1
|
Tiddy IC, Schneider K, Elmer KR. Environmental correlates of adaptive diversification in postglacial freshwater fishes. JOURNAL OF FISH BIOLOGY 2024; 104:517-535. [PMID: 37984834 DOI: 10.1111/jfb.15621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 11/22/2023]
Abstract
Determining how environmental conditions contribute to divergence among populations and drive speciation is fundamental to resolving mechanisms and understanding outcomes in evolutionary biology. Postglacial freshwater fish species in the Northern Hemisphere are ideal biological systems to explore the effects of environment on diversification in morphology, ecology, and genetics (ecomorph divergences) within lakes. To date, various environmental factors have been implicated in the presence of multiple ecomorphs within particular lakes or regions. However, concerted evidence for generalizable patterns in environmental variables associated with speciation across geographical regions and across species and genera has been lacking. Here, we aimed to identify key biotic and abiotic factors associated with ecological divergence of postglacial freshwater fish species into multiple sympatric ecomorphs, focusing on species in the well-studied, widespread, and co-distributed genera Gasterosteus, Salvelinus, and Coregonus (stickleback, charr, and whitefish, respectively). We found that the presence of multiple sympatric ecomorphs tended to be associated with increasing lake surface area, maximum depth, and nutrient availability. In addition, predation, competition, and prey availability were suggested to play a role in divergence into multiple ecomorphs, but the effects of biotic factors require further study. Although we identified several environmental factors correlated with the presence of multiple ecomorphs, there were substantial data gaps across species and regions. An improved understanding of these systems may provide insight into both generalizable environmental factors involved in speciation in other systems, and potential ecological and evolutionary responses of species complexes when these variables are altered by environmental change.
Collapse
Affiliation(s)
- Isabelle C Tiddy
- School of Biodiversity, One Health & Veterinary Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Kevin Schneider
- School of Biodiversity, One Health & Veterinary Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Kathryn R Elmer
- School of Biodiversity, One Health & Veterinary Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| |
Collapse
|
2
|
Burress ED, Muñoz MM. Phenotypic rate and state are decoupled in response to river-to-lake transitions in cichlid fishes. Evolution 2023; 77:2365-2377. [PMID: 37624672 DOI: 10.1093/evolut/qpad143] [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: 01/21/2023] [Revised: 07/10/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023]
Abstract
Geographic access to isolated ecosystems is an important catalyst of adaptive radiation. Cichlid fishes repeatedly colonized rift, crater, and volcanic lakes from surrounding rivers. We test the "lake effect" on the phenotypic rate and state across 253 cichlid species. The rate of evolution was consistently higher (~10-fold) in lakes, and consistent across different dimensions of the phenotype. Rate shifts tended to occur coincident with or immediately following river-to-lake transitions, generally resulting in 2- to 5-fold faster rates than in the founding riverine lineage. By contrast, river- and lake-dwelling cichlids exhibit considerable overlap in phenotypes, generally with less disparity in lakes, but often different evolutionary optima. Taken together, these results suggest that lake radiations rapidly expand into niches largely already represented by ancestral riverine lineages, albeit in different frequencies. Lakes may provide ecological opportunity via ecological release (e.g., from predators/competitors) but need not be coupled with access to novel ecological niches.
Collapse
Affiliation(s)
- Edward D Burress
- Department of Ecology and Evolution, Yale University, New Haven, CT, United States
| | - Martha M Muñoz
- Department of Ecology and Evolution, Yale University, New Haven, CT, United States
| |
Collapse
|
3
|
Estivals G, Duponchelle F, García-Dávila C, Römer U, Mariac C, Renno JF. Exceptional Genetic Differentiation at a Micro-geographic Scale in Apistogramma agassizii (Steindachner, 1875) from the Peruvian Amazon: Sympatric Speciation? Evol Biol 2022. [DOI: 10.1007/s11692-022-09587-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
|
4
|
Early stages of sympatric homoploid hybrid speciation in crater lake cichlid fishes. Nat Commun 2022; 13:5893. [PMID: 36202802 PMCID: PMC9537415 DOI: 10.1038/s41467-022-33319-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/13/2022] [Indexed: 11/27/2022] Open
Abstract
Homoploid hybrid speciation (i.e., hybrid speciation without a change in ploidy) has traditionally been considered to be rare in animals. Only few accepted empirical examples of homoploid hybrid speciation in nature exist, and in only one previous case (insects) was it convincingly shown that this process occurred in complete sympatry. Here, we report an instance of sympatric homoploid hybrid speciation in Midas cichlid fishes in Crater Lake Xiloá, Nicaragua. The hybrid lineage, albeit at an early stage of speciation, has genomically and phenotypically diverged from both of its two parental species. Together with a distinct stable isotope signature this suggests that this hybrid lineages occupies a different trophic niche compared to the other sympatric Midas cichlid species in Crater Lake Xiloá. Here, the authors present a rare example of sympatric homoploid hybrid speciation, without ploidy changes, in the Midas cichlid fishes from Nicaragua. Midas cichlid hybrids occupy a different ecological niche, likely facilitated by body shape adaptations.
Collapse
|
5
|
Bracamonte SE, Hofmann MJ, Lozano-Martín C, Eizaguirre C, Barluenga M. Divergent and non-parallel evolution of MHC IIB in the Neotropical Midas cichlid species complex. BMC Ecol Evol 2022; 22:41. [PMID: 35365100 PMCID: PMC8974093 DOI: 10.1186/s12862-022-01997-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 03/21/2022] [Indexed: 01/09/2023] Open
Abstract
Background Ecological diversification is the result of divergent natural selection by contrasting habitat characteristics that favours the evolution of distinct phenotypes. This process can happen in sympatry and in allopatry. Habitat-specific parasite communities have the potential to drive diversification among host populations by imposing selective pressures on their host's immune system. In particular, the hyperdiverse genes of the major histocompatibility complex (MHC) are implicated in parasite-mediated host divergence. Here, we studied the extent of divergence at MHC, and discuss how it may have contributed to the Nicaraguan Midas cichlid species complex diversification, one of the most convincing examples of rapid sympatric parallel speciation. Results We genotyped the MHC IIB for individuals from six sympatric Midas cichlid assemblages, each containing species that have adapted to exploit similar habitats. We recovered large allelic and functional diversity within the species complex. While most alleles were rare, functional groups of alleles (supertypes) were common, suggesting that they are key to survival and that they were maintained during colonization and subsequent radiations. We identified lake-specific and habitat-specific signatures for both allelic and functional diversity, but no clear pattern of parallel divergence among ecomorphologically similar phenotypes. Conclusions Colonization and demographic effects of the fish could have contributed to MHC evolution in the Midas cichlid in conjunction with habitat-specific selective pressures, such as parasites associated to alternative preys or environmental features. Additional ecological data will help evaluating the role of host–parasite interactions in the Midas cichlid radiations and aid in elucidating the potential role of non-parallel features differentiating crater lake species assemblages. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-01997-9.
Collapse
Affiliation(s)
- Seraina E Bracamonte
- Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal 2, 28006, Madrid, Spain
| | - Melinda J Hofmann
- Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal 2, 28006, Madrid, Spain
| | - Carlos Lozano-Martín
- Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal 2, 28006, Madrid, Spain
| | - Christophe Eizaguirre
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Marta Barluenga
- Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal 2, 28006, Madrid, Spain.
| |
Collapse
|
6
|
The macroparasite fauna of cichlid fish from Nicaraguan lakes, a model system for understanding host-parasite diversification and speciation. Sci Rep 2022; 12:3944. [PMID: 35273219 PMCID: PMC8913791 DOI: 10.1038/s41598-022-07647-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 02/15/2022] [Indexed: 01/28/2023] Open
Abstract
The Nicaraguan lakes represent an ideal continent-island-like setting to study the colonization patterns of both fish and their parasites. The dominant fish fauna are cichlids, particularly the Midas cichlid species complex Amphilophus spp., a well-studied model for recent sympatric speciation. Here, we characterized the Midas cichlid macroparasite diversity in Nicaraguan lakes. We evaluated patterns of parasite diversity across host populations. Morphological and molecular analyses were conducted, revealing a macroparasite fauna composed by 37 taxa, including platyhelminths, nematodes, copepods, branchiurans, hirudineans and oribatids. Three invasive species are reported for the first time. The Midas cichlid was infected by 22 parasite taxa, 18 shared with other cichlids. Eight taxa conformed the core parasite fauna of the Midas cichlid. The large lakes had higher parasite diversity than the smaller and isolated crater lakes, although parasite infracommunity diversity was lower. Environmental factors along with the differential distribution of intermediate hosts, the potential resistance gained by their hosts after colonization of new lakes, competitive exclusion among parasites, or the introduction of exotic fish, may determine the observed pattern of parasite heterogeneous distribution. Our study provides a ground to explore the evolutionary history of both, hosts and parasites within the context of speciation and diversification processes.
Collapse
|
7
|
Burress ED, Piálek L, Casciotta J, Almirón A, Říčan O. Rapid Parallel Morphological and Mechanical Diversification of South American Pike Cichlids (Crenicichla). Syst Biol 2022; 72:120-133. [PMID: 35244182 DOI: 10.1093/sysbio/syac018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/24/2022] [Accepted: 03/01/2022] [Indexed: 11/13/2022] Open
Abstract
Explosive bouts of diversification are one of the most conspicuous features of the tree of life. When such bursts are repeated in similar environments it suggests some degree of predictability in the evolutionary process. We assess parallel adaptive radiation of South American pike cichlids (Crenicichla) using phylogenomics and phylogenetic comparative methods. We find that species flocks in the Uruguay and Iguazú River basins rapidly diversified into the same set of ecomorphs that reflect feeding ecology. Both adaptive radiations involve expansion of functional morphology, resulting in unique jaw phenotypes. Yet, form and function were decoupled such that most ecomorphs share similar mechanical properties of the jaws (i.e., jaw motion during a feeding strike). Prey mobility explained six to nine-fold differences in the rate of morphological evolution, but had no effect on the rate of mechanical evolution. We find no evidence of gene flow between species flocks or with surrounding coastal lineages that may explain their rapid diversification. When compared to cichlids of the East African Great Lakes and other prominent adaptive radiations, pike cichlids share many themes, including rapid expansion of phenotypic diversity, specialization along the benthic-to-pelagic habitat and soft-to-hard prey axes, and the evolution of conspicuous functional innovations. Yet, decoupled evolution of form and function and the absence of hybridization as a catalyzing force are departures from patterns observed in other adaptive radiations. Many-to-one mapping of morphology to mechanical properties is a mechanism by which pike cichlids exhibit a diversity of feeding ecologies while avoiding exacerbating underlying mechanical trade-offs.
Collapse
Affiliation(s)
- Edward D Burress
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Lubomír Piálek
- Department of Zoology, Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Jorge Casciotta
- División Zoología Vertebrados, Facultad de Ciencias Naturales y Museo,UNLP, Paseo del Bosque, 1900 La Plata, Buenos Aires, Argentina.,CIC,Comisión de Investigaciones Científicas de la Provincia de Buenos Aires, La Plata, Argentina
| | - Adriana Almirón
- División Zoología Vertebrados, Facultad de Ciencias Naturales y Museo,UNLP, Paseo del Bosque, 1900 La Plata, Buenos Aires, Argentina
| | - Oldřich Říčan
- Department of Zoology, Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic
| |
Collapse
|
8
|
Cárcamo-Tejer V, Vila I, Llanquín-Rosas F, Sáez-Arteaga A, Guerrero-Jiménez C. Phylogeography of high Andean killifishes Orestias (Teleostei: Cyprinodontidae) in Caquena and Lauca sub-basins of the Altiplano (Chile): mitochondrial and nuclear analysis of an endangered fish. PeerJ 2021; 9:e11917. [PMID: 34484986 DOI: 10.7717/peerj.11917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 07/15/2021] [Indexed: 11/20/2022] Open
Abstract
From the early Miocene, the uplift of the Andes Mountains, intense volcanic activity and the occurrence of successive periods of dryness and humidity would have differentially influenced the modification of Altiplano watersheds, and consequently the evolutionary history of the taxa that live there. We analyzed Orestias populations from the Caquena and Lauca Altiplanic sub-basins of northern Chile to determine their genetic differentiation and relationship to their geographical distribution using mitochondrial (D-loop) and nuclear (microsatellite) molecular markers and to reconstruct its biogeographic history on these sub-basins. The results allowed reconstructing and reevaluating the evolutionary history of the genus in the area; genic diversity and differentiation together with different founding genetic groups suggest that Orestias have been spread homogeneously in the study area and would have experienced local disturbances that promoted isolation and diversification in restricted zones of their distribution.
Collapse
Affiliation(s)
- Violeta Cárcamo-Tejer
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Región Metropolitana, Chile
| | - Irma Vila
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Región Metropolitana, Chile
| | - Francisco Llanquín-Rosas
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Región Metropolitana, Chile
| | - Alberto Sáez-Arteaga
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Temuco, Región de la Araucanía, Chile
| | - Claudia Guerrero-Jiménez
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Temuco, Región de la Araucanía, Chile
| |
Collapse
|
9
|
Sowersby W, Cerca J, Wong BBM, Lehtonen TK, Chapple DG, Leal-Cardín M, Barluenga M, Ravinet M. Pervasive admixture and the spread of a large-lipped form in a cichlid fish radiation. Mol Ecol 2021; 30:5551-5571. [PMID: 34418206 DOI: 10.1111/mec.16139] [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: 12/15/2019] [Revised: 07/31/2021] [Accepted: 08/11/2021] [Indexed: 12/30/2022]
Abstract
Adaptive radiations have proven important for understanding the mechanisms and processes underlying biological diversity. The convergence of form and function, as well as admixture and adaptive introgression, are common in adaptive radiations. However, distinguishing between these two scenarios remains a challenge for evolutionary research. The Midas cichlid species complex (Amphilophus spp.) is a prime example of adaptive radiation, with phenotypic diversification occurring at various stages of genetic differentiation. One species, A. labiatus, has large fleshy lips, is associated with rocky lake substrates, and occurs patchily within Lakes Nicaragua and Managua. By contrast, the similar, but thin-lipped, congener, A. citrinellus, is more common and widespread. We investigated the evolutionary history of the large-lipped form, specifically regarding whether the trait has evolved independently in both lakes from ancestral thin-lipped populations, or via dispersal and/or admixture events. We collected samples from distinct locations in both lakes, and assessed differences in morphology and ecology. Using RAD-seq, we genotyped thousands of SNPs to measure population structure and divergence, demographic history, and admixture. We found significant between-species differences in ecology and morphology, local intraspecific differences in body shape and trophic traits, but only limited intraspecific variation in lip shape. Despite clear ecological differences, our genomic approach uncovered pervasive admixture between the species and low genomic differentiation, with species within lakes being genetically more similar than species between lakes. Taken together, our results suggest a single origin of large-lips, followed by pervasive admixture and adaptive introgression, with morphology being driven by local ecological opportunities, despite ongoing gene-flow.
Collapse
Affiliation(s)
- Will Sowersby
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia.,Department of Biology, Osaka City University, Osaka, Japan
| | - José Cerca
- Frontiers of Evolutionary Zoology Research Group, Natural History Museum, University of Oslo, Oslo, Norway.,Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, California, USA.,Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Bob B M Wong
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Topi K Lehtonen
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia.,Department of Biology, University of Turku, Turku, Finland.,Organismal and Evolutionary Biology, University of Helsinki, Helsinki, Finland
| | - David G Chapple
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Mariana Leal-Cardín
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain.,Universidad de Alcalá de Henares, Madrid, Spain
| | - Marta Barluenga
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
| | - Mark Ravinet
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway.,Division of Population Genetics, National Institute of Genetics, Mishima, Japan.,School of Life Sciences, University of Nottingham, Nottingham, UK
| |
Collapse
|
10
|
Xiong P, Hulsey CD, Fruciano C, Wong WY, Nater A, Kautt AF, Simakov O, Pippel M, Kuraku S, Meyer A, Franchini P. The comparative genomic landscape of adaptive radiation in crater lake cichlid fishes. Mol Ecol 2021; 30:955-972. [PMID: 33305470 PMCID: PMC8607476 DOI: 10.1111/mec.15774] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 11/21/2020] [Accepted: 11/30/2020] [Indexed: 12/13/2022]
Abstract
Factors ranging from ecological opportunity to genome composition might explain why only some lineages form adaptive radiations. While being rare, particular systems can provide natural experiments within an identical ecological setting where species numbers and phenotypic divergence in two closely related lineages are notably different. We investigated one such natural experiment using two de novo assembled and 40 resequenced genomes and asked why two closely related Neotropical cichlid fish lineages, the Amphilophus citrinellus species complex (Midas cichlids; radiating) and Archocentrus centrarchus (Flyer cichlid; nonradiating), have resulted in such disparate evolutionary outcomes. Although both lineages inhabit many of the same Nicaraguan lakes, whole-genome inferred demography suggests that priority effects are not likely to be the cause of the dissimilarities. Also, genome-wide levels of selection, transposable element dynamics, gene family expansion, major chromosomal rearrangements and the number of genes under positive selection were not markedly different between the two lineages. To more finely investigate particular subsets of the genome that have undergone adaptive divergence in Midas cichlids, we also examined if there was evidence for 'molecular pre-adaptation' in regions identified by QTL mapping of repeatedly diverging adaptive traits. Although most of our analyses failed to pinpoint substantial genomic differences, we did identify functional categories containing many genes under positive selection that provide candidates for future studies on the propensity of Midas cichlids to radiate. Our results point to a disproportionate role of local, rather than genome-wide factors underlying the propensity for these cichlid fishes to adaptively radiate.
Collapse
Affiliation(s)
- Peiwen Xiong
- Department of BiologyUniversity of KonstanzKonstanzGermany
| | - C. Darrin Hulsey
- Department of BiologyUniversity of KonstanzKonstanzGermany
- School of Biology and Environmental ScienceUniversity College DublinDublinIreland
| | - Carmelo Fruciano
- Department of BiologyUniversity of KonstanzKonstanzGermany
- National Research Council (CNR) – IRBIMMessinaItaly
| | - Wai Y. Wong
- Department of Molecular Evolution and DevelopmentUniversity of ViennaViennaAustria
| | | | - Andreas F. Kautt
- Department of BiologyUniversity of KonstanzKonstanzGermany
- Department of Organismic and Evolutionary BiologyHarvard UniversityCambridgeMAUSA
| | - Oleg Simakov
- Department of Molecular Evolution and DevelopmentUniversity of ViennaViennaAustria
| | - Martin Pippel
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
| | - Shigehiro Kuraku
- Laboratory for PhyloinformaticsRIKEN Center for Biosystems Dynamics Research (BDR)KobeJapan
| | - Axel Meyer
- Department of BiologyUniversity of KonstanzKonstanzGermany
| | | |
Collapse
|
11
|
Koene JP, Elmer KR, Adams CE. Intraspecific variation and structuring of phenotype in a lake-dwelling species are driven by lake size and elevation. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa137] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
The fragmented, heterogeneous and relatively depauperate ecosystems of recently glaciated lakes present contrasting ecological opportunities for resident fish. Across a species, local adaptation may induce diverse and distinct phenotypic responses to various selection pressures. We tested for intraspecific phenotypic structuring by population in a common native lake-dwelling fish species across a medium-scale geographic region with considerable variation in lake types. We investigated potential lake-characteristic drivers of trophic morphology. Using geometric morphometric techniques, we quantified the head shapes of 759 adult brown trout (Salmo trutta L.) from 28 lakes and reservoirs across Scotland. Multivariate statistical analyses showed that almost all populations differed from one another. Trout from larger and deeper lakes had deeper, but shorter heads, and smaller eyes. Higher elevation lakes were associated with fish with shorter heads and jaws. Within-population shape variation also differed by population, and was positively correlated with lake surface area and depth. Trout within reservoirs differed subtly from those in natural lakes, having larger eyes, shorter jaws and greater variability. This study documents an extraordinary morphological variation between and within populations of brown trout, and demonstrates the role of the extrinsic environment in driving phenotypic structuring over a medium-scale and varied geographic area.
Collapse
Affiliation(s)
- J Peter Koene
- Scottish Centre for Ecology and the Natural Environment (SCENE), University of Glasgow, Rowardennan, Glasgow, UK
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Science, University of Glasgow, Glasgow, UK
| | - Kathryn R Elmer
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Science, University of Glasgow, Glasgow, UK
| | - Colin E Adams
- Scottish Centre for Ecology and the Natural Environment (SCENE), University of Glasgow, Rowardennan, Glasgow, UK
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Science, University of Glasgow, Glasgow, UK
| |
Collapse
|
12
|
Öhlund G, Bodin M, Nilsson KA, Öhlund SO, Mobley KB, Hudson AG, Peedu M, Brännström Å, Bartels P, Præbel K, Hein CL, Johansson P, Englund G. Ecological speciation in European whitefish is driven by a large-gaped predator. Evol Lett 2020; 4:243-256. [PMID: 32547784 PMCID: PMC7293097 DOI: 10.1002/evl3.167] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 12/21/2019] [Accepted: 02/02/2020] [Indexed: 12/15/2022] Open
Abstract
Lake‐dwelling fish that form species pairs/flocks characterized by body size divergence are important model systems for speciation research. Although several sources of divergent selection have been identified in these systems, their importance for driving the speciation process remains elusive. A major problem is that in retrospect, we cannot distinguish selection pressures that initiated divergence from those acting later in the process. To address this issue, we studied the initial stages of speciation in European whitefish (Coregonus lavaretus) using data from 358 populations of varying age (26–10,000 years). We find that whitefish speciation is driven by a large‐growing predator, the northern pike (Esox lucius). Pike initiates divergence by causing a largely plastic differentiation into benthic giants and pelagic dwarfs: ecotypes that will subsequently develop partial reproductive isolation and heritable differences in gill raker number. Using an eco‐evolutionary model, we demonstrate how pike's habitat specificity and large gape size are critical for imposing a between‐habitat trade‐off, causing prey to mature in a safer place or at a safer size. Thereby, we propose a novel mechanism for how predators may cause dwarf/giant speciation in lake‐dwelling fish species.
Collapse
Affiliation(s)
- Gunnar Öhlund
- Department of Ecology and Environmental Science Umeå University Umeå SE-901 87 Sweden.,Department of Business Administration, Technology, and Social Sciences Luleå University of Technology Luleå SE-971 87 Sweden.,Department of Wildlife, Fish, and Environmental Studies SLU Umeå SE-901 83 Sweden
| | - Mats Bodin
- Department of Ecology and Environmental Science Umeå University Umeå SE-901 87 Sweden.,Department of Mathematics and Mathematical Statistics Umeå University Umeå SE-901 87 Sweden
| | - Karin A Nilsson
- Department of Ecology and Environmental Science Umeå University Umeå SE-901 87 Sweden.,Department of Integrative Biology University of Guelph Guelph ON N1G 2W1 Canada
| | - Sven-Ola Öhlund
- Department of Ecology and Environmental Science Umeå University Umeå SE-901 87 Sweden
| | - Kenyon B Mobley
- Department of Ecology and Environmental Science Umeå University Umeå SE-901 87 Sweden.,Max Planck Institute for Evolutionary Biology Plön D-24302 Germany.,Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences University of Helsinki Helsinki 00014 Finland
| | - Alan G Hudson
- Department of Ecology and Environmental Science Umeå University Umeå SE-901 87 Sweden.,School of Biological Sciences, Life Sciences Building University of Bristol Bristol BS8 1TQ United Kingdom
| | - Mikael Peedu
- Department of Ecology and Environmental Science Umeå University Umeå SE-901 87 Sweden
| | - Åke Brännström
- Department of Mathematics and Mathematical Statistics Umeå University Umeå SE-901 87 Sweden.,Evolution and Ecology Program International Institute for Applied Systems Analysis Laxenburg A-2361 Austria
| | - Pia Bartels
- Department of Ecology and Environmental Science Umeå University Umeå SE-901 87 Sweden
| | - Kim Præbel
- Norwegian College of Fishery Science UiT The Arctic University of Norway Tromsø N-9037 Norway
| | - Catherine L Hein
- Department of Ecology and Environmental Science Umeå University Umeå SE-901 87 Sweden.,Climate Impacts Research Centre (CIRC) Abisko Scientific Research Station Abisko SE-981 07 Sweden
| | - Petter Johansson
- Department of Ecology and Environmental Science Umeå University Umeå SE-901 87 Sweden
| | - Göran Englund
- Department of Ecology and Environmental Science Umeå University Umeå SE-901 87 Sweden
| |
Collapse
|
13
|
Resource trait specialisation in an introduced fish population with reduced genetic diversity. Biol Invasions 2020. [DOI: 10.1007/s10530-020-02264-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
14
|
Pérez-Miranda F, Mejia O, López B, Říčan O. Molecular clocks, biogeography and species diversity in Herichthys with evaluation of the role of Punta del Morro as a vicariant brake along the Mexican Transition Zone in the context of local and global time frame of cichlid diversification. PeerJ 2020; 8:e8818. [PMID: 32391194 PMCID: PMC7195834 DOI: 10.7717/peerj.8818] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 02/28/2020] [Indexed: 11/20/2022] Open
Abstract
Using molecular dated phylogenies and biogeographic reconstructions, the species diversity, biogeography and time frame of evolution of the genus Herichthys were evaluated. In particular, we test the role of Punta del Morro (PdM) as a vicariant brake along the Mexican Transition Zone in the context of local and global time frame of cichlid diversification using several sets of calibrations. Species diversity in Herichthys is complex and the here employed dating methods suggest young age and rapid divergence for many species while species delimitation methods did not resolve these young species including both sympatric species pairs. Based on our molecular clock dating analyses, Herichthys has colonized its present distribution area significantly prior to the suggested vicariance by PdM (10-17.1 Ma vs. 5 to 7.5 Ma). The PdM constraint is in conflict with all other paleogeographic and fossil constraints including novel ones introduced in this study that are, however, congruent among each other. Our study demonstrates that any cichlid datings significantly older or younger than the bounds presented by our analyses and discussion have to be taken as highly questionable from the point of view of Middle American paleogeography and cichlid biogeography unless we allow the option that cichlid biogeography is completely independent from ecological and geological constraints.
Collapse
Affiliation(s)
- Fabian Pérez-Miranda
- Laboratorio de Variación Biológica y Evolución, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Omar Mejia
- Laboratorio de Variación Biológica y Evolución, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Benjamín López
- Laboratorio de Variación Biológica y Evolución, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Oldřich Říčan
- Departament of Zoology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| |
Collapse
|
15
|
Jacobs A, Carruthers M, Yurchenko A, Gordeeva NV, Alekseyev SS, Hooker O, Leong JS, Minkley DR, Rondeau EB, Koop BF, Adams CE, Elmer KR. Parallelism in eco-morphology and gene expression despite variable evolutionary and genomic backgrounds in a Holarctic fish. PLoS Genet 2020; 16:e1008658. [PMID: 32302300 PMCID: PMC7164584 DOI: 10.1371/journal.pgen.1008658] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 02/06/2020] [Indexed: 01/05/2023] Open
Abstract
Understanding the extent to which ecological divergence is repeatable is essential for predicting responses of biodiversity to environmental change. Here we test the predictability of evolution, from genotype to phenotype, by studying parallel evolution in a salmonid fish, Arctic charr (Salvelinus alpinus), across eleven replicate sympatric ecotype pairs (benthivorous-planktivorous and planktivorous-piscivorous) and two evolutionary lineages. We found considerable variability in eco-morphological divergence, with several traits related to foraging (eye diameter, pectoral fin length) being highly parallel even across lineages. This suggests repeated and predictable adaptation to environment. Consistent with ancestral genetic variation, hundreds of loci were associated with ecotype divergence within lineages of which eight were shared across lineages. This shared genetic variation was maintained despite variation in evolutionary histories, ranging from postglacial divergence in sympatry (ca. 10-15kya) to pre-glacial divergence (ca. 20-40kya) with postglacial secondary contact. Transcriptome-wide gene expression (44,102 genes) was highly parallel across replicates, involved biological processes characteristic of ecotype morphology and physiology, and revealed parallelism at the level of regulatory networks. This expression divergence was not only plastic but in part genetically controlled by parallel cis-eQTL. Lastly, we found that the magnitude of phenotypic divergence was largely correlated with the genetic differentiation and gene expression divergence. In contrast, the direction of phenotypic change was mostly determined by the interplay of adaptive genetic variation, gene expression, and ecosystem size. Ecosystem size further explained variation in putatively adaptive, ecotype-associated genomic patterns within and across lineages, highlighting the role of environmental variation and stochasticity in parallel evolution. Together, our findings demonstrate the parallel evolution of eco-morphology and gene expression within and across evolutionary lineages, which is controlled by the interplay of environmental stochasticity and evolutionary contingencies, largely overcoming variable evolutionary histories and genomic backgrounds.
Collapse
Affiliation(s)
- Arne Jacobs
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Madeleine Carruthers
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Andrey Yurchenko
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Natalia V. Gordeeva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Sergey S. Alekseyev
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Oliver Hooker
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
- Scottish Centre for Ecology and the Natural Environment, University of Glasgow, Rowardennan, Loch Lomond, Glasgow, United Kingdom
| | - Jong S. Leong
- Biology/Centre for Biomedical Research, University of Victoria, British Columbia, Canada
| | - David R. Minkley
- Biology/Centre for Biomedical Research, University of Victoria, British Columbia, Canada
| | - Eric B. Rondeau
- Biology/Centre for Biomedical Research, University of Victoria, British Columbia, Canada
| | - Ben F. Koop
- Biology/Centre for Biomedical Research, University of Victoria, British Columbia, Canada
| | - Colin E. Adams
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
- Scottish Centre for Ecology and the Natural Environment, University of Glasgow, Rowardennan, Loch Lomond, Glasgow, United Kingdom
| | - Kathryn R. Elmer
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| |
Collapse
|
16
|
Olave M, Meyer A. Implementing Large Genomic Single Nucleotide Polymorphism Data Sets in Phylogenetic Network Reconstructions: A Case Study of Particularly Rapid Radiations of Cichlid Fish. Syst Biol 2020; 69:848-862. [DOI: 10.1093/sysbio/syaa005] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 01/09/2020] [Accepted: 01/23/2020] [Indexed: 12/23/2022] Open
Abstract
AbstractThe Midas cichlids of the Amphilophus citrinellus spp. species complex from Nicaragua (13 species) are an extraordinary example of adaptive and rapid radiation ($<$24,000 years old). These cichlids are a very challenging group to infer its evolutionary history in phylogenetic analyses, due to the apparent prevalence of incomplete lineage sorting (ILS), as well as past and current gene flow. Assuming solely a vertical transfer of genetic material from an ancestral lineage to new lineages is not appropriate in many cases of genes transferred horizontally in nature. Recently developed methods to infer phylogenetic networks under such circumstances might be able to circumvent these problems. These models accommodate not just ILS, but also gene flow, under the multispecies network coalescent (MSNC) model, processes that are at work in young, hybridizing, and/or rapidly diversifying lineages. There are currently only a few programs available that implement MSNC for estimating phylogenetic networks. Here, we present a novel way to incorporate single nucleotide polymorphism (SNP) data into the currently available PhyloNetworks program. Based on simulations, we demonstrate that SNPs can provide enough power to recover the true phylogenetic network. We also show that it can accurately infer the true network more often than other similar SNP-based programs (PhyloNet and HyDe). Moreover, our approach results in a faster algorithm compared to the original pipeline in PhyloNetworks, without losing power. We also applied our new approach to infer the phylogenetic network of Midas cichlid radiation. We implemented the most comprehensive genomic data set to date (RADseq data set of 679 individuals and $>$37K SNPs from 19 ingroup lineages) and present estimated phylogenetic networks for this extremely young and fast-evolving radiation of cichlid fish. We demonstrate that the MSNC is more appropriate than the multispecies coalescent alone for the analysis of this rapid radiation. [Genomics; multispecies network coalescent; phylogenetic networks; phylogenomics; RADseq; SNPs.]
Collapse
Affiliation(s)
- Melisa Olave
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Axel Meyer
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| |
Collapse
|
17
|
Franchini P, Xiong P, Fruciano C, Schneider RF, Woltering JM, Hulsey CD, Meyer A. MicroRNA Gene Regulation in Extremely Young and Parallel Adaptive Radiations of Crater Lake Cichlid Fish. Mol Biol Evol 2019; 36:2498-2511. [PMID: 31397871 DOI: 10.1093/molbev/msz168] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 07/03/2019] [Accepted: 07/17/2019] [Indexed: 12/20/2022] Open
Abstract
AbstractCichlid fishes provide textbook examples of explosive phenotypic diversification and sympatric speciation, thereby making them ideal systems for studying the molecular mechanisms underlying rapid lineage divergence. Despite the fact that gene regulation provides a critical link between diversification in gene function and speciation, many genomic regulatory mechanisms such as microRNAs (miRNAs) have received little attention in these rapidly diversifying groups. Therefore, we investigated the posttranscriptional regulatory role of miRNAs in the repeated sympatric divergence of Midas cichlids (Amphilophus spp.) from Nicaraguan crater lakes. Using miRNA and mRNA sequencing of embryos from five Midas species, we first identified miRNA binding sites in mRNAs and highlighted the presences of a surprising number of novel miRNAs in these adaptively radiating species. Then, through analyses of expression levels, we identified putative miRNA/gene target pairs with negatively correlated expression level that were consistent with the role of miRNA in downregulating mRNA. Furthermore, we determined that several miRNA/gene pairs show convergent expression patterns associated with the repeated benthic/limnetic sympatric species divergence implicating these miRNAs as potential molecular mechanisms underlying replicated sympatric divergence. Finally, as these candidate miRNA/gene pairs may play a central role in phenotypic diversification in these cichlids, we characterized the expression domains of selected miRNAs and their target genes via in situ hybridization, providing further evidence that miRNA regulation likely plays a role in the Midas cichlid adaptive radiation. These results provide support for the hypothesis that extremely quickly evolving miRNA regulation can contribute to rapid evolutionary divergence even in the presence of gene flow.
Collapse
Affiliation(s)
- Paolo Franchini
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Peiwen Xiong
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Carmelo Fruciano
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
- Institut de biologie de l’Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, PSL Université Paris, Paris, France
| | - Ralf F Schneider
- Marine Ecology, Helmholtz-Zentrum für Ozeanforschung Kiel (GEOMAR), Düsternbrooker Weg 20, Kiel, Germany
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Joost M Woltering
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Christopher Darrin Hulsey
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
| |
Collapse
|
18
|
Richards EJ, Servedio MR, Martin CH. Searching for Sympatric Speciation in the Genomic Era. Bioessays 2019; 41:e1900047. [PMID: 31245871 PMCID: PMC8175013 DOI: 10.1002/bies.201900047] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 04/22/2019] [Indexed: 12/25/2022]
Abstract
Sympatric speciation illustrates how natural and sexual selection may create new species in isolation without geographic barriers. However, recent genomic reanalyses of classic examples of sympatric speciation reveal complex histories of secondary gene flow from outgroups into the radiation. In contrast, the rich theoretical literature on this process distinguishes among a diverse range of models based on simple genetic histories and different types of reproductive isolating barriers. Thus, there is a need to revisit how to connect theoretical models of sympatric speciation and their predictions to empirical case studies in the face of widespread gene flow. Here, theoretical differences among different types of sympatric speciation and speciation-with-gene-flow models are reviewed and summarized, and genomic analyses are proposed for distinguishing which models apply to case studies based on the timing and function of adaptive introgression. Investigating whether secondary gene flow contributed to reproductive isolation is necessary to test whether predictions of theory are ultimately borne out in nature.
Collapse
Affiliation(s)
- Emilie J. Richards
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill NC
| | - Maria R. Servedio
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill NC
| | - Christopher H. Martin
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill NC
- Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, CA
| |
Collapse
|
19
|
Gidmark NJ, Pos K, Matheson B, Ponce E, Westneat MW. Functional Morphology and Biomechanics of Feeding in Fishes. FEEDING IN VERTEBRATES 2019. [DOI: 10.1007/978-3-030-13739-7_9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
|
20
|
Moser FN, van Rijssel JC, Mwaiko S, Meier JI, Ngatunga B, Seehausen O. The onset of ecological diversification 50 years after colonization of a crater lake by haplochromine cichlid fishes. Proc Biol Sci 2018; 285:rspb.2018.0171. [PMID: 30111604 DOI: 10.1098/rspb.2018.0171] [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: 01/23/2018] [Accepted: 07/23/2018] [Indexed: 12/29/2022] Open
Abstract
Adaptive radiation research typically relies on the study of evolution in retrospective, leaving the predictive value of the concept hard to evaluate. Several radiations, including the cichlid fishes in the East African Great Lakes, have been studied extensively, yet no study has investigated the onset of the intraspecific processes of niche expansion and differentiation shortly after colonization of an adaptive zone by cichlids. Haplochromine cichlids of one of the two lineages that seeded the Lake Victoria radiation recently arrived in Lake Chala, a lake perfectly suited for within-lake cichlid speciation. Here, we infer the colonization and demographic history, quantify phenotypic, ecological and genomic diversity and diversification, and investigate the selection regime to ask if the population shows signs of diversification resembling the onset of adaptive radiation. We find that since their arrival in the lake, haplochromines have colonized a wide range of depth habitats associated with ecological and morphological expansion and the beginning of phenotypic differentiation and potentially nascent speciation, consistent with the very early onset of an adaptive radiation process. Moreover, we demonstrate evidence of rugged phenotypic fitness surfaces, indicating that current ecological selection may contribute to the phenotypic diversification.
Collapse
Affiliation(s)
- Florian N Moser
- Department of Aquatic Ecology, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.,Department of Fish Ecology and Evolution, EAWAG, 6047 Kastanienbaum, Switzerland
| | - Jacco C van Rijssel
- Department of Aquatic Ecology, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.,Department of Fish Ecology and Evolution, EAWAG, 6047 Kastanienbaum, Switzerland.,Wageningen Marine Research, Wageningen University and Research, Ijmuiden, The Netherlands
| | - Salome Mwaiko
- Department of Fish Ecology and Evolution, EAWAG, 6047 Kastanienbaum, Switzerland
| | - Joana I Meier
- Department of Aquatic Ecology, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.,Department of Fish Ecology and Evolution, EAWAG, 6047 Kastanienbaum, Switzerland
| | - Benjamin Ngatunga
- Tanzania Fisheries Research Institute, Box 9750, Dar Es Salaam, Tanzania
| | - Ole Seehausen
- Department of Aquatic Ecology, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland .,Department of Fish Ecology and Evolution, EAWAG, 6047 Kastanienbaum, Switzerland
| |
Collapse
|
21
|
Härer A, Meyer A, Torres‐Dowdall J. Convergent phenotypic evolution of the visual system via different molecular routes: How Neotropical cichlid fishes adapt to novel light environments. Evol Lett 2018; 2:341-354. [PMID: 30283686 PMCID: PMC6121847 DOI: 10.1002/evl3.71] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 06/21/2018] [Accepted: 06/21/2018] [Indexed: 12/17/2022] Open
Abstract
How predictable is evolution? This remains a fundamental but contested issue in evolutionary biology. When independent lineages colonize the same environment, we are presented with a natural experiment that allows us to ask if genetic and ecological differences promote species-specific evolutionary outcomes or whether species phenotypically evolve in a convergent manner in response to shared selection pressures. If so, are the molecular mechanisms underlying phenotypic convergence the same? In Nicaragua, seven species of cichlid fishes concurrently colonized two novel photic environments. Hence, their visual system represents a compelling model to address these questions, particularly since the adaptive value of phenotypic changes is well-understood. By analyzing retinal transcriptomes, we found that differential expression of genes responsible for color vision (cone opsins and cyp27c1) produced rapid and mostly convergent changes of predicted visual sensitivities. Notably, these changes occurred in the same direction in all species although there were differences in underlying gene expression patterns illustrating nonconvergence at the molecular level. Adaptive phenotypes evolved deterministically, even when species differ substantially in ecology and genetic variation. This provides strong evidence that phenotypic evolution of the visual system occurred in response to similar selective forces of the photic environment.
Collapse
Affiliation(s)
- Andreas Härer
- Zoology and Evolutionary Biology, Department of BiologyUniversity of KonstanzGermany
| | - Axel Meyer
- Zoology and Evolutionary Biology, Department of BiologyUniversity of KonstanzGermany
- Radcliffe Institute for Advanced StudyHarvard UniversityCambridgeMassachusetts02138
| | - Julián Torres‐Dowdall
- Zoology and Evolutionary Biology, Department of BiologyUniversity of KonstanzGermany
- Zukunftskolleg, University of KonstanzKonstanzGermany
| |
Collapse
|
22
|
Kautt AF, Machado‐Schiaffino G, Meyer A. Lessons from a natural experiment: Allopatric morphological divergence and sympatric diversification in the Midas cichlid species complex are largely influenced by ecology in a deterministic way. Evol Lett 2018; 2:323-340. [PMID: 30283685 PMCID: PMC6121794 DOI: 10.1002/evl3.64] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 05/31/2018] [Accepted: 06/06/2018] [Indexed: 12/15/2022] Open
Abstract
Explaining why some lineages diversify while others do not and how are key objectives in evolutionary biology. Young radiations of closely related species derived from the same source population provide an excellent opportunity to disentangle the relative contributions of possible drivers of diversification. In these settings, lineage-specific effects are shared and can be ruled out. Moreover, the relevant demographic and ecological parameters can be estimated accurately. Midas cichlid fish in Nicaragua have repeatedly colonized several crater lakes, diverged from the same source populations, and, interestingly, diversified in some of them but not others. Here, using the most comprehensive molecular and geometric morphometric data set on Midas cichlids to date (∼20,000 SNPs, 12 landmarks, ∼700 individuals), we aim to understand why and how crater lake populations diverge and why some of them are more prone to diversify in sympatry than others. Taking ancestor-descendant relationships into account, we find that Midas cichlids diverged in parallel from their source population mostly-but not exclusively-by evolving more slender body shapes in all six investigated crater lakes. Admixture among crater lakes has possibly facilitated this process in one case, but overall, admixture and secondary waves of colonization cannot predict morphological divergence and intralacustrine diversification. Instead, morphological divergence is larger the more dissimilar a crater lake is compared to the source lake and happens rapidly after colonization followed by a slow-down with time. Our data also provide some evidence that founder effects may positively contribute to divergence. The depth of a crater lake is positively associated with variation in body shapes (and number of species), presumably by providing more ecological opportunities. In conclusion, we find that parallel morphological divergence in allopatry and the propensity for diversification in sympatry across the entire Midas cichlid fish radiation is partly predictable and mostly driven by ecology.
Collapse
Affiliation(s)
- Andreas F. Kautt
- Department of BiologyUniversity of KonstanzUniversitätsstraße 1078457KonstanzGermany
| | - Gonzalo Machado‐Schiaffino
- Department of BiologyUniversity of KonstanzUniversitätsstraße 1078457KonstanzGermany
- Current Address: Genetics Area, Department of Functional BiologyUniversity of Oviedo33006OviedoSpain
| | - Axel Meyer
- Department of BiologyUniversity of KonstanzUniversitätsstraße 1078457KonstanzGermany
- Radcliffe Institute for Advanced StudyHarvard UniversityCambridgeMassachusetts02138
| |
Collapse
|
23
|
Roman I, Bourgeois Y, Reyes-Velasco J, Jensen OP, Waldman J, Boissinot S. Contrasted patterns of divergence and gene flow among five fish species in a Mongolian rift lake following glaciation. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly083] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Ivana Roman
- Department of Biology, Queens College, the City University of New York, Flushing, NY, USA
| | - Yann Bourgeois
- New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
| | - Jacobo Reyes-Velasco
- New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
| | - Olaf P Jensen
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, USA
| | - John Waldman
- Department of Biology, Queens College, the City University of New York, Flushing, NY, USA
| | - Stephane Boissinot
- New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
| |
Collapse
|
24
|
Chiozzi G, Stiassny MLJ, de Marchi G, Lamboj A, Fasola M, Fruciano C. A diversified kettle of fish: phenotypic variation in the endemic cichlid genus Danakilia of the Danakil Depression of northeastern Africa. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly085] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Giorgio Chiozzi
- Dipartimento di Scienze della Terra e dell’Ambiente, Università degli Studi di Pavia, Pavia, Italy
- Museo di Storia Naturale di Milano, Corso Venezia, Milano, Italy
| | - Melanie L J Stiassny
- Department of Ichthyology, American Museum of Natural History, New York, NY, USA
| | - Giuseppe de Marchi
- Dipartimento di Scienze della Terra e dell’Ambiente, Università degli Studi di Pavia, Pavia, Italy
| | - Anton Lamboj
- Department of Integrative Zoology, University of Vienna, UZA, Vienna, Austria
| | - Mauro Fasola
- Dipartimento di Scienze della Terra e dell’Ambiente, Università degli Studi di Pavia, Pavia, Italy
| | - Carmelo Fruciano
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| |
Collapse
|
25
|
Raffini F, Fruciano C, Meyer A. Gene(s) and individual feeding behavior: Exploring eco-evolutionary dynamics underlying left-right asymmetry in the scale-eating cichlid fish Perissodus microlepis. Ecol Evol 2018; 8:5495-5507. [PMID: 29938068 PMCID: PMC6010907 DOI: 10.1002/ece3.4070] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Revised: 03/22/2018] [Accepted: 03/26/2018] [Indexed: 01/09/2023] Open
Abstract
The scale‐eating cichlid fish Perissodus microlepis is a textbook example of bilateral asymmetry due to its left or right‐bending heads and of negative frequency‐dependent selection, which is proposed to maintain this stable polymorphism. The mechanisms that underlie this asymmetry remain elusive. Several studies had initially postulated a simple genetic basis for this trait, but this explanation has been questioned, particularly by reports observing a unimodal distribution of mouth shapes. We hypothesize that this unimodal distribution might be due to a combination of genetic and phenotypically plastic components. Here, we expanded on previous work by investigating a formerly identified candidate SNP associated to mouth laterality, documenting inter‐individual variation in feeding preference using stable isotope analyses, and testing their association with mouth asymmetry. Our results suggest that this polymorphism is influenced by both a polygenic basis and inter‐individual non‐genetic variation, possibly due to feeding experience, individual specialization, and intraspecific competition. We introduce a hypothesis potentially explaining the simultaneous maintenance of left, right, asymmetric and symmetric mouth phenotypes due to the interaction between diverse eco‐evolutionary dynamics including niche construction and balancing selection. Future studies will have to further tease apart the relative contribution of genetic and environmental factors and their interactions in an integrated fashion.
Collapse
Affiliation(s)
- Francesca Raffini
- Lehrstuhl für Zoologie und Evolutionsbiologie Department of Biology University of Konstanz Konstanz Germany.,International Max Planck Research School (IMPRS) for Organismal Biology University of Konstanz Konstanz Germany
| | - Carmelo Fruciano
- Lehrstuhl für Zoologie und Evolutionsbiologie Department of Biology University of Konstanz Konstanz Germany.,School of Earth, Environmental & Biological Sciences Queensland University of Technology Brisbane QLD Australia.,Institut de biologie de l'Ecole normale supérieure (IBENS) Ecole normale supérieure, CNRS, INSERM PSL Université, Paris France
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie Department of Biology University of Konstanz Konstanz Germany.,International Max Planck Research School (IMPRS) for Organismal Biology University of Konstanz Konstanz Germany.,Radcliffe Institute for Advanced Study Harvard University Cambridge Massachusetts
| |
Collapse
|
26
|
Foote AD. Sympatric Speciation in the Genomic Era. Trends Ecol Evol 2017; 33:85-95. [PMID: 29198471 DOI: 10.1016/j.tree.2017.11.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 11/03/2017] [Accepted: 11/07/2017] [Indexed: 10/18/2022]
Abstract
Sympatric speciation has been of key interest to biologists investigating how natural and sexual selection drive speciation without the confounding variable of geographic isolation. The advent of the genomic era has provided a more nuanced and quantitative understanding of the different and often complex modes of speciation by which sympatric sister taxa arose, and a reassessment of some of the most compelling empirical case studies of sympatric speciation. However, I argue that genomic studies based on contemporary populations may never be able to provide unequivocal evidence of true primary sympatric speciation, and there is a need to incorporate palaeogenomic studies into this field. This inability to robustly distinguish cases of primary and secondary 'divergence with gene flow' may be inconsequential, as both are useful for understanding the role of large effect barrier loci in the progression from localised genic isolation to genome-wide reproductive isolation. I argue that they can be of equivalent interest due to shared underlying mechanisms driving divergence and potentially leaving similar patterns of coalescence.
Collapse
Affiliation(s)
- Andrew D Foote
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK.
| |
Collapse
|
27
|
Hauser FE, Ilves KL, Schott RK, Castiglione GM, López-Fernández H, Chang BSW. Accelerated Evolution and Functional Divergence of the Dim Light Visual Pigment Accompanies Cichlid Colonization of Central America. Mol Biol Evol 2017; 34:2650-2664. [PMID: 28957507 DOI: 10.1093/molbev/msx192] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Cichlids encompass one of the most diverse groups of fishes in South and Central America, and show extensive variation in life history, morphology, and colouration. While studies of visual system evolution in cichlids have focussed largely on the African rift lake species flocks, Neotropical cichlids offer a unique opportunity to investigate visual system evolution at broader temporal and geographic scales. South American cichlid colonization of Central America has likely promoted accelerated rates of morphological evolution in Central American lineages as they encountered reduced competition, renewed ecological opportunity, and novel aquatic habitats. To investigate whether such transitions have influenced molecular evolution of vision in Central American cichlids, we sequenced the dim-light rhodopsin gene in 101 Neotropical cichlid species, spanning the diversity of the clade. We find strong evidence for increased rates of evolution in Central American cichlid rhodopsin relative to South American lineages, and identify several sites under positive selection in rhodopsin that likely contribute to adaptation to different photic environments. We expressed a Neotropical cichlid rhodopsin protein invitro for the first time, and found that while its spectral tuning properties were characteristic of typical vertebrate rhodopsin pigments, the rate of decay of its active signalling form was much slower, consistent with dim light adaptation in other vertebrate rhodopsins. Using site-directed mutagenesis combined with spectroscopic assays, we found that a key amino acid substitution present in some Central American cichlids accelerates the rate of decay of active rhodopsin, which may mediate adaptation to clear water habitats.
Collapse
Affiliation(s)
- Frances E Hauser
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Katriina L Ilves
- Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
- Department of Biology, Pace University, New York, NY
| | - Ryan K Schott
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Gianni M Castiglione
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Hernán López-Fernández
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
- Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
| | - Belinda S W Chang
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada
| |
Collapse
|
28
|
Burress ED, Alda F, Duarte A, Loureiro M, Armbruster JW, Chakrabarty P. Phylogenomics of pike cichlids (Cichlidae: Crenicichla): the rapid ecological speciation of an incipient species flock. J Evol Biol 2017; 31:14-30. [PMID: 29044782 DOI: 10.1111/jeb.13196] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 08/13/2017] [Accepted: 10/12/2017] [Indexed: 12/18/2022]
Abstract
The rapid rise of phenotypic and ecological diversity in independent lake-dwelling groups of cichlids is emblematic of the East African Great Lakes. In this study, we show that similar ecologically based diversification has occurred in pike cichlids (Crenicichla) throughout the Uruguay River drainage of South America. We collected genomic data from nearly 500 ultraconserved element (UCEs) loci and >260 000 base pairs across 33 species, to obtain a phylogenetic hypothesis for the major species groups and to evaluate the relationships and genetic structure among five closely related, endemic, co-occurring species (the Uruguay River species flock; URSF). Additionally, we evaluated ecological divergence of the URSF based on body and lower pharyngeal jaw (LPJ) shape and gut contents. Across the genus, we recovered novel relationships among the species groups. We found strong support for the monophyly of the URSF; however, relationships among these species remain problematic, likely because of the rapid and recent evolution of this clade. Clustered co-ancestry analysis recovered most species as well delimited genetic groups. The URSF species exhibit species-specific body and LPJ shapes associated with specialized trophic roles. Collectively, our results suggest that the URSF consists of incipient species that arose via ecological speciation associated with the exploration of novel trophic roles.
Collapse
Affiliation(s)
- E D Burress
- Department of Biological Sciences and Auburn University Museum of Natural History, Auburn University, Auburn, AL, USA
| | - F Alda
- Museum of Natural Science, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - A Duarte
- Sección Zoología Vertebrados, Departmento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - M Loureiro
- Sección Zoología Vertebrados, Departmento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay.,Sección Ictología, Departmento de Zoología, Museo Nacional de Historia Natural, Montevideo, Uruguay
| | - J W Armbruster
- Department of Biological Sciences and Auburn University Museum of Natural History, Auburn University, Auburn, AL, USA
| | - P Chakrabarty
- Museum of Natural Science, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| |
Collapse
|
29
|
Eckerström‐Liedholm S, Sowersby W, Gonzalez‐Voyer A, Rogell B. Time‐limited environments affect the evolution of egg–body size allometry. Evolution 2017; 71:1900-1910. [DOI: 10.1111/evo.13286] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 05/23/2017] [Accepted: 05/23/2017] [Indexed: 11/28/2022]
Affiliation(s)
| | - Will Sowersby
- Department of ZoologyStockholm University Stockholm 114 18 Sweden
| | - Alejandro Gonzalez‐Voyer
- Department of ZoologyStockholm University Stockholm 114 18 Sweden
- Instituto de EcologíaUniversidad Nacional Autónoma de México Apartado Postal 70–275, Ciudad Universitaria 04510 Cd México Mexico
| | - Björn Rogell
- Department of ZoologyStockholm University Stockholm 114 18 Sweden
| |
Collapse
|
30
|
Recknagel H, Hooker OE, Adams CE, Elmer KR. Ecosystem size predicts eco-morphological variability in a postglacial diversification. Ecol Evol 2017; 7:5560-5570. [PMID: 28811875 PMCID: PMC5552947 DOI: 10.1002/ece3.3013] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 03/08/2017] [Accepted: 03/26/2017] [Indexed: 02/03/2023] Open
Abstract
Identifying the processes by which new phenotypes and species emerge has been a long‐standing effort in evolutionary biology. Young adaptive radiations provide a model to study patterns of morphological and ecological diversification in environmental context. Here, we use the recent radiation (ca. 12k years old) of the freshwater fish Arctic charr (Salvelinus alpinus) to identify abiotic and biotic environmental factors associated with adaptive morphological variation. Arctic charr are exceptionally diverse, and in postglacial lakes there is strong evidence of repeated parallel evolution of similar morphologies associated with foraging. We measured head depth (a trait reflecting general eco‐morphology and foraging ecology) of 1,091 individuals across 30 lake populations to test whether fish morphological variation was associated with lake bathymetry and/or ecological parameters. Across populations, we found a significant relationship between the variation in head depth of the charr and abiotic environmental characteristics: positively with ecosystem size (i.e., lake volume, surface area, depth) and negatively with the amount of littoral zone. In addition, extremely robust‐headed phenotypes tended to be associated with larger and deeper lakes. We identified no influence of co‐existing biotic community on Arctic charr trophic morphology. This study evidences the role of the extrinsic environment as a facilitator of rapid eco‐morphological diversification.
Collapse
Affiliation(s)
- Hans Recknagel
- Institute of Biodiversity Animal Health & Comparative Medicine College of Medical, Veterinary & Life Sciences University of Glasgow Glasgow UK
| | - Oliver E Hooker
- Institute of Biodiversity Animal Health & Comparative Medicine College of Medical, Veterinary & Life Sciences University of Glasgow Glasgow UK.,PR Statistics Glasgow UK
| | - Colin E Adams
- Institute of Biodiversity Animal Health & Comparative Medicine College of Medical, Veterinary & Life Sciences University of Glasgow Glasgow UK
| | - Kathryn R Elmer
- Institute of Biodiversity Animal Health & Comparative Medicine College of Medical, Veterinary & Life Sciences University of Glasgow Glasgow UK
| |
Collapse
|
31
|
Machado-Schiaffino G, Kautt AF, Torres-Dowdall J, Baumgarten L, Henning F, Meyer A. Incipient speciation driven by hypertrophied lips in Midas cichlid fishes? Mol Ecol 2017; 26:2348-2362. [PMID: 28133841 DOI: 10.1111/mec.14029] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 12/22/2016] [Accepted: 01/11/2017] [Indexed: 01/03/2023]
Abstract
Sympatric speciation has been debated in evolutionary biology for decades. Although it has gained in acceptance recently, still only a handful of empirical examples are seen as valid (e.g. crater lake cichlids). In this study, we disentangle the role of hypertrophied lips in the repeated adaptive radiations of Nicaraguan crater lake cichlid fish. We assessed the role of disruptive selection and assortative mating during the early stages of divergence and found a functional trade-off in feeding behaviour between thick- and thin-lipped ecotypes, suggesting that this trait is a target of disruptive selection. Thick-lipped fish perform better on nonevasive prey at the cost of a poorer performance on evasive prey. Using enclosures in the wild, we found that thick-lipped fish perform significantly better in rocky than in sandy habitats. We found almost no mixed pairs during two breeding seasons and hence significant assortative mating. Genetic differentiation between ecotypes seems to be related to the time since colonization, being subtle in L. Masaya (1600 generations ago) and absent in the younger L. Apoyeque (<600 generations ago). Genome-wide differentiation between ecotypes was higher in the old source lakes than in the young crater lakes. Our results suggest that hypertrophied lips might be promoting incipient sympatric speciation through divergent selection (ecological divergence in feeding performance) and nonrandom mating (assortative mating) in the young Nicaraguan crater lakes. Nonetheless, further manipulative experiments are needed in order to confirm the role of hypertrophied lips as the main cue for assortative mating.
Collapse
Affiliation(s)
| | - Andreas F Kautt
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Julian Torres-Dowdall
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Lukas Baumgarten
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Frederico Henning
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Axel Meyer
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
| |
Collapse
|
32
|
Hofmann MJ, Bracamonte SE, Eizaguirre C, Barluenga M. Molecular characterization of MHC class IIB genes of sympatric Neotropical cichlids. BMC Genet 2017; 18:15. [PMID: 28201988 PMCID: PMC5310070 DOI: 10.1186/s12863-017-0474-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 01/13/2017] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The Major Histocompatibility Complex (MHC) is a key component of the adaptive immune system of all vertebrates and consists of the most polymorphic genes known to date. Due to this complexity, however, MHC remains to be characterized in many species including any Neotropical cichlid fish. Neotropical crater lake cichlids are ideal models to study evolutionary processes as they display one of the most convincing examples of sympatric and repeated parallel radiation events within and among isolated crater lakes. RESULTS Here, we characterized the genes of MHC class IIB chain of the Midas cichlid species complex (Amphilophus cf. citrinellus) including fish from five lakes in Nicaragua. We designed 19 new specific primers anchored in a stepwise fashion in order to detect all alleles present. We obtained 866 genomic DNA (gDNA) sequences from thirteen individuals and 756 additional sequences from complementary DNA (cDNA) of seven of those individuals. We identified 69 distinct alleles with up to 25 alleles per individual. We also found considerable intron length variation and mismatches of alleles detected in cDNA and gDNA suggesting that some loci have undergone pseudogenization. Lastly, we created a model of protein structure homology for each allele and identified their key structural components. CONCLUSIONS Overall, the Midas cichlid has one of the most diverse repertoires of MHC class IIB genes known, which could serve as a powerful tool to elucidate the process of divergent radiations, colonization and speciation in sympatry.
Collapse
Affiliation(s)
- Melinda J Hofmann
- Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal, 2, 28006, Madrid, Spain
| | - Seraina E Bracamonte
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Duesternbrooker weg 20, 24105, Kiel, Germany
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 310, 12587, Berlin, Germany
| | - Christophe Eizaguirre
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Duesternbrooker weg 20, 24105, Kiel, Germany
- Queen Mary University of London, School of Biological and Chemical Sciences, Mile End Road, London, E1 4NS, UK
| | - Marta Barluenga
- Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal, 2, 28006, Madrid, Spain.
| |
Collapse
|
33
|
Ford AGP, Rüber L, Newton J, Dasmahapatra KK, Balarin JD, Bruun K, Day JJ. Niche divergence facilitated by fine-scale ecological partitioning in a recent cichlid fish adaptive radiation. Evolution 2016; 70:2718-2735. [PMID: 27659769 PMCID: PMC5132037 DOI: 10.1111/evo.13072] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 08/29/2016] [Accepted: 09/10/2016] [Indexed: 12/22/2022]
Abstract
Ecomorphological differentiation is a key feature of adaptive radiations, with a general trend for specialization and niche expansion following divergence. Ecological opportunity afforded by invasion of a new habitat is thought to act as an ecological release, facilitating divergence, and speciation. Here, we investigate trophic adaptive morphology and ecology of an endemic clade of oreochromine cichlid fishes (Alcolapia) that radiated along a herbivorous trophic axis following colonization of an isolated lacustrine environment, and demonstrate phenotype‐environment correlation. Ecological and morphological divergence of the Alcolapia species flock are examined in a phylogenomic context, to infer ecological niche occupation within the radiation. Species divergence is observed in both ecology and morphology, supporting the importance of ecological speciation within the radiation. Comparison with an outgroup taxon reveals large‐scale ecomorphological divergence but shallow genomic differentiation within the Alcolapia adaptive radiation. Ancestral morphological reconstruction suggests lake colonization by a generalist oreochromine phenotype that diverged in Lake Natron to varied herbivorous morphologies akin to specialist herbivores in Lakes Tanganyika and Malawi.
Collapse
Affiliation(s)
- Antonia G P Ford
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, United Kingdom.,Current Address: School of Biological Sciences, Bangor University, ECW Building, Deiniol Road, Bangor, Gwynedd, LL57 2UW, Wales, United Kingdom
| | - Lukas Rüber
- Naturhistorisches Museum der Burgergemeinde Bern, Bernastrasse 15, 3005, Bern, Switzerland.,Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012, Bern, Switzerland
| | - Jason Newton
- NERC Life Sciences Mass Spectrometry Facility, SUERC, Rankine Avenue, Scottish Enterprise Technology Park, East Kilbride, G75 0QF, United Kingdom
| | | | | | - Kristoffer Bruun
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, United Kingdom
| | - Julia J Day
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, United Kingdom
| |
Collapse
|
34
|
Arbour JH, López-Fernández H. Continental cichlid radiations: functional diversity reveals the role of changing ecological opportunity in the Neotropics. Proc Biol Sci 2016; 283:20160556. [PMID: 27512144 PMCID: PMC5013758 DOI: 10.1098/rspb.2016.0556] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 07/20/2016] [Indexed: 11/12/2022] Open
Abstract
Adaptive radiations have been hypothesized to contribute broadly to the diversity of organisms. Models of adaptive radiation predict that ecological opportunity and ecological release, the availability of empty ecological niches and the response by adapting lineages to occupy them, respectively, drive patterns of phenotypic and lineage diversification. Adaptive radiations driven by 'ecological opportunity' are well established in island systems; it is less clear if ecological opportunity influences continent-wide diversification. We use Neotropical cichlid fishes to test if variation in rates of functional evolution is consistent with changing ecological opportunity. Across a functional morphological axis associated with ram-suction feeding traits, evolutionary rates declined through time as lineages diversified in South America. Evolutionary rates of ram-suction functional morphology also appear to have accelerated as cichlids colonized Central America and encountered renewed opportunity. Our results suggest that ecological opportunity may play an important role in shaping patterns of morphological diversity of even broadly distributed lineages like Neotropical cichlids.
Collapse
Affiliation(s)
- Jessica Hilary Arbour
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Wilcocks Street, Toronto, Ontario, Canada M5S 3B2 Department of Biology, University of Washington, Kincaid Hall, Seattle, WA 206-221-7568, USA Department of Natural History, Royal Ontario Museum, 100 Queen's Park, Toronto, Ontario, Canada M5S 2C6
| | - Hernán López-Fernández
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Wilcocks Street, Toronto, Ontario, Canada M5S 3B2 Department of Natural History, Royal Ontario Museum, 100 Queen's Park, Toronto, Ontario, Canada M5S 2C6
| |
Collapse
|
35
|
Kern EMA, Robinson D, Gass E, Godwin J, Langerhans RB. Correlated evolution of personality, morphology and performance. Anim Behav 2016; 117:79-86. [PMID: 29398712 PMCID: PMC5791543 DOI: 10.1016/j.anbehav.2016.04.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Evolutionary change in one trait can elicit evolutionary changes in other traits due to genetic correlations. This constrains the independent evolution of traits and can lead to unpredicted ecological and evolutionary outcomes. Animals might frequently exhibit genetic associations among behavioural and morphological-physiological traits, because the physiological mechanisms behind animal personality can have broad multitrait effects and because many selective agents influence the evolution of multiple types of traits. However, we currently know little about genetic correlations between animal personalities and nonbehavioural traits. We tested for associations between personality, morphology and locomotor performance by comparing zebrafish (Danio rerio) collected from the wild and then selectively bred for either a proactive or reactive stress coping style ('bold' or 'shy' phenotypes). Based on adaptive hypotheses of correlational selection in the wild, we predicted that artificial selection for boldness would produce correlated evolutionary responses of larger caudal regions and higher fast-start escape performance (and the opposite for shyness). After four to seven generations, morphology and locomotor performance differed between personality lines: bold zebrafish exhibited a larger caudal region and higher fast-start performance than fish in the shy line, matching predictions. Individual-level phenotypic correlations suggested that pleiotropy or physical gene linkage likely explained the correlated response of locomotor performance, while the correlated response of body shape may have reflected linkage disequilibrium, which is breaking down each generation in the laboratory. Our results indicate that evolution of personality can result in concomitant changes in morphology and whole-organism performance, and vice versa.
Collapse
Affiliation(s)
- Elizabeth M. A. Kern
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, U.S.A
- W.M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC, U.S.A
| | - Detric Robinson
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, U.S.A
- W.M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC, U.S.A
| | - Erika Gass
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, U.S.A
- W.M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC, U.S.A
| | - John Godwin
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, U.S.A
- W.M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC, U.S.A
| | - R. Brian Langerhans
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, U.S.A
- W.M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC, U.S.A
| |
Collapse
|
36
|
Kautt AF, Machado-Schiaffino G, Torres-Dowdall J, Meyer A. Incipient sympatric speciation in Midas cichlid fish from the youngest and one of the smallest crater lakes in Nicaragua due to differential use of the benthic and limnetic habitats? Ecol Evol 2016; 6:5342-57. [PMID: 27551387 PMCID: PMC4984508 DOI: 10.1002/ece3.2287] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 06/08/2016] [Accepted: 06/09/2016] [Indexed: 12/21/2022] Open
Abstract
Understanding how speciation can occur without geographic isolation remains a central objective in evolutionary biology. Generally, some form of disruptive selection and assortative mating are necessary for sympatric speciation to occur. Disruptive selection can arise from intraspecific competition for resources. If this competition leads to the differential use of habitats and variation in relevant traits is genetically determined, then assortative mating can be an automatic consequence (i.e., habitat isolation). In this study, we caught Midas cichlid fish from the limnetic (middle of the lake) and benthic (shore) habitats of Crater Lake Asososca Managua to test whether some of the necessary conditions for sympatric speciation due to intraspecific competition and habitat isolation are given. Lake As. Managua is very small (<900 m in diameter), extremely young (maximally 1245 years of age), and completely isolated. It is inhabited by, probably, only a single endemic species of Midas cichlids, Amphilophus tolteca. We found that fish from the limnetic habitat were more elongated than fish collected from the benthic habitat, as would be predicted from ecomorphological considerations. Stable isotope analyses confirmed that the former also exhibit a more limnetic lifestyle than the latter. Furthermore, split‐brood design experiments in the laboratory suggest that phenotypic plasticity is unlikely to explain much of the observed differences in body elongation that we observed in the field. Yet, neutral markers (microsatellites) did not reveal any genetic clustering in the population. Interestingly, demographic inferences based on RAD‐seq data suggest that the apparent lack of genetic differentiation at neutral markers could simply be due to a lack of time, as intraspecific competition may only have begun a few hundred generations ago.
Collapse
Affiliation(s)
- Andreas F Kautt
- Department of Biology University of Konstanz Universitätsstrasse 10 78457 Konstanz Germany
| | | | - Julian Torres-Dowdall
- Department of Biology University of Konstanz Universitätsstrasse 10 78457 Konstanz Germany
| | - Axel Meyer
- Department of Biology University of Konstanz Universitätsstrasse 10 78457 Konstanz Germany
| |
Collapse
|
37
|
Kautt AF, Machado-Schiaffino G, Meyer A. Multispecies Outcomes of Sympatric Speciation after Admixture with the Source Population in Two Radiations of Nicaraguan Crater Lake Cichlids. PLoS Genet 2016; 12:e1006157. [PMID: 27362536 PMCID: PMC4928843 DOI: 10.1371/journal.pgen.1006157] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 06/09/2016] [Indexed: 12/19/2022] Open
Abstract
The formation of species in the absence of geographic barriers (i.e. sympatric speciation) remains one of the most controversial topics in evolutionary biology. While theoretical models have shown that this most extreme case of primary divergence-with-gene-flow is possible, only a handful of accepted empirical examples exist. And even for the most convincing examples uncertainties remain; complex histories of isolation and secondary contact can make species falsely appear to have originated by sympatric speciation. This alternative scenario is notoriously difficult to rule out. Midas cichlids inhabiting small and remote crater lakes in Nicaragua are traditionally considered to be one of the best examples of sympatric speciation and lend themselves to test the different evolutionary scenarios that could lead to apparent sympatric speciation since the system is relatively small and the source populations known. Here we reconstruct the evolutionary history of two small-scale radiations of Midas cichlids inhabiting crater lakes Apoyo and Xiloá through a comprehensive genomic data set. We find no signs of differential admixture of any of the sympatric species in the respective radiations. Together with coalescent simulations of different demographic models our results support a scenario of speciation that was initiated in sympatry and does not result from secondary contact of already partly diverged populations. Furthermore, several species seem to have diverged simultaneously, making Midas cichlids an empirical example of multispecies outcomes of sympatric speciation. Importantly, however, the demographic models strongly support an admixture event from the source population into both crater lakes shortly before the onset of the radiations within the lakes. This opens the possibility that the formation of reproductive barriers involved in sympatric speciation was facilitated by genetic variants that evolved in a period of isolation between the initial founding population and the secondary migrants that came from the same source population. Thus, the exact mechanisms by which these species arose might be different from what had been thought before.
Collapse
Affiliation(s)
- Andreas F. Kautt
- Department of Biology, University of Konstanz, Konstanz, Baden-Württemberg, Germany
| | | | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Baden-Württemberg, Germany
- * E-mail:
| |
Collapse
|
38
|
Fruciano C, Franchini P, Raffini F, Fan S, Meyer A. Are sympatrically speciating Midas cichlid fish special? Patterns of morphological and genetic variation in the closely related species Archocentrus centrarchus. Ecol Evol 2016; 6:4102-14. [PMID: 27516867 PMCID: PMC4877357 DOI: 10.1002/ece3.2184] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 04/18/2016] [Accepted: 04/22/2016] [Indexed: 12/14/2022] Open
Abstract
Established empirical cases of sympatric speciation are scarce, although there is an increasing consensus that sympatric speciation might be more common than previously thought. Midas cichlid fish are one of the few substantiated cases of sympatric speciation, and they formed repeated radiations in crater lakes. In contrast, in the same environment, such radiation patterns have not been observed in other species of cichlids and other families of fish. We analyze morphological and genetic variation in a cichlid species (Archocentrus centrarchus) that co-inhabits several crater lakes with the Midas species complex. In particular, we analyze variation in body and pharyngeal jaw shape (two ecologically important traits in sympatrically divergent Midas cichlids) and relate that to genetic variation in mitochondrial control region and microsatellites. Using these four datasets, we analyze variation between and within two Nicaraguan lakes: a crater lake where multiple Midas cichlids have been described and a lake where the source population lives. We do not observe any within-lake clustering consistent across morphological traits and genetic markers, suggesting the absence of sympatric divergence in A. centrarchus. Genetic differentiation between lakes was low and morphological divergence absent. Such morphological similarity between lakes is found not only in average morphology, but also when analyzing covariation between traits and degree of morphospace occupation. A combined analysis of the mitochondrial control region in A. centrarchus and Midas cichlids suggests that a difference between lineages in the timing of crater lake colonization cannot be invoked as an explanation for the difference in their levels of diversification. In light of our results, A. centrarchus represents the ideal candidate to study the genomic differences between these two lineages that might explain why some lineages are more likely to speciate and diverge in sympatry than others.
Collapse
Affiliation(s)
- Carmelo Fruciano
- Department of Biology Chair of Zoology and Evolutionary Biology University of Konstanz Universitätsstrasse 1078457 Konstanz Germany; School of Earth, Environmental & Biological Sciences Queensland University of Technology Brisbane Qld 4000 Australia
| | - Paolo Franchini
- Department of Biology Chair of Zoology and Evolutionary Biology University of Konstanz Universitätsstrasse 10 78457 Konstanz Germany
| | - Francesca Raffini
- Department of Biology Chair of Zoology and Evolutionary Biology University of Konstanz Universitätsstrasse 1078457 Konstanz Germany; International Max Planck Research School (IMPRS) for Organismal Biology Max-Planck-Institut für Ornithologie Am Obstberg 178315 Radolfzell Germany
| | - Shaohua Fan
- Department of Biology Chair of Zoology and Evolutionary Biology University of Konstanz Universitätsstrasse 10 78457 Konstanz Germany
| | - Axel Meyer
- Department of Biology Chair of Zoology and Evolutionary Biology University of Konstanz Universitätsstrasse 10 78457 Konstanz Germany
| |
Collapse
|
39
|
Fine-scale behavioural differences distinguish resource use by ecomorphs in a closed ecosystem. Sci Rep 2016; 6:24369. [PMID: 27098197 PMCID: PMC4838883 DOI: 10.1038/srep24369] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 03/16/2016] [Indexed: 11/19/2022] Open
Abstract
Temporal differences in habitat use and foraging specialisms between ecomorphs represent aspects of behavioural phenotype that are poorly understood with regard to the origin and maintenance of ecological diversity. We tested the role of behaviour in resource use divergence of two Arctic charr (Salvelinus alpinus) phenotypes, a slim, putatively pelagic-dwelling morph and a robust, putatively littoral-dwelling generalist morph, over an annual cycle, using biotelemetry and stable isotopes. Pelagic morph charr exhibited significantly greater δC13 depletion, concordant with increased zooplanktivory, than for the Littoral morph. Although three-dimensional space-use of the morphs strongly overlapped, on average, the Littoral morph used that habitat 19.3% more than the Pelagic morph. Pelagic morph fish were significantly more active, further from the lake bed and at greater depth than Littoral fish (annual means respectively, Pelagic, 0.069BLs−1, 8.21 m and 14.11 m; Littoral, 0.047BLs−1, 5.87 m and 10.47 m). Patterns of habitat use differed between ecomorphs at key times, such as during autumn and at ice break, likely related to spawning and resumption of intensive foraging respectively. Extensive space-use overlap, but fine-scale differences in habitat use between charr ecomorphs, suggests the importance of competition for generating and maintaining polymorphism, and its potential for promoting reproductive isolation and evolution in sympatry.
Collapse
|
40
|
Lemaire P, Piette J. Tunicates: exploring the sea shores and roaming the open ocean. A tribute to Thomas Huxley. Open Biol 2016; 5:150053. [PMID: 26085517 PMCID: PMC4632506 DOI: 10.1098/rsob.150053] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This review is a tribute to the remarkable contributions of Thomas Huxley to the biology of tunicates, the likely sister group of vertebrates. In 1851, the great biologist and philosopher published two landmark papers on pelagic tunicates in the Philosophical Transactions of the Royal Society. They were dedicated to the description of the adult anatomy and life cycle of thaliaceans and appendicularians, the pelagic relatives of ascidians. In the first part of this review, we discuss the novel anatomical observations and evolutionary hypotheses made by Huxley, which would have a lasting influence on tunicate biology. We also briefly comment on the more philosophical reflections of Huxley on individuality. In the second part, we stress the originality and relevance of past and future studies of tunicates in the resolution of major biological issues. In particular, we focus on the complex relationship between genotype and phenotype and the phenomenon of developmental system drift. We propose that more than 150 years after Huxley's papers, tunicate embryos are still worth studying in their own right, independently of their evolutionary proximity to vertebrates, as they provide original and crucial insights into the process of animal evolution. Tunicates are still at the forefront of biological research.
Collapse
Affiliation(s)
- Patrick Lemaire
- Centre de Recherches de Biochimie Macromoléculaire. UMR 5237, Centre National de la Recherche Scientifique, Université de Montpellier, 1919 Route de Mende, 34293, Montpellier cedex 5, France
| | - Jacques Piette
- Centre de Recherches de Biochimie Macromoléculaire. UMR 5237, Centre National de la Recherche Scientifique, Université de Montpellier, 1919 Route de Mende, 34293, Montpellier cedex 5, France
| |
Collapse
|
41
|
Kavembe GD, Kautt AF, Machado-Schiaffino G, Meyer A. Eco-morphological differentiation in Lake Magadi tilapia, an extremophile cichlid fish living in hot, alkaline and hypersaline lakes in East Africa. Mol Ecol 2016; 25:1610-25. [DOI: 10.1111/mec.13461] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 11/01/2015] [Accepted: 11/03/2015] [Indexed: 12/25/2022]
Affiliation(s)
- Geraldine D. Kavembe
- Chair in Zoology and Evolutionary Biology; Department of Biology; University of Konstanz; Universitätsstrasse 10 78457 Konstanz Germany
- Department of Biology; School of Pure and Applied Sciences; South Eastern Kenya University; P. O. Box 170 90200 Kitui Kenya
| | - Andreas F. Kautt
- Chair in Zoology and Evolutionary Biology; Department of Biology; University of Konstanz; Universitätsstrasse 10 78457 Konstanz Germany
- International Max Planck Research School for Organismal Biology; University of Konstanz; Universitätsstrasse 10 78457 Konstanz Germany
| | - Gonzalo Machado-Schiaffino
- Chair in Zoology and Evolutionary Biology; Department of Biology; University of Konstanz; Universitätsstrasse 10 78457 Konstanz Germany
| | - Axel Meyer
- Chair in Zoology and Evolutionary Biology; Department of Biology; University of Konstanz; Universitätsstrasse 10 78457 Konstanz Germany
- International Max Planck Research School for Organismal Biology; University of Konstanz; Universitätsstrasse 10 78457 Konstanz Germany
| |
Collapse
|
42
|
Šklíba J, Lövy M, Koeppen SCW, Pleštilová L, Vitámvás M, Nevo E, Šumbera R. Activity of free-living subterranean blind mole ratsSpalax galili(Rodentia: Spalacidae) in an area of supposed sympatric speciation. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12741] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jan Šklíba
- Department of Zoology; Faculty of Science; University of South Bohemia; Branišovská 31 37005 České Budějovice Czech Republic
| | - Matěj Lövy
- Department of Zoology; Faculty of Science; University of South Bohemia; Branišovská 31 37005 České Budějovice Czech Republic
| | - Stephan C. W. Koeppen
- Department of General Zoology; Faculty of Biology; University of Duisburg-Essen; Universitätsstr. 5 45141 Essen Germany
| | - Lucie Pleštilová
- Department of Zoology; Faculty of Science; University of South Bohemia; Branišovská 31 37005 České Budějovice Czech Republic
| | - Miloš Vitámvás
- Department of Zoology; Faculty of Science; University of South Bohemia; Branišovská 31 37005 České Budějovice Czech Republic
| | - Eviatar Nevo
- Institute of Evolution; University of Haifa; Haifa 31905 Israel
| | - Radim Šumbera
- Department of Zoology; Faculty of Science; University of South Bohemia; Branišovská 31 37005 České Budějovice Czech Republic
| |
Collapse
|
43
|
Malabarba LR, Malabarba MC, Reis RE. Descriptions of five new species of the Neotropical cichlid genus Gymnogeophagus Miranda Ribeiro, 1918 (Teleostei: Cichliformes) from the rio Uruguay drainage. NEOTROPICAL ICHTHYOLOGY 2015. [DOI: 10.1590/1982-0224-20140188] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
ABSTRACT Gymnogeophagus is a Neotropical cichlid genus distributed in the río Paraguay, rio Paraná and rio Uruguay drainages and also in the coastal rivers of Uruguay and southern Brazil. Its monophyly is supported by two derived features: the absence of supraneurals and the presence of a forward spine in the first dorsal-fin pterygiophore. Herein, five new species of Gymnogeophagus are described from middle to upper tributaries of the rio Uruguay drainage and from the rio Negro. All these new species belong to a clade, which includes G. gymnogenys , easily recognized by sharing two synapomorphies: the absence of an oblique bar between the dorsal border of the eye and the nape, and the possession of a black bar originating in the dorsal contour near the dorsal-fin origin and directed downward and backward on the dorsum. A key to all species of Gymnogeophagus is provided.
Collapse
|
44
|
Burress ED. Ecological diversification associated with the pharyngeal jaw diversity of Neotropical cichlid fishes. J Anim Ecol 2015; 85:302-13. [PMID: 26476003 DOI: 10.1111/1365-2656.12457] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 10/08/2015] [Indexed: 01/10/2023]
Abstract
Innovations can facilitate bursts of diversification by increasing access to novel resources and the attainment of novel functional designs. Pharyngognathy, exhibited by highly diverse groups such as wrasses and cichlid fishes, is hypothesized to increase foraging capacity and efficiency. Here, I test the hypothesis that pharyngeal jaw shape and tooth morphology are adaptive in an ecologically diverse radiation of Neotropical cichlid fishes that spans North, Central and South America. I partitioned species into generalized trophic guilds using published stomach content analyses and quantified shape variation of the lower pharyngeal jaw (LPJ) using geometric morphometrics. Additionally, I tested for convergence in LPJ shape and trophic guild by mapping the phylogeny onto the principal components and testing for shifts towards similar evolutionary regimes. Major LPJ shape variation included the length and orientation (i.e. narrow or wide) of the lateral processes and length of the medial process, which varied based on the proportion of fishes and plants consumed. Pharyngeal tooth number, diversity and the frequency of tooth types were not evenly distributed among trophic guilds. There were seven distinct evolutionary regimes that converged upon four optima. Pharyngeal jaw diversification is associated with the exploitation of novel resources among Neotropical cichlids such that pharyngeal specialization has increased access to otherwise poorly accessible resources, such as resources that are difficult to crush (e.g. hard-shelled organisms) and assimilate (e.g. algae).
Collapse
Affiliation(s)
- Edward D Burress
- Department of Biological Sciences and Auburn University Museum of Natural History, Auburn University, Auburn, AL, 36849, USA
| |
Collapse
|
45
|
Cruz-Jofré F, Morales P, Vila I, Esquer-Garrigos Y, Hugueny B, Gaubert P, Poulin E, Méndez MA. Geographical isolation and genetic differentiation: the case ofOrestias ascotanensis(Teleostei: Cyprinodontidae), an Andean killifish inhabiting a highland salt pan. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12704] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Franco Cruz-Jofré
- Laboratorio de Genética y Evolución; Departamento de Ciencias Ecológicas; Facultad de Ciencias; Universidad de Chile; Las Palmeras 3425 Casilla 653 Ñuñoa Santiago Chile
- Escuela de Medicina Veterinaria; Facultad de Medicina Veterinaria y Recursos Naturales; Universidad Santo Tomás; Avenida Limonares 190 Viña del Mar Chile
| | - Pamela Morales
- Laboratorio de Genética y Evolución; Departamento de Ciencias Ecológicas; Facultad de Ciencias; Universidad de Chile; Las Palmeras 3425 Casilla 653 Ñuñoa Santiago Chile
| | - Irma Vila
- Laboratorio de Limnología; Departamento de Ciencias Ecológicas; Facultad de Ciencias; Universidad de Chile; Las Palmeras 3425, Casilla 653 Ñuñoa Santiago Chile
| | - Yareli Esquer-Garrigos
- UMR BOREA; Département Milieux et Peuplements Aquatiques; MNHN-CNRS 7208-IRD 207-UPMC; Muséum National d'Histoire Naturelle; 43 rue Cuvier 75231 Paris France
| | - Bernard Hugueny
- UMR BOREA; Département Milieux et Peuplements Aquatiques; MNHN-CNRS 7208-IRD 207-UPMC; Muséum National d'Histoire Naturelle; 43 rue Cuvier 75231 Paris France
| | - Philippe Gaubert
- UMR BOREA; Département Milieux et Peuplements Aquatiques; MNHN-CNRS 7208-IRD 207-UPMC; Muséum National d'Histoire Naturelle; 43 rue Cuvier 75231 Paris France
- Institut des Sciences de l'Evolution de Montpellier (ISEM), UM2/CNRS/IRD; Université de Montpellier; Place Eugène Bataillon, CC 64 34095 Montpellier, Cedex 05 France
| | - Elie Poulin
- Laboratorio de Ecología Molecular; Departamento de Ciencias Ecológicas; Facultad de Ciencias; Universidad de Chile; Las Palmeras 3425, Casilla 653 Ñuñoa Santiago Chile
- Instituto de Ecología y Biodiversidad (IEB), Departamento de Ciencias Ecológicas; Facultad de Ciencias; Universidad de Chile; Las Palmeras 3425, Casilla 653 Ñuñoa Santiago Chile
| | - Marco A. Méndez
- Laboratorio de Genética y Evolución; Departamento de Ciencias Ecológicas; Facultad de Ciencias; Universidad de Chile; Las Palmeras 3425 Casilla 653 Ñuñoa Santiago Chile
- Instituto de Ecología y Biodiversidad (IEB), Departamento de Ciencias Ecológicas; Facultad de Ciencias; Universidad de Chile; Las Palmeras 3425, Casilla 653 Ñuñoa Santiago Chile
| |
Collapse
|
46
|
Kusche H, Elmer KR, Meyer A. Sympatric ecological divergence associated with a color polymorphism. BMC Biol 2015; 13:82. [PMID: 26437665 PMCID: PMC4594650 DOI: 10.1186/s12915-015-0192-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 09/12/2015] [Indexed: 01/24/2023] Open
Abstract
Background Color polymorphisms are a conspicuous feature of many species and a way to address broad ecological and evolutionary questions. Three potential major evolutionary fates of color polymorphisms are conceivable over time: maintenance, loss, or speciation. However, the understanding of color polymorphisms and their evolutionary implications is frequently impaired by sex-linkage of coloration, unknown inheritance patterns, difficulties in phenotypic characterization, and a lack of evolutionary replicates. Hence, the role of color polymorphisms in promoting ecological and evolutionary diversification remains poorly understood. In this context, we assessed the ecological and evolutionary consequences of a color polymorphic study system that is not hampered by these restrictions: the repeated adaptive radiations of the gold/dark Midas cichlid fishes (the Amphilophus citrinellus species complex) from the great lakes and crater lakes of Nicaragua, Central America. Results We conducted multi-trait morphological and ecological analyses from ten populations of this young adaptive radiation (<6,000 years old), which revealed sympatric ecological differentiation associated with the conspicuous binary (gold/dark) color polymorphism. Varying degrees of intraspecific ecological divergence were observed across the ten color morph pairs, but most pairs exhibited a consistently parallel ecological and evolutionary trajectory across populations. Specifically, gold Midas cichlids are frequently deeper-bodied, have more robust pharyngeal jaws, and feed at a lower trophic level compared to conspecific, sympatric dark individuals. A common garden experiment suggests there is a genetic correlation of color and eco-morphological traits. Conclusions We demonstrate unprecedented ecological and evolutionary consequences of color polymorphism in this adaptive radiation. Across the species complex, sympatric conspecific individuals differed in eco-morphology depending on color morph (gold/dark) and the axis of differentiation tended to be consistent across replicates. The consistent divergence across wild populations and the common garden experiment suggests that color is genetically correlated to ecology. Because Midas cichlids are known to mate color assortatively, the putative genetic correlation of this color polymorphism with an eco-morphological divergence suggests an innate potential to promote ecological and evolutionary divergence across this species complex. However, there are to date no examples of speciation based on color in this radiation, suggesting long-term maintenance of this color polymorphism. Electronic supplementary material The online version of this article (doi:10.1186/s12915-015-0192-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Henrik Kusche
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany. .,International Max Planck Research School for Organismal Biology, University of Konstanz, 78457, Konstanz, Germany. .,Present address: Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval, 1030 Avenue de la Médecine, Québec, G1V 0A6, QC, Canada.
| | - Kathryn R Elmer
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany. .,Present address: Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK.
| | - Axel Meyer
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany. .,International Max Planck Research School for Organismal Biology, University of Konstanz, 78457, Konstanz, Germany.
| |
Collapse
|
47
|
Collin H, Fumagalli L. The role of geography and ecology in shaping repeated patterns of morphological and genetic differentiation between European minnows (Phoxinus phoxinus) from the Pyrenees and the Alps. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12611] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hélène Collin
- Département d'Ecologie et Evolution; Laboratoire de Biologie de la Conservation, Biophore; Université de Lausanne; Lausanne 1015 Switzerland
- Institute of Integrative Biology; Department of Evolution; Ecology and Behaviour; University of Liverpool; Liverpool L69 7ZB UK
| | - Luca Fumagalli
- Département d'Ecologie et Evolution; Laboratoire de Biologie de la Conservation, Biophore; Université de Lausanne; Lausanne 1015 Switzerland
| |
Collapse
|
48
|
Ford AGP, Dasmahapatra KK, Rüber L, Gharbi K, Cezard T, Day JJ. High levels of interspecific gene flow in an endemic cichlid fish adaptive radiation from an extreme lake environment. Mol Ecol 2015; 24:3421-40. [PMID: 25997156 PMCID: PMC4973668 DOI: 10.1111/mec.13247] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 05/13/2015] [Accepted: 05/13/2015] [Indexed: 12/30/2022]
Abstract
Studying recent adaptive radiations in isolated insular systems avoids complicating causal events and thus may offer clearer insight into mechanisms generating biological diversity. Here, we investigate evolutionary relationships and genomic differentiation within the recent radiation of Alcolapia cichlid fish that exhibit extensive phenotypic diversification, and which are confined to the extreme soda lakes Magadi and Natron in East Africa. We generated an extensive RAD data set of 96 individuals from multiple sampling sites and found evidence for genetic admixture between species within Lake Natron, with the highest levels of admixture between sympatric populations of the most recently diverged species. Despite considerable environmental separation, populations within Lake Natron do not exhibit isolation by distance, indicating panmixia within the lake, although individuals within lineages clustered by population in phylogenomic analysis. Our results indicate exceptionally low genetic differentiation across the radiation despite considerable phenotypic trophic variation, supporting previous findings from smaller data sets; however, with the increased power of densely sampled SNPs, we identify genomic peaks of differentiation (FST outliers) between Alcolapia species. While evidence of ongoing gene flow and interspecies hybridization in certain populations suggests that Alcolapia species are incompletely reproductively isolated, the identification of outlier SNPs under diversifying selection indicates the radiation is undergoing adaptive divergence.
Collapse
Affiliation(s)
- Antonia G P Ford
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
| | | | - Lukas Rüber
- Naturhistorisches Museum der Burgergemeinde Bern, Bernastrasse 15, Bern, 3005, Switzerland
| | - Karim Gharbi
- Edinburgh Genomics, Ashworth Laboratories, The University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Timothee Cezard
- Edinburgh Genomics, Ashworth Laboratories, The University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Julia J Day
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
| |
Collapse
|
49
|
Martin CH, Cutler JS, Friel JP, Dening Touokong C, Coop G, Wainwright PC. Complex histories of repeated gene flow in Cameroon crater lake cichlids cast doubt on one of the clearest examples of sympatric speciation. Evolution 2015; 69:1406-1422. [PMID: 25929355 DOI: 10.1111/evo.12674] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 04/20/2015] [Indexed: 12/19/2022]
Abstract
One of the most celebrated examples of sympatric speciation in nature are monophyletic radiations of cichlid fishes endemic to Cameroon crater lakes. However, phylogenetic inference of monophyly may not detect complex colonization histories involving some allopatric isolation, such as double invasions obscured by genome-wide gene flow. Population genomic approaches are better suited to test hypotheses of sympatric speciation in these cases. Here, we use comprehensive sampling from all four sympatric crater lake cichlid radiations in Cameroon and outgroups across Africa combined with next-generation sequencing to genotype tens of thousands of SNPs. We find considerable evidence of gene flow between all four radiations and neighboring riverine populations after initial colonization. In a few cases, some sympatric species are more closely related to outgroups than others, consistent with secondary gene flow facilitating their speciation. Our results do not rule out sympatric speciation in Cameroon cichlids, but rather reveal a complex history of speciation with gene flow, including allopatric and sympatric phases, resulting in both reproductively isolated species and incipient species complexes. The best remaining non-cichlid examples of sympatric speciation all involve assortative mating within microhabitats. We speculate that this feature may be necessary to complete the process of sympatric speciation in nature.
Collapse
Affiliation(s)
- Christopher H Martin
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina
| | - Joseph S Cutler
- Department of Conservation Biology, University of California, Santa Cruz, California
| | - John P Friel
- Alabama Museum of Natural History, University of Alabama, Tuscaloosa, Alabama
| | | | - Graham Coop
- Center for Population Biology and Department of Evolution & Ecology, University of California, Davis, California
| | - Peter C Wainwright
- Center for Population Biology and Department of Evolution & Ecology, University of California, Davis, California
| |
Collapse
|
50
|
Analyzing Fluctuating Asymmetry with Geometric Morphometrics: Concepts, Methods, and Applications. Symmetry (Basel) 2015. [DOI: 10.3390/sym7020843] [Citation(s) in RCA: 208] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
|