of Field Ornithology, Department of Biology, University of Oxford, Oxford, UK
| | - Ashley T Sendell-Price
- Edward Grey Institute of Field Ornithology, Department of Biology, University of Oxford, Oxford, UK
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Graeme Oatley
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Fiona Robertson
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Dominique Potvin
- School of Science, Technology and Engineering, University of the Sunshine Coast, Petrie, Queensland, Australia
| | - Melanie Massaro
- Gulbali Institute and School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Albury, New South Wales, Australia
| | | | - Sonya M Clegg
- Edward Grey Institute of Field Ornithology, Department of Biology, University of Oxford, Oxford, UK
- Centre for Planetary Health and Food Security, Griffith University, Brisbane, Queensland, Australia
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4
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Meier JI, McGee MD, Marques DA, Mwaiko S, Kishe M, Wandera S, Neumann D, Mrosso H, Chapman LJ, Chapman CA, Kaufman L, Taabu-Munyaho A, Wagner CE, Bruggmann R, Excoffier L, Seehausen O. Cycles of fusion and fission enabled rapid parallel adaptive radiations in African cichlids. Science 2023; 381:eade2833. [PMID: 37769075 DOI: 10.1126/science.ade2833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 08/21/2023] [Indexed: 09/30/2023]
Abstract
Although some lineages of animals and plants have made impressive adaptive radiations when provided with ecological opportunity, the propensities to radiate vary profoundly among lineages for unknown reasons. In Africa's Lake Victoria region, one cichlid lineage radiated in every lake, with the largest radiation taking place in a lake less than 16,000 years old. We show that all of its ecological guilds evolved in situ. Cycles of lineage fusion through admixture and lineage fission through speciation characterize the history of the radiation. It was jump-started when several swamp-dwelling refugial populations, each of which were of older hybrid descent, met in the newly forming lake, where they fused into a single population, resuspending old admixture variation. Each population contributed a different set of ancient alleles from which a new adaptive radiation assembled in record time, involving additional fusion-fission cycles. We argue that repeated fusion-fission cycles in the history of a lineage make adaptive radiation fast and predictable.
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Affiliation(s)
- Joana I Meier
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre for Ecology, Evolution, and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, Switzerland
- Department of Zoology, University of Cambridge, Cambridge, UK
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Matthew D McGee
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre for Ecology, Evolution, and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, Switzerland
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - David A Marques
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre for Ecology, Evolution, and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, Switzerland
- Natural History Museum Basel, Basel, Switzerland
| | - Salome Mwaiko
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre for Ecology, Evolution, and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, Switzerland
| | - Mary Kishe
- Tanzania Fisheries Research Institute (TAFIRI), Dar es Salaam, Tanzania
| | - Sylvester Wandera
- National Fisheries Resources Research Institute (NAFIRRI), Jinja, Uganda
| | - Dirk Neumann
- Leipniz Institute for Biodiversity Change, Hamburg, Germany
| | - Hilary Mrosso
- Tanzania Fisheries Research Institute (TAFIRI), Dar es Salaam, Tanzania
| | - Lauren J Chapman
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Colin A Chapman
- Wilson Center, Washington, DC, USA
- Biology Department, Vancouver Island University, Nanaimo, British Columbia, Canada
- School of Life Sciences, University of KwaZulu-Natal, Scottsville, Pietermaritzburg, South Africa
- Shaanxi Key Laboratory for Animal Conservation, Northwest University, Xi'an, China
- Biology Department, Vancouver Island University, Nanaimo, British Columbia, Canada
| | - Les Kaufman
- Boston University Marine Program, Department of Biology, Boston University, Boston, MA, USA
| | | | | | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit and Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Laurent Excoffier
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Ole Seehausen
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre for Ecology, Evolution, and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, Switzerland
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Rohwer VG, Hagler SJ, Van Doren BM, Fuentes M, Billerman SM. Lower survival of hybrid grosbeaks, but not towhees, suggests a molt divide disfavors hybrids. Evolution 2023; 77:1956-1966. [PMID: 37345673 DOI: 10.1093/evolut/qpad112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 05/29/2023] [Accepted: 06/21/2023] [Indexed: 06/23/2023]
Abstract
Although avian hybrid zones in the Great Plains have been studied for almost 70 years, we know surprisingly little about the fitness costs to hybrids that keep these zones narrow. We compare age ratios in grosbeaks (Pheucticus ludovicianus and P. melanocephalus) and towhees (Pipilo erythropthalums and P. maculatus), two species pairs that differ in their life histories and molt schedules, to evaluate survival between hybrids and parentals. We then contrast molt and migratory divides as possible sources of selection against hybrids. Hybrid grosbeaks had 27%-33% lower survival relative to their parentals, whereas hybrid towhees had survival rates similar to parentals. Age ratio data for hybrid grosbeaks suggest high mortality in older birds, as expected if selection operates after the first year of life. This pattern is consistent with parental species of grosbeaks having contrasting molt schedules relative to migration, suggesting high mortality costs to hybrids driven by molt biology, which are expressed later in life. Contrasts in molt schedules are absent in towhees. While migratory divides may exist for towhees and grosbeaks, the low adult survival of hybrid grosbeaks suggest that molt may be an important and underappreciated source of selection maintaining this and other narrow avian hybrid zones.
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Affiliation(s)
- Vanya G Rohwer
- Cornell University Museum of Vertebrates, Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, United States
| | - Samantha J Hagler
- Cornell University Museum of Vertebrates, Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, United States
- Cornell Lab of Ornithology, Ithaca, NY, United States
| | - Benjamin M Van Doren
- Cornell Lab of Ornithology, Ithaca, NY, United States
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, United States
| | - Miguel Fuentes
- Manning College of Information and Computer Sciences, University of Massachusetts-Amherst, Amherst, MA, United States
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6
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Wharton D. Backcrossing as a species restoration technique. Zoo Biol 2023; 42:490-508. [PMID: 36967628 DOI: 10.1002/zoo.21765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/15/2023] [Accepted: 03/12/2023] [Indexed: 08/15/2023]
Abstract
An investigation was conducted on the phenotypic results of mouse hybridization and seven generations of backcrossing, observing reciprocal F1 hybrids and backcrosses of Mus spretus and a laboratory strain of Mus domesticus C57BL/6J. F1 hybrids, backcrosses, and pure control specimens were measured for 6 body characteristics, 4 pelage coloration characteristics, 14 behaviors, and reproduction as reflected in litter size. Backcrossing was pursued for seven generations to FBC7 (i.e., "Backcross 7" or seven generations from commencement of backcrossing from an F1 hybrid female) where species restoration is mathematically calculated to be at 99.7%. Except for a minority of FBC7 M. spretus specimens failing to conform completely to one pelage characteristic, FBC7 specimens were indistinguishable from controls both subjectively and in all areas of measurement. The M. spretus backcross line was followed generation by generation and was largely conforming to controls by FBC4 at latest. The same effect was observed in the reciprocal M. domesticus backcross line. Fertility was negatively affected in F1 hybrids but restored or improved in backcross generations. Discussion is offered on hybridization and backcrossing as it occurs in nature and how it has been used or could be used as an additional ex situ tool in wildlife conservation efforts. It is concluded that conservation-oriented backcrossing is a practical species/subspecies restoration technique and has the potential to make genetic rescue feasible with minimal gene flow at the binomial level. Backcrossing is most applicable in closely monitored ex situ settings (1) where only one sex remains of a given taxon; and (2) where inbreeding depression seriously threatens a remnant taxon's ability to recover, and the only gene flow option is from another distinct species.
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Affiliation(s)
- Dan Wharton
- Conservation Science (Emeritus), Chicago Zoological Society, Brookfield, Illinois, USA
- City Zoos (retired), Wildlife Conservation Society, Bronx, New York, USA
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7
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Lackey ACR, Murray AC, Mirza NA, Powell THQ. The role of sexual isolation during rapid ecological divergence: Evidence for a new dimension of isolation in Rhagoletis pomonella. J Evol Biol 2023. [PMID: 37173822 DOI: 10.1111/jeb.14179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 03/05/2023] [Accepted: 03/23/2023] [Indexed: 05/15/2023]
Abstract
The pace of divergence and likelihood of speciation often depends on how and when different types of reproductive barriers evolve. Questions remain about how reproductive isolation evolves after initial divergence. We tested for the presence of sexual isolation (reduced mating between populations due to divergent mating preferences and traits) in Rhagoletis pomonella flies, a model system for incipient ecological speciation. We measured the strength of sexual isolation between two very recently diverged (~170 generations) sympatric populations, adapted to different host fruits (hawthorn and apple). We found that flies from both populations were more likely to mate within than between populations. Thus, sexual isolation may play an important role in reducing gene flow allowed by early-acting ecological barriers. We also tested how warmer temperatures predicted under climate change could alter sexual isolation and found that sexual isolation was markedly asymmetric under warmer temperatures - apple males and hawthorn females mated randomly while apple females and hawthorn males mated more within populations than between. Our findings provide a window into the early speciation process and the role of sexual isolation after initial ecological divergence, in addition to examining how environmental conditions could shape the likelihood of further divergence.
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Affiliation(s)
- Alycia C R Lackey
- University of Louisville, Louisville, Kentucky, USA
- Binghamton University, Binghamton, New York, USA
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8
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Godin JGJ, Le Roy A, Burns AL, Seebacher F, Ward AJ. Pace-of-life syndrome: linking personality, metabolism and colour ornamentation in male guppies. Anim Behav 2022. [DOI: 10.1016/j.anbehav.2022.09.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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9
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dos Santos P, Brilhante MÂ, Messerschmid TFE, Serrano HC, Kadereit G, Branquinho C, de Vos JM. Plant growth forms dictate adaptations to the local climate. FRONTIERS IN PLANT SCIENCE 2022; 13:1023595. [PMID: 36479511 PMCID: PMC9720395 DOI: 10.3389/fpls.2022.1023595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 10/31/2022] [Indexed: 06/17/2023]
Abstract
Adaptive radiation is a significant driver of biodiversity. Primarily studied in animal systems, mechanisms that trigger adaptive radiations remain poorly understood in plants. A frequently claimed indicator of adaptive radiation in plants is growth form diversity when tied to the occupation of different habitats. However, it remains obscure whether morphological adaptations manifest as growth form diversity per se or as its constituent traits. We use the classic Aeonium radiation from the Canary Islands to ask whether adaptation across climatic space is structured by growth form evolution. Using morphological sampling with site-associated climate in a phylogenetic context, we find that growth forms dictate adaptations to the local environment. Furthermore, we demonstrate that the response of specific traits to analogous environments is antagonistic when growth forms are different. This finding suggests for the first time that growth forms represent particular ecological functions, allowing the co-occurrence of closely related species, being a product of divergent selection during evolution in sympatry.
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Affiliation(s)
- Patrícia dos Santos
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & Global Change and Sustainability Institute (CHANGE), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- Department of Environmental Sciences – Botany, University of Basel, Basel, Switzerland
| | - Miguel Ângelo Brilhante
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Lisbon, Portugal
| | - Thibaud F. E. Messerschmid
- Botanischer Garten München-Nymphenburg und Botanischen Staatssammlung, Staatliche Naturwissenschaftliche Sammlungen Bayerns, Munich, Germany
- Prinzessin Therese von Bayern Lehrstuhl für Systematik, Biodiversität & Evolution der Pflanzen, Ludwig-Maximilans-Universität München, Munich, Germany
| | - Helena Cristina Serrano
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & Global Change and Sustainability Institute (CHANGE), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Gudrun Kadereit
- Botanischer Garten München-Nymphenburg und Botanischen Staatssammlung, Staatliche Naturwissenschaftliche Sammlungen Bayerns, Munich, Germany
- Prinzessin Therese von Bayern Lehrstuhl für Systematik, Biodiversität & Evolution der Pflanzen, Ludwig-Maximilans-Universität München, Munich, Germany
| | - Cristina Branquinho
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & Global Change and Sustainability Institute (CHANGE), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Jurriaan M. de Vos
- Department of Environmental Sciences – Botany, University of Basel, Basel, Switzerland
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10
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Dobreva MP, Camacho J, Abzhanov A. Time to synchronize our clocks: Connecting developmental mechanisms and evolutionary consequences of heterochrony. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2022; 338:87-106. [PMID: 34826199 DOI: 10.1002/jez.b.23103] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 09/27/2021] [Accepted: 10/12/2021] [Indexed: 06/13/2023]
Abstract
Heterochrony, defined as a change in the timing of developmental events altering the course of evolution, was first recognized by Ernst Haeckel in 1866. Haeckel's original definition was meant to explain the observed parallels between ontogeny and phylogeny, but the interpretation of his work became a source of controversy over time. Heterochrony took its modern meaning following the now classical work in the 1970-80s by Steven J. Gould, Pere Alberch, and co-workers. Predicted and described heterochronic scenarios emphasize the many ways in which developmental changes can influence evolution. However, while important examples of heterochrony detected with comparative morphological methods have multiplied, the more mechanistic understanding of this phenomenon lagged conspicuously behind. Considering the rapid progress in imaging and molecular tools available now for developmental biologists, this review aims to stress the need to take heterochrony research to the next level. It is time to synchronize the different levels of heterochrony research into a single analysis flow: from studies on organismal-level morphology to cells to molecules and genes, using complementary techniques. To illustrate how to achieve a more comprehensive understanding of phyletic morphological diversification associated with heterochrony, we discuss several recent case studies at various phylogenetic scales that combine morphological, cellular, and molecular analyses. Such a synergistic approach offers to more fully integrate phylogenetic and ontogenetic dimensions of the fascinating evolutionary phenomenon of heterochrony.
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Affiliation(s)
| | - Jasmin Camacho
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Arkhat Abzhanov
- Department of Life Sciences, Imperial College London, Ascot, UK
- Department of Life Sciences, Natural History Museum, London, UK
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11
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Ottenburghs J. The genic view of hybridization in the Anthropocene. Evol Appl 2021; 14:2342-2360. [PMID: 34745330 PMCID: PMC8549621 DOI: 10.1111/eva.13223] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 03/10/2021] [Accepted: 03/10/2021] [Indexed: 12/24/2022] Open
Abstract
Human impact is noticeable around the globe, indicating that a new era might have begun: the Anthropocene. Continuing human activities, including land-use changes, introduction of non-native species and rapid climate change, are altering the distributions of countless species, often giving rise to human-mediated hybridization events. While the interbreeding of different populations or species can have detrimental effects, such as genetic extinction, it can be beneficial in terms of adaptive introgression or an increase in genetic diversity. In this paper, I first review the different mechanisms and outcomes of anthropogenic hybridization based on literature from the last five years (2016-2020). The most common mechanisms leading to the interbreeding of previously isolated taxa include habitat change (51% of the studies) and introduction of non-native species (34% intentional and 19% unintentional). These human-induced hybridization events most often result in introgression (80%). The high incidence of genetic exchange between the hybridizing taxa indicates that the application of a genic view of speciation (and introgression) can provide crucial insights on how to address hybridization events in the Anthropocene. This perspective considers the genome as a dynamic collection of genetic loci with distinct evolutionary histories, giving rise to a heterogenous genomic landscape in terms of genetic differentiation and introgression. First, understanding this genomic landscape can lead to a better selection of diagnostic genetic markers to characterize hybrid populations. Second, describing how introgression patterns vary across the genome can help to predict the likelihood of negative processes, such as demographic and genetic swamping, as well as positive outcomes, such as adaptive introgression. It is especially important to not only quantify how much genetic material introgressed, but also what has been exchanged. Third, comparing introgression patterns in pre-Anthropocene hybridization events with current human-induced cases might provide novel insights into the likelihood of genetic swamping or species collapse during an anthropogenic hybridization event. However, this comparative approach remains to be tested before it can be applied in practice. Finally, the genic view of introgression can be combined with conservation genomic studies to determine the legal status of hybrids and take appropriate measures to manage anthropogenic hybridization events. The interplay between evolutionary and conservation genomics will result in the constant exchange of ideas between these fields which will not only improve our knowledge on the origin of species, but also how to conserve and protect them.
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Affiliation(s)
- Jente Ottenburghs
- Wildlife Ecology and ConservationWageningen University & ResearchWageningenThe Netherlands
- Forest Ecology and Forest ManagementWageningen University & ResearchWageningenThe Netherlands
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12
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Reilly SB, Stubbs AL, Arida E, Karin BR, Arifin U, Kaiser H, Bi K, Iskandar DT, McGuire JA. Phylogenomic Analysis Reveals Dispersal-Driven Speciation and Divergence with Gene Flow in Lesser Sunda Flying Lizards (Genus Draco). Syst Biol 2021; 71:221-241. [PMID: 34117769 DOI: 10.1093/sysbio/syab043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 05/30/2021] [Accepted: 06/02/2021] [Indexed: 12/13/2022] Open
Abstract
The Lesser Sunda Archipelago offers exceptional potential as a model system for studying the dynamics of dispersal-driven diversification. The geographic proximity of the islands suggests the possibility for successful dispersal, but this is countered by the permanence of the marine barriers and extreme intervening currents that are expected to hinder gene flow. Phylogenetic and species delimitation analyses of flying lizards (genus Draco) using single mitochondrial genes, complete mitochondrial genomes, and exome-capture data sets identified 9-11 deeply divergent lineages including single-island endemics, lineages that span multiple islands, and parapatrically-distributed non-sister lineages on the larger islands. Population clustering and PCA confirmed these genetic boundaries with isolation-by-distance playing a role in some islands or island sets. While gdi estimates place most candidate species comparisons in the ambiguous zone, migration estimates suggest 9 or 10 species exist with nuclear introgression detected across some intra-island contact zones. Initial entry of Draco into the archipelago occurred at 5.5-7.5 Ma, with most inter-island colonization events having occurred between 1-3 Ma. Biogeographical model testing favors scenarios integrating geographic distance and historical island connectivity, including an initial stepping-stone dispersal process from the Greater Sunda Shelf through the Sunda Arc as far eastward as Lembata Island. However, rather than reaching the adjacent island of Pantar by dispersing over the 15-km wide Alor Strait, Draco ultimately reached Pantar (and much of the rest of the archipelago) by way of a circuitous route involving at least five over-water dispersal events. These findings suggest that historical geological and oceanographic conditions heavily influenced dispersal pathways and gene flow, which in turn drove species formation and shaped species boundaries.
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Affiliation(s)
- Sean B Reilly
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Alexander L Stubbs
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Evy Arida
- Museum Zoologicum Bogoriense, Indonesian Institute of Sciences, Cibinong, Indonesia
| | - Benjamin R Karin
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Umilaela Arifin
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, Indonesia
| | - Hinrich Kaiser
- Department of Vertebrate Zoology, Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany; and Department of Biology, Victor Valley College, Victorville, California 92395, USA
| | - Ke Bi
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA.,Computational Genomics Resource Laboratory, California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
| | | | - Jimmy A McGuire
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
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13
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Zhang L, Hood GR, Carroo I, Ott JR, Egan SP. Context-Dependent Reproductive Isolation: Host Plant Variability Drives Fitness of Hybrid Herbivores. Am Nat 2021; 197:732-739. [PMID: 33989147 DOI: 10.1086/714139] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractThe role of divergent selection between alternative environments in promoting reproductive isolation (RI) between lineages is well recognized. However, most studies view each divergent environment as homogenous, thereby overlooking the potential role within-environment variation plays in RI between differentiating lineages. Here, we test the importance of microenvironmental variation in RI by using individual trees of two host plants, each harboring locally adapted populations of the cynipid wasp Belonocnema treatae. We compared the fitness surrogate (survival) of offspring from hybrid crosses with resident crosses across individual trees on each of two primary host plants, Quercus virginiana and Q. geminata. We found evidence of weak hybrid inviability between host-associated lineages of B. treatae despite strong genomic differentiation. However, averaging across environments masked great variation in hybrid fitness on individual trees, where hybrids performed worse than, equal to, or better than residents. Thus, considering the environmental context of hybridization is critical to improving the predictability of divergence under variable selection.
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14
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Colombelli‐Négrel D, Kleindorfer S. Behavioural response to songs between genetically diverged allopatric populations of Darwin's small tree finch in the Galápagos. J Evol Biol 2021; 34:816-829. [PMID: 33714212 PMCID: PMC8251970 DOI: 10.1111/jeb.13783] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 02/01/2021] [Accepted: 03/03/2021] [Indexed: 11/26/2022]
Abstract
Empirical data that identify contemporary mechanisms of divergence shed light on how species could multiply. In this study, we measured population genetic structure, song syllable diversity and response to simulated intruder song in Darwin's small tree finch (Camarhynchus parvulus) on Santa Cruz and Floreana Islands, Galápagos archipelago. Our aim was to test whether the magnitude of contemporary behavioural response in resident birds was consistent with patterns of genetic or cultural differences between populations. We analysed genetic structure and the occurrence of song syllable types, and experimentally measured the response of resident birds to intruder bird song from different geographical origin (i.e., island) or syllable type. We discovered a weak signal of population genetic structure between Santa Cruz and Floreana Islands. Although some song syllables occurred on both islands, others were unique to each island; Santa Cruz Island males used more unique syllables than Floreana Island males. Both Santa Cruz and Floreana resident males discriminated their response towards a simulated intruder song based on the geographical origin of the intruder song, but not on the syllable type sung by the intruder. We conclude that the populations are diverging in genetic and cultural traits and identified a signal of contemporary behavioural response that could maintain divergence upon secondary contact.
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Affiliation(s)
| | - Sonia Kleindorfer
- College of Science and EngineeringFlinders UniversityAdelaideSouth AustraliaAustralia
- Konrad Lorenz Research Centre for Behaviour and CognitionDepartment of Behavioural and Cognitive BiologyUniversity of ViennaViennaAustria
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15
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Kagawa K, Seehausen O. The propagation of admixture-derived adaptive radiation potential. Proc Biol Sci 2020; 287:20200941. [PMID: 32900317 PMCID: PMC7542789 DOI: 10.1098/rspb.2020.0941] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 08/19/2020] [Indexed: 12/05/2022] Open
Abstract
Adaptive radiations (ARs) frequently show remarkable repeatability where single lineages undergo multiple independent episodes of AR in distant places and long-separate time points. Genetic variation generated through hybridization between distantly related lineages can promote AR. This mechanism, however, requires rare coincidence in space and time between a hybridization event and opening of ecological opportunity, because hybridization generates large genetic variation only locally and it will persist only for a short period. Hence, hybridization seems unlikely to explain recurrent AR in the same lineage. Contrary to these expectations, our evolutionary computer simulations demonstrate that admixture variation can geographically spread and persist for long periods if the hybrid population becomes separated into isolated sub-lineages. Subsequent secondary hybridization of some of these can reestablish genetic polymorphisms from the ancestral hybridization in places far from the birthplace of the hybrid clade and long after the ancestral hybridization event. Consequently, simulations revealed conditions where exceptional genetic variation, once generated through a rare hybridization event, can facilitate multiple ARs exploiting ecological opportunities available at distant points in time and space.
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Affiliation(s)
- Kotaro Kagawa
- Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, 6047 Kastanienbaum, Switzerland
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Hochschulstrasse 6, 3012 Bern, Switzerland
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba, Stendai, Miyagi 980-8578, Japan
| | - Ole Seehausen
- Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, 6047 Kastanienbaum, Switzerland
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Hochschulstrasse 6, 3012 Bern, Switzerland
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16
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Muschick M, Soria-Carrasco V, Feder JL, Gompert Z, Nosil P. Adaptive zones shape the magnitude of premating reproductive isolation in Timema stick insects. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190541. [PMID: 32654646 DOI: 10.1098/rstb.2019.0541] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Simpson's fossil-record inspired model of 'adaptive zones' proposes that evolution is dominated by small fluctuations within adaptive zones, occasionally punctuated by larger shifts between zones. This model can help explain why the process of population divergence often results in weak or moderate reproductive isolation (RI), rather than strong RI and distinct species. Applied to the speciation process, the adaptive zones hypothesis makes two inter-related predictions: (i) large shifts between zones are relatively rare, (ii) when large shifts do occur they generate stronger RI than shifts within zones. Here, we use ecological, phylogenetic and behavioural data to test these predictions in Timema stick insects. We show that host use in Timema is dominated by moderate shifts within the systematic divisions of flowering plants and conifers, with only a few extreme shifts between these divisions. However, when extreme shifts occur, they generate greater RI than do more moderate shifts. Our results support the adaptive zones model, and suggest that the net contribution of ecological shifts to diversification is dependent on both their magnitude and frequency. We discuss the generality of our findings in the light of emerging evidence from diverse taxa that the evolution of RI is not always the only factor determining the origin of species diversity. This article is part of the theme issue 'Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.
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Affiliation(s)
- Moritz Muschick
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK.,Department of Fish Ecology and Evolution, Eawag, Swiss Federal Institute for Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland.,Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Víctor Soria-Carrasco
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK.,Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Zach Gompert
- Department of Biology, Utah State University, Logan, UT 84322, USA
| | - Patrik Nosil
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK.,Center for Evolution and Functional Ecology, CNRS, 34000 Montpellier, France
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17
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Tinghitella RM, Lackey ACR, Durso C, Koop JAH, Boughman JW. The ecological stage changes benefits of mate choice and drives preference divergence. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190546. [PMID: 32654644 DOI: 10.1098/rstb.2019.0546] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Preference divergence is thought to contribute to reproductive isolation. Ecology can alter the way selection acts on female preferences, making them most likely to diverge when ecological conditions vary among populations. We present a novel mechanism for ecologically dependent sexual selection, termed 'the ecological stage' to highlight its ecological dependence. Our hypothesized mechanism emphasizes that males and females interact over mating in a specific ecological context, and different ecological conditions change the costs and benefits of mating interactions, selecting for different preferences in distinct environments and different male traits, especially when traits are condition dependent. We test key predictions of this mechanism in a sympatric three-spine stickleback species pair. We used a maternal half-sib split-clutch design for both species, mating females to attractive and unattractive males and raising progeny on alternate diets that mimic the specialized diets of the species in nature. We estimated the benefits of mate choice for an indicator trait (male nuptial colour) by measuring many fitness components across the lifetimes of both sons and daughters from these crosses. We analysed fitness data using a combination of aster and mixed models. We found that many benefits of mating with high-colour males depended on both species and diet. These results support the ecological stage hypothesis for sticklebacks. Finally, we discuss the potential role of this mechanism for other taxa and highlight its ability to enhance reproductive isolation as speciation proceeds, thus facilitating the evolution of strong reproductive isolation. This article is part of the theme issue 'Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.
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Affiliation(s)
| | - Alycia C R Lackey
- Biological Sciences Department, Binghamton University, Binghamton, NY, USA
| | - Catherine Durso
- Engineering and Computer Science, University of Denver, Denver, CO, USA
| | - Jennifer A H Koop
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL, USA
| | - Janette W Boughman
- Department of Integrative Biology and Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI, USA
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18
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Mandarin fish (Sinipercidae) genomes provide insights into innate predatory feeding. Commun Biol 2020; 3:361. [PMID: 32647268 PMCID: PMC7347838 DOI: 10.1038/s42003-020-1094-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 06/12/2020] [Indexed: 01/04/2023] Open
Abstract
Mandarin fishes (Sinipercidae) are piscivores that feed solely on live fry. Unlike higher vertebrates, teleosts exhibit feeding behavior driven mainly by genetic responses, with no modification by learning from parents. Mandarin fishes could serve as excellent model organisms for studying feeding behavior. We report a long-read, chromosomal-scale genome assembly for Siniperca chuatsi and genome assemblies for Siniperca kneri, Siniperca scherzeri and Coreoperca whiteheadi. Positive selection analysis revealed rapid adaptive evolution of genes related to predatory feeding/aggression, growth, pyloric caeca and euryhalinity. Very few gill rakers are observed in mandarin fishes; analogously, we found that zebrafish deficient in edar had a gill raker loss phenotype and a more predatory habit, with reduced intake of zooplankton but increased intake of prey fish. Higher expression of bmp4, which could inhibit edar expression and gill raker development through binding of a Xvent-1 site upstream of edar, may cause predatory feeding in Siniperca. He, Li, and Lv et al. took a genomics approach to study innate feeding behavior in mandarin fish. They identify genes related to predatory feeding that underwent rapid adaptive evolution. They also functionally validate the role of bmp4-edar pathway in inducing predatory feeding in zebrafish.
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19
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Feller AF, Selz OM, McGee MD, Meier JI, Mwaiko S, Seehausen O. Rapid generation of ecologically relevant behavioral novelty in experimental cichlid hybrids. Ecol Evol 2020; 10:7445-7462. [PMID: 32760540 PMCID: PMC7391563 DOI: 10.1002/ece3.6471] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 05/15/2020] [Accepted: 05/16/2020] [Indexed: 01/25/2023] Open
Abstract
The East African cichlid radiations are characterized by repeated and rapid diversification into many distinct species with different ecological specializations and by a history of hybridization events between nonsister species. Such hybridization might provide important fuel for adaptive radiation. Interspecific hybrids can have extreme trait values or novel trait combinations and such transgressive phenotypes may allow some hybrids to explore ecological niches neither of the parental species could tap into. Here, we investigate the potential of second-generation (F2) hybrids between two generalist cichlid species from Lake Malawi to exploit a resource neither parental species is specialized on: feeding by sifting sand. Some of the F2 hybrids phenotypically resembled fish of species that are specialized on sand sifting. We combined experimental behavioral and morphometric approaches to test whether the F2 hybrids are transgressive in both morphology and behavior related to sand sifting. We then performed a quantitative trait loci (QTL) analysis using RADseq markers to investigate the genetic architecture of morphological and behavioral traits. We show that transgression is present in several morphological traits, that novel trait combinations occur, and we observe transgressive trait values in sand sifting behavior in some of the F2 hybrids. Moreover, we find QTLs for morphology and for sand sifting behavior, suggesting the existence of some loci with moderate to large effects. We demonstrate that hybridization has the potential to rapidly generate novel and ecologically relevant phenotypes that may be suited to a niche neither of the parental species occupies. Interspecific hybridization may thereby contribute to the rapid generation of ecological diversity in cichlid radiations.
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Affiliation(s)
- Anna F. Feller
- Division of Aquatic Ecology and EvolutionInstitute of Ecology and EvolutionUniversity of BernBernSwitzerland
- Department of Fish Ecology and EvolutionCentre of Ecology, Evolution and BiogeochemistryEAWAG Swiss Federal Institute of Aquatic Science and TechnologyKastanienbaumSwitzerland
| | - Oliver M. Selz
- Department of Fish Ecology and EvolutionCentre of Ecology, Evolution and BiogeochemistryEAWAG Swiss Federal Institute of Aquatic Science and TechnologyKastanienbaumSwitzerland
| | - Matthew D. McGee
- Department of Fish Ecology and EvolutionCentre of Ecology, Evolution and BiogeochemistryEAWAG Swiss Federal Institute of Aquatic Science and TechnologyKastanienbaumSwitzerland
- School of Biological SciencesMonash UniversityClaytonVic.Australia
| | - Joana I. Meier
- Division of Aquatic Ecology and EvolutionInstitute of Ecology and EvolutionUniversity of BernBernSwitzerland
- Department of Fish Ecology and EvolutionCentre of Ecology, Evolution and BiogeochemistryEAWAG Swiss Federal Institute of Aquatic Science and TechnologyKastanienbaumSwitzerland
- Department of ZoologyUniversity of CambridgeCambridgeUK
- St John’s CollegeUniversity of CambridgeCambridgeUK
| | - Salome Mwaiko
- Department of Fish Ecology and EvolutionCentre of Ecology, Evolution and BiogeochemistryEAWAG Swiss Federal Institute of Aquatic Science and TechnologyKastanienbaumSwitzerland
| | - Ole Seehausen
- Division of Aquatic Ecology and EvolutionInstitute of Ecology and EvolutionUniversity of BernBernSwitzerland
- Department of Fish Ecology and EvolutionCentre of Ecology, Evolution and BiogeochemistryEAWAG Swiss Federal Institute of Aquatic Science and TechnologyKastanienbaumSwitzerland
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20
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Friis G, Milá B. Change in sexual signalling traits outruns morphological divergence across an ecological gradient in the post-glacial radiation of the songbird genus Junco. J Evol Biol 2020; 33:1276-1293. [PMID: 32603490 DOI: 10.1111/jeb.13671] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 06/15/2020] [Accepted: 06/22/2020] [Indexed: 12/30/2022]
Abstract
The relative roles of natural and sexual selection in promoting evolutionary lineage divergence remains controversial and difficult to assess in natural systems. Local adaptation through natural selection is known to play a central role in promoting evolutionary divergence, yet secondary sexual traits can vary widely among species in recent radiations, suggesting that sexual selection may also be important in the early stages of speciation. Here, we compare rates of divergence in ecologically relevant traits (morphology) and sexually selected signalling traits (coloration) relative to neutral structure in genome-wide molecular markers and examine patterns of variation in sexual dichromatism to explore the roles of natural and sexual selection in the diversification of the songbird genus Junco (Aves: Passerellidae). Juncos include divergent lineages in Central America and several dark-eyed junco (J. hyemalis) lineages that diversified recently as the group recolonized North America following the last glacial maximum (ca. 18,000 years ago). We found an accelerated rate of divergence in sexually selected characters relative to ecologically relevant traits. Moreover, sexual dichromatism measurements suggested a positive relationship between the degree of colour divergence and the strength of sexual selection when controlling for neutral genetic distance. We also found a positive correlation between dichromatism and latitude, which coincides with the geographic axis of decreasing lineage age in juncos but also with a steep ecological gradient. Finally, we found significant associations between genome-wide variants linked to functional genes and proxies of both sexual and natural selection. These results suggest that the joint effects of sexual and ecological selection have played a prominent role in the junco radiation.
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Affiliation(s)
- Guillermo Friis
- Department of Biodiversity and Evolutionary Biology, National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
| | - Borja Milá
- Department of Biodiversity and Evolutionary Biology, National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
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21
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Kleindorfer S, Dudaniec RY. Hybridization fluctuates with rainfall in Darwin’s tree finches. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Hybridization in natural populations may be an adaptive response to shifting climatic regimes, but understanding this can be limited by the timing of sampling effort and confident identification of hybrids. On the Galapagos Islands, Darwin’s finches regularly hybridize; the islands also show extreme annual variation in rainfall, but the effect of annual rainfall on the frequency of finch hybridization is little known. Across a 20-year period on Floreana Island, we compare patterns of hybridization in sympatric Darwin’s tree finches (N = 425; Camaryhnchus spp.) and test for an effect of annual rainfall on (1) the frequency of hybrids (C. pauper × C. parvulus) and (2) the percentage of male hybrid birds produced per year (hybrid recruitment). Annual rainfall correlated with recruitment positively for hybrids, negatively for C. parvulus and not at all for C. pauper. Furthermore, the percentage of hybrids (range: 12–56%) and C. parvulus did not change with sampling year, but the critically endangered C. pauper declined. Our findings indicate that hybrid recruitment is recurring and variable according to annual rainfall in Camarhynchus Darwin’s finches.
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Affiliation(s)
- Sonia Kleindorfer
- Flinders University, College of Science and Engineering, Bedford Park, Adelaide, Australia
- Konrad Lorenz Research Center for Behaviour and Cognition and Department of Behavioural and Cognitive Biology, University of Vienna, Vienna, Austria
| | - Rachael Y Dudaniec
- Macquarie University, Department of Biological Sciences, North Ryde, Sydney, Australia
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22
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Quintero I, Landis MJ. Interdependent Phenotypic and Biogeographic Evolution Driven by Biotic Interactions. Syst Biol 2019; 69:739-755. [DOI: 10.1093/sysbio/syz082] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 12/06/2019] [Accepted: 12/10/2019] [Indexed: 11/13/2022] Open
Abstract
Abstract
Biotic interactions are hypothesized to be one of the main processes shaping trait and biogeographic evolution during lineage diversification. Theoretical and empirical evidence suggests that species with similar ecological requirements either spatially exclude each other, by preventing the colonization of competitors or by driving coexisting populations to extinction, or show niche divergence when in sympatry. However, the extent and generality of the effect of interspecific competition in trait and biogeographic evolution has been limited by a dearth of appropriate process-generating models to directly test the effect of biotic interactions. Here, we formulate a phylogenetic parametric model that allows interdependence between trait and biogeographic evolution, thus enabling a direct test of central hypotheses on how biotic interactions shape these evolutionary processes. We adopt a Bayesian data augmentation approach to estimate the joint posterior distribution of trait histories, range histories, and coevolutionary process parameters under this analytically intractable model. Through simulations, we show that our model is capable of distinguishing alternative scenarios of biotic interactions. We apply our model to the radiation of Darwin’s finches—a classic example of adaptive divergence—and find limited support for in situ trait divergence in beak size, but stronger evidence for convergence in traits such as beak shape and tarsus length and for competitive exclusion throughout their evolutionary history. These findings are more consistent with presympatric, rather than postsympatric, niche divergence. Our modeling framework opens new possibilities for testing more complex hypotheses about the processes underlying lineage diversification. More generally, it provides a robust probabilistic methodology to model correlated evolution of continuous and discrete characters. [Bayesian; biotic interactions; competition; data augmentation; historical biogeography; trait evolution.]
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Affiliation(s)
- Ignacio Quintero
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA
- Département de Biologie, Institut de Biologie de l’ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Michael J Landis
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
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23
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Saarman NP, Opiro R, Hyseni C, Echodu R, Opiyo EA, Dion K, Johnson T, Aksoy S, Caccone A. The population genomics of multiple tsetse fly (Glossina fuscipes fuscipes) admixture zones in Uganda. Mol Ecol 2019; 28:66-85. [PMID: 30471158 DOI: 10.1111/mec.14957] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 10/26/2018] [Accepted: 11/05/2018] [Indexed: 11/28/2022]
Abstract
Understanding the mechanisms that enforce, maintain or reverse the process of speciation is an important challenge in evolutionary biology. This study investigates the patterns of divergence and discusses the processes that form and maintain divergent lineages of the tsetse fly Glossina fuscipes fuscipes in Uganda. We sampled 251 flies from 18 sites spanning known genetic lineages and the four admixture zones between them. We apply population genomics, hybrid zone and approximate Bayesian computation to the analysis of three types of genetic markers: 55,267 double-digest restriction site-associated DNA (ddRAD) SNPs to assess genome-wide admixture, 16 microsatellites to provide continuity with published data and accurate biogeographic modelling, and a 491-bp fragment of mitochondrial cytochrome oxidase I and II to infer maternal inheritance patterns. Admixture zones correspond with regions impacted by the reorganization of Uganda's river networks that occurred during the formation of the West African Rift system over the last several hundred thousand years. Because tsetse fly population distributions are defined by rivers, admixture zones likely represent both old and new regions of secondary contact. Our results indicate that older hybrid zones contain mostly parental types, while younger zones contain variable hybrid types resulting from multiple generations of interbreeding. These findings suggest that reproductive barriers are nearly complete in the older admixture zones, while nearly absent in the younger admixture zones. Findings are consistent with predictions of hybrid zone theory: Populations in zones of secondary contact transition rapidly from early to late stages of speciation or collapse all together.
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Affiliation(s)
- Norah P Saarman
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut
| | - Robert Opiro
- Department of Biology, Faculty of Science, Gulu University, Uganda
| | - Chaz Hyseni
- Department of Biology, University of Mississippi, Oxford, Mississippi
| | - Richard Echodu
- Department of Biology, Faculty of Science, Gulu University, Uganda
| | | | - Kirstin Dion
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut
| | - Thomas Johnson
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut
| | - Serap Aksoy
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut
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24
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Guðbrandsson J, Kapralova KH, Franzdóttir SR, Bergsveinsdóttir ÞM, Hafstað V, Jónsson ZO, Snorrason SS, Pálsson A. Extensive genetic differentiation between recently evolved sympatric Arctic charr morphs. Ecol Evol 2019; 9:10964-10983. [PMID: 31641448 PMCID: PMC6802010 DOI: 10.1002/ece3.5516] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 07/11/2019] [Accepted: 07/12/2019] [Indexed: 12/22/2022] Open
Abstract
The availability of diverse ecological niches can promote adaptation of trophic specializations and related traits, as has been repeatedly observed in evolutionary radiations of freshwater fish. The role of genetics, environment, and history in ecologically driven divergence and adaptation, can be studied on adaptive radiations or populations showing ecological polymorphism. Salmonids, especially the Salvelinus genus, are renowned for both phenotypic diversity and polymorphism. Arctic charr (Salvelinus alpinus) invaded Icelandic streams during the glacial retreat (about 10,000 years ago) and exhibits many instances of sympatric polymorphism. Particularly, well studied are the four morphs in Lake Þingvallavatn in Iceland. The small benthic (SB), large benthic (LB), planktivorous (PL), and piscivorous (PI) charr differ in many regards, including size, form, and life history traits. To investigate relatedness and genomic differentiation between morphs, we identified variable sites from RNA-sequencing data from three of those morphs and verified 22 variants in population samples. The data reveal genetic differences between the morphs, with the two benthic morphs being more similar and the PL-charr more genetically different. The markers with high differentiation map to all linkage groups, suggesting ancient and pervasive genetic separation of these three morphs. Furthermore, GO analyses suggest differences in collagen metabolism, odontogenesis, and sensory systems between PL-charr and the benthic morphs. Genotyping in population samples from all four morphs confirms the genetic separation and indicates that the PI-charr are less genetically distinct than the other three morphs. The genetic separation of the other three morphs indicates certain degree of reproductive isolation. The extent of gene flow between the morphs and the nature of reproductive barriers between them remain to be elucidated.
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Affiliation(s)
- Jóhannes Guðbrandsson
- Institute of Life and Environmental SciencesUniversity of IcelandReykjavikIceland
- Marine and Freshwater Research InstituteReykjavikIceland
| | - Kalina H. Kapralova
- Institute of Life and Environmental SciencesUniversity of IcelandReykjavikIceland
| | - Sigríður R. Franzdóttir
- Institute of Life and Environmental SciencesUniversity of IcelandReykjavikIceland
- Biomedical CenterUniversity of IcelandReykjavikIceland
| | | | - Völundur Hafstað
- Institute of Life and Environmental SciencesUniversity of IcelandReykjavikIceland
| | - Zophonías O. Jónsson
- Institute of Life and Environmental SciencesUniversity of IcelandReykjavikIceland
- Biomedical CenterUniversity of IcelandReykjavikIceland
| | | | - Arnar Pálsson
- Institute of Life and Environmental SciencesUniversity of IcelandReykjavikIceland
- Biomedical CenterUniversity of IcelandReykjavikIceland
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25
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Wollenberg Valero KC, Marshall JC, Bastiaans E, Caccone A, Camargo A, Morando M, Niemiller ML, Pabijan M, Russello MA, Sinervo B, Werneck FP, Sites JW, Wiens JJ, Steinfartz S. Patterns, Mechanisms and Genetics of Speciation in Reptiles and Amphibians. Genes (Basel) 2019; 10:genes10090646. [PMID: 31455040 PMCID: PMC6769790 DOI: 10.3390/genes10090646] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/21/2019] [Accepted: 08/05/2019] [Indexed: 12/22/2022] Open
Abstract
In this contribution, the aspects of reptile and amphibian speciation that emerged from research performed over the past decade are reviewed. First, this study assesses how patterns and processes of speciation depend on knowing the taxonomy of the group in question, and discuss how integrative taxonomy has contributed to speciation research in these groups. This study then reviews the research on different aspects of speciation in reptiles and amphibians, including biogeography and climatic niches, ecological speciation, the relationship between speciation rates and phenotypic traits, and genetics and genomics. Further, several case studies of speciation in reptiles and amphibians that exemplify many of these themes are discussed. These include studies of integrative taxonomy and biogeography in South American lizards, ecological speciation in European salamanders, speciation and phenotypic evolution in frogs and lizards. The final case study combines genomics and biogeography in tortoises. The field of amphibian and reptile speciation research has steadily moved forward from the assessment of geographic and ecological aspects, to incorporating other dimensions of speciation, such as genetic mechanisms and evolutionary forces. A higher degree of integration among all these dimensions emerges as a goal for future research.
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Affiliation(s)
| | - Jonathon C Marshall
- Department of Zoology, Weber State University, 1415 Edvalson Street, Dept. 2505, Ogden, UT 84401, USA
| | - Elizabeth Bastiaans
- Department of Biology, State University of New York, College at Oneonta, Oneonta, NY 13820, USA
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | - Arley Camargo
- Centro Universitario de Rivera, Universidad de la República, Ituzaingó 667, Rivera 40000, Uruguay
| | - Mariana Morando
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC, CENPAT-CONICET) Bv. Brown 2915, Puerto Madryn U9120ACD, Argentina
| | - Matthew L Niemiller
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL 35899, USA
| | - Maciej Pabijan
- Department of Comparative Anatomy, Institute of Zoology and Biomedical Research, Jagiellonian University, ul. Gronostajowa 9, 30-387 Kraków, Poland
| | - Michael A Russello
- Department of Biology, University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna, BC V1V 1V7, Canada
| | - Barry Sinervo
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Coastal Biology Building, 130 McAllister Way, Santa Cruz, CA 95060, USA
| | - Fernanda P Werneck
- Programa de Coleções Científicas Biológicas, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus 69060-000, Brazil
| | - Jack W Sites
- Department of Biological and Marine Sciences, University of Hull, Cottingham Road, Hull HU6 7RX, UK
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Sebastian Steinfartz
- Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig, Talstrasse 33, 04103 Leipzig, Germany
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26
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McRobie HR, Moncrief ND, Mundy NI. Multiple origins of melanism in two species of North American tree squirrel (Sciurus). BMC Evol Biol 2019; 19:140. [PMID: 31296164 PMCID: PMC6625063 DOI: 10.1186/s12862-019-1471-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 06/30/2019] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND While our understanding of the genetic basis of convergent evolution has improved there are still many uncertainties. Here we investigate the repeated evolution of dark colouration (melanism) in eastern fox squirrels (Sciurus niger; hereafter "fox squirrels") and eastern gray squirrels (S. carolinensis; hereafter "gray squirrels"). RESULTS We show that convergent evolution of melanism has arisen by independent genetic mechanisms in two populations of the fox squirrel. In a western population, melanism is associated with a 24 bp deletion in the melanocortin-1-receptor gene (MC1RΔ24 allele), whereas in a south-eastern population, melanism is associated with a point substitution in the agouti signalling protein gene causing a Gly121Cys mutation. The MC1R∆24 allele is also associated with melanism in gray squirrels, and, remarkably, all the MC1R∆24 haplotypes are identical in the two species. Evolutionary analyses show that the MC1R∆24 haplotype is more closely related to other MC1R haplotypes in the fox squirrel than in the gray squirrel. Modelling supports the possibility of gene flow between the two species. CONCLUSIONS The presence of the MC1R∆24 allele and melanism in gray squirrels is likely due to introgression from fox squirrels, although we cannot completely rule out alternative hypotheses including introgression from gray squirrels to fox squirrels, or an ancestral polymorphism. Convergent melanism in these two species of tree squirrels has evolved by at least two and probably three different evolutionary routes.
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Affiliation(s)
- Helen R McRobie
- School of Life Sciences, Anglia Ruskin University, Cambridge, CB1 1PT, UK.
| | - Nancy D Moncrief
- Virginia Museum of Natural History, Martinsville, VA, 24112, USA
| | - Nicholas I Mundy
- Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
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27
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Friedline CJ, Faske TM, Lind BM, Hobson EM, Parry D, Dyer RJ, Johnson DM, Thompson LM, Grayson KL, Eckert AJ. Evolutionary genomics of gypsy moth populations sampled along a latitudinal gradient. Mol Ecol 2019; 28:2206-2223. [PMID: 30834645 DOI: 10.1111/mec.15069] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 01/31/2019] [Accepted: 02/13/2019] [Indexed: 01/05/2023]
Abstract
The European gypsy moth (Lymantria dispar L.) was first introduced to Massachusetts in 1869 and within 150 years has spread throughout eastern North America. This large-scale invasion across a heterogeneous landscape allows examination of the genetic signatures of adaptation potentially associated with rapid geographical spread. We tested the hypothesis that spatially divergent natural selection has driven observed changes in three developmental traits that were measured in a common garden for 165 adult moths sampled from six populations across a latitudinal gradient covering the entirety of the range. We generated genotype data for 91,468 single nucleotide polymorphisms based on double digest restriction-site associated DNA sequencing and used these data to discover genome-wide associations for each trait, as well as to test for signatures of selection on the discovered architectures. Genetic structure across the introduced range of gypsy moth was low in magnitude (FST = 0.069), with signatures of bottlenecks and spatial expansion apparent in the rare portion of the allele frequency spectrum. Results from applications of Bayesian sparse linear mixed models were consistent with the presumed polygenic architectures of each trait. Further analyses indicated spatially divergent natural selection acting on larval development time and pupal mass, with the linkage disequilibrium component of this test acting as the main driver of observed patterns. The populations most important for these signals were two range-edge populations established less than 30 generations ago. We discuss the importance of rapid polygenic adaptation to the ability of non-native species to invade novel environments.
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Affiliation(s)
| | - Trevor M Faske
- Department of Biology, Virginia Commonwealth University, Richmond, Virginia
| | - Brandon M Lind
- Integrative Life Sciences Ph.D. Program, Virginia Commonwealth University, Richmond, Virginia
| | - Erin M Hobson
- Department of Biology, Virginia Commonwealth University, Richmond, Virginia
| | - Dylan Parry
- Department of Environmental & Forest Biology, State University of New York, Syracuse, New York
| | - Rodney J Dyer
- Center for Environmental Studies, Virginia Commonwealth University, Richmond, Virginia
| | - Derek M Johnson
- Department of Biology, Virginia Commonwealth University, Richmond, Virginia
| | - Lily M Thompson
- Department of Biology, University of Richmond, Richmond, Virginia
| | | | - Andrew J Eckert
- Department of Biology, Virginia Commonwealth University, Richmond, Virginia
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28
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Xue HJ, Segraves KA, Wei J, Zhang B, Nie RE, Li WZ, Yang XK. Chemically mediated sexual signals restrict hybrid speciation in a flea beetle. Behav Ecol 2018. [DOI: 10.1093/beheco/ary105] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Huai-Jun Xue
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Kari A Segraves
- Department of Biology, Syracuse University, Syracuse, NY, USA
- Archbold Biological Station, Venus, FL, USA
| | - Jing Wei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bin Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Rui-E Nie
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Wen-Zhu Li
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xing-Ke Yang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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29
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Sottas C, Reif J, Kuczyński L, Reifová R. Interspecific competition promotes habitat and morphological divergence in a secondary contact zone between two hybridizing songbirds. J Evol Biol 2018; 31:914-923. [PMID: 29603471 DOI: 10.1111/jeb.13275] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 03/22/2018] [Indexed: 01/25/2023]
Abstract
Interspecific competition is assumed to play an important role in the ecological differentiation of species and speciation. However, empirical evidence for competition's role in speciation remains surprisingly scarce. Here, we studied the role of interspecific competition in the ecological differentiation and speciation of two closely related songbird species, the Common Nightingale (Luscinia megarhynchos) and the Thrush Nightingale (Luscinia luscinia). Both species are insectivorous and ecologically very similar. They hybridize in a secondary contact zone, which is a mosaic of sites where both species co-occur (syntopy) and sites where only one species is present (allotopy). We analysed fine-scale habitat data for both species in both syntopic and allotopic sites and looked for associations between habitat use and bill morphology, which have been previously shown to be more divergent in sympatry than in allopatry. We found that the two nightingale species differ in habitat use in allotopic sites, where L. megarhynchos occurred in drier habitats and at slightly higher elevations, but not in syntopic sites. Birds from allotopic sites also showed higher interspecific divergence in relative bill size compared to birds from syntopic sites. Finally, we found an association between bill morphology and elevation. Our results are consistent with the view that interspecific competition in nightingales has resulted in partial habitat segregation in sympatry and that the habitat-specific food supply has in turn very likely led to bill size divergence. Such ecological divergence may enhance prezygotic as well as extrinsic postzygotic isolation and thus accelerate the completion of the speciation process.
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Affiliation(s)
- Camille Sottas
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jiří Reif
- Institute for Environmental Studies, Faculty of Science, Charles University, Prague, Czech Republic.,Department of Zoology and Laboratory of Ornithology, Faculty of Science, Palacký University in Olomouc, Olomouc, Czech Republic
| | - Lechosław Kuczyński
- Population Ecology Lab, Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - Radka Reifová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
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30
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Testo WL, Sundue MA. Are rates of species diversification and body size evolution coupled in the ferns? AMERICAN JOURNAL OF BOTANY 2018; 105:525-535. [PMID: 29637539 DOI: 10.1002/ajb2.1044] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 11/09/2017] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY Understanding the relationship between phenotypic evolution and lineage diversification is a central goal of evolutionary biology. To extend our understanding of the role morphological evolution plays in the diversification of plants, we examined the relationship between leaf size evolution and lineage diversification across ferns. METHODS We tested for an association between body size evolution and lineage diversification using a comparative phylogenetic approach that combined a time-calibrated phylogeny and leaf size data set for 2654 fern species. Rates of leaf size change and lineage diversification were estimated using BAMM, and rate correlations were performed for rates obtained for all families and individual species. Rates and patterns of rate-rate correlation were also analyzed separately for terrestrial and epiphytic taxa. KEY RESULTS We find no significant correlation between rates of leaf area change and lineage diversification, nor was there a difference in this pattern when growth habit is considered. Our results are consistent with the findings of an earlier study that reported decoupled rates of body size evolution and diversification in the Polypodiaceae, but conflict with a recent study that reported a positive correlation between body size evolution and lineage diversification rates in the tree fern family Cyatheaceae. CONCLUSIONS Our findings indicate that lineage diversification in ferns is largely decoupled from shifts in body size, in contrast to several other groups of organisms. Speciation in ferns appears to be primarily driven by hybridization and isolation along elevational gradients, rather than adaptive radiations featuring prominent morphological restructuring. The exceptional diversity of leaf morphologies in ferns appears to reflect a combination of ecophysiological constraints and adaptations that are not key innovations.
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Affiliation(s)
- Weston L Testo
- The Pringle Herbarium, University of Vermont, 27 Colchester Drive, Burlington, VT, 05405, USA
| | - Michael A Sundue
- The Pringle Herbarium, University of Vermont, 27 Colchester Drive, Burlington, VT, 05405, USA
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31
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Varela SAM, Matos M, Schlupp I. The role of mate-choice copying in speciation and hybridization. Biol Rev Camb Philos Soc 2018; 93:1304-1322. [DOI: 10.1111/brv.12397] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Revised: 12/27/2017] [Accepted: 01/05/2018] [Indexed: 12/16/2022]
Affiliation(s)
- Susana A. M. Varela
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências; Universidade de Lisboa; 1749-016 Lisboa Portugal
| | - Margarida Matos
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências; Universidade de Lisboa; 1749-016 Lisboa Portugal
| | - Ingo Schlupp
- Department of Biology; University of Oklahoma; Norman OK 73019 U.S.A
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32
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Guðbrandsson J, Franzdóttir SR, Kristjánsson BK, Ahi EP, Maier VH, Kapralova KH, Snorrason SS, Jónsson ZO, Pálsson A. Differential gene expression during early development in recently evolved and sympatric Arctic charr morphs. PeerJ 2018; 6:e4345. [PMID: 29441236 PMCID: PMC5807978 DOI: 10.7717/peerj.4345] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 01/19/2018] [Indexed: 02/06/2023] Open
Abstract
Phenotypic differences between closely related taxa or populations can arise through genetic variation or be environmentally induced, leading to altered transcription of genes during development. Comparative developmental studies of closely related species or variable populations within species can help to elucidate the molecular mechanisms related to evolutionary divergence and speciation. Studies of Arctic charr (Salvelinus alpinus) and related salmonids have revealed considerable phenotypic variation among populations and in Arctic charr many cases of extensive variation within lakes (resource polymorphism) have been recorded. One example is the four Arctic charr morphs in the ∼10,000 year old Lake Thingvallavatn, which differ in numerous morphological and life history traits. We set out to investigate the molecular and developmental roots of this polymorphism by studying gene expression in embryos of three of the morphs reared in a common garden set-up. We performed RNA-sequencing, de-novo transcriptome assembly and compared gene expression among morphs during an important timeframe in early development, i.e., preceding the formation of key trophic structures. Expectedly, developmental time was the predominant explanatory variable. As the data were affected by some form of RNA-degradation even though all samples passed quality control testing, an estimate of 3'-bias was the second most common explanatory variable. Importantly, morph, both as an independent variable and as interaction with developmental time, affected the expression of numerous transcripts. Transcripts with morph effect, separated the three morphs at the expression level, with the two benthic morphs being more similar. However, Gene Ontology analyses did not reveal clear functional enrichment of transcripts between groups. Verification via qPCR confirmed differential expression of several genes between the morphs, including regulatory genes such as AT-Rich Interaction Domain 4A (arid4a) and translin (tsn). The data are consistent with a scenario where genetic divergence has contributed to differential expression of multiple genes and systems during early development of these sympatric Arctic charr morphs.
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Affiliation(s)
- Jóhannes Guðbrandsson
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
- Freshwater Division, Marine and Freshwater Research Institute, Reykjavík, Iceland
| | - Sigríður Rut Franzdóttir
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
- Biomedical Center, University of Iceland, Reykjavík, Iceland
| | | | - Ehsan Pashay Ahi
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
- Karl-Franzens-Universität, Graz, Austria
| | - Valerie Helene Maier
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
- Biomedical Center, University of Iceland, Reykjavík, Iceland
| | | | | | - Zophonías Oddur Jónsson
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
- Biomedical Center, University of Iceland, Reykjavík, Iceland
| | - Arnar Pálsson
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
- Biomedical Center, University of Iceland, Reykjavík, Iceland
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33
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Pfennig KS, Kelly AL, Pierce AA. Hybridization as a facilitator of species range expansion. Proc Biol Sci 2018; 283:rspb.2016.1329. [PMID: 27683368 DOI: 10.1098/rspb.2016.1329] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 09/01/2016] [Indexed: 01/02/2023] Open
Abstract
Explaining the evolution of species geographical ranges is fundamental to understanding how biodiversity is distributed and maintained. The solution to this classic problem in ecology and evolution remains elusive: we still do not fully know how species geographical ranges evolve and what factors fuel range expansions. Resolving this problem is now more crucial than ever with increasing biodiversity loss, global change and movement of species by humans. Here, we describe and evaluate the hypothesis that hybridization between species can contribute to species range expansion. We discuss how such a process can occur and the empirical data that are needed to test this hypothesis. We also examine how species can expand into new environments via hybridization with a resident species, and yet remain distinct species. Generally, hybridization may play an underappreciated role in influencing the evolution of species ranges. Whether-and to what extent-hybridization has such an effect requires further study across more diverse taxa.
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Affiliation(s)
- Karin S Pfennig
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA
| | - Audrey L Kelly
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA
| | - Amanda A Pierce
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA
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34
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Cui R, Delclos PJ, Schumer M, Rosenthal GG. Early social learning triggers neurogenomic expression changes in a swordtail fish. Proc Biol Sci 2018; 284:rspb.2017.0701. [PMID: 28515207 DOI: 10.1098/rspb.2017.0701] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Accepted: 04/18/2017] [Indexed: 01/06/2023] Open
Abstract
Mate choice can play a pivotal role in the nature and extent of reproductive isolation between species. Mating preferences are often dependent on an individual's social experience with adult phenotypes throughout development. We show that olfactory preference in a swordtail fish (Xiphophorus malinche) is affected by previous experience with adult olfactory signals. We compare transcriptome-wide gene expression levels of pooled sensory and brain tissues between three treatment groups that differ by social experience: females with no adult exposure, females exposed to conspecifics and females exposed to heterospecifics. We identify potential functionally relevant genes and biological pathways differentially expressed not only between control and exposure groups, but also between groups exposed to conspecifics and heterospecifics. Based on our results, we speculate that vomeronasal receptor type 2 paralogs may detect species-specific pheromone components and thus play an important role in reproductive isolation between species.
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Affiliation(s)
- Rongfeng Cui
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Pablo J Delclos
- Department of Biology, Texas A&M University, College Station, TX 77843, USA.,Centro de Investigaciones Científicas de las Huastecas 'Aguazarca', Calnali, 43240 Hidalgo, Mexico
| | - Molly Schumer
- Department of Biology, Texas A&M University, College Station, TX 77843, USA.,Centro de Investigaciones Científicas de las Huastecas 'Aguazarca', Calnali, 43240 Hidalgo, Mexico.,Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Gil G Rosenthal
- Department of Biology, Texas A&M University, College Station, TX 77843, USA.,Centro de Investigaciones Científicas de las Huastecas 'Aguazarca', Calnali, 43240 Hidalgo, Mexico
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35
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Advancing Understanding of Amphibian Evolution, Ecology, Behavior, and Conservation with Massively Parallel Sequencing. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_61] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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36
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Shapiro JA. Living Organisms Author Their Read-Write Genomes in Evolution. BIOLOGY 2017; 6:E42. [PMID: 29211049 PMCID: PMC5745447 DOI: 10.3390/biology6040042] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 11/17/2017] [Accepted: 11/28/2017] [Indexed: 12/18/2022]
Abstract
Evolutionary variations generating phenotypic adaptations and novel taxa resulted from complex cellular activities altering genome content and expression: (i) Symbiogenetic cell mergers producing the mitochondrion-bearing ancestor of eukaryotes and chloroplast-bearing ancestors of photosynthetic eukaryotes; (ii) interspecific hybridizations and genome doublings generating new species and adaptive radiations of higher plants and animals; and, (iii) interspecific horizontal DNA transfer encoding virtually all of the cellular functions between organisms and their viruses in all domains of life. Consequently, assuming that evolutionary processes occur in isolated genomes of individual species has become an unrealistic abstraction. Adaptive variations also involved natural genetic engineering of mobile DNA elements to rewire regulatory networks. In the most highly evolved organisms, biological complexity scales with "non-coding" DNA content more closely than with protein-coding capacity. Coincidentally, we have learned how so-called "non-coding" RNAs that are rich in repetitive mobile DNA sequences are key regulators of complex phenotypes. Both biotic and abiotic ecological challenges serve as triggers for episodes of elevated genome change. The intersections of cell activities, biosphere interactions, horizontal DNA transfers, and non-random Read-Write genome modifications by natural genetic engineering provide a rich molecular and biological foundation for understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations.
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Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology, University of Chicago GCIS W123B, 979 E. 57th Street, Chicago, IL 60637, USA.
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37
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Scheriau CL, Nuerk NM, Sharbel TF, Koch MA. Cryptic gene pools in the Hypericum perforatum-H. maculatum complex: diploid persistence versus trapped polyploid melting. ANNALS OF BOTANY 2017; 120:955-966. [PMID: 29182722 PMCID: PMC5710527 DOI: 10.1093/aob/mcx110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 08/09/2017] [Indexed: 05/24/2023]
Abstract
BACKGROUND AND AIMS In Central Europe Hypericum perforatum and Hypericum maculatum show significant hybridization and introgression as a consequence of Pleistocene range fluctuations, and their gene pools are merging on higher ploidy levels. This paper discusses whether polyploid hybrid gene pools are trapped in the ecological climatic niche space of their diploid ancestors, and tests the idea of geographical parthenogenesis. METHODS DNA sequence information of nuclear ribosomal DNA and plastid loci, ploidy level estimates and ecological niche modelling are used to characterize the various diploid and polyploid gene pools and unravel spatio-temporal patterns of gene flow among them. KEY RESULTS On the diploid level, the three gene pools are clearly distinct between and within species of H. perforatum (two gene pools) and H. maculatum, and their divergence dates back to the first half of the Pleistocene. All polyploids in Central Europe show high levels of past and contemporary gene flow between all three gene pools. The correlation of genetic and geographical distances breaks down if the latter is larger than 250 km, indicating recent and ongoing gene flow. The two species are ecologically differentiated, but in particular hybrids among all three gene pools do not show significant niche differences compared to their parental gene pools, except for some combinations with H. maculatum. CONCLUSIONS Inter- and intraspecific gene flow between inter- and intra-species gene pools is limited on the diploid level, and the geographical distribution of the diploids largely reflects Pleistocene evolutionary history. Secondary contact promoted hybridization and introgression on the polyploid level, enabling offspring to escape the diploid gene pools. However, the hybrid polyploids do not show significant niche differences compared to their diploid progenitors. It is concluded that the observed absence of niche divergence has precluded further differentiation and geographical partitioning of new polyploid lineages being effectively separated from the parental lines. The predominantly apomictic reproducing polyploids are trapped in the polyploid gene pool and the ecological climatic niche space of their diploid ancestors.
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Affiliation(s)
- Charlotte L Scheriau
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Nicolai M Nuerk
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Timothy F Sharbel
- Global Institute for Food Security, Seed Developmental Biology Program, University of Saskatchewan, Canada
| | - Marcus A Koch
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, Germany
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38
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Peters KJ, Myers SA, Dudaniec RY, O'Connor JA, Kleindorfer S. Females drive asymmetrical introgression from rare to common species in Darwin's tree finches. J Evol Biol 2017; 30:1940-1952. [PMID: 28833876 DOI: 10.1111/jeb.13167] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 08/15/2017] [Indexed: 01/06/2023]
Abstract
The consequences of hybridization for biodiversity depend on the specific ecological and evolutionary context in which it occurs. Understanding patterns of gene flow among hybridizing species is crucial for determining the evolutionary trajectories of species assemblages. The recently discovered hybridization between two species of Darwin's tree finches (Camarhynchus parvulus and C. pauper) on Floreana Island, Galápagos, presents an exciting opportunity to investigate the mechanisms causing hybridization and its potential evolutionary consequences under conditions of recent habitat disturbance and the introduction of invasive pathogens. In this study, we combine morphological and genetic analysis with pairing observations to explore the extent, direction and drivers of hybridization and to test whether hybridization patterns are a result of asymmetrical pairing preference driven by females of the rarer species (C. pauper). We found asymmetrical introgression from the critically endangered, larger-bodied C. pauper to the common, smaller-bodied C. parvulus, which was associated with a lack of selection against heterospecific males by C. pauper females. Examination of pairing data showed that C. parvulus females paired assortatively, whereas C. pauper females showed no such pattern. This study shows how sex-specific drivers can determine the direction of gene flow in hybridizing species. Furthermore, our results suggest the existence of a hybrid swarm comprised of C. parvulus and hybrid birds. We discuss the influence of interspecific abundance differences and susceptibility to the invasive parasite Philornis downsi on the observed hybridization and recommend that the conservation of this iconic species group should be managed jointly rather than species-specific.
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Affiliation(s)
- K J Peters
- School of Biological Sciences, Flinders University, Adelaide, SA, Australia
| | - S A Myers
- Southern Seas Ecology Laboratory, School of Earth and Environmental Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - R Y Dudaniec
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| | - J A O'Connor
- Department of Environment, Water and Natural Resources, Adelaide, SA, Australia
| | - S Kleindorfer
- School of Biological Sciences, Flinders University, Adelaide, SA, Australia
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39
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Abstract
Many of the most important evolutionary variations that generated phenotypic adaptations and originated novel taxa resulted from complex cellular activities affecting genome content and expression. These activities included (i) the symbiogenetic cell merger that produced the mitochondrion-bearing ancestor of all extant eukaryotes, (ii) symbiogenetic cell mergers that produced chloroplast-bearing ancestors of photosynthetic eukaryotes, and (iii) interspecific hybridizations and genome doublings that generated new species and adaptive radiations of higher plants and animals. Adaptive variations also involved horizontal DNA transfers and natural genetic engineering by mobile DNA elements to rewire regulatory networks, such as those essential to viviparous reproduction in mammals. In the most highly evolved multicellular organisms, biological complexity scales with 'non-coding' DNA content rather than with protein-coding capacity in the genome. Coincidentally, 'non-coding' RNAs rich in repetitive mobile DNA sequences function as key regulators of complex adaptive phenotypes, such as stem cell pluripotency. The intersections of cell fusion activities, horizontal DNA transfers and natural genetic engineering of Read-Write genomes provide a rich molecular and biological foundation for understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations.
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Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology, University of Chicago, GCISW123B, 979 E. 57th Street, Chicago, IL 60637, USA
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40
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Riesch R, Muschick M, Lindtke D, Villoutreix R, Comeault AA, Farkas TE, Lucek K, Hellen E, Soria-Carrasco V, Dennis SR, de Carvalho CF, Safran RJ, Sandoval CP, Feder J, Gries R, Crespi BJ, Gries G, Gompert Z, Nosil P. Transitions between phases of genomic differentiation during stick-insect speciation. Nat Ecol Evol 2017; 1:82. [PMID: 28812654 DOI: 10.1038/s41559-017-0082] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Accepted: 01/12/2017] [Indexed: 01/17/2023]
Abstract
Speciation can involve a transition from a few genetic loci that are resistant to gene flow to genome-wide differentiation. However, only limited data exist concerning this transition and the factors promoting it. Here, we study phases of speciation using data from >100 populations of 11 species of Timema stick insects. Consistent with early phases of genic speciation, adaptive colour-pattern loci reside in localized genetic regions of accentuated differentiation between populations experiencing gene flow. Transitions to genome-wide differentiation are also observed with gene flow, in association with differentiation in polygenic chemical traits affecting mate choice. Thus, intermediate phases of speciation are associated with genome-wide differentiation and mate choice, but not growth of a few genomic islands. We also find a gap in genomic differentiation between sympatric taxa that still exchange genes and those that do not, highlighting the association between differentiation and complete reproductive isolation. Our results suggest that substantial progress towards speciation may involve the alignment of multi-faceted aspects of differentiation.
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Affiliation(s)
- Rüdiger Riesch
- School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK
| | - Moritz Muschick
- Aquatic Ecology &Evolution, Institute of Ecology and Evolution, University of Bern, CH-3012, Bern, Switzerland
| | - Dorothea Lindtke
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, South Yorkshire S10 2TN, UK
| | - Romain Villoutreix
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, South Yorkshire S10 2TN, UK
| | - Aaron A Comeault
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Timothy E Farkas
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06369, USA
| | - Kay Lucek
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, South Yorkshire S10 2TN, UK
| | - Elizabeth Hellen
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, South Yorkshire S10 2TN, UK
| | - Víctor Soria-Carrasco
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, South Yorkshire S10 2TN, UK
| | - Stuart R Dennis
- Department of Aquatic Ecology, Eawag Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600 Dübendorf, Zurich, Switzerland
| | - Clarissa F de Carvalho
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, South Yorkshire S10 2TN, UK
| | - Rebecca J Safran
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309, USA
| | - Cristina P Sandoval
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, California 93106, USA
| | - Jeff Feder
- Department of Biology, Notre Dame University, South Bend, Indiana 11111, USA
| | - Regine Gries
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Bernard J Crespi
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Gerhard Gries
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Zach Gompert
- Department of Biology, Utah State University, Logan, Utah 84322, USA
| | - Patrik Nosil
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, South Yorkshire S10 2TN, UK
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41
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Lackey ACR, Boughman JW. Evolution of reproductive isolation in stickleback fish. Evolution 2016; 71:357-372. [PMID: 27901265 DOI: 10.1111/evo.13114] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 10/15/2016] [Accepted: 10/24/2016] [Indexed: 12/21/2022]
Abstract
To understand how new species form and what causes their collapse, we examined how reproductive isolation evolves during the speciation process, considering species pairs with little to extensive divergence, including a recently collapsed pair. We estimated many reproductive barriers in each of five sets of stickleback fish species pairs using our own data and decades of previous work. We found that the types of barriers important early in the speciation process differ from those important late. Two premating barriers-habitat and sexual isolation-evolve early in divergence and remain two of the strongest barriers throughout speciation. Premating isolation evolves before postmating isolation, and extrinsic isolation is far stronger than intrinsic. Completing speciation, however, may require postmating intrinsic incompatibilities. Reverse speciation in one species pair was characterized by significant loss of sexual isolation. We present estimates of barrier strengths before and after collapse of a species pair; such detail regarding the loss of isolation has never before been documented. Additionally, despite significant asymmetries in individual barriers, which can limit speciation, total isolation was essentially symmetric between species. Our study provides important insight into the order of barrier evolution and the relative importance of isolating barriers during speciation and tests fundamental predictions of ecological speciation.
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Affiliation(s)
- Alycia C R Lackey
- Department of Integrative Biology, Michigan State University, East Lansing, Michigan.,Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, Michigan.,BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan.,Department of Biological Sciences, Watershed Studies Institute, Murray State University, 2112 Biology Building, Murray, State University, Murray, Kentucky, 42071
| | - Janette W Boughman
- Department of Integrative Biology, Michigan State University, East Lansing, Michigan.,Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, Michigan.,BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan
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42
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Meier JI, Sousa VC, Marques DA, Selz OM, Wagner CE, Excoffier L, Seehausen O. Demographic modelling with whole-genome data reveals parallel origin of similar Pundamilia cichlid species after hybridization. Mol Ecol 2016; 26:123-141. [PMID: 27613570 DOI: 10.1111/mec.13838] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 08/15/2016] [Accepted: 08/22/2016] [Indexed: 01/15/2023]
Abstract
Modes and mechanisms of speciation are best studied in young species pairs. In older taxa, it is increasingly difficult to distinguish what happened during speciation from what happened after speciation. Lake Victoria cichlids in the genus Pundamilia encompass a complex of young species and polymorphic populations. One Pundamilia species pair, P. pundamilia and P. nyererei, is particularly well suited to study speciation because sympatric population pairs occur with different levels of phenotypic differentiation and reproductive isolation at different rocky islands within the lake. Genetic distances between allopatric island populations of the same nominal species often exceed those between the sympatric species. It thus remained unresolved whether speciation into P. nyererei and P. pundamilia occurred once, followed by geographical range expansion and interspecific gene flow in local sympatry, or if the species pair arose repeatedly by parallel speciation. Here, we use genomic data and demographic modelling to test these alternative evolutionary scenarios. We demonstrate that gene flow plays a strong role in shaping the observed patterns of genetic similarity, including both gene flow between sympatric species and gene flow between allopatric populations, as well as recent and early gene flow. The best supported model for the origin of P. pundamilia and P. nyererei population pairs at two different islands is one where speciation happened twice, whereby the second speciation event follows shortly after introgression from an allopatric P. nyererei population that arose earlier. Our findings support the hypothesis that very similar species may arise repeatedly, potentially facilitated by introgressed genetic variation.
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Affiliation(s)
- Joana I Meier
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland.,CMPG, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland.,Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, CH-6047, Kastanienbaum, Switzerland
| | - Vitor C Sousa
- CMPG, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, CH-1015, Switzerland
| | - David A Marques
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland.,CMPG, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland.,Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, CH-6047, Kastanienbaum, Switzerland
| | - Oliver M Selz
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland.,Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, CH-6047, Kastanienbaum, Switzerland
| | - Catherine E Wagner
- Biodiversity Institute & Department of Botany, University of Wyoming, Berry Center, 1000 E. University Ave, Laramie, WY, 82071, USA
| | - Laurent Excoffier
- CMPG, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, CH-1015, Switzerland
| | - Ole Seehausen
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland.,Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, CH-6047, Kastanienbaum, Switzerland
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43
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Chaves JA, Cooper EA, Hendry AP, Podos J, De León LF, Raeymaekers JAM, MacMillan W, Uy JAC. Genomic variation at the tips of the adaptive radiation of Darwin's finches. Mol Ecol 2016; 25:5282-5295. [DOI: 10.1111/mec.13743] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 06/27/2016] [Accepted: 06/28/2016] [Indexed: 01/22/2023]
Affiliation(s)
- Jaime A. Chaves
- Department of Biology; University of Miami; Coral Gables FL 33146 USA
- Universidad San Francisco de Quito, USFQ; Colegio de Ciencias Biológicas y Ambientales; y Extensión Galápagos Campus Cumbayá Quito Ecuador
| | - Elizabeth A. Cooper
- Department of Biology; University of Miami; Coral Gables FL 33146 USA
- Department of Genetics and Biochemistry; Clemson University; Clemson SC 29634 USA
| | - Andrew P. Hendry
- Redpath Museum; Department of Biology; McGill University; Montréal QC Canada
| | - Jeffrey Podos
- Department of Biology; University of Massachusetts Amherst; Amherst MA 01003 USA
| | - Luis F. De León
- Centro de Biodiversidad y Descubrimiento de Drogas; Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP); Ciudad del Saber Panama Panama
- Department of Biology; University of Massachusetts Boston; 100 Morrissey Blvd Boston MA 02125 USA
| | - Joost A. M. Raeymaekers
- Laboratory of Biodiversity and Evolutionary Genomics; University of Leuven; B-3000 Leuven Belgium
- Center for Biodiversity Dynamics; Department of Biology; Norwegian University of Science and Technology; N-7491 Trondheim Norway
| | | | - J. Albert C. Uy
- Department of Biology; University of Miami; Coral Gables FL 33146 USA
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44
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Mitchell SM, Muehlbauer LK, Freedberg S. Nuclear introgression without mitochondrial introgression in two turtle species exhibiting sex-specific trophic differentiation. Ecol Evol 2016; 6:3280-8. [PMID: 27252833 PMCID: PMC4870212 DOI: 10.1002/ece3.2087] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 02/15/2016] [Accepted: 02/22/2016] [Indexed: 12/24/2022] Open
Abstract
Despite the presence of reproductive barriers between species, interspecific gene introgression has been documented in a range of natural systems. Comparing patterns of genetic introgression in biparental versus matrilineal markers can potentially reveal sex-specific barriers to interspecific gene flow. Hybridization has been documented in the freshwater turtles Graptemys geographica and G. pseudogeographica, whose ranges are largely sympatric. Morphological differentiation between the species is restricted to females, with female G. geographica possessing large heads and jaws compared to the narrow heads of G. pseudogeographica females. If hybrid females are morphologically intermediate, they may be less successful at exploiting parental feeding niches, thereby limiting the introgression of maternally inherited, but not biparental, molecular markers. We paired sequence data with stable isotope analysis and examined sex-specific genetic introgression and trophic differentiation in sympatric populations of G. geographica and G. pseudogeographica. We observed introgression from G. pseudogeographica into G. geographica at three nuclear loci, but not at the mitochondrial locus. Analysis of ∂(15)N and ∂(13)C was consistent with species differences in trophic positioning in females, but not males. These results suggest that ecological divergence in females may reduce the opportunity for gene flow in this system.
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Affiliation(s)
- Sarah M Mitchell
- Department of Ecology, Evolution, and Organismal Biology Iowa State University Ames Iowa 50011-1020
| | - Laura K Muehlbauer
- Department of Biology St. Olaf College 1520 St. Olaf Avenue Northfield Minnesota 55057
| | - Steven Freedberg
- Department of Biology St. Olaf College 1520 St. Olaf Avenue Northfield Minnesota 55057
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45
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Pfennig KS. Reinforcement as an initiator of population divergence and speciation. Curr Zool 2016; 62:145-154. [PMID: 29491902 PMCID: PMC5804236 DOI: 10.1093/cz/zow033] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 12/29/2015] [Indexed: 02/02/2023] Open
Abstract
When hybridization results in reduced fitness, natural selection is expected to favor the evolution of traits that minimize the likelihood of hybridizing in the first place. This process, termed reinforcement (or, more generally, reproductive character displacement), thereby contributes to the evolution of enhanced reproductive isolation between hybridizing groups. By enhancing reproductive isolation in this way, reinforcement plays an important role in the final stages of speciation. However, reinforcement can also contribute to the early stages of speciation. Specifically, because selection to avoid hybridization occurs only in sympatric populations, the unfolding of reinforcement can lead to the evolution of traits in sympatric populations that reduce reproduction between conspecifics in sympatry versus those in allopatry. Thus, reinforcement between species can lead to reproductive isolation—and possibly speciation—between populations in sympatry versus those in allopatry or among different sympatric populations. Here, I describe how this process can occur, the conditions under which it is most likely to occur, and the empirical data needed to evaluate the hypothesis that reinforcement can initiate speciation.
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Affiliation(s)
- Karin S Pfennig
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA
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46
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Jančúchová-Lásková J, Landová E, Frynta D. Experimental Crossing of Two Distinct Species of Leopard Geckos, Eublepharis angramainyu and E. macularius: Viability, Fertility and Phenotypic Variation of the Hybrids. PLoS One 2015; 10:e0143630. [PMID: 26633648 PMCID: PMC4669172 DOI: 10.1371/journal.pone.0143630] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 11/07/2015] [Indexed: 12/01/2022] Open
Abstract
Hybridization between distinct species of animals and subsequent genetic introgression plays a considerable role in the speciation process and the emergence of adaptive characters. Fitness of between-species hybrids usually sharply decreases with the divergence time of the concerned species and the divergence depth, which still allows for a successful crossing differs among principal clades of vertebrates. Recently, a review of hybridization events among distinct lizard species revealed that lizards belong to vertebrates with a highly developed ability to hybridize. In spite of this, reliable reports of experimental hybridizations between genetically fairly divergent species are only exceptional. Here, we show the results of the crossing of two distinct allopatric species of eyelid geckos possessing temperature sex determination and lacking sex chromosomes: Eublepharis macularius distributed in Pakistan/Afghanistan area and E. angramainyu, which inhabits Mesopotamia and adjacent areas. We demonstrated that F1 hybrids were viable and fertile, and the introgression of E. angramainyu genes into the E. macularius genome can be enabled via a backcrossing. The examined hybrids (except those of the F2 generation) displayed neither malformations nor a reduced survival. Analyses of morphometric and coloration traits confirmed phenotypic distinctness of both parental species and their F1 hybrids. These findings contrast with long-term geographic and an evolutionary separation of the studied species. Thus, the occurrence of fertile hybrids of comparably divergent species, such as E. angramainyu and E. macularius, may also be expected in other taxa of squamates. This would violate the current estimates of species diversity in lizards.
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Affiliation(s)
| | - Eva Landová
- Department of Zoology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Daniel Frynta
- Department of Zoology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
- * E-mail:
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47
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Grant PR, Grant BR. Introgressive hybridization and natural selection in Darwin's finches. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12702] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Peter R. Grant
- Department of Ecology and Evolutionary Biology; Princeton University; Princeton NJ 08544-1003 USA
| | - B. Rosemary Grant
- Department of Ecology and Evolutionary Biology; Princeton University; Princeton NJ 08544-1003 USA
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48
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King KC, Stelkens RB, Webster JP, Smith DF, Brockhurst MA. Hybridization in Parasites: Consequences for Adaptive Evolution, Pathogenesis, and Public Health in a Changing World. PLoS Pathog 2015; 11:e1005098. [PMID: 26336070 PMCID: PMC4559376 DOI: 10.1371/journal.ppat.1005098] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Kayla C. King
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | | | - Joanne P. Webster
- Department of Pathology and Pathogen Biology, Centre for Emerging, Endemic and Exotic Diseases (CEEED), Royal Veterinary College, University of London, London, United Kingdom
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49
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Saarman NP, Pogson GH. Introgression between invasive and native blue mussels (genusMytilus) in the central California hybrid zone. Mol Ecol 2015; 24:4723-38. [DOI: 10.1111/mec.13340] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 07/28/2015] [Accepted: 07/29/2015] [Indexed: 01/05/2023]
Affiliation(s)
- Norah P. Saarman
- Department of Ecology and Evolutionary Biology; Yale University; PO Box 208106 New Haven CT 06520-8106 USA
| | - Grant H. Pogson
- Department of Ecology and Evolutionary Biology; UC Santa Cruz; Santa Cruz CA 95064 USA
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50
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Bhullar BAS, Morris ZS, Sefton EM, Tok A, Tokita M, Namkoong B, Camacho J, Burnham DA, Abzhanov A. A molecular mechanism for the origin of a key evolutionary innovation, the bird beak and palate, revealed by an integrative approach to major transitions in vertebrate history. Evolution 2015; 69:1665-77. [PMID: 25964090 DOI: 10.1111/evo.12684] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2014] [Accepted: 04/08/2015] [Indexed: 12/17/2022]
Abstract
The avian beak is a key evolutionary innovation whose flexibility has permitted birds to diversify into a range of disparate ecological niches. We approached the problem of the mechanism behind this innovation using an approach bridging paleontology, comparative anatomy, and experimental developmental biology. First, we used fossil and extant data to show the beak is distinctive in consisting of fused premaxillae that are geometrically distinct from those of ancestral archosaurs. To elucidate underlying developmental mechanisms, we examined candidate gene expression domains in the embryonic face: the earlier frontonasal ectodermal zone (FEZ) and the later midfacial WNT-responsive region, in birds and several reptiles. This permitted the identification of an autapomorphic median gene expression region in Aves. To test the mechanism, we used inhibitors of both pathways to replicate in chicken the ancestral amniote expression. Altering the FEZ altered later WNT responsiveness to the ancestral pattern. Skeletal phenotypes from both types of experiments had premaxillae that clustered geometrically with ancestral fossil forms instead of beaked birds. The palatal region was also altered to a more ancestral phenotype. This is consistent with the fossil record and with the tight functional association of avian premaxillae and palate in forming a kinetic beak.
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Affiliation(s)
- Bhart-Anjan S Bhullar
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts, 02138. .,Department of Organismal Biology and Anatomy, University of Chicago, 1027 E. 57th St., Anatomy 306, Chicago, Illinois, 60637. .,Department of Geology and Geophysics, Yale University, P.O. Box 208109, New Haven, Connecticut, 06520. .,Peabody Museum of Natural History, Yale University, P.O. Box 208109, New Haven, Connecticut, 06520.
| | - Zachary S Morris
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts, 02138
| | - Elizabeth M Sefton
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts, 02138.,Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, Massachusetts, 02138
| | - Atalay Tok
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts, 02138
| | - Masayoshi Tokita
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts, 02138
| | - Bumjin Namkoong
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts, 02138
| | - Jasmin Camacho
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts, 02138
| | - David A Burnham
- Biodiversity Institute and Natural History Museum, University of Kansas, 1345 Jayhawk Boulevard, Lawrence, Kansas, 66045
| | - Arhat Abzhanov
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts, 02138. .,Current address: Department of Life Sciences, Imperial College London, Silwood Park Campus Buckhurst Road, Ascot, Berkshire SL5 7PY, United Kingdom. .,Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom.
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