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Tan A, St. John M, Chau D, Clair C, Chan H, Holzman R, Martin CH. A multi-peak performance landscape for scale biting in an adaptive radiation of pupfishes. J Exp Biol 2024; 227:jeb247615. [PMID: 39054887 PMCID: PMC11418179 DOI: 10.1242/jeb.247615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 07/19/2024] [Indexed: 07/27/2024]
Abstract
The physical interactions between organisms and their environment ultimately shape diversification rates, but the contributions of biomechanics to evolutionary divergence are frequently overlooked. Here, we estimated a performance landscape for biting in an adaptive radiation of Cyprinodon pupfishes, including scale-biting and molluscivore specialists, and compared performance peaks with previous estimates of the fitness landscape in this system. We used high-speed video to film feeding strikes on gelatin cubes by scale eater, molluscivore, generalist and hybrid pupfishes and measured bite dimensions. We then measured five kinematic variables from 227 strikes using the SLEAP machine-learning model. We found a complex performance landscape with two distinct peaks best predicted gel-biting performance, corresponding to a significant non-linear interaction between peak gape and peak jaw protrusion. Only scale eaters and their hybrids were able to perform strikes within the highest performance peak, characterized by larger peak gapes and greater jaw protrusion. A performance valley separated this peak from a lower performance peak accessible to all species, characterized by smaller peak gapes and less jaw protrusion. However, most individuals exhibited substantial variation in strike kinematics and species could not be reliably distinguished by their strikes, indicating many-to-many mapping of morphology to performance. The two performance peaks observed in the lab were partially consistent with estimates of a two-peak fitness landscape measured in the wild, with the exception of the new performance peak for scale eaters. We thus reveal a new bimodal non-linear biomechanical model that connects morphology to performance to fitness in a sympatric radiation of trophic niche specialists.
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Affiliation(s)
- Anson Tan
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720-3140, USA
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Michelle St. John
- Department of Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Dylan Chau
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720-3140, USA
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Chloe Clair
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720-3140, USA
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - HoWan Chan
- Department of BioSciences, Rice University, Houston, TX 77005, USA
| | - Roi Holzman
- School of Zoology, Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
- Inter-University Institute for Marine Sciences, Eilat 8810302, Israel
| | - Christopher H. Martin
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720-3140, USA
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, USA
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2
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Dunker JC, St. John ME, Martin CH. Phenotypic covariation predicts diversification in an adaptive radiation of pupfishes. Ecol Evol 2024; 14:e11642. [PMID: 39114171 PMCID: PMC11303982 DOI: 10.1002/ece3.11642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 06/07/2024] [Accepted: 06/12/2024] [Indexed: 08/10/2024] Open
Abstract
Phenotypic covariation among suites of traits may constrain or promote diversification both within and between species, yet few studies have empirically tested this relationship. In this study, we investigate whether phenotypic covariation of craniofacial traits is associated with diversification in an adaptive radiation of pupfishes found only on San Salvador Island, Bahamas (SSI). The radiation includes generalist, durophagous, and lepidophagous species. We compared phenotypic variation and covariation (i.e., the P matrix) between (1) allopatric populations of generalist pupfish from neighboring islands and estuaries in the Caribbean, (2) SSI pupfish allopatric lake populations with only generalist pupfish, and (3) SSI lake populations containing the full radiation in sympatry. Additionally, we examine patterns observed in the P matrices of two independent lab-reared F2 hybrid crosses of the two most morphologically distinct members of the radiation to make inferences about the underlying mechanisms contributing to the variation in craniofacial traits in SSI pupfishes. We found that the P matrix of SSI allopatric generalist populations exhibited higher levels of mean trait correlation, constraints, and integration with simultaneously lower levels of flexibility compared to allopatric generalist populations on other Caribbean islands and sympatric populations of all three species on SSI. We also document that while many craniofacial traits appear to result from additive genetic effects, variation in key traits such as head depth, maxilla length, and lower jaw length may be produced via non-additive genetic mechanisms. Ultimately, this study suggests that differences in phenotypic covariation significantly contribute to producing and maintaining organismal diversity.
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Affiliation(s)
- Julia C. Dunker
- Department of Integrative BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Michelle E. St. John
- Department of Integrative BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
- Present address:
Department of BiologyUniversity of OklahomaNormanOklahomaUSA
| | - Christopher H. Martin
- Department of Integrative BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
- Museum of Vertebrate ZoologyUniversity of CaliforniaBerkeleyCaliforniaUSA
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3
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St John ME, Dunker JC, Richards EJ, Romero S, Martin CH. Parallel evolution of integrated craniofacial traits in trophic specialist pupfishes. Ecol Evol 2024; 14:e11640. [PMID: 38979003 PMCID: PMC11228360 DOI: 10.1002/ece3.11640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 05/14/2024] [Accepted: 06/13/2024] [Indexed: 07/10/2024] Open
Abstract
Populations may adapt to similar environments via parallel or non-parallel genetic changes, but the frequency of these alternative mechanisms and underlying contributing factors are still poorly understood outside model systems. We used QTL mapping to investigate the genetic basis of highly divergent craniofacial traits between the scale-eater (Cyprinodon desquamator) and molluscivore (C. brontotheroides) pupfish adapting to two different hypersaline lake environments on San Salvador Island, Bahamas. We lab-reared F2 scale-eater x molluscivore intercrosses from two different lake populations, estimated linkage maps, scanned for significant QTL for 29 skeletal and craniofacial traits, female mate preference, and sex. We compared the location of QTL between lakes to quantify parallel and non-parallel genetic changes. We detected significant QTL for six craniofacial traits in at least one lake. However, nearly all shared QTL loci were associated with a different craniofacial trait within each lake. Therefore, our estimate of parallel evolution of craniofacial genetic architecture could range from one out of six identical trait QTL (low parallelism) to five out of six integrated trait QTL (high parallelism). We suggest that pleiotropy and trait integration can affect estimates of parallel evolution, particularly within rapid radiations. We also observed increased adaptive introgression in shared QTL regions, suggesting that gene flow contributed to parallel evolution. Overall, our results suggest that the same genomic regions may contribute to parallel adaptation across integrated suites of craniofacial traits, rather than specific traits, and highlight the need for a more expansive definition of parallel evolution.
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Affiliation(s)
| | - Julia C Dunker
- Department of Integrative Biology University of California Berkeley California USA
| | - Emilie J Richards
- Department of Ecology, Evolution and Behavior University of Minnesota Minneapolis Minnesota USA
| | - Stephanie Romero
- Department of Evolution and Ecology University of California Davis California USA
| | - Christopher H Martin
- Department of Integrative Biology University of California Berkeley California USA
- Museum of Vertebrate Zoology University of California Berkeley California USA
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4
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Tetrault E, Aaronson B, Gilbert MC, Albertson RC. Foraging-induced craniofacial plasticity is associated with an early, robust and dynamic transcriptional response. Proc Biol Sci 2024; 291:20240215. [PMID: 38654651 PMCID: PMC11040245 DOI: 10.1098/rspb.2024.0215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 03/19/2024] [Indexed: 04/26/2024] Open
Abstract
Phenotypic plasticity is the ability of a single genotype to vary its phenotype in response to the environment. Plasticity of the skeletal system in response to mechanical input is widely studied, but the timing of its transcriptional regulation is not well understood. Here, we used the cichlid feeding apparatus to examine the transcriptional dynamics of skeletal plasticity over time. Using three closely related species that vary in their ability to remodel bone and a panel of 11 genes, including well-studied skeletal differentiation markers and newly characterized environmentally sensitive genes, we examined plasticity at one, two, four and eight weeks following the onset of alternate foraging challenges. We found that the plastic species exhibited environment-specific bursts in gene expression beginning at one week, followed by a sharp decline in levels, while the species with more limited plasticity exhibited consistently low levels of gene expression. This trend held across nearly all genes, suggesting that it is a hallmark of the larger plasticity regulatory network. We conclude that plasticity of the cichlid feeding apparatus is not the result of slowly accumulating gene expression difference over time, but rather is stimulated by early bursts of environment-specific gene expression followed by a return to homeostatic levels.
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Affiliation(s)
- Emily Tetrault
- Molecular and Cell Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
| | - Ben Aaronson
- Department of Biology, University of Massachusetts, Amherst, MA 01003, USA
| | - Michelle C. Gilbert
- Department of Biology, Pennsylvania State University, State College, PA 16802, USA
| | - R. Craig Albertson
- Department of Biology, University of Massachusetts, Amherst, MA 01003, USA
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5
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Tan A, St. John M, Chau D, Clair C, Chan H, Holzman R, Martin CH. Multiple performance peaks for scale-biting in an adaptive radiation of pupfishes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.22.573139. [PMID: 38187684 PMCID: PMC10769438 DOI: 10.1101/2023.12.22.573139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
The physical interactions between organisms and their environment ultimately shape their rate of speciation and adaptive radiation, but the contributions of biomechanics to evolutionary divergence are frequently overlooked. Here we investigated an adaptive radiation of Cyprinodon pupfishes to measure the relationship between feeding kinematics and performance during adaptation to a novel trophic niche, lepidophagy, in which a predator removes only the scales, mucus, and sometimes tissue from their prey using scraping and biting attacks. We used high-speed video to film scale-biting strikes on gelatin cubes by scale-eater, molluscivore, generalist, and hybrid pupfishes and subsequently measured the dimensions of each bite. We then trained the SLEAP machine-learning animal tracking model to measure kinematic landmarks and automatically scored over 100,000 frames from 227 recorded strikes. Scale-eaters exhibited increased peak gape and greater bite length; however, substantial within-individual kinematic variation resulted in poor discrimination of strikes by species or strike type. Nonetheless, a complex performance landscape with two distinct peaks best predicted gel-biting performance, corresponding to a significant nonlinear interaction between peak gape and peak jaw protrusion in which scale-eaters and their hybrids occupied a second performance peak requiring larger peak gape and greater jaw protrusion. A bite performance valley separating scale-eaters from other species may have contributed to their rapid evolution and is consistent with multiple estimates of a multi-peak fitness landscape in the wild. We thus present an efficient deep-learning automated pipeline for kinematic analyses of feeding strikes and a new biomechanical model for understanding the performance and rapid evolution of a rare trophic niche.
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Affiliation(s)
- Anson Tan
- Department of Integrative Biology, University of California, Berkeley
- Museum of Vertebrate Zoology, University of California, Berkeley
| | | | - Dylan Chau
- Department of Integrative Biology, University of California, Berkeley
- Museum of Vertebrate Zoology, University of California, Berkeley
| | - Chloe Clair
- Department of Integrative Biology, University of California, Berkeley
- Museum of Vertebrate Zoology, University of California, Berkeley
| | | | - Roi Holzman
- School of Zoology, Tel Aviv University, Eilat, Israel
- Inter-University Institute for Marine Sciences, Eilat, Israel
| | - Christopher H. Martin
- Department of Integrative Biology, University of California, Berkeley
- Museum of Vertebrate Zoology, University of California, Berkeley
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6
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Palominos MF, Muhl V, Richards EJ, Miller CT, Martin CH. Jaw size variation is associated with a novel craniofacial function for galanin receptor 2 in an adaptive radiation of pupfishes. Proc Biol Sci 2023; 290:20231686. [PMID: 37876194 PMCID: PMC10598438 DOI: 10.1098/rspb.2023.1686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/02/2023] [Indexed: 10/26/2023] Open
Abstract
Understanding the genetic basis of novel adaptations in new species is a fundamental question in biology. Here we demonstrate a new role for galr2 in vertebrate craniofacial development using an adaptive radiation of trophic specialist pupfishes endemic to San Salvador Island, Bahamas. We confirmed the loss of a putative Sry transcription factor binding site upstream of galr2 in scale-eating pupfish and found significant spatial differences in galr2 expression among pupfish species in Meckel's cartilage using in situ hybridization chain reaction (HCR). We then experimentally demonstrated a novel role for Galr2 in craniofacial development by exposing embryos to Garl2-inhibiting drugs. Galr2-inhibition reduced Meckel's cartilage length and increased chondrocyte density in both trophic specialists but not in the generalist genetic background. We propose a mechanism for jaw elongation in scale-eaters based on the reduced expression of galr2 due to the loss of a putative Sry binding site. Fewer Galr2 receptors in the scale-eater Meckel's cartilage may result in their enlarged jaw lengths as adults by limiting opportunities for a circulating Galr2 agonist to bind to these receptors during development. Our findings illustrate the growing utility of linking candidate adaptive SNPs in non-model systems with highly divergent phenotypes to novel vertebrate gene functions.
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Affiliation(s)
- M. Fernanda Palominos
- Department of Integrative Biology, University of California, 3101 Valley Life Sciences Building, Berkeley, CA 94720, USA
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
| | - Vanessa Muhl
- Department of Integrative Biology, University of California, 3101 Valley Life Sciences Building, Berkeley, CA 94720, USA
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
| | - Emilie J. Richards
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN, USA
| | - Craig T. Miller
- Department of Molecular & Cell Biology, University of California, Berkeley, CA, USA
| | - Christopher H. Martin
- Department of Integrative Biology, University of California, 3101 Valley Life Sciences Building, Berkeley, CA 94720, USA
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
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7
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van Rijssel JC, Moser FN, Mwaiko S, Seehausen O. Strong species structure but weak geographical structure in demersal Lake Victoria cichlids. Ecol Evol 2022; 12:e9669. [PMID: 36582774 PMCID: PMC9790821 DOI: 10.1002/ece3.9669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 12/05/2022] [Accepted: 12/09/2022] [Indexed: 12/27/2022] Open
Abstract
Studying phenotypic and genetic differentiation between very young species can be very informative with regard to learning about processes of speciation. Identifying and characterizing genetic species structure and distinguishing it from spatial genetic structure within a species is a prerequisite for this and is often not given sufficient attention. Young radiations of cichlid fish are classical speciation study systems. However, it is only during the past decade that population genomics based on next-generation sequencing has begun to provide the power to resolve species and distinguish speciation from spatial population structure for the youngest of these radiations. The Lake Victoria haplochromine cichlids constitute the youngest large cichlid fish radiation, probably <20,000 years old. Earlier work showed that communities of rocky reef cichlids are composed of many reciprocally monophyletic species despite their very recent origins. Here, we build on this work by studying assemblages of offshore demersal cichlids, adding analyses of within-species spatial structure to the sympatric species structure. We sampled seven multispecies communities along a 6-km-long transect from one side of the Mwanza Gulf to the other side. We investigated whether phenotypically diagnosed putative species are reciprocally monophyletic and whether such monophyly is stable across species geographic ranges. We show that all species are genetically strongly differentiated in sympatry, that they are reciprocally monophyletic, and that monophyly is stable across distribution ranges. We found significant differentiation between geographically distinct populations in two species, but no or weak isolation by distance. We further found subtle but significant morphological differences between all species and a linear relationship between genomic and morphological distance which suggests that differences in morphology begin to accumulate after speciation has already affected genome-wide restrictions of gene flow.
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Affiliation(s)
- Jacco C. van Rijssel
- Department of Fish Ecology & EvolutionEAWAG Centre for Ecology, Evolution and BiogeochemistryKastanienbaumSwitzerland
- Institute of Ecology and Evolution, Aquatic EcologyUniversity of BernBernSwitzerland
- Wageningen Marine ResearchWageningen UniversityIJmuidenThe Netherlands
| | - Florian N. Moser
- Department of Fish Ecology & EvolutionEAWAG Centre for Ecology, Evolution and BiogeochemistryKastanienbaumSwitzerland
- Institute of Ecology and Evolution, Aquatic EcologyUniversity of BernBernSwitzerland
| | - Salome Mwaiko
- Department of Fish Ecology & EvolutionEAWAG Centre for Ecology, Evolution and BiogeochemistryKastanienbaumSwitzerland
- Institute of Ecology and Evolution, Aquatic EcologyUniversity of BernBernSwitzerland
| | - Ole Seehausen
- Department of Fish Ecology & EvolutionEAWAG Centre for Ecology, Evolution and BiogeochemistryKastanienbaumSwitzerland
- Institute of Ecology and Evolution, Aquatic EcologyUniversity of BernBernSwitzerland
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8
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Heras J, Martin CH. Minimal overall divergence of the gut microbiome in an adaptive radiation of Cyprinodon pupfishes despite potential adaptive enrichment for scale-eating. PLoS One 2022; 17:e0273177. [PMID: 36112615 PMCID: PMC9481044 DOI: 10.1371/journal.pone.0273177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 08/03/2022] [Indexed: 11/18/2022] Open
Abstract
Adaptive radiations offer an excellent opportunity to understand the eco-evolutionary dynamics of gut microbiota and host niche specialization. In a laboratory common garden, we compared the gut microbiota of two novel derived trophic specialist pupfishes, a scale-eater and a molluscivore, to closely related and distant outgroup generalist populations, spanning both rapid trophic evolution within 10 kya and stable generalist diets persisting over 11 Mya. We predicted an adaptive and highly divergent microbiome composition in the trophic specialists reflecting their rapid rates of craniofacial and behavioral diversification. We sequenced 16S rRNA amplicons of gut microbiomes from lab-reared adult pupfishes raised under identical conditions and fed the same high protein diet. In contrast to our predictions, gut microbiota largely reflected phylogenetic distance among species, rather than generalist or specialist life history, in support of phylosymbiosis. However, we did find significant enrichment of Burkholderiaceae bacteria in replicated lab-reared scale-eater populations. These bacteria sometimes digest collagen, the major component of fish scales, supporting an adaptive shift. We also found some enrichment of Rhodobacteraceae and Planctomycetia in lab-reared molluscivore populations, but these bacteria target cellulose. Overall phylogenetic conservation of microbiome composition contrasts with predictions of adaptive radiation theory and observations of rapid diversification in all other trophic traits in these hosts, including craniofacial morphology, foraging behavior, aggression, and gene expression, suggesting that the functional role of these minor shifts in microbiota will be important for understanding the role of the microbiome in trophic diversification.
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Affiliation(s)
- Joseph Heras
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, United States of America
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, United States of America
| | - Christopher H. Martin
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, United States of America
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, United States of America
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9
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Patton AH, Richards EJ, Gould KJ, Buie LK, Martin CH. Hybridization alters the shape of the genotypic fitness landscape, increasing access to novel fitness peaks during adaptive radiation. eLife 2022; 11:e72905. [PMID: 35616528 PMCID: PMC9135402 DOI: 10.7554/elife.72905] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 04/14/2022] [Indexed: 12/30/2022] Open
Abstract
Estimating the complex relationship between fitness and genotype or phenotype (i.e. the adaptive landscape) is one of the central goals of evolutionary biology. However, adaptive walks connecting genotypes to organismal fitness, speciation, and novel ecological niches are still poorly understood and processes for surmounting fitness valleys remain controversial. One outstanding system for addressing these connections is a recent adaptive radiation of ecologically and morphologically novel pupfishes (a generalist, molluscivore, and scale-eater) endemic to San Salvador Island, Bahamas. We leveraged whole-genome sequencing of 139 hybrids from two independent field fitness experiments to identify the genomic basis of fitness, estimate genotypic fitness networks, and measure the accessibility of adaptive walks on the fitness landscape. We identified 132 single nucleotide polymorphisms (SNPs) that were significantly associated with fitness in field enclosures. Six out of the 13 regions most strongly associated with fitness contained differentially expressed genes and fixed SNPs between trophic specialists; one gene (mettl21e) was also misexpressed in lab-reared hybrids, suggesting a potential intrinsic genetic incompatibility. We then constructed genotypic fitness networks from adaptive alleles and show that scale-eating specialists are the most isolated of the three species on these networks. Intriguingly, introgressed and de novo variants reduced fitness landscape ruggedness as compared to standing variation, increasing the accessibility of genotypic fitness paths from generalist to specialists. Our results suggest that adaptive introgression and de novo mutations alter the shape of the fitness landscape, providing key connections in adaptive walks circumventing fitness valleys and triggering the evolution of novelty during adaptive radiation.
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Affiliation(s)
- Austin H Patton
- Department of Integrative Biology, University of California, BerkeleyBerkeleyUnited States
- Museum of Vertebrate Zoology, University of California, BerkeleyBerkeleyUnited States
| | - Emilie J Richards
- Department of Integrative Biology, University of California, BerkeleyBerkeleyUnited States
- Museum of Vertebrate Zoology, University of California, BerkeleyBerkeleyUnited States
| | - Katelyn J Gould
- Department of Biology, University of North CarolinaChapel HillUnited States
| | - Logan K Buie
- Department of Biology, University of North CarolinaChapel HillUnited States
| | - Christopher H Martin
- Department of Integrative Biology, University of California, BerkeleyBerkeleyUnited States
- Museum of Vertebrate Zoology, University of California, BerkeleyBerkeleyUnited States
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10
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Blázquez M, Hernández-Moreno LS, Gasulla F, Pérez-Vargas I, Pérez-Ortega S. The Role of Photobionts as Drivers of Diversification in an Island Radiation of Lichen-Forming Fungi. Front Microbiol 2022; 12:784182. [PMID: 35046912 PMCID: PMC8763358 DOI: 10.3389/fmicb.2021.784182] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/02/2021] [Indexed: 01/04/2023] Open
Abstract
Speciation in oceanic islands has attracted the interest of scientists since the 19th century. One of the most striking evolutionary phenomena that can be studied in islands is adaptive radiation, that is, when a lineage gives rise to different species by means of ecological speciation. Some of the best-known examples of adaptive radiation are charismatic organisms like the Darwin finches of the Galapagos and the cichlid fishes of the great African lakes. In these and many other examples, a segregation of the trophic niche has been shown to be an important diversification driver. Radiations are known in other groups of organisms, such as lichen-forming fungi. However, very few studies have investigated their adaptive nature, and none have focused on the trophic niche. In this study, we explore the role of the trophic niche in a putative radiation of endemic species from the Macaronesian Region, the Ramalina decipiens group. The photobiont diversity was studied by Illumina MiSeq sequencing of the ITS2 region of 197 specimens spanning the phylogenetic breadth and geographic range of the group. A total of 66 amplicon sequence variants belonging to the four main clades of the algal genus Trebouxia were found. Approximately half of the examined thalli showed algal coexistence, but in most of them, a single main photobiont amounted to more than 90% of the reads. However, there were no significant differences in photobiont identity and in the abundance of ITS2 reads across the species of the group. We conclude that a segregation of the trophic niche has not occurred in the R. decipiens radiation.
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Affiliation(s)
- Miguel Blázquez
- Department of Mycology, Real Jardín Botánico (CSIC), Madrid, Spain.,Open Access Publication Support Program, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain.,Escuela Internacional de Doctorado, Universidad Rey Juan Carlos, Móstoles, Spain
| | - Lucía S Hernández-Moreno
- Department of Mycology, Real Jardín Botánico (CSIC), Madrid, Spain.,Open Access Publication Support Program, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Francisco Gasulla
- Department of Life Sciences, Universidad de Alcalá, Alcalá de Henares, Spain
| | - Israel Pérez-Vargas
- Department of Botany, Ecology and Plant Physiology, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | - Sergio Pérez-Ortega
- Department of Mycology, Real Jardín Botánico (CSIC), Madrid, Spain.,Open Access Publication Support Program, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
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11
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García-Navas V, Tobias JA, Schweizer M, Wegmann D, Schodde R, Norman JA, Christidis L. Trophic niche shifts and phenotypic trait evolution are largely decoupled in Australasian parrots. BMC Ecol Evol 2021; 21:212. [PMID: 34837943 PMCID: PMC8626917 DOI: 10.1186/s12862-021-01940-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 11/11/2021] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Trophic shifts from one dietary niche to another have played major roles in reshaping the evolutionary trajectories of a wide range of vertebrate groups, yet their consequences for morphological disparity and species diversity differ among groups. METHODS Here, we use phylogenetic comparative methods to examine whether the evolution of nectarivory and other trophic shifts have driven predictable evolutionary pathways in Australasian psittaculid parrots in terms of ecological traits such as body size, beak shape, and dispersal capacity. RESULTS We found no evidence for an 'early-burst' scenario of lineage or morphological diversification. The best-fitting models indicate that trait evolution in this group is characterized by abrupt phenotypic shifts (evolutionary jumps), with no sign of multiple phenotypic optima correlating with different trophic strategies. Thus, our results point to the existence of weak directional selection and suggest that lineages may be evolving randomly or slowly toward adaptive peaks they have not yet reached. CONCLUSIONS This study adds to a growing body of evidence indicating that the relationship between avian morphology and feeding ecology may be more complex than usually assumed and highlights the importance of adding more flexible models to the macroevolutionary toolbox.
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Affiliation(s)
- Vicente García-Navas
- Department of Integrative Ecology, Doñana Biological Station EBD (CSIC), Seville, Spain.
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.
- Centre for Ecology, Evolution and Environmental Changes (cE3c), University of Lisbon, Lisbon, Portugal.
| | - Joseph A Tobias
- Department of Life Sciences (Silwood Park), Faculty of Natural Sciences, Imperial College London, London, UK
| | | | - Daniel Wegmann
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Richard Schodde
- Australian National Wildlife Collection, CSIRO Sustainable Ecosystems, Canberra, Australia
| | | | - Les Christidis
- Southern Cross University, Coffs Harbour, NSW, Australia
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12
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Cohen HE, Kane EA. Biting kinematics do not differ between ecologically divergent populations of Trinidadian guppies. J Zool (1987) 2021. [DOI: 10.1111/jzo.12924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- H. E. Cohen
- Department of Biology Georgia Southern University Statesboro GA USA
| | - E. A. Kane
- Department of Biology University of Louisiana at Lafayette Lafayette LA USA
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13
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de Alencar LRV, Quental TB. Linking population-level and microevolutionary processes to understand speciation dynamics at the macroevolutionary scale. Ecol Evol 2021; 11:5828-5843. [PMID: 34141187 PMCID: PMC8207422 DOI: 10.1002/ece3.7511] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 03/17/2021] [Indexed: 11/05/2022] Open
Abstract
Although speciation dynamics have been described for several taxonomic groups in distinct geographic regions, most macroevolutionary studies still lack a detailed mechanistic view on how or why speciation rates change. To help partially fill this gap, we suggest that the interaction between the time taken by a species to geographically expand and the time populations take to evolve reproductive isolation should be considered when we are trying to understand macroevolutionary patterns. We introduce a simple conceptual index to guide our discussion on how demographic and microevolutionary processes might produce speciation dynamics at macroevolutionary scales. Our framework is developed under different scenarios: when speciation is mediated by geographical or resource-partitioning opportunities, and when diversity is limited or not. We also discuss how organismal intrinsic properties and different overall geographical settings can influence the tempo and mode of speciation. We argue that specific conditions observed at the microscale might produce a pulse in speciation rates even without a pulse in either climate or physical barriers. We also propose a hypothesis to reconcile the apparent inconsistency between speciation measured at the microscale and macroscale, and emphasize that diversification rates are better seen as an emergent property. We hope to bring the reader's attention to interesting mechanisms to be further studied, to motivate the development of new theoretical models that connect microevolution and macroevolution, and to inspire new empirical and methodological approaches to more adequately investigate speciation dynamics either using neontological or paleontological data.
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Affiliation(s)
| | - Tiago Bosisio Quental
- Departamento de EcologiaInstituto de BiociênciasUniversidade de São PauloSão PauloBrazil
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14
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McGirr JA, Martin CH. Few Fixed Variants between Trophic Specialist Pupfish Species Reveal Candidate Cis-Regulatory Alleles Underlying Rapid Craniofacial Divergence. Mol Biol Evol 2021; 38:405-423. [PMID: 32877534 PMCID: PMC7826174 DOI: 10.1093/molbev/msaa218] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Investigating closely related species that rapidly evolved divergent feeding morphology is a powerful approach to identify genetic variation underlying variation in complex traits. This can also lead to the discovery of novel candidate genes influencing natural and clinical variation in human craniofacial phenotypes. We combined whole-genome resequencing of 258 individuals with 50 transcriptomes to identify candidate cis-acting genetic variation underlying rapidly evolving craniofacial phenotypes within an adaptive radiation of Cyprinodon pupfishes. This radiation consists of a dietary generalist species and two derived trophic niche specialists-a molluscivore and a scale-eating species. Despite extensive morphological divergence, these species only diverged 10 kya and produce fertile hybrids in the laboratory. Out of 9.3 million genome-wide SNPs and 80,012 structural variants, we found very few alleles fixed between species-only 157 SNPs and 87 deletions. Comparing gene expression across 38 purebred F1 offspring sampled at three early developmental stages, we identified 17 fixed variants within 10 kb of 12 genes that were highly differentially expressed between species. By measuring allele-specific expression in F1 hybrids from multiple crosses, we found that the majority of expression divergence between species was explained by trans-regulatory mechanisms. We also found strong evidence for two cis-regulatory alleles affecting expression divergence of two genes with putative effects on skeletal development (dync2li1 and pycr3). These results suggest that SNPs and structural variants contribute to the evolution of novel traits and highlight the utility of the San Salvador Island pupfish system as an evolutionary model for craniofacial development.
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Affiliation(s)
- Joseph A McGirr
- Environmental Toxicology Department, University of California, Davis, CA
| | - Christopher H Martin
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, CA
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15
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Martin CH, Gould KJ. Surprising spatiotemporal stability of a multi-peak fitness landscape revealed by independent field experiments measuring hybrid fitness. Evol Lett 2020; 4:530-544. [PMID: 33312688 PMCID: PMC7719547 DOI: 10.1002/evl3.195] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 07/23/2020] [Accepted: 09/14/2020] [Indexed: 12/14/2022] Open
Abstract
The effect of the environment on fitness in natural populations is a fundamental question in evolutionary biology. However, experimental manipulations of both environment and phenotype at the same time are rare. Thus, the relative importance of the competitive environment versus intrinsic organismal performance in shaping the location, height, and fluidity of fitness peaks and valleys remains largely unknown. Here, we experimentally tested the effect of competitor frequency on the complex fitness landscape driving adaptive radiation of a generalist and two trophic specialist pupfishes, a scale-eater and molluscivore, endemic to hypersaline lakes on San Salvador Island (SSI), Bahamas. We manipulated phenotypes, by generating 3407 F4/F5 lab-reared hybrids, and competitive environment, by altering the frequency of rare transgressive hybrids between field enclosures in two independent lake populations. We then tracked hybrid survival and growth rates across these four field enclosures for 3-11 months. In contrast to competitive speciation theory, we found no evidence that the frequency of hybrid phenotypes affected their survival. Instead, we observed a strikingly similar fitness landscape to a previous independent field experiment, each supporting multiple fitness peaks for generalist and molluscivore phenotypes and a large fitness valley isolating the divergent scale-eater phenotype. These features of the fitness landscape were stable across manipulated competitive environments, multivariate trait axes, and spatiotemporal heterogeneity. We suggest that absolute performance constraints and divergent gene regulatory networks shape macroevolutionary (interspecific) fitness landscapes in addition to microevolutionary (intraspecific) competitive dynamics. This interplay between organism and environment underlies static and dynamic features of the adaptive landscape.
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Affiliation(s)
- Christopher H. Martin
- Department of Integrative BiologyUniversity of California, BerkeleyBerkeleyCalifornia94720
- Museum of Vertebrate ZoologyUniversity of California, BerkeleyBerkeleyCalifornia94720
| | - Katelyn J. Gould
- Department of BiologyUniversity of North Carolina at Chapel HillChapel HillNorth Carolina27515
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16
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McGirr JA, Martin CH. Ecological divergence in sympatry causes gene misexpression in hybrids. Mol Ecol 2020; 29:2707-2721. [PMID: 32557903 PMCID: PMC8209238 DOI: 10.1111/mec.15512] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 05/21/2020] [Accepted: 06/01/2020] [Indexed: 12/17/2022]
Abstract
Ecological speciation occurs when reproductive isolation evolves as a byproduct of adaptive divergence between populations. Selection favouring gene regulatory divergence between species could result in transgressive levels of gene expression in F1 hybrids that may lower hybrid fitness. We combined 58 resequenced genomes with 124 transcriptomes to identify patterns of hybrid gene misexpression that may be driven by adaptive regulatory divergence within a young radiation of Cyprinodon pupfishes, which consists of a dietary generalist and two trophic specialists-a molluscivore and a scale-eater. We found more differential gene expression between closely related sympatric specialists than between allopatric generalist populations separated by 1,000 km. Intriguingly, 9.6% of genes that were differentially expressed between sympatric species were also misexpressed in F1 hybrids. A subset of these genes were in highly differentiated genomic regions and enriched for functions important for trophic specialization, including head, muscle and brain development. These regions also included genes that showed evidence of hard selective sweeps and were significantly associated with oral jaw length-the most rapidly diversifying skeletal trait in this radiation. Our results indicate that divergent ecological selection in sympatry can contribute to hybrid gene misexpression which may act as a reproductive barrier between nascent species.
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Affiliation(s)
- Joseph A. McGirr
- Department of Biology, University of North Carolina, Chapel
Hill, NC 27514
| | - Christopher H. Martin
- Department of Biology, University of North Carolina, Chapel
Hill, NC 27514
- Department of Integrative Biology and Museum of Vertebrate
Zoology, University of California, Berkeley, CA 94720
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17
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St. John ME, Dixon K, Martin CH. Oral shelling within an adaptive radiation of pupfishes: Testing the adaptive function of a novel nasal protrusion and behavioural preference. JOURNAL OF FISH BIOLOGY 2020; 97:163-171. [PMID: 32278332 PMCID: PMC8183458 DOI: 10.1111/jfb.14344] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/05/2020] [Accepted: 04/08/2020] [Indexed: 06/11/2023]
Abstract
Dietary specialization on hard prey items, such as mollusks and crustaceans, is commonly observed in a diverse array of fish species. Many fish consume these types of prey by crushing the shell to consume the soft tissue within, but a few fishes extricate the soft tissue without breaking the shell using a method known as oral shelling. Oral shelling involves pulling a mollusc from its shell and it may be a way to subvert an otherwise insurmountable shell defence. However, the biomechanical requirements and potential adaptations for oral shelling are unknown. Here, we test the hypothesis that a novel nasal protrusion is an adaptation for oral shelling in the durophagous pupfish (Cyprinodon brontotheroides). We first demonstrate oral shelling in this species and then predict that a larger nasal protrusion would allow pupfish to consume larger snails. Durophagous pupfish are found within an endemic radiation of pupfish on San Salvador Island, Bahamas. We took advantage of closely related sympatric species and outgroups to test: (a) whether durophagous pupfish shell and consume more snails than other species, (b) if F1 and F2 durophagous hybrids consume similar amounts of snails as purebred durophagous pupfish, and (c) if nasal protrusion size in parental and hybrid populations increases the maximum size of consumed snails. We found that durophagous pupfish and their hybrids consumed the most snails, but did not find a strong association between nasal protrusion size and maximum snail size consumed within the parental or F2 hybrid population, suggesting that the size of their novel nasal protrusion does not provide a major benefit in oral shelling. Instead, we suggest that the nasal protrusion may increase feeding efficiency, act as a sensory organ, or is a sexually selected trait, and that a strong feeding preference may be most important for oral shelling.
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Affiliation(s)
- Michelle E. St. John
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
| | - Kristi Dixon
- Department of Biology, University of North Carolina at Chapel Hill, 120 South Rd., NC 27599, USA
| | - Christopher H. Martin
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
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18
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St John ME, Holzman R, Martin CH. Rapid adaptive evolution of scale-eating kinematics to a novel ecological niche. J Exp Biol 2020; 223:jeb217570. [PMID: 32029459 PMCID: PMC7097200 DOI: 10.1242/jeb.217570] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 01/29/2020] [Indexed: 01/08/2023]
Abstract
The origins of novel trophic specialization, in which organisms begin to exploit resources for the first time, may be explained by shifts in behavior such as foraging preferences or feeding kinematics. One way to investigate behavioral mechanisms underlying ecological novelty is by comparing prey capture kinematics among species. We investigated the contribution of kinematics to the origins of a novel ecological niche for scale-eating within a microendemic adaptive radiation of pupfishes on San Salvador Island, Bahamas. We compared prey capture kinematics across three species of pupfish while they consumed shrimp and scales in the lab, and found that scale-eating pupfish exhibited peak gape sizes twice as large as in other species, but also attacked prey with a more obtuse angle between their lower jaw and suspensorium. We then investigated how this variation in feeding kinematics could explain scale-biting performance by measuring bite size (surface area removed) from standardized gelatin cubes. We found that a combination of larger peak gape and more obtuse lower jaw and suspensorium angles resulted in approximately 40% more surface area removed per strike, indicating that scale-eaters may reside on a performance optimum for scale biting. To test whether feeding performance could contribute to reproductive isolation between species, we also measured F1 hybrids and found that their kinematics and performance more closely resembled generalists, suggesting that F1 hybrids may have low fitness in the scale-eating niche. Ultimately, our results suggest that the evolution of strike kinematics in this radiation is an adaptation to the novel niche of scale eating.
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Affiliation(s)
- Michelle E St John
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Roi Holzman
- School of Zoology, Tel Aviv University, Eilat 6997801, Israel
- Inter-University Institute for Marine Sciences, Eilat 8810302, Israel
| | - Christopher H Martin
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, USA
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19
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Quach QN, Reynolds RG, Revell LJ. Historical allopatry and secondary contact or primary intergradation in the Puerto Rican crested anole, Anolis cristatellus, on Vieques Island in the Caribbean. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
AbstractRecent work has revealed surprisingly deep mitochondrial genetic divergence in the lizard Anolis cristatellus among samples obtained from the small Caribbean island of Vieques. Here we sought to determine whether this had resulted from natural or anthropogenic causes, and (if the former) whether divergence occurred in a biogeographical context of allopatry followed by secondary contact, or via isolation-by-distance across the species’ historical range. We first estimated a mitochondrial gene tree for 379 samples and then genotyped 3407 single nucleotide polymorphic sites from 48 individuals using a modified genotyping-by-sequencing approach. We found that A. cristatellus samples from Vieques belong to two highly divergent mitochondrial subclades, but the geographical distribution of these haplogroups indicates that this pattern is probably natural in origin. Analysis of our single nucleotide polymorphic dataset revealed differentiation that is consistent with isolation-by-distance between the western and eastern ends of Vieques, suggesting that the overall pattern of divergence probably reflects primary intergradation with a mitochondrial break on the historical Puerto Rico Bank palaeo-island that happened to coincide with the present-day location of Vieques. Our findings help to underline the growing consensus that results from a single genetic marker can prove highly misleading in studies of historical population genetic structure.
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Affiliation(s)
- Quynh N Quach
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA
| | - R Graham Reynolds
- Department of Biology, University of North Carolina Asheville, Asheville, NC, USA
| | - Liam J Revell
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA
- Departamento de Ecología, Universidad Católica de la Santísima Concepción, Concepción, Chile
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20
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Sutra N, Kusumi J, Montenegro J, Kobayashi H, Fujimoto S, Masengi KWA, Nagano AJ, Toyoda A, Matsunami M, Kimura R, Yamahira K. Evidence for sympatric speciation in a Wallacean ancient lake. Evolution 2019; 73:1898-1915. [DOI: 10.1111/evo.13821] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 08/03/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Nobu Sutra
- Tropical Biosphere Research CenterUniversity of the Ryukyus Okinawa 903‐0213 Japan
| | - Junko Kusumi
- Faculty of Social and Cultural StudiesKyushu University Fukuoka 819‐0395 Japan
| | - Javier Montenegro
- Tropical Biosphere Research CenterUniversity of the Ryukyus Okinawa 903‐0213 Japan
| | - Hirozumi Kobayashi
- Tropical Biosphere Research CenterUniversity of the Ryukyus Okinawa 903‐0213 Japan
| | - Shingo Fujimoto
- Graduate School of MedicineUniversity of the Ryukyus Okinawa 903‐0125 Japan
| | | | | | - Atsushi Toyoda
- Comparative Genomics LaboratoryNational Institute of Genetics Mishima 411‐8540 Japan
| | | | - Ryosuke Kimura
- Graduate School of MedicineUniversity of the Ryukyus Okinawa 903‐0125 Japan
| | - Kazunori Yamahira
- Tropical Biosphere Research CenterUniversity of the Ryukyus Okinawa 903‐0213 Japan
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21
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Martin CH, McGirr JA, Richards EJ, St. John ME. How to Investigate the Origins of Novelty: Insights Gained from Genetic, Behavioral, and Fitness Perspectives. Integr Org Biol 2019; 1:obz018. [PMID: 33791533 PMCID: PMC7671130 DOI: 10.1093/iob/obz018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Biologists are drawn to the most extraordinary adaptations in the natural world, often referred to as evolutionary novelties, yet rarely do we understand the microevolutionary context underlying the origins of novel traits, behaviors, or ecological niches. Here we discuss insights gained into the origins of novelty from a research program spanning biological levels of organization from genotype to fitness in Caribbean pupfishes. We focus on a case study of the origins of novel trophic specialists on San Salvador Island, Bahamas and place this radiation in the context of other rapid radiations. We highlight questions that can be addressed about the origins of novelty at different biological levels, such as measuring the isolation of novel phenotypes on the fitness landscape, locating the spatial and temporal origins of adaptive variation contributing to novelty, detecting dysfunctional gene regulation due to adaptive divergence, and connecting behaviors with novel traits. Evolutionary novelties are rare, almost by definition, and we conclude that integrative case studies can provide insights into this rarity relative to the dynamics of adaptation to more common ecological niches and repeated parallel speciation, such as the relative isolation of novel phenotypes on fitness landscapes and the transient availability of ecological, genetic, and behavioral opportunities.
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Affiliation(s)
- C H Martin
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
| | - J A McGirr
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - E J Richards
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
| | - M E St. John
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
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22
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McGirr JA, Martin CH. Hybrid gene misregulation in multiple developing tissues within a recent adaptive radiation of Cyprinodon pupfishes. PLoS One 2019; 14:e0218899. [PMID: 31291291 PMCID: PMC6619667 DOI: 10.1371/journal.pone.0218899] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/11/2019] [Indexed: 12/24/2022] Open
Abstract
Genetic incompatibilities constitute the final stages of reproductive isolation and speciation, but little is known about incompatibilities that occur within recent adaptive radiations among closely related diverging populations. Crossing divergent species to form hybrids can break up coadapted variation, resulting in genetic incompatibilities within developmental networks shaping divergent adaptive traits. We crossed two closely related sympatric Cyprinodon pupfish species–a dietary generalist and a specialized molluscivore–and measured expression levels in their F1 hybrids to identify regulatory variation underlying the novel craniofacial morphology found in this recent microendemic adaptive radiation. We extracted mRNA from eight day old whole-larvae tissue and from craniofacial tissues dissected from 17–20 day old larvae to compare gene expression between a total of seven F1 hybrids and 24 individuals from parental species populations. We found 3.9% of genes differentially expressed between generalists and molluscivores in whole-larvae tissues and 0.6% of genes differentially expressed in craniofacial tissue. We found that 2.1% of genes were misregulated in whole-larvae hybrids whereas 19.1% of genes were misregulated in hybrid craniofacial tissues, after correcting for sequencing biases. We also measured allele specific expression across 15,429 heterozygous sites to identify putative compensatory regulatory mechanisms underlying differential expression between generalists and molluscivores. Together, our results highlight the importance of considering misregulation as an early indicator of genetic incompatibilities in the context of rapidly diverging adaptive radiations and suggests that compensatory regulatory divergence drives hybrid gene misregulation in developing tissues that give rise to novel craniofacial traits.
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Affiliation(s)
- Joseph A. McGirr
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail:
| | - Christopher H. Martin
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, California, United States of America
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23
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St. John ME, McGirr JA, Martin CH. The behavioral origins of novelty: did increased aggression lead to scale-eating in pupfishes? Behav Ecol 2019; 30:557-569. [PMID: 30971862 PMCID: PMC6450202 DOI: 10.1093/beheco/ary196] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 11/08/2018] [Accepted: 12/14/2018] [Indexed: 11/13/2022] Open
Abstract
Behavioral changes in a new environment are often assumed to precede the origins of evolutionary novelties. Here, we examined whether an increase in aggression is associated with a novel scale-eating trophic niche within a recent radiation of Cyprinodon pupfishes endemic to San Salvador Island, Bahamas. We measured aggression using multiple behavioral assays and used transcriptomic analyses to identify differentially expressed genes in aggression and other behavioral pathways across 3 sympatric species in the San Salvador radiation (generalist, snail-eating specialist, and scale-eating specialist) and 2 generalist outgroups. Surprisingly, we found increased behavioral aggression and differential expression of aggression-related pathways in both the scale-eating and snail-eating specialists, despite their independent evolutionary origins. Increased behavioral aggression varied across both sex and stimulus context in both species. Our results indicate that aggression is not unique to scale-eating specialists. Instead, selection may increase aggression in other contexts such as niche specialization in general or mate competition. Alternatively, increased aggression may result from indirect selection on craniofacial traits, pigmentation, or metabolism-all traits which are highly divergent, exhibit signs of selective sweeps, and are affected by aggression-related genetic pathways which are differentially expressed in this system. In conclusion, the evolution of a novel predatory trophic niche within a recent adaptive radiation does not have clear-cut behavioral origins as previously assumed, highlighting the multivariate nature of adaptation and the complex integration of behavior with other phenotypic traits.
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Affiliation(s)
| | - Joseph A McGirr
- Department of Biology, University of North Carolina at Chapel Hill, NC, USA
| | - Christopher H Martin
- Department of Biology, University of North Carolina at Chapel Hill, NC, USA
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA
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24
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Lencer ES, McCune AR. An embryonic staging series up to hatching for Cyprinodon variegatus: An emerging fish model for developmental, evolutionary, and ecological research. J Morphol 2018; 279:1559-1578. [PMID: 30368863 DOI: 10.1002/jmor.20870] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 06/17/2018] [Accepted: 06/22/2018] [Indexed: 11/08/2022]
Abstract
Using multiple taxa to research development is necessary for making general conclusions about developmental patterns and mechanisms. We present a staging series for Cyprinodon variegatus as a basis for further study of the developmental biology of fishes in the genus Cyprinodon and for comparative work on teleost fishes beyond the standard models. Cyprinodon are small, euryhaline fishes, widely distributed in fresh, brackish, and hypersaline waters of southern and eastern North America. Cyprinodontids are closely related to fundulids, providing a comparative reference point to the embryological model, Fundulus heteroclitus. Ecologists and evolutionary biologists commonly study Cyprinodon, and we have been using Cyprinodon to study skull variation and its genetic basis among closely related species. We divided embryonic development of C. variegatus into 34 morphologically identifiable stages. We reference our staging series to that already defined for a related model species, Oryzias latipes (medaka) that is studied by a large community of researchers. We provide a description of the early chondrogenesis and ossification of skull and caudal fin bones during the latter stages of embryonic development. We show that Cyprinodon are tractable for studying development. Eggs can be obtained easily from breeding pairs and our study provides a staging system to facilitate future developmental studies.
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Affiliation(s)
- Ezra S Lencer
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York
| | - Amy R McCune
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York
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25
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Jones KS, Weisrock DW. Genomic data reject the hypothesis of sympatric ecological speciation in a clade of Desmognathus salamanders. Evolution 2018; 72:2378-2393. [PMID: 30246244 DOI: 10.1111/evo.13606] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 09/05/2018] [Indexed: 12/22/2022]
Abstract
Closely related taxa with dissimilar morphologies are often considered to have diverged via natural selection favoring different phenotypes. However, some studies have found these scenarios to be paired with limited or no genetic differentiation. Desmognathus quadramaculatus and D. marmoratus are sympatric salamander species thought to represent a case of ecological speciation based on distinct morphologies, but the results of previous studies have not resolved corresponding patterns of lineage divergence. Here, we use genome-wide data to test this hypothesis of ecological speciation. Population structure analyses partitioned individuals geographically, but not morphologically, into two adjacent regions of western North Carolina: Pisgah and Nantahala. Phylogenetic analyses confirmed the nominal species are nonmonophyletic and resolved deep divergence between the two geographic clusters. Model-testing overwhelmingly supported the hypothesis that lineage divergence followed geography. Finally, ecological niche modeling showed that Pisgah and Nantahala individuals occupy different climatic niches, and geographic boundaries for the two lineages correspond to differences in precipitation regimes across southern Appalachia. Overall, we reject the previous hypothesis of ecological speciation based on microhabitat partitioning. Instead, our results suggest that there are two cryptic lineages, each containing the same pair of morphotypes.
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Affiliation(s)
- Kara S Jones
- Department of Biology, University of Kentucky, Lexington, Kentucky 40506
| | - David W Weisrock
- Department of Biology, University of Kentucky, Lexington, Kentucky 40506
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26
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Foster KL, Piller KR. Disentangling the drivers of diversification in an imperiled group of freshwater fishes (Cyprinodontiformes: Goodeidae). BMC Evol Biol 2018; 18:116. [PMID: 30021522 PMCID: PMC6052539 DOI: 10.1186/s12862-018-1220-3] [Citation(s) in RCA: 18] [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: 12/04/2017] [Accepted: 06/20/2018] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND One of the most perplexing questions in evolutionary biology is why some lineages diversify into many species, and others do not. In many cases, ecological opportunity has played an important role, leading to diversification along trophic or habitat-based axes. The Goodeidae (Teleostomi: Cyprinodontiformes) are a family of freshwater fishes with two subfamilies: Goodeinae (42 species, viviparous, heterogeneous habitats, Mesa Central of Mexico) and Empetrichthyinae (4 species, oviparous, homogeneous habitats, Great Basin of the United States). These discrepant sets of characteristics and their sister-group relationship make the goodeids amenable to a comparative study of diversification. We gathered lateral body images from more than 1600 specimens of all extant species in the family. Geometric morphometric, and phylogenetic comparative analyses were used to address whether higher species diversity correlates with higher rates of morphological shape evolution and whether there are differences in functional/habitat modules between the two subfamilies. RESULTS This study recovered a higher rate of overall body shape evolution in the Goodeinae that is nearly double in magnitude compared to the Empetrichthyinae. A modularity test indicated that the Goodeinae displayed elevated rates of morphological evolution in comparison to the Empetrichthyinae when only trunk (locomotor) regions were compared between subfamilies. No significant differences in evolutionary shape rates were recovered when the trophic (head) regions were compared between subfamilies. DISCUSSION These results support the hypothesis that Mexican goodeids radiated via an ecological opportunity scenario into a wide-array of novel habitats in the island-like Mesa Central as evidenced by their high rate of shape evolution, relative to the Empetrichthyinae. This study quantitatively unraveled the drivers of evolution and eliminated trophic specialization as a driving force within the Goodeidae. CONCLUSIONS A combination of phylogenetic and morphometric data, and phylogenetic comparative analyses were used to examine body shape rate evolution within the Goodeidae. Results support the hypothesis that species in the subfamily Goodeinae on the central Mexican plateau had a higher rate of body shape evolution relative to its sister subfamily Empetrichthyinae in the Great Basin suggesting that the Goodeinae diversified via an ecological opportunity scenario along habitat, rather than trophic axes.
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Affiliation(s)
- Kimberly L. Foster
- Department of Biological Sciences, Southeastern Louisiana University, Hammond, LA 70402 USA
- Present Address: Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008-5410 USA
| | - Kyle R. Piller
- Department of Biological Sciences, Southeastern Louisiana University, Hammond, LA 70402 USA
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27
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Martin CH, Turner BJ. Long-distance dispersal over land by fishes: extremely rare ecological events become probable over millennial timescales. Proc Biol Sci 2018; 285:20172436. [PMID: 29925610 PMCID: PMC6030530 DOI: 10.1098/rspb.2017.2436] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 05/23/2018] [Indexed: 01/01/2023] Open
Affiliation(s)
- Christopher H Martin
- Department of Biology, University of North Carolina at Chapel Hill, NC 27599, USA
| | - Bruce J Turner
- Department of Biological Sciences, Virginia Tech, VA, USA
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28
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Higham TE, Rogers SM, Langerhans RB, Jamniczky HA, Lauder GV, Stewart WJ, Martin CH, Reznick DN. Speciation through the lens of biomechanics: locomotion, prey capture and reproductive isolation. Proc Biol Sci 2017; 283:rspb.2016.1294. [PMID: 27629033 DOI: 10.1098/rspb.2016.1294] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 08/24/2016] [Indexed: 11/12/2022] Open
Abstract
Speciation is a multifaceted process that involves numerous aspects of the biological sciences and occurs for multiple reasons. Ecology plays a major role, including both abiotic and biotic factors. Whether populations experience similar or divergent ecological environments, they often adapt to local conditions through divergence in biomechanical traits. We investigate the role of biomechanics in speciation using fish predator-prey interactions, a primary driver of fitness for both predators and prey. We highlight specific groups of fishes, or specific species, that have been particularly valuable for understanding these dynamic interactions and offer the best opportunities for future studies that link genetic architecture to biomechanics and reproductive isolation (RI). In addition to emphasizing the key biomechanical techniques that will be instrumental, we also propose that the movement towards linking biomechanics and speciation will include (i) establishing the genetic basis of biomechanical traits, (ii) testing whether similar and divergent selection lead to biomechanical divergence, and (iii) testing whether/how biomechanical traits affect RI. Future investigations that examine speciation through the lens of biomechanics will propel our understanding of this key process.
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Affiliation(s)
- Timothy E Higham
- Department of Biology, University of California, Riverside, CA, USA
| | - Sean M Rogers
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - R Brian Langerhans
- Department of Biological Sciences and W.M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC, USA
| | - Heather A Jamniczky
- Department of Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - George V Lauder
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | | | | | - David N Reznick
- Department of Biology, University of California, Riverside, CA, USA
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29
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Martin CH, Höhna S. New evidence for the recent divergence of Devil's Hole pupfish and the plausibility of elevated mutation rates in endangered taxa. Mol Ecol 2017; 27:831-838. [DOI: 10.1111/mec.14404] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 08/18/2017] [Accepted: 09/15/2017] [Indexed: 01/06/2023]
Affiliation(s)
- Christopher H. Martin
- Department of Biology; University of North Carolina at Chapel Hill; Chapel Hill NC USA
| | - Sebastian Höhna
- Department of Integrative Biology; University of California; Berkeley CA USA
- Department of Statistics; University of California; Berkeley CA USA
- Division of Evolutionary Biology; Ludwig-Maximilians-Universität; München Germany
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30
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Hernandez LP, Adriaens D, Martin CH, Wainwright PC, Masschaele B, Dierick M. Building trophic specializations that result in substantial niche partitioning within a young adaptive radiation. J Anat 2017; 232:173-185. [PMID: 29161774 DOI: 10.1111/joa.12742] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2017] [Indexed: 02/06/2023] Open
Abstract
Dietary partitioning often accompanies the increased morphological diversity seen during adaptive radiations within aquatic systems. While such niche partitioning would be expected in older radiations, it is unclear how significant morphological divergence occurs within a shorter time period. Here we show how differential growth in key elements of the feeding mechanism can bring about pronounced functional differences among closely related species. An incredibly young adaptive radiation of three Cyprinodon species residing within hypersaline lakes in San Salvador Island, Bahamas, has recently been described. Characterized by distinct head shapes, gut content analyses revealed three discrete feeding modes in these species: basal detritivory as well as derived durophagy and lepidophagy (scale-feeding). We dissected, cleared and stained, and micro-CT scanned species to assess functionally relevant differences in craniofacial musculoskeletal elements. The widespread feeding mode previously described for cyprinodontiforms, in which the force of the bite may be secondary to the requisite dexterity needed to pick at food items, is modified within both the scale specialist and the durophagous species. While the scale specialist has greatly emphasized maxillary retraction, using it to overcome the poor mechanical advantage associated with scale-eating, the durophage has instead stabilized the maxilla. In all species the bulk of the adductor musculature is composed of AM A1. However, the combined masses of both adductor mandibulae (AM) A1 and A3 in the scale specialist were five times that of the other species, showing the importance of growth in functional divergence. The scale specialist combines plesiomorphic jaw mechanisms with both a hypertrophied AM A1 and a slightly modified maxillary anatomy (with substantial functional implications) to generate a bite that is both strong and allows a wide range of motion in the upper jaw, two attributes that normally tradeoff mechanically. Thus, a significant feeding innovation (scale-eating, rarely seen in fishes) may evolve based largely on allometric changes in ancestral structures. Alternatively, the durophage shows reduced growth with foreshortened jaws that are stabilized by an immobile maxilla. Overall, scale specialists showed the most divergent morphology, suggesting that selection for scale-biting might be stronger or act on a greater number of traits than selection for either detritivory or durophagy. The scale specialist has colonized an adaptive peak that few lineages have climbed. Thus, heterochronic changes in growth can quickly produce functionally relevant change among closely related species.
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Affiliation(s)
- Luz Patricia Hernandez
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | - Dominique Adriaens
- Evolutionary Morphology of Vertebrates, Ghent University, Ghent, Belgium
| | - Christopher H Martin
- Department of Biology, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Peter C Wainwright
- Department of Evolution & Ecology, University of California, Davis, Davis, CA, USA
| | - Bert Masschaele
- Department of Subatomic and Radiation Physics, Ghent University, Ghent, Belgium
| | - Manuel Dierick
- Department of Subatomic and Radiation Physics, Ghent University, Ghent, Belgium
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31
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Richards EJ, Martin CH. Adaptive introgression from distant Caribbean islands contributed to the diversification of a microendemic adaptive radiation of trophic specialist pupfishes. PLoS Genet 2017; 13:e1006919. [PMID: 28796803 PMCID: PMC5552031 DOI: 10.1371/journal.pgen.1006919] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 07/12/2017] [Indexed: 12/19/2022] Open
Abstract
Rapid diversification often involves complex histories of gene flow that leave variable and conflicting signatures of evolutionary relatedness across the genome. Identifying the extent and source of variation in these evolutionary relationships can provide insight into the evolutionary mechanisms involved in rapid radiations. Here we compare the discordant evolutionary relationships associated with species phenotypes across 42 whole genomes from a sympatric adaptive radiation of Cyprinodon pupfishes endemic to San Salvador Island, Bahamas and several outgroup pupfish species in order to understand the rarity of these trophic specialists within the larger radiation of Cyprinodon. 82% of the genome depicts close evolutionary relationships among the San Salvador Island species reflecting their geographic proximity, but the vast majority of variants fixed between specialist species lie in regions with discordant topologies. Top candidate adaptive introgression regions include signatures of selective sweeps and adaptive introgression of genetic variation from a single population in the northwestern Bahamas into each of the specialist species. Hard selective sweeps of genetic variation on San Salvador Island contributed 5 times more to speciation of trophic specialists than adaptive introgression of Caribbean genetic variation; however, four of the 11 introgressed regions came from a single distant island and were associated with the primary axis of oral jaw divergence within the radiation. For example, standing variation in a proto-oncogene (ski) known to have effects on jaw size introgressed into one San Salvador Island specialist from an island 300 km away approximately 10 kya. The complex emerging picture of the origins of adaptive radiation on San Salvador Island indicates that multiple sources of genetic variation contributed to the adaptive phenotypes of novel trophic specialists on the island. Our findings suggest that a suite of factors, including rare adaptive introgression, may be necessary for adaptive radiation in addition to ecological opportunity.
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Affiliation(s)
- Emilie J. Richards
- Biology Department, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Christopher H. Martin
- Biology Department, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
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32
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Lencer ES, Warren WC, Harrison R, McCune AR. The Cyprinodon variegatus genome reveals gene expression changes underlying differences in skull morphology among closely related species. BMC Genomics 2017; 18:424. [PMID: 28558659 PMCID: PMC5450241 DOI: 10.1186/s12864-017-3810-7] [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: 01/20/2017] [Accepted: 05/22/2017] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Understanding the genetic and developmental origins of phenotypic novelty is central to the study of biological diversity. In this study we identify modifications to the expression of genes at four developmental stages that may underlie jaw morphological differences among three closely related species of pupfish (genus Cyprinodon) from San Salvador Island, Bahamas. Pupfishes on San Salvador Island are trophically differentiated and include two endemic species that have evolved jaw morphologies unlike that of any other species in the genus Cyprinodon. RESULTS We find that gene expression differs significantly across recently diverged species of pupfish. Genes such as Bmp4 and calmodulin, previously implicated in jaw diversification in African cichlid fishes and Galapagos finches, were not found to be differentially expressed among species of pupfish. Instead we find multiple growth factors and cytokine/chemokine genes to be differentially expressed among these pupfish taxa. These include both genes and pathways known to affect craniofacial development, such as Wnt signaling, as well as novel genes and pathways not previously implicated in craniofacial development. These data highlight both shared and potentially unique sources of jaw diversity in pupfish and those identified in other evolutionary model systems such as Galapagos finches and African cichlids. CONCLUSIONS We identify modifications to the expression of genes involved in Wnt signaling, Igf signaling, and the inflammation response as promising avenues for future research. Our project provides insight into the magnitude of gene expression changes contributing to the evolution of morphological novelties, such as jaw structure, in recently diverged pupfish species.
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Affiliation(s)
- Ezra S Lencer
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14850, USA.
| | - Wesley C Warren
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, 63108, USA
| | - Richard Harrison
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14850, USA
| | - Amy R McCune
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14850, USA
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33
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de la Harpe M, Paris M, Karger DN, Rolland J, Kessler M, Salamin N, Lexer C. Molecular ecology studies of species radiations: current research gaps, opportunities and challenges. Mol Ecol 2017; 26:2608-2622. [PMID: 28316112 DOI: 10.1111/mec.14110] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Revised: 02/11/2017] [Accepted: 03/06/2017] [Indexed: 12/28/2022]
Abstract
Understanding the drivers and limits of species radiations is a crucial goal of evolutionary genetics and molecular ecology, yet research on this topic has been hampered by the notorious difficulty of connecting micro- and macroevolutionary approaches to studying the drivers of diversification. To chart the current research gaps, opportunities and challenges of molecular ecology approaches to studying radiations, we examine the literature in the journal Molecular Ecology and revisit recent high-profile examples of evolutionary genomic research on radiations. We find that available studies of radiations are highly unevenly distributed among taxa, with many ecologically important and species-rich organismal groups remaining severely understudied, including arthropods, plants and fungi. Most studies employed molecular methods suitable over either short or long evolutionary time scales, such as microsatellites or restriction site-associated DNA sequencing (RAD-seq) in the former case and conventional amplicon sequencing of organellar DNA in the latter. The potential of molecular ecology studies to address and resolve patterns and processes around the species level in radiating groups of taxa is currently limited primarily by sample size and a dearth of information on radiating nuclear genomes as opposed to organellar ones. Based on our literature survey and personal experience, we suggest possible ways forward in the coming years. We touch on the potential and current limitations of whole-genome sequencing (WGS) in studies of radiations. We suggest that WGS and targeted ('capture') resequencing emerge as the methods of choice for scaling up the sampling of populations, species and genomes, including currently understudied organismal groups and the genes or regulatory elements expected to matter most to species radiations.
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Affiliation(s)
- Marylaure de la Harpe
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg, CH-1700, Switzerland.,Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria
| | - Margot Paris
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg, CH-1700, Switzerland
| | - Dirk N Karger
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, Zürich, CH-8008, Switzerland
| | - Jonathan Rolland
- Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne, CH-1015, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge, Lausanne, CH-1015, Switzerland
| | - Michael Kessler
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, Zürich, CH-8008, Switzerland
| | - Nicolas Salamin
- Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne, CH-1015, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge, Lausanne, CH-1015, Switzerland
| | - Christian Lexer
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg, CH-1700, Switzerland.,Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria
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34
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Affiliation(s)
- Josephine R. Paris
- Biosciences College of Life and Environmental Sciences University of Exeter Exeter UK
| | - Jamie R. Stevens
- Biosciences College of Life and Environmental Sciences University of Exeter Exeter UK
| | - Julian M. Catchen
- Department of Animal Biology University of Illinois at Urbana–Champaign Urbana IL 61801 USA
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35
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McGirr JA, Martin CH. Novel Candidate Genes Underlying Extreme Trophic Specialization in Caribbean Pupfishes. Mol Biol Evol 2017; 34:873-888. [PMID: 28028132 PMCID: PMC5850223 DOI: 10.1093/molbev/msw286] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The genetic changes responsible for evolutionary transitions from generalist to specialist phenotypes are poorly understood. Here we examine the genetic basis of craniofacial traits enabling novel trophic specialization in a sympatric radiation of Cyprinodon pupfishes endemic to San Salvador Island, Bahamas. This recent radiation consists of a generalist species and two novel specialists: a small-jawed "snail-eater" and a large-jawed "scale-eater." We genotyped 12 million single nucleotide polymorphisms (SNPs) by whole-genome resequencing of 37 individuals of all three species from nine populations and integrated genome-wide divergence scans with association mapping to identify divergent regions containing putatively causal SNPs affecting jaw size-the most rapidly diversifying trait in this radiation. A mere 22 fixed variants accompanied extreme ecological divergence between generalist and scale-eater species. We identified 31 regions (20 kb) containing variants fixed between specialists that were significantly associated with variation in jaw size which contained 11 genes annotated for skeletal system effects and 18 novel candidate genes never previously associated with craniofacial phenotypes. Six of these 31 regions showed robust signs of hard selective sweeps after accounting for demographic history. Our data are consistent with predictions based on quantitative genetic models of adaptation, suggesting that the effect sizes of regions influencing jaw phenotypes are positively correlated with distance between fitness peaks on a complex adaptive landscape.
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Affiliation(s)
- Joseph A. McGirr
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC
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36
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Naumenko SA, Logacheva MD, Popova NV, Klepikova AV, Penin AA, Bazykin GA, Etingova AE, Mugue NS, Kondrashov AS, Yampolsky LY. Transcriptome‐based phylogeny of endemic Lake Baikal amphipod species flock: fast speciation accompanied by frequent episodes of positive selection. Mol Ecol 2017; 26:536-553. [DOI: 10.1111/mec.13927] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 10/11/2016] [Accepted: 10/12/2016] [Indexed: 12/15/2022]
Affiliation(s)
- Sergey A. Naumenko
- Belozersky Institute of Physico‐Chemical Biology Lomonosov Moscow State University Moscow Russia
- Institute for Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences Moscow Russia
- Genetics and Genome Biology Program The Hospital For Sick Children Toronto ON Canada
| | - Maria D. Logacheva
- Belozersky Institute of Physico‐Chemical Biology Lomonosov Moscow State University Moscow Russia
- Institute for Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences Moscow Russia
- Pirogov Russian National Research Medical University Moscow Russia
| | - Nina V. Popova
- Belozersky Institute of Physico‐Chemical Biology Lomonosov Moscow State University Moscow Russia
| | - Anna V. Klepikova
- Belozersky Institute of Physico‐Chemical Biology Lomonosov Moscow State University Moscow Russia
- Institute for Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences Moscow Russia
| | - Aleksey A. Penin
- Belozersky Institute of Physico‐Chemical Biology Lomonosov Moscow State University Moscow Russia
- Institute for Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences Moscow Russia
| | - Georgii A. Bazykin
- Belozersky Institute of Physico‐Chemical Biology Lomonosov Moscow State University Moscow Russia
- Institute for Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences Moscow Russia
- Pirogov Russian National Research Medical University Moscow Russia
- Skolkovo Institute of Science and Technology Skolkovo Russia
| | - Anna E. Etingova
- Baikal Museum Irkutsk Research Center Russian Academy of Sciences Listvyanka, Irkutsk region Russia
| | - Nikolai S. Mugue
- Laboratory of Molecular Genetics Russian Institute for Fisheries and Oceanography (VNIRO) Moscow Russia
- Laboratory of Experimental Embryology Koltsov Institute of Developmental Biology Moscow Russia
| | - Alexey S. Kondrashov
- Belozersky Institute of Physico‐Chemical Biology Lomonosov Moscow State University Moscow Russia
- Department of Ecology and Evolution University of Michigan Ann Arbor MI USA
| | - Lev Y. Yampolsky
- Department of Biological Sciences East Tennessee State University Johnson City TN USA
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37
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Martin CH, Erickson PA, Miller CT. The genetic architecture of novel trophic specialists: larger effect sizes are associated with exceptional oral jaw diversification in a pupfish adaptive radiation. Mol Ecol 2016; 26:624-638. [PMID: 27873369 DOI: 10.1111/mec.13935] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 10/20/2016] [Accepted: 10/25/2016] [Indexed: 12/14/2022]
Abstract
The genetic architecture of adaptation is fundamental to understanding the mechanisms and constraints governing diversification. However, most case studies focus on loss of complex traits or parallel speciation in similar environments. It is still unclear how the genetic architecture of these local adaptive processes compares to the architecture of evolutionary transitions contributing to morphological and ecological novelty. Here, we identify quantitative trait loci (QTL) between two trophic specialists in an excellent case study for examining the origins of ecological novelty: a sympatric radiation of pupfishes endemic to San Salvador Island, Bahamas, containing a large-jawed scale-eater and a short-jawed molluscivore with a skeletal nasal protrusion. These specialized niches and trophic traits are unique among over 2000 related species. Measurements of the fitness landscape on San Salvador demonstrate multiple fitness peaks and a larger fitness valley isolating the scale-eater from the putative ancestral intermediate phenotype of the generalist, suggesting that more large-effect QTL should contribute to its unique phenotype. We evaluated this prediction using an F2 intercross between these specialists. We present the first linkage map for pupfishes and detect significant QTL for sex and eight skeletal traits. Large-effect QTL contributed more to enlarged scale-eater jaws than the molluscivore nasal protrusion, consistent with predictions from the adaptive landscape. The microevolutionary genetic architecture of large-effect QTL for oral jaws parallels the exceptional diversification rates of oral jaws within the San Salvador radiation observed over macroevolutionary timescales and may have facilitated exceptional trophic novelty in this system.
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Affiliation(s)
- Christopher H Martin
- Department of Biology, University of North Carolina at Chapel Hill, Campus Box 3280, 120 South Rd, Chapel Hill, NC 27599-3280, USA
| | - Priscilla A Erickson
- Molecular and Cell Biology Department, University of California, Berkeley, CA 94720, USA.,Department of Biology, University of Virginia, 229 Gilmer Hall, 485 McCormick Road, P.O. Box 400328, Charlottesville, VA 22904, USA
| | - Craig T Miller
- Molecular and Cell Biology Department, University of California, Berkeley, CA 94720, USA
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38
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Stroud JT, Losos JB. Ecological Opportunity and Adaptive Radiation. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2016. [DOI: 10.1146/annurev-ecolsys-121415-032254] [Citation(s) in RCA: 271] [Impact Index Per Article: 33.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- James T. Stroud
- Department of Biological Sciences, Florida International University, Miami, Florida 33199
- Fairchild Tropical Botanic Garden, Coral Gables, Florida 33156;
| | - Jonathan B. Losos
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 01238;
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39
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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.
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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
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40
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Martin CH. The cryptic origins of evolutionary novelty: 1000-fold faster trophic diversification rates without increased ecological opportunity or hybrid swarm. Evolution 2016; 70:2504-2519. [PMID: 27593215 DOI: 10.1111/evo.13046] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 08/10/2016] [Accepted: 08/18/2016] [Indexed: 01/15/2023]
Abstract
Ecological opportunity is frequently proposed as the sole ingredient for adaptive radiation into novel niches. An additional trigger may be genome-wide hybridization resulting from "hybrid swarm." However, these hypotheses have been difficult to test due to the rarity of comparable control environments lacking adaptive radiations. Here I exploit such a pattern in microendemic radiations of Caribbean pupfishes. I show that a sympatric three species radiation on San Salvador Island, Bahamas diversified 1445 times faster than neighboring islands in jaw length due to the evolution of a novel scale-eating adaptive zone from a generalist ancestral niche. I then sampled 22 generalist populations on seven neighboring islands and measured morphological diversity, stomach content diversity, dietary isotopic diversity, genetic diversity, lake/island areas, macroalgae richness, and Caribbean-wide patterns of gene flow. None of these standard metrics of ecological opportunity or gene flow were associated with adaptive radiation, except for slight increases in macroalgae richness. Thus, exceptional trophic diversification is highly localized despite myriad generalist populations in comparable environmental and genetic backgrounds. This study provides a strong counterexample to the ecological and hybrid swarm theories of adaptive radiation and suggests that diversification of novel specialists on a sparse fitness landscape is constrained by more than ecological opportunity and gene flow.
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Affiliation(s)
- Christopher H Martin
- Department of Biology, University of North Carolina at Chapel Hill, Campus Box 3280, 120 South Road, Chapel Hill, North Carolina, 27599-3280.
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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.
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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:
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Martin CH. Context dependence in complex adaptive landscapes: frequency and trait-dependent selection surfaces within an adaptive radiation of Caribbean pupfishes. Evolution 2016; 70:1265-82. [PMID: 27130447 DOI: 10.1111/evo.12932] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 04/14/2016] [Indexed: 01/16/2023]
Abstract
The adaptive landscape provides the foundational bridge between micro- and macroevolution. One well-known caveat to this perspective is that fitness surfaces depend on ecological context, including competitor frequency, traits measured, and resource abundance. However, this view is based largely on intraspecific studies. It is still unknown how context-dependence affects the larger features of peaks and valleys on the landscape which ultimately drive speciation and adaptive radiation. Here, I explore this question using one of the most complex fitness landscapes measured in the wild in a sympatric pupfish radiation endemic to San Salvador Island, Bahamas by tracking survival and growth of laboratory-reared F2 hybrids. I present new analyses of the effects of competitor frequency, dietary isotopes, and trait subsets on this fitness landscape. Contrary to expectations, decreasing competitor frequency increased survival only among very common phenotypes, whereas less common phenotypes rarely survived despite few competitors, suggesting that performance, not competitor frequency, shapes large-scale features of the fitness landscape. Dietary isotopes were weakly correlated with phenotype and growth, but did not explain additional survival variation. Nonlinear fitness surfaces varied substantially among trait subsets, revealing one-, two-, and three-peak landscapes, demonstrating the complexity of selection in the wild, even among similar functional traits.
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Affiliation(s)
- Christopher H Martin
- Department of Biology, University of North Carolina at Chapel Hill, Campus Box 3280, 120 South Road, Chapel Hill, North Carolina, 27599-3280.
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Lencer ES, Riccio ML, McCune AR. Changes in growth rates of oral jaw elements produce evolutionary novelty in bahamian pupfish. J Morphol 2016; 277:935-47. [DOI: 10.1002/jmor.20547] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 03/29/2016] [Accepted: 04/01/2016] [Indexed: 11/11/2022]
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Campagna L, Gronau I, Silveira LF, Siepel A, Lovette IJ. Distinguishing noise from signal in patterns of genomic divergence in a highly polymorphic avian radiation. Mol Ecol 2015; 24:4238-51. [DOI: 10.1111/mec.13314] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 07/03/2015] [Indexed: 01/10/2023]
Affiliation(s)
- Leonardo Campagna
- Fuller Evolutionary Biology Program; Cornell Laboratory of Ornithology; 159 Sapsucker Woods Road Ithaca NY 14850 USA
- Department of Ecology and Evolutionary Biology; Cornell University; 215 Tower Road Ithaca NY 14853 USA
| | - Ilan Gronau
- Efi Arazi School of Computer Science; Herzliya Interdisciplinary Center (IDC); P.O. Box 167, Kanfei Nesharim St. Herzliya 46150 Israel
| | - Luís Fábio Silveira
- Seção de Aves; Museu de Zoologia, Universidade de São Paulo (MZUSP); Caixa Postal 42.494 CEP 04218-970 São Paulo SP Brazil
| | - Adam Siepel
- Watson School of Biological Sciences; Simons Center for Quantitative Biology; Cold Spring Harbor Laboratory; One Bungtown Road Cold Spring Harbor NY 11724 USA
| | - Irby J. Lovette
- Fuller Evolutionary Biology Program; Cornell Laboratory of Ornithology; 159 Sapsucker Woods Road Ithaca NY 14850 USA
- Department of Ecology and Evolutionary Biology; Cornell University; 215 Tower Road Ithaca NY 14853 USA
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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.
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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
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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.
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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
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Papadopoulou A, Knowles LL. Genomic tests of the species-pump hypothesis: Recent island connectivity cycles drive population divergence but not speciation in Caribbean crickets across the Virgin Islands. Evolution 2015; 69:1501-1517. [DOI: 10.1111/evo.12667] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 04/13/2015] [Indexed: 01/16/2023]
Affiliation(s)
- Anna Papadopoulou
- Department of Ecology and Evolutionary Biology; Museum of Zoology; University of Michigan; Ann Arbor Michigan 48109
| | - L. Lacey Knowles
- Department of Ecology and Evolutionary Biology; Museum of Zoology; University of Michigan; Ann Arbor Michigan 48109
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Sovic MG, Fries AC, Gibbs HL. AftrRAD: a pipeline for accurate and efficient de novo assembly of RADseq data. Mol Ecol Resour 2015; 15:1163-71. [PMID: 25641221 DOI: 10.1111/1755-0998.12378] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 12/29/2014] [Accepted: 01/15/2015] [Indexed: 11/28/2022]
Abstract
An increase in studies using restriction site-associated DNA sequencing (RADseq) methods has led to a need for both the development and assessment of novel bioinformatic tools that aid in the generation and analysis of these data. Here, we report the availability of AftrRAD, a bioinformatic pipeline that efficiently assembles and genotypes RADseq data, and outputs these data in various formats for downstream analyses. We use simulated and experimental data sets to evaluate AftrRAD's ability to perform accurate de novo assembly of loci, and we compare its performance with two other commonly used programs, stacks and pyrad. We demonstrate that AftrRAD is able to accurately assemble loci, while accounting for indel variation among alleles, in a more computationally efficient manner than currently available programs. AftrRAD run times are not strongly affected by the number of samples in the data set, making this program a useful tool when multicore systems are not available for parallel processing, or when data sets include large numbers of samples.
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Affiliation(s)
- Michael G Sovic
- Department of Evolution, Ecology, and Organismal Biology, Aronoff Laboratory, The Ohio State University, 318 W. 12th Ave, Columbus, OH, 43210, USA.,Ohio Biodiversity Conservation Partnership, Aronoff Laboratory, The Ohio State University, 318 W. 12th Ave, Columbus, OH, 43210, USA
| | - Anthony C Fries
- Department of Evolution, Ecology, and Organismal Biology, Aronoff Laboratory, The Ohio State University, 318 W. 12th Ave, Columbus, OH, 43210, USA
| | - H Lisle Gibbs
- Department of Evolution, Ecology, and Organismal Biology, Aronoff Laboratory, The Ohio State University, 318 W. 12th Ave, Columbus, OH, 43210, USA.,Ohio Biodiversity Conservation Partnership, Aronoff Laboratory, The Ohio State University, 318 W. 12th Ave, Columbus, OH, 43210, USA
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Rieseberg L, Vines T, Gow J, Geraldes A. Editorial 2015. Mol Ecol 2015; 24:1-17. [DOI: 10.1111/mec.12997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 11/10/2014] [Indexed: 11/30/2022]
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Abstract
The extraordinary species richness of freshwater fishes has attracted much research on mechanisms and modes of speciation. We here review research on speciation in freshwater fishes in light of speciation theory, and place this in a context of broad-scale diversity patterns in freshwater fishes. We discuss several major repeated themes in freshwater fish speciation and the speciation mechanisms they are frequently associated with. These include transitions between marine and freshwater habitats, transitions between discrete freshwater habitats, and ecological transitions within habitats, as well as speciation without distinct niche shifts. Major research directions in the years to come include understanding the transition from extrinsic environment-dependent to intrinsic reproductive isolation and its influences on species persistence and understanding the extrinsic and intrinsic constraints to speciation and how these relate to broad-scale diversification patterns through time.
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Affiliation(s)
- Ole Seehausen
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, CH-3012 Bern, Switzerland
- Department of Fish Ecology and Evolution, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Center of Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland
| | - Catherine E. Wagner
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, CH-3012 Bern, Switzerland
- Department of Fish Ecology and Evolution, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Center of Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland
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