1
|
Coulmance F, Akkaynak D, Le Poul Y, Höppner MP, McMillan WO, Puebla O. Phenotypic and genomic dissection of colour pattern variation in a reef fish radiation. Mol Ecol 2024; 33:e17047. [PMID: 37337919 DOI: 10.1111/mec.17047] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 05/04/2023] [Accepted: 05/30/2023] [Indexed: 06/21/2023]
Abstract
Coral reefs rank among the most diverse species assemblages on Earth. A particularly striking aspect of coral reef communities is the variety of colour patterns displayed by reef fishes. Colour pattern is known to play a central role in the ecology and evolution of reef fishes through, for example, signalling or camouflage. Nevertheless, colour pattern is a complex trait in reef fishes-actually a collection of traits-that is difficult to analyse in a quantitative and standardized way. This is the challenge that we address in this study using the hamlets (Hypoplectrus spp., Serranidae) as a model system. Our approach involves a custom underwater camera system to take orientation- and size-standardized photographs in situ, colour correction, alignment of the fish images with a combination of landmarks and Bézier curves, and principal component analysis on the colour value of each pixel of each aligned fish. This approach identifies the major colour pattern elements that contribute to phenotypic variation in the group. Furthermore, we complement the image analysis with whole-genome sequencing to run a multivariate genome-wide association study for colour pattern variation. This second layer of analysis reveals sharp association peaks along the hamlet genome for each colour pattern element and allows to characterize the phenotypic effect of the single nucleotide polymorphisms that are most strongly associated with colour pattern variation at each association peak. Our results suggest that the diversity of colour patterns displayed by the hamlets is generated by a modular genomic and phenotypic architecture.
Collapse
Affiliation(s)
- Floriane Coulmance
- Leibniz Center for Tropical Marine Research, Bremen, Germany
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Oldenburg, Germany
- Smithsonian Tropical Research Institute (STRI), Panama, Republic of Panama
| | - Derya Akkaynak
- Hatter Department of Marine Technologies, University of Haifa, Haifa, Israel
- Interuniversity Institute of Marine Sciences, Eilat, Israel
| | - Yann Le Poul
- Ludwig-Maximilians-Universität München, Munich, Germany
| | - Marc P Höppner
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - W Owen McMillan
- Smithsonian Tropical Research Institute (STRI), Panama, Republic of Panama
| | - Oscar Puebla
- Leibniz Center for Tropical Marine Research, Bremen, Germany
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Oldenburg, Germany
- Smithsonian Tropical Research Institute (STRI), Panama, Republic of Panama
| |
Collapse
|
2
|
Hench K, Helmkampf M, McMillan WO, Puebla O. Rapid radiation in a highly diverse marine environment. Proc Natl Acad Sci U S A 2022; 119:e2020457119. [PMID: 35042790 PMCID: PMC8794831 DOI: 10.1073/pnas.2020457119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 11/18/2021] [Indexed: 12/16/2022] Open
Abstract
Rapid diversification is often observed when founding species invade isolated or newly formed habitats that provide ecological opportunity for adaptive radiation. However, most of the Earth's diversity arose in diverse environments where ecological opportunities appear to be more constrained. Here, we present a striking example of a rapid radiation in a highly diverse marine habitat. The hamlets, a group of reef fishes from the wider Caribbean, have radiated into a stunning diversity of color patterns but show low divergence across other ecological axes. Although the hamlet lineage is ∼26 My old, the radiation appears to have occurred within the last 10,000 generations in a burst of diversification that ranks among the fastest in fishes. As such, the hamlets provide a compelling backdrop to uncover the genomic elements associated with phenotypic diversification and an excellent opportunity to build a broader comparative framework for understanding the drivers of adaptive radiation. The analysis of 170 genomes suggests that color pattern diversity is generated by different combinations of alleles at a few large-effect loci. Such a modular genomic architecture of diversification has been documented before in Heliconius butterflies, capuchino finches, and munia finches, three other tropical radiations that took place in highly diverse and complex environments. The hamlet radiation also occurred in a context of high effective population size, which is typical of marine populations. This allows for the accumulation of new variants through mutation and the retention of ancestral genetic variation, both of which appear to be important in this radiation.
Collapse
Affiliation(s)
- Kosmas Hench
- Ecology Department, Leibniz Centre for Tropical Marine Research, 28359 Bremen, Germany;
| | - Martin Helmkampf
- Ecology Department, Leibniz Centre for Tropical Marine Research, 28359 Bremen, Germany
| | - W Owen McMillan
- Smithsonian Tropical Research Institute, Apartado Postal 0843-03092, Republic of Panama
| | - Oscar Puebla
- Ecology Department, Leibniz Centre for Tropical Marine Research, 28359 Bremen, Germany;
- Smithsonian Tropical Research Institute, Apartado Postal 0843-03092, Republic of Panama
- Institute for Chemistry and Biology of the Marine Environment, 26111 Oldenburg, Germany
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, 24105 Kiel, Germany
| |
Collapse
|
3
|
Ng CKC, Tan J. Cryptic species and grey zone speciation of the Barbodes binotatus complex (Teleostei, Cyprinidae) in Sundaland. JOURNAL OF FISH BIOLOGY 2021; 99:1256-1273. [PMID: 34159593 DOI: 10.1111/jfb.14829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 06/03/2021] [Accepted: 06/12/2021] [Indexed: 06/13/2023]
Abstract
Morphology-based taxonomy of freshwater fish is effective when there are representative specimens covering large regions. However, in Sundaland, where the presence of cryptic species is high, the technique has its limitations. This is compounded by uncritical descriptions of holotypes in old literature. We demonstrate the problem using Barbodes binotatus first described from an ink drawing. Several species in the Barbodes genus of Sundaland exhibit morphological similarity to B. binotatus. We applied new DNA sequences of 16S, cytochrome c oxidase subunit I (COI), cytochrome b (Cytb) and recombination-activating gene 1 (RAG1), and pigmentation markers to clarify species complex boundaries in the Malay Peninsula, namely B. aff. binotatus "Malay Peninsula", Barbodes cf. banksi and Barbodes rhombeus. Results suggest B. binotatus-like specimens in the Malay Peninsula are B. rhombeus based on a threshold of 3% COI genetic divergence. B. aff. binotatus recorded in Sumatra, Borneo and the Philippines are likely valid but undescribed species. However, if the 2% COI threshold is applied, some populations in the northern Malay Peninsula would qualify as new and undescribed species. The implications of the 2% threshold and the likelihood of "grey zone" incipient populations are discussed. We further found a rapid visual method, not reported previously, to delineate B. aff. binotatus and B. cf. banksi, but it requires further validation. Additionally, we offer fresh perspectives by discussing the roles of biological species concept, morphological species concept, genetic species concept and mate recognition concept in the B. binotatus complex. Our findings reinforce the standpoint that species delineation is not entirely a binary process, but there is a spectrum to consider, especially in biogeography intersection regions.
Collapse
Affiliation(s)
- Casey Keat-Chuan Ng
- School of Biological Sciences, Universiti Sains Malaysia, Pulau Pinang, Malaysia
| | - Ji Tan
- Department of Agricultural and Food Sciences, Faculty of Science, Universiti Tunku Abdul Rahman, Kampar, Malaysia
| |
Collapse
|
4
|
Casas L, Saenz-Agudelo P, Villegas-Ríos D, Irigoien X, Saborido-Rey F. Genomic landscape of geographically structured colour polymorphism in a temperate marine fish. Mol Ecol 2021; 30:1281-1296. [PMID: 33455028 PMCID: PMC7986630 DOI: 10.1111/mec.15805] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 01/06/2021] [Accepted: 01/08/2021] [Indexed: 12/14/2022]
Abstract
The study of phenotypic variation patterns among populations is fundamental to elucidate the drivers of evolutionary processes. Empirical evidence that supports ongoing genetic divergence associated with phenotypic variation remains very limited for marine species where larval dispersal is a common homogenizing force. We present a genome‐wide analysis of a marine fish, Labrus bergylta, comprising 144 samples distributed from Norway to Spain, a large geographical area that harbours a gradient of phenotypic differentiation. We analysed 39,602 biallelic single nucleotide polymorphisms and found a clear latitudinal gradient of genomic differentiation strongly correlated with the variation in phenotypic morph frequencies observed across the North Atlantic. We also detected a strong association between the latitude and the number of loci that appear to be under divergent selection, which increased with differences in coloration but not with overall genetic differentiation. Our results demonstrate that strong reproductive isolation is occurring between sympatric colour morphs of L. bergylta found at the southern areas and provide important new insights into the genomic changes shaping early stages of differentiation that might precede speciation with gene flow.
Collapse
Affiliation(s)
- Laura Casas
- Institute of Marine Research (IIM-CSIC), Vigo, Spain
| | - Pablo Saenz-Agudelo
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - David Villegas-Ríos
- Institute of Marine Research (IIM-CSIC), Vigo, Spain.,Instituto Mediterráneo de Estudios Avanzados (IMEDEA-CSIC-UiB), Esporles, Mallorca, Spain
| | - Xabier Irigoien
- AZTI - Marine Research, Herrera Kaia, Pasaia (Gipuzkoa), Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | | |
Collapse
|
5
|
Martin CH, Gould KJ. Surprising spatiotemporal stability of a multi-peak fitness landscape revealed by independent field experiments measuring hybrid fitness. Evol Lett 2020; 4:530-544. [PMID: 33312688 PMCID: PMC7719547 DOI: 10.1002/evl3.195] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 07/23/2020] [Accepted: 09/14/2020] [Indexed: 12/14/2022] Open
Abstract
The effect of the environment on fitness in natural populations is a fundamental question in evolutionary biology. However, experimental manipulations of both environment and phenotype at the same time are rare. Thus, the relative importance of the competitive environment versus intrinsic organismal performance in shaping the location, height, and fluidity of fitness peaks and valleys remains largely unknown. Here, we experimentally tested the effect of competitor frequency on the complex fitness landscape driving adaptive radiation of a generalist and two trophic specialist pupfishes, a scale-eater and molluscivore, endemic to hypersaline lakes on San Salvador Island (SSI), Bahamas. We manipulated phenotypes, by generating 3407 F4/F5 lab-reared hybrids, and competitive environment, by altering the frequency of rare transgressive hybrids between field enclosures in two independent lake populations. We then tracked hybrid survival and growth rates across these four field enclosures for 3-11 months. In contrast to competitive speciation theory, we found no evidence that the frequency of hybrid phenotypes affected their survival. Instead, we observed a strikingly similar fitness landscape to a previous independent field experiment, each supporting multiple fitness peaks for generalist and molluscivore phenotypes and a large fitness valley isolating the divergent scale-eater phenotype. These features of the fitness landscape were stable across manipulated competitive environments, multivariate trait axes, and spatiotemporal heterogeneity. We suggest that absolute performance constraints and divergent gene regulatory networks shape macroevolutionary (interspecific) fitness landscapes in addition to microevolutionary (intraspecific) competitive dynamics. This interplay between organism and environment underlies static and dynamic features of the adaptive landscape.
Collapse
Affiliation(s)
- Christopher H. Martin
- Department of Integrative BiologyUniversity of California, BerkeleyBerkeleyCalifornia94720
- Museum of Vertebrate ZoologyUniversity of California, BerkeleyBerkeleyCalifornia94720
| | - Katelyn J. Gould
- Department of BiologyUniversity of North Carolina at Chapel HillChapel HillNorth Carolina27515
| |
Collapse
|
6
|
Picq S, Sperling J, Cheng CJ, Carlson BA, Gallant JR. Genetic drift does not sufficiently explain patterns of electric signal variation among populations of the mormyrid electric fish Paramormyrops kingsleyae. Evolution 2020; 74:911-935. [PMID: 32187650 PMCID: PMC7816287 DOI: 10.1111/evo.13953] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 02/13/2020] [Accepted: 02/20/2020] [Indexed: 11/28/2022]
Abstract
Communication signals serve crucial survival and reproductive functions. In Gabon, the widely distributed mormyrid fish Paramormyrops kingsleyae emits an electric organ discharge (EOD) signal with a dual role in communication and electrolocation that exhibits remarkable variation: populations of P. kingsleyae have either biphasic or triphasic EODs, a feature that characterizes interspecific signal diversity among the Paramormyrops genus. We quantified variation in EODs of 327 P. kingsleyae from nine populations and compared it to genetic variation estimated from microsatellite loci. We found no correlation between electric signal and genetic distances, suggesting that EOD divergence cannot be explained by drift alone. An alternative hypothesis is that EOD differences are used for mate discrimination, which would require P. kingsleyae be capable of differentiating between divergent EOD waveforms. Using a habituation-dishabituation assay, we found that P. kingsleyae can discriminate between biphasic and triphasic EOD types. Nonetheless, patterns of genetic and electric organ morphology divergence provide evidence for hybridization between these signal types. Although reproductive isolation with respect to signal type is incomplete, our results suggest that EOD variation in P. kingsleyae could be a cue for assortative mating.
Collapse
Affiliation(s)
- Sophie Picq
- Michigan State University Department of Integrative Biology, East Lansing MI 48824 USA
| | - Joshua Sperling
- Cornell University Department of Neurobiology and Behavior, Ithaca NY 14853 USA
| | - Catherine J. Cheng
- Cornell University Department of Neurobiology and Behavior, Ithaca NY 14853 USA
| | - Bruce A. Carlson
- Washington University in St. Louis Department of Biology, St. Louis, MO 63130 USA
| | - Jason R. Gallant
- Michigan State University Department of Integrative Biology, East Lansing MI 48824 USA
| |
Collapse
|
7
|
Abstract
Egg trading-whereby simultaneous hermaphrodites exchange each other's eggs for fertilization-constitutes one of the few rigorously documented and most widely cited examples of direct reciprocity among unrelated individuals. Yet how egg trading may initially invade a population of nontrading simultaneous hermaphrodites is still unresolved. Here, we address this question with an analytical model that considers mate encounter rates and costs of egg production in a population that may include traders (who provide eggs for fertilization only if their partners also have eggs to reciprocate), providers (who provide eggs regardless of whether their partners have eggs to reciprocate), and withholders (cheaters who mate only in the male role and just use their eggs to elicit egg release from traders). Our results indicate that a combination of intermediate mate encounter rates, sufficiently high costs of egg production, and a sufficiently high probability that traders detect withholders (in which case eggs are not provided) is conducive to the evolution of egg trading. Under these conditions, traders can invade-and resist invasion from-providers and withholders alike. The prediction that egg trading evolves only under these specific conditions is consistent with the rare occurrence of this mating system among simultaneous hermaphrodites.
Collapse
|
8
|
MARTIN CHRISTOPHERH, RICHARDS EMILIEJ. The paradox behind the pattern of rapid adaptive radiation: how can the speciation process sustain itself through an early burst? ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2019; 50:569-593. [PMID: 36237480 PMCID: PMC9555815 DOI: 10.1146/annurev-ecolsys-110617-062443] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/27/2023]
Abstract
Rapid adaptive radiation poses a distinct question apart from speciation and adaptation: what happens after one speciation event? That is, how are some lineages able to continue speciating through a rapid burst? This question connects global macroevolutionary patterns to microevolutionary processes. Here we review major features of rapid radiations in nature and their mismatch with theoretical models and what is currently known about speciation mechanisms. Rapid radiations occur on three major diversification axes - species richness, phenotypic disparity, and ecological diversity - with exceptional outliers on each axis. The paradox is that the hallmark early stage of adaptive radiation, a rapid burst of speciation and niche diversification, is contradicted by most existing speciation models which instead predict continuously decelerating speciation rates and niche subdivision through time. Furthermore, while speciation mechanisms such as magic traits, phenotype matching, and physical linkage of co-adapted alleles promote speciation, it is often not discussed how these mechanisms could promote multiple speciation events in rapid succession. Additional mechanisms beyond ecological opportunity are needed to understand how rapid radiations occur. We review the evidence for five emerging theories: 1) the 'transporter' hypothesis: introgression and the ancient origins of adaptive alleles, 2) the 'signal complexity' hypothesis: the dimensionality of sexual traits, 3) the connectivity of fitness landscapes, 4) 'diversity begets diversity', and 5) flexible stem/'plasticity first'. We propose new questions and predictions to guide future work on the mechanisms underlying the rare origins of rapid radiation.
Collapse
Affiliation(s)
- CHRISTOPHER H. MARTIN
- Department of Biology, University of North Carolina at Chapel Hill, NC, USA
- Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA
| | - EMILIE J. RICHARDS
- Department of Biology, University of North Carolina at Chapel Hill, NC, USA
- Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA
| |
Collapse
|
9
|
Matschiner M, Salzburger W. Evolution: Genomic Signatures of Mimicry and Mimicry of Genomic Signatures. Curr Biol 2019; 29:R363-R365. [PMID: 31112685 DOI: 10.1016/j.cub.2019.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
How new species form in the ocean, and thus what determines the diversity of fish in the sea, is not well understood. A study in Caribbean coral-reef fishes sheds light on the genomic underpinnings of diversification in the marine realm.
Collapse
Affiliation(s)
- Michael Matschiner
- Department of Palaeontology and Museum, University of Zurich, Zurich, Switzerland; Centre of Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Norway.
| | - Walter Salzburger
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland.
| |
Collapse
|
10
|
Behavioural syndromes as a link between ecology and mate choice: a field study in a reef fish population. Anim Behav 2019. [DOI: 10.1016/j.anbehav.2019.02.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
11
|
Inter-chromosomal coupling between vision and pigmentation genes during genomic divergence. Nat Ecol Evol 2019; 3:657-667. [PMID: 30833758 DOI: 10.1038/s41559-019-0814-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 01/11/2019] [Indexed: 12/30/2022]
Abstract
Recombination between loci underlying mate choice and ecological traits is a major evolutionary force acting against speciation with gene flow. The evolution of linkage disequilibrium between such loci is therefore a fundamental step in the origin of species. Here, we show that this process can take place in the absence of physical linkage in hamlets-a group of closely related reef fishes from the wider Caribbean that differ essentially in colour pattern and are reproductively isolated through strong visually-based assortative mating. Using full-genome analysis, we identify four narrow genomic intervals that are consistently differentiated among sympatric species in a backdrop of extremely low genomic divergence. These four intervals include genes involved in pigmentation (sox10), axial patterning (hoxc13a), photoreceptor development (casz1) and visual sensitivity (SWS and LWS opsins) that develop islands of long-distance and inter-chromosomal linkage disequilibrium as species diverge. The relatively simple genomic architecture of species differences facilitates the evolution of linkage disequilibrium in the presence of gene flow.
Collapse
|
12
|
Campbell MA, Robertson DR, Vargas MI, Allen GR, McMillan WO. Multilocus molecular systematics of the circumtropical reef-fish genus Abudefduf (Pomacentridae): history, geography and ecology of speciation. PeerJ 2018; 6:e5357. [PMID: 30128183 PMCID: PMC6097498 DOI: 10.7717/peerj.5357] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 07/11/2018] [Indexed: 01/05/2023] Open
Abstract
We investigated a pantropical sub-family and genus of damselfishes, the sergeant-majors (Pomacentridae: Abudefdufinae: Abudefduf), to identify the tempo and mechanisms of speciation in the lineage. We examined sequence capture data from 500 loci and 20 species, with multiple individuals sampled from across the geographic ranges of widespread species. Utilizing a maximum likelihood framework, as well as a time-calibrated Bayesian phylogeny, the following key questions are addressed: What is the historical tempo of speciation? What are the relative contributions of vicariant, peripatric and parapatric speciation to sergeant-major diversity? How is speciation related to major variation in trophic ecology? The approximately 20 species of sergeant-majors fall into three main lineages. The ancestral condition appears to be benthivory, which is predominant in two lineages comprising six species. The remaining species of sergeant-majors, of which there are at least 15, fall within a clade composed entirely of planktivores. This clade is sister to a benthivore clade that included one species, Abudefduf notatus, in transition to planktivory. Most speciation of sergeant-majors, which appeared ∼24 million years ago, occurred in the last 10 million years. Present distributional patterns indicate vicariant speciation precipitated by the closure of land barriers between both sides of the Atlantic and the Pacific, and the emergence of land between the Indian and Pacific Oceans. Within this backdrop, frequent oscillations in sea level over the last 10 million years also appear to have generated conditions suitable for both peripatric and vicariant speciation, and most speciation within the genus appears linked to these changes in sea level. Diversification within the genus has been concentrated in planktivorous seargeant-majors rather than benthivores. The root cause is unclear, but does not appear to be related to differences in dispersal potential, which is greater in the planktivorous species, due to the ability of their post-larval juveniles to raft with floating debris. This elevated speciation rate in planktivores and their propensity to form local endemics may reflect relaxation of selective pressures (e.g., on crypticity) that limit speciation in benthivorous sergeant-majors. Finally, our data allow us to clarify relationships of geminate sergeant-major species, indicating that there are subdivisions within the Atlantic for both benthivore and planktivore geminate pairs that may have misled previous studies.
Collapse
Affiliation(s)
| | - D Ross Robertson
- Smithsonian Tropical Research Institute, Balboa, Republic of Panama
| | - Marta I Vargas
- Smithsonian Tropical Research Institute, Balboa, Republic of Panama
| | - Gerald R Allen
- Western Australian Museum, Welshpool, Western Australia, Australia
| | - W O McMillan
- Smithsonian Tropical Research Institute, Balboa, Republic of Panama
| |
Collapse
|
13
|
Theodosiou L, McMillan WO, Puebla O. Recombination in the eggs and sperm in a simultaneously hermaphroditic vertebrate. Proc Biol Sci 2017; 283:rspb.2016.1821. [PMID: 27974520 DOI: 10.1098/rspb.2016.1821] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 11/14/2016] [Indexed: 01/15/2023] Open
Abstract
When there is no recombination (achiasmy) in one sex, it is in the heterogametic one. This observation is so consistent that it constitutes one of the few patterns in biology that may be regarded as a 'rule' and Haldane (Haldane 1922 J. Genet. 12, 101-109. (doi:10.1007/BF02983075)) proposed that it might be driven by selection against recombination in the sex chromosomes. Yet differences in recombination rates between the sexes (heterochiasmy) have also been reported in hermaphroditic species that lack sex chromosomes. In plants-the vast majority of which are hermaphroditic-selection at the haploid stage has been proposed to drive heterochiasmy. Yet few data are available for hermaphroditic animals, and barely any for hermaphroditic vertebrates. Here, we leverage reciprocal crosses between two black hamlets (Hypoplectrus nigricans, Serranidae), simultaneously hermaphroditic reef fishes from the wider Caribbean, to generate high-density egg- and sperm-specific linkage maps for each parent. We find globally higher recombination rates in the eggs, with dramatically pronounced heterochiasmy at the chromosome peripheries. We suggest that this pattern may be due to female meiotic drive, and that this process may be an important source of heterochiasmy in animals. We also identify a large non-recombining region that may play a role in speciation and local adaptation in Hypoplectrus.
Collapse
Affiliation(s)
- L Theodosiou
- Max-Planck-Institute for Evolutionary Biology, Research Group for Community Dynamics, August-Thienemann-Straße 2, 24306 Plön, Germany
| | - W O McMillan
- Smithsonian Tropical Research Institute, Apartado Postal 0843-03092, Panamá, República de Panamá
| | - O Puebla
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Evolutionary Ecology of Marine Fishes, Düsternbrooker Weg 20, 24105 Kiel, Germany .,Faculty of Mathematics and Natural Sciences, University of Kiel, Christian-Albrechts-Platz 4, 24118 Kiel, Germany.,Smithsonian Tropical Research Institute, Apartado Postal 0843-03092, Panamá, República de Panamá
| |
Collapse
|
14
|
Hench K, Mcmillan WO, Betancur-R R, Puebla O. Temporal changes in hamlet communities (Hypoplectrus spp., Serranidae) over 17 years. JOURNAL OF FISH BIOLOGY 2017; 91:1475-1490. [PMID: 28994100 DOI: 10.1111/jfb.13481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 08/29/2017] [Indexed: 06/07/2023]
Abstract
Transect surveys of hamlet communities (Hypoplectrus spp., Serranidae) covering 14 000 m2 across 16 reefs off La Parguera, Puerto Rico, are presented and compared with a previous survey conducted in the year 2000. The hamlet community has noticeably changed over 17 years, with a > 30% increase in relative abundance of the yellowtail hamlet Hypoplectrus chlorurus on the inner reefs at the expense of the other hamlet species. The data also suggest that the density of H. chlorurus has declined and that its distribution has shifted towards shallower depths. Considering that H. chlorurus has been previously identified as one of the few fish showing a positive association with seawater turbidity on the inner reefs of La Parguera and that sedimentation of terrestrial origin has increased over recent decades on these reefs, it is proposed that turbidity may constitute an important but so far overlooked ecological driver of hamlet communities.
Collapse
Affiliation(s)
- K Hench
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Evolutionary Ecology of Marine Fishes, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - W O Mcmillan
- Smithsonian Tropical Research Institute, Apartado Postal 0843-03092, Panamá, República de Panamá
| | - R Betancur-R
- Department of Biology, University of Puerto Rico - Río Piedras, PO Box 23360, San Juan, Puerto Rico
| | - O Puebla
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Evolutionary Ecology of Marine Fishes, Düsternbrooker Weg 20, 24105 Kiel, Germany
| |
Collapse
|
15
|
Milá B, Van Tassell JL, Calderón JA, Rüber L, Zardoya R. Cryptic lineage divergence in marine environments: genetic differentiation at multiple spatial and temporal scales in the widespread intertidal goby Gobiosoma bosc. Ecol Evol 2017; 7:5514-5523. [PMID: 28770087 PMCID: PMC5528222 DOI: 10.1002/ece3.3161] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 05/22/2017] [Accepted: 05/23/2017] [Indexed: 01/01/2023] Open
Abstract
The adaptive radiation of the seven-spined gobies (Gobiidae: Gobiosomatini) represents a classic example of how ecological specialization and larval retention can drive speciation through local adaptation. However, geographically widespread and phenotypically uniform species also do occur within Gobiosomatini. This lack of phenotypic variation across large geographic areas could be due to recent colonization, widespread gene flow, or stabilizing selection acting across environmental gradients. We use a phylogeographic approach to test these alternative hypotheses in the naked goby Gobiosoma bosc, a widespread and phenotypically invariable intertidal fish found along the Atlantic Coast of North America. Using DNA sequence from 218 individuals sampled at 15 localities, we document marked intraspecific genetic structure in mitochondrial and nuclear genes at three main geographic scales: (i) between Gulf of Mexico and Atlantic Coast, (ii) between the west coast of the Florida peninsula and adjacent Gulf of Mexico across the Apalachicola Bay, and (iii) at local scales of a few hundred kilometers. Clades on either side of Florida diverged about 8 million years ago, whereas some populations along the East Cost show divergent phylogroups that have differentiated within the last 200,000 years. The absence of noticeable phenotypic or ecological differentiation among lineages suggests the role of stabilizing selection on ancestral phenotypes, together with isolation in allopatry due to reduced dispersal and restricted gene flow, as the most likely explanation for their divergence. Haplotype phylogenies and spatial patterns of genetic diversity reveal frequent population bottlenecks followed by rapid population growth, particularly along the Gulf of Mexico. The magnitude of the genetic divergence among intraspecific lineages suggests the existence of cryptic species within Gobiosoma and indicates that modes of speciation can vary among lineages within Gobiidae.
Collapse
Affiliation(s)
- Borja Milá
- National Museum of Natural SciencesSpanish National Research Council (CSIC)MadridSpain
| | - James L. Van Tassell
- Department of IchthyologyAmerican Museum of Natural HistoryNew York, NY 10024USA
| | - Jatziri A. Calderón
- National Museum of Natural SciencesSpanish National Research Council (CSIC)MadridSpain
| | - Lukas Rüber
- Naturhistorisches Museum der BurgergemeindeBernBernastrasse 15, 3005 BernSwitzerland
- Institute of Ecology and EvolutionUniversity of BernBaltzerstrasse 6, 3012 BernSwitzerland
| | - Rafael Zardoya
- National Museum of Natural SciencesSpanish National Research Council (CSIC)MadridSpain
| |
Collapse
|
16
|
|
17
|
Bernal MA, Gaither MR, Simison WB, Rocha LA. Introgression and selection shaped the evolutionary history of sympatric sister-species of coral reef fishes (genus: Haemulon). Mol Ecol 2016; 26:639-652. [PMID: 27873385 DOI: 10.1111/mec.13937] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 10/18/2016] [Accepted: 11/16/2016] [Indexed: 12/25/2022]
Abstract
Closely related marine species with large overlapping ranges provide opportunities to study mechanisms of speciation, particularly when there is evidence of gene flow between such lineages. Here, we focus on a case of hybridization between the sympatric sister-species Haemulon maculicauda and H. flaviguttatum, using Sanger sequencing of mitochondrial and nuclear loci, as well as 2422 single nucleotide polymorphisms (SNPs) obtained via restriction site-associated DNA sequencing (RADSeq). Mitochondrial markers revealed a shared haplotype for COI and low divergence for CytB and CR between the sister-species. On the other hand, complete lineage sorting was observed at the nuclear loci and most of the SNPs. Under neutral expectations, the smaller effective population size of mtDNA should lead to fixation of mutations faster than nDNA. Thus, these results suggest that hybridization in the recent past (0.174-0.263 Ma) led to introgression of the mtDNA, with little effect on the nuclear genome. Analyses of the SNP data revealed 28 loci potentially under divergent selection between the two species. The combination of mtDNA introgression and limited nuclear DNA introgression provides a mechanism for the evolution of independent lineages despite recurrent hybridization events. This study adds to the growing body of research that exemplifies how genetic divergence can be maintained in the presence of gene flow between closely related species.
Collapse
Affiliation(s)
- Moisés A Bernal
- Integrative Systems Biology Lab, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, 23955-6900 Thuwal, Kingdom of Saudi Arabia.,Institute for Biodiversity, Science and Sustainability, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA, 94118, USA
| | - Michelle R Gaither
- Institute for Biodiversity, Science and Sustainability, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA, 94118, USA.,School of Biological and Biomedical Sciences, Durham University, South Road, Durham, DH1 3LE, UK
| | - W Brian Simison
- Center for Comparative Genomics, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA, 94118, USA
| | - Luiz A Rocha
- Institute for Biodiversity, Science and Sustainability, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA, 94118, USA
| |
Collapse
|
18
|
Rueger T, Gardiner NM, Jones GP. Size matters: male and female mate choice leads to size-assortative pairing in a coral reef cardinalfish. Behav Ecol 2016. [DOI: 10.1093/beheco/arw082] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
|
19
|
Svensson EI, Nordén A, Waller JT, Runemark A. Linking intra- and interspecific assortative mating: Consequences for asymmetric sexual isolation. Evolution 2016; 70:1165-79. [DOI: 10.1111/evo.12939] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 04/22/2016] [Accepted: 04/27/2016] [Indexed: 12/28/2022]
Affiliation(s)
- Erik I. Svensson
- Evolutionary Ecology Unit, Department of Biology; Lund University; SE-223 62 Lund Sweden
| | - Anna Nordén
- Evolutionary Ecology Unit, Department of Biology; Lund University; SE-223 62 Lund Sweden
| | - John T. Waller
- Evolutionary Ecology Unit, Department of Biology; Lund University; SE-223 62 Lund Sweden
| | - Anna Runemark
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences; University of Oslo; Oslo Norway
| |
Collapse
|
20
|
Picq S, McMillan WO, Puebla O. Population genomics of local adaptation versus speciation in coral reef fishes (Hypoplectrus spp, Serranidae). Ecol Evol 2016; 6:2109-24. [PMID: 27099711 PMCID: PMC4831444 DOI: 10.1002/ece3.2028] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 01/18/2016] [Indexed: 12/13/2022] Open
Abstract
Are the population genomic patterns underlying local adaptation and the early stages of speciation similar? Addressing this question requires a system in which (i) local adaptation and the early stages of speciation can be clearly identified and distinguished, (ii) the amount of genetic divergence driven by the two processes is similar, and (iii) comparisons can be repeated both taxonomically (for local adaptation) and geographically (for speciation). Here, we report just such a situation in the hamlets (Hypoplectrus spp), brightly colored reef fishes from the wider Caribbean. Close to 100,000 SNPs genotyped in 126 individuals from three sympatric species sampled in three repeated populations provide genome-wide levels of divergence that are comparable among allopatric populations (F st estimate = 0.0042) and sympatric species (F st estimate = 0.0038). Population genetic, clustering, and phylogenetic analyses reveal very similar patterns for local adaptation and speciation, with a large fraction of the genome undifferentiated (F st estimate ≈ 0), a very small proportion of F st outlier loci (0.05-0.07%), and remarkably few repeated outliers (1-3). Nevertheless, different loci appear to be involved in the two processes in Hypoplectrus, with only 7% of the most differentiated SNPs and outliers shared between populations and species comparisons. In particular, a tropomyosin (Tpm4) and a previously identified hox (HoxCa) locus emerge as candidate loci (repeated outliers) for local adaptation and speciation, respectively. We conclude that marine populations may be locally adapted notwithstanding shallow levels of genetic divergence, and that from a population genomic perspective, this process does not appear to differ fundamentally from the early stages of speciation.
Collapse
Affiliation(s)
- Sophie Picq
- Evolutionary Ecology of Marine Fishes GEOMAR Helmholtz Centre for Ocean Research Kiel Düsternbrooker Weg 2024105 Kiel Germany; Faculty of Mathematics and Natural Sciences University of Kiel Christian-Albrechts-Platz 424118 Kiel Germany
| | - W Owen McMillan
- Smithsonian Tropical Research Institute Apartado Postal 0843-03092 Panamá República de Panamá
| | - Oscar Puebla
- Evolutionary Ecology of Marine Fishes GEOMAR Helmholtz Centre for Ocean Research Kiel Düsternbrooker Weg 2024105 Kiel Germany; Faculty of Mathematics and Natural Sciences University of Kiel Christian-Albrechts-Platz 424118 Kiel Germany; Smithsonian Tropical Research Institute Apartado Postal 0843-03092 Panamá República de Panamá
| |
Collapse
|
21
|
Gaither MR, Bernal MA, Coleman RR, Bowen BW, Jones SA, Simison WB, Rocha LA. Genomic signatures of geographic isolation and natural selection in coral reef fishes. Mol Ecol 2015; 24:1543-57. [PMID: 25753379 DOI: 10.1111/mec.13129] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2014] [Revised: 02/20/2015] [Accepted: 02/24/2015] [Indexed: 01/17/2023]
Abstract
The drivers of speciation remain among the most controversial topics in evolutionary biology. Initially, Darwin emphasized natural selection as a primary mechanism of speciation, but the architects of the modern synthesis largely abandoned that view in favour of divergence by geographic isolation. The balance between selection and isolation is still at the forefront of the evolutionary debate, especially for the world's tropical oceans where biodiversity is high, but isolating barriers are few. Here, we identify the drivers of speciation in Pacific reef fishes of the genus Acanthurus by comparative genome scans of two peripheral populations that split from a large Central-West Pacific lineage at roughly the same time. Mitochondrial sequences indicate that populations in the Hawaiian Archipelago and the Marquesas Islands became isolated approximately 0.5 Ma. The Hawaiian lineage is morphologically indistinguishable from the widespread Pacific form, but the Marquesan form is recognized as a distinct species that occupies an unusual tropical ecosystem characterized by upwelling, turbidity, temperature fluctuations, algal blooms and little coral cover. An analysis of 3737 SNPs reveals a strong signal of selection at the Marquesas, with 59 loci under disruptive selection including an opsin Rh2 locus. While both the Hawaiian and Marquesan populations indicate signals of drift, the former shows a weak signal of selection that is comparable with populations in the Central-West Pacific. This contrast between closely related lineages reveals one population diverging due primarily to geographic isolation and genetic drift, and the other achieving taxonomic species status under the influence of selection.
Collapse
Affiliation(s)
- Michelle R Gaither
- School of Biological and Biomedical Sciences, Durham University, South Road, Durham, DH1 3LE, UK; Section of Ichthyology, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA, 94118, USA
| | | | | | | | | | | | | |
Collapse
|
22
|
Rudnicki R, Zwoleński P. Model of phenotypic evolution in hermaphroditic populations. J Math Biol 2015; 70:1295-321. [PMID: 24832543 PMCID: PMC4365287 DOI: 10.1007/s00285-014-0798-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 04/28/2014] [Indexed: 11/29/2022]
Abstract
We consider an individual based model of phenotypic evolution in hermaphroditic populations which includes random and assortative mating of individuals. By increasing the number of individuals to infinity we obtain a nonlinear transport equation, which describes the evolution of phenotypic distribution. The main result of the paper is a theorem on asymptotic stability of trait distribution. This theorem is applied to models with the offspring trait distribution given by additive and multiplicative random perturbations of the parental mean trait.
Collapse
Affiliation(s)
- Ryszard Rudnicki
- Institute of Mathematics, Polish Academy of Sciences, Bankowa 14, 40-007 Katowice, Poland
| | - Paweł Zwoleński
- Institute of Mathematics, Polish Academy of Sciences, Bankowa 14, 40-007 Katowice, Poland
| |
Collapse
|
23
|
Puebla O, Bermingham E, McMillan WO. Genomic atolls of differentiation in coral reef fishes (Hypoplectrus spp., Serranidae). Mol Ecol 2014; 23:5291-303. [PMID: 25231270 DOI: 10.1111/mec.12926] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 08/28/2014] [Accepted: 09/12/2014] [Indexed: 12/20/2022]
Abstract
Because the vast majority of species are well diverged, relatively little is known about the genomic architecture of speciation during the early stages of divergence. Species within recent evolutionary radiations are often minimally diverged from a genomic perspective, and therefore provide rare opportunities to address this question. Here, we leverage the hamlet radiation (Hypoplectrus spp., brightly coloured reef fishes from the tropical western Atlantic) to characterize genomic divergence during the early stages of speciation. Transect surveys and spawning observations in Belize, Honduras and Panama confirm that sympatric barred (H. puella), black (H. nigricans) and butter (H. unicolor) hamlets are phenotypically distinct and reproductively isolated, although hybrid spawnings and individuals with intermediate phenotypes are seen on rare occasions. A survey of approximately 100 000 restriction site-associated SNPs in 126 samples from the three species across the three replicate populations reveals extremely slight genomewide divergence among species (FST = 0.0038), indicating that ecomorphological differences and functional reproductive isolation are maintained in sympatry in a backdrop of extraordinary genomic similarity. Nonetheless, a very small proportion of SNPs (0.05% on average) are identified as FST outliers among sympatric species. Remarkably, a single SNP is identified as an outlier in repeated populations for the same species pair. A minicontig assembled de novo around this SNP falls into the genomic region containing the HoxCa10 and HoxCa11 genes in 10 teleost species, suggesting an important role for Hox gene evolution in this radiation. This finding, if confirmed, would provide a better understanding of the links between micro- and macroevolutionary processes.
Collapse
Affiliation(s)
- O Puebla
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Evolutionary Ecology of Marine Fishes, Düsternbrooker Weg 20, Kiel, 24105, Germany; Smithsonian Tropical Research Institute, Apartado Postal, 0843-03092, Panamá, República de Panamá
| | | | | |
Collapse
|
24
|
Bernardi G. Speciation in fishes. Mol Ecol 2013; 22:5487-502. [PMID: 24118417 DOI: 10.1111/mec.12494] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 08/08/2013] [Accepted: 08/14/2013] [Indexed: 12/27/2022]
Abstract
The field of speciation has seen much renewed interest in the past few years, with theoretical and empirical advances that have moved it from a descriptive field to a predictive and testable one. The goal of this review is to provide a general background on research on speciation as it pertains to fishes. Three major components to the question are first discussed: the spatial, ecological and sexual factors that influence speciation mechanisms. We then move to the latest developments in the field of speciation genomics. Affordable and rapidly available, massively parallel sequencing data allow speciation studies to converge into a single comprehensive line of investigation, where the focus has shifted to the search for speciation genes and genomic islands of speciation. We argue that fish present a very diverse array of scenarios, making them an ideal model to study speciation processes.
Collapse
Affiliation(s)
- Giacomo Bernardi
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, 100 Shaffer Road, Santa Cruz, CA, 95076, USA
| |
Collapse
|