1
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Brandon AA, Michael C, Carmona Baez A, Moore EC, Ciccotto PJ, Roberts NB, Roberts RB, Powder KE. Distinct genetic origins of eumelanin levels and barring patterns in cichlid fishes. PLoS One 2024; 19:e0306614. [PMID: 38976656 PMCID: PMC11230561 DOI: 10.1371/journal.pone.0306614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 06/20/2024] [Indexed: 07/10/2024] Open
Abstract
Pigment patterns are incredibly diverse across vertebrates and are shaped by multiple selective pressures from predator avoidance to mate choice. A common pattern across fishes, but for which we know little about the underlying mechanisms, is repeated melanic vertical bars. To understand the genetic factors that modify the level or pattern of vertical barring, we generated a genetic cross of 322 F2 hybrids between two cichlid species with distinct barring patterns, Aulonocara koningsi and Metriaclima mbenjii. We identify 48 significant quantitative trait loci that underlie a series of seven phenotypes related to the relative pigmentation intensity, and four traits related to patterning of the vertical bars. We find that genomic regions that generate variation in the level of eumelanin produced are largely independent of those that control the spacing of vertical bars. Candidate genes within these intervals include novel genes and those newly-associated with vertical bars, which could affect melanophore survival, fate decisions, pigment biosynthesis, and pigment distribution. Together, this work provides insights into the regulation of pigment diversity, with direct implications for an animal's fitness and the speciation process.
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Affiliation(s)
- A. Allyson Brandon
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, United States of America
| | - Cassia Michael
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, United States of America
| | - Aldo Carmona Baez
- Department of Biological Sciences, Genetics and Genomics Academy, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Emily C. Moore
- Department of Biological Sciences, Genetics and Genomics Academy, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Patrick J. Ciccotto
- Department of Biology, Warren Wilson College, Swannanoa, North Carolina, United States of America
| | - Natalie B. Roberts
- Department of Biological Sciences, Genetics and Genomics Academy, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Reade B. Roberts
- Department of Biological Sciences, Genetics and Genomics Academy, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Kara E. Powder
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, United States of America
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2
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Cataño Tenorio I, Joya CD, Márquez EJ. Spatial population genetic structure of Caquetaia kraussii (Steindachner, 1878) evidenced by species-specific microsatellite loci in the middle and low basin of the Cauca River, Colombia. PLoS One 2024; 19:e0304799. [PMID: 38833482 PMCID: PMC11149877 DOI: 10.1371/journal.pone.0304799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 05/17/2024] [Indexed: 06/06/2024] Open
Abstract
The adaptative responses and divergent evolution shown in the environments habited by the Cichlidae family allow to understand different biological properties, including fish genetic diversity and structure studies. In a zone that has been historically submitted to different anthropogenic pressures, this study assessed the genetic diversity and population structure of cichlid Caquetaia kraussii, a sedentary species with parental care that has a significant ecological role for its contribution to redistribution and maintenance of sedimentologic processes in its distribution area. This study developed de novo 16 highly polymorphic species-specific microsatellite loci that allowed the estimation of the genetic diversity and differentiation in 319 individuals from natural populations in the area influenced by the Ituango hydroelectric project in the Colombian Cauca River. Caquetaia kraussii exhibits high genetic diversity levels (Ho: 0.562-0.885; He: 0.583-0.884) in relation to the average neotropical cichlids and a three group-spatial structure: two natural groups upstream and downstream the Nechí River mouth, and one group of individuals with high relatedness degree, possibly independently formed by founder effect in the dam zone. The three genetic groups show recent bottlenecks, but only the two natural groups have effective population size that suggest their long-term permanence. The information generated is relevant not only for management programs and species conservation purposes, but also for broadening the available knowledge on the factors influencing neotropical cichlids population genetics.
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Affiliation(s)
- Isaí Cataño Tenorio
- Sede Medellín, Facultad de Ciencias, Escuela de Biociencias, Grupo de Investigación de Biotecnología Animal, Universidad Nacional de Colombia, Medellín, Colombia
| | - Cristhian Danilo Joya
- Sede Medellín, Facultad de Ciencias, Escuela de Biociencias, Grupo de Investigación de Biotecnología Animal, Universidad Nacional de Colombia, Medellín, Colombia
| | - Edna Judith Márquez
- Sede Medellín, Facultad de Ciencias, Escuela de Biociencias, Grupo de Investigación de Biotecnología Animal, Universidad Nacional de Colombia, Medellín, Colombia
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3
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Choi N, Mathevon N, Hebets EA, Beauchaud M. Influence of ambient water coloration on habitat and conspecific choice in the female Lake Malawi cichlid, Metriaclima zebra. Curr Zool 2024; 70:214-224. [PMID: 38726246 PMCID: PMC11078059 DOI: 10.1093/cz/zoad015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/19/2023] [Indexed: 05/12/2024] Open
Abstract
Female cichlid fish living in African great lakes are known to have sensory systems that are adapted to ambient light environments. These sensory system adaptations are hypothesized to have influenced the evolution of the diverse male nuptial coloration. In rock-dwelling Lake Malawi mbuna cichlids, however, the extent to which ambient light environments influence female sensory systems and potentially associated male nuptial coloration remains unknown. Yet, the ubiquitous blue flank coloration and UV reflection of male mbuna cichlids suggest the potential impacts of the blue-shifted ambient light environment on these cichlid's visual perception and male nuptial coloration in the shallow water depth in Lake Malawi. In the present study, we explored whether and how the sensory bias of females influences intersexual communication in the mbuna cichlid, Metriaclima zebra. A series of choice experiments in various light environments showed that M. zebra females 1) have a preference for the blue-shifted light environment, 2) prefer to interact with males in blue-shifted light environments, 3) do not show a preference between dominant and subordinate males in full-spectrum, long-wavelength filtered, and short-wavelength filtered light environments, and 4) show a "reversed" preference for subordinate males in the UV-filtered light environment. These results suggest that the visual perception of M. zebra females may be biased to the ambient light spectra in their natural habitat by local adaptation and that this sensory bias may influence the evolution of blue and UV reflective patterns in male nuptial coloration.
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Affiliation(s)
- Noori Choi
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
- ENES Bioacoustics Research Laboratory, CRNL, CNRS, Inserm, Université de Saint-Etienne, Saint-Etienne, France
- Max Planck Institute of Animal Behavior, Konstanz, Germany
| | - Nicolas Mathevon
- ENES Bioacoustics Research Laboratory, CRNL, CNRS, Inserm, Université de Saint-Etienne, Saint-Etienne, France
| | - Eileen A Hebets
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Marilyn Beauchaud
- ENES Bioacoustics Research Laboratory, CRNL, CNRS, Inserm, Université de Saint-Etienne, Saint-Etienne, France
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4
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Wang J, Tai J, Zhang W, He K, Lan H, Liu H. Comparison of seven complete mitochondrial genomes from Lamprologus and Neolamprologus (Chordata, Teleostei, Perciformes) and the phylogenetic implications for Cichlidae. Zookeys 2023; 1184:115-132. [PMID: 38314327 PMCID: PMC10838552 DOI: 10.3897/zookeys.1184.107091] [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: 05/27/2023] [Accepted: 10/27/2023] [Indexed: 02/06/2024] Open
Abstract
In this study, mitochondrial genomes (mitogenomes) of seven cichlid species (Lamprologuskungweensis, L.meleagris, L.ornatipinnis, Neolamprologusbrevis, N.caudopunctatus, N.leleupi, and N.similis) are characterized for the first time. The newly sequenced mitogenomes contained 37 typical genes [13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs) and 22 transfer RNA genes (tRNAs)]. The mitogenomes were 16,562 ~ 16,587 bp in length with an A + T composition of 52.1~58.8%. The cichlid mitogenomes had a comparable nucleotide composition, A + T content was higher than the G + C content. The AT-skews of most mitogenomes were inconspicuously positive and the GC-skews were negative, indicating higher occurrences of C than G. Most PCGs started with the conventional start codon, ATN. There was no essential difference in the codon usage patterns of these seven species. Using Ka/Ks, we found the fastest-evolving gene were atp8. But the results of p-distance indicated that the fastest-evolving gene was nad6. Phylogenetic analysis revealed that L.meleagris did not cluster with Lamprologus species, but with species from the genus Neolamprologus. The novel information obtained about these mitogenomes will contribute to elucidating the complex relationships among cichlid species.
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Affiliation(s)
- Jiachen Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China Nanjing Forestry University Nanjing China
| | - Jingzhe Tai
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China Nanjing Forestry University Nanjing China
| | - Wenwen Zhang
- Institute of Environmental Sciences, Ministry of Ecology and Environment of China State Environmental Protection Scientific Observation and Research Station for Ecological Environment of Wuyi Mountains Research Center for Biodiversity Conservation and Biosafety, Nanjing 210042, China Institute of Environmental Sciences, Ministry of Ecology and Environment of China State Environmental Protection Scientific Observation and Research Station for Ecological Environment of Wuyi Mountains Research Center for Biodiversity Conservation and Biosafety Nanjing China
| | - Ke He
- Zhejiang Agriculture and Forestry University, Hangzhou 311300, China Zhejiang Agriculture and Forestry University Hangzhou China
| | - Hong Lan
- Zhejiang Open University, Hangzhou 310012, China Zhejiang Open University Hangzhou China
| | - Hongyi Liu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China Nanjing Forestry University Nanjing China
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5
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Roberts-Hugghis AS, Burress ED, Lam B, Wainwright PC. The cichlid pharyngeal jaw novelty enhances evolutionary integration in the feeding apparatus. Evolution 2023; 77:1917-1929. [PMID: 37326103 DOI: 10.1093/evolut/qpad109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 06/14/2023] [Indexed: 06/17/2023]
Abstract
The modified pharyngeal jaw system of cichlid fishes is widely viewed as a key innovation that substantially facilitated the evolutionary exuberance of this iconic evolutionary radiation. We conduct comparative phylogenetic analyses of integration, disparity, and rate of evolution among feeding-related, skeletal structures in Neotropical cichlids and North American centrarchids, which lack the specialized pharyngeal jaw. Contrasting evolutionary patterns in these two continental radiations, we test a classic decoupling hypothesis. Specifically, we ask whether the modified pharyngeal jaw in cichlids resulted in enhanced evolutionary independence of the oral and pharyngeal jaws, leading to increased diversity of trophic structures. Contrary to this prediction, we find significantly stronger evolutionary integration between the oral and pharyngeal jaws in cichlids compared to centrarchids, although the two groups do not differ in patterns of integration within each jaw system. Further, though we find no significant differences in disparity, centrarchids show faster rates of morphological evolution. Our results suggest that the modified pharyngeal jaw resulted in less evolutionary independence and slower rates of evolution within the feeding system. Thus, we raise the possibility that the cichlid novelty enhances feeding performance, but does not prompt increased morphological diversification within the feeding apparatus, as has long been thought.
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Affiliation(s)
| | - Edward D Burress
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, United States
| | - Brian Lam
- Department of Evolution and Ecology, University of California-Davis, Davis, CA, United States
| | - Peter C Wainwright
- Department of Evolution and Ecology, University of California-Davis, Davis, CA, United States
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6
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Brandon AA, Michael C, Carmona Baez A, Moore EC, Ciccotto PJ, Roberts NB, Roberts RB, Powder KE. Distinct genetic origins of eumelanin intensity and barring patterns in cichlid fishes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.02.547430. [PMID: 37461734 PMCID: PMC10349982 DOI: 10.1101/2023.07.02.547430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Pigment patterns are incredibly diverse across vertebrates and are shaped by multiple selective pressures from predator avoidance to mate choice. A common pattern across fishes, but for which we know little about the underlying mechanisms, is repeated melanic vertical bars. In order to understand genetic factors that modify the level or pattern of vertical barring, we generated a genetic cross of 322 F2 hybrids between two cichlid species with distinct barring patterns, Aulonocara koningsi and Metriaclima mbenjii. We identify 48 significant quantitative trait loci that underlie a series of seven phenotypes related to the relative pigmentation intensity, and four traits related to patterning of the vertical bars. We find that genomic regions that generate variation in the level of eumelanin produced are largely independent of those that control the spacing of vertical bars. Candidate genes within these intervals include novel genes and those newly-associated with vertical bars, which could affect melanophore survival, fate decisions, pigment biosynthesis, and pigment distribution. Together, this work provides insights into the regulation of pigment diversity, with direct implications for an animal's fitness and the speciation process.
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Affiliation(s)
- A. Allyson Brandon
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
| | - Cassia Michael
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
| | - Aldo Carmona Baez
- Department of Biological Sciences, and Genetics and Genomics Academy, North Carolina State University, Raleigh, NC 27695, USA
| | - Emily C. Moore
- Department of Biological Sciences, and Genetics and Genomics Academy, North Carolina State University, Raleigh, NC 27695, USA
- Department of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | | | - Natalie B. Roberts
- Department of Biological Sciences, and Genetics and Genomics Academy, North Carolina State University, Raleigh, NC 27695, USA
| | - Reade B. Roberts
- Department of Biological Sciences, and Genetics and Genomics Academy, North Carolina State University, Raleigh, NC 27695, USA
| | - Kara E. Powder
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
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7
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Estivals G, Duponchelle F, García-Dávila C, Römer U, Mariac C, Renno JF. Exceptional Genetic Differentiation at a Micro-geographic Scale in Apistogramma agassizii (Steindachner, 1875) from the Peruvian Amazon: Sympatric Speciation? Evol Biol 2022. [DOI: 10.1007/s11692-022-09587-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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8
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Masonick P, Meyer A, Hulsey CD. Phylogenomic analyses show repeated evolution of hypertrophied lips among Lake Malawi cichlid fishes. Genome Biol Evol 2022; 14:6568296. [PMID: 35417557 PMCID: PMC9017819 DOI: 10.1093/gbe/evac051] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/03/2022] [Indexed: 11/27/2022] Open
Abstract
Cichlid fishes have repeatedly evolved an astounding diversity of trophic morphologies. For example, hypertrophied lips have evolved multiple times in both African and Neotropical cichlids and could have even evolved convergently within single species assemblages such as African Lake Malawi cichlids. However, the extremely high diversification rate in Lake Malawi cichlids and extensive potential for hybridization has cast doubt on whether even genome-level phylogenetic reconstructions could delineate if these types of adaptations have evolved once or multiple times. To examine the evolution of this iconic trait using protein-coding and noncoding single nucleotide polymorphisms (SNPs), we analyzed the genomes of 86 Lake Malawi cichlid species, including 33 de novo resequenced genomes. Surprisingly, genome-wide protein-coding SNPs exhibited enough phylogenetic informativeness to reconstruct interspecific and intraspecific relationships of hypertrophied lip cichlids, although noncoding SNPs provided better support. However, thinning of noncoding SNPs indicated most discrepancies come from the relatively smaller number of protein-coding sites and not from fundamental differences in their phylogenetic informativeness. Both coding and noncoding reconstructions showed that several “sand-dwelling” hypertrophied lip species, sampled intraspecifically, form a clade interspersed with a few other nonhypertrophied lip lineages. We also recovered Abactochromis labrosus within the rock-dwelling “mbuna” lineage, starkly contrasting with the affinities of other hypertrophied lip taxa found in the largely sand-dwelling “nonmbuna” component of this radiation. Comparative analyses coupled with tests for introgression indicate there is no widespread introgression between the hypertrophied lip lineages and taken together suggest this trophic phenotype has likely evolved at least twice independently within-lake Malawi.
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Affiliation(s)
- Paul Masonick
- Department of Biology, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
| | - Axel Meyer
- Department of Biology, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
| | - C Darrin Hulsey
- Department of Biology, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany.,Current Address: School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
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9
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Durán-Castillo M, Hudson A, Wilson Y, Field DL, Twyford AD. A phylogeny of Antirrhinum reveals parallel evolution of alpine morphology. THE NEW PHYTOLOGIST 2022; 233:1426-1439. [PMID: 34170548 DOI: 10.1111/nph.17581] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 06/20/2021] [Indexed: 06/13/2023]
Abstract
Parallel evolution of similar morphologies in closely related lineages provides insight into the repeatability and predictability of evolution. In the genus Antirrhinum (snapdragons), as in other plants, a suite of morphological characters are associated with adaptation to alpine environments. We tested for parallel trait evolution in Antirrhinum by investigating phylogenetic relationships using restriction-site associated DNA (RAD) sequencing. We then associated phenotypic information to our phylogeny to reconstruct the patterns of morphological evolution and related this to evidence for hybridisation between emergent lineages. Phylogenetic analyses showed that the alpine character syndrome is present in multiple groups, suggesting that Antirrhinum has repeatedly colonised alpine habitats. Dispersal to novel environments happened in the presence of intraspecific and interspecific gene flow. We found support for a model of parallel evolution in Antirrhinum. Hybridisation in natural populations, and a complex genetic architecture underlying the alpine morphology syndrome, support an important role of natural selection in maintaining species divergence in the face of gene flow.
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Affiliation(s)
- Mario Durán-Castillo
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Andrew Hudson
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Yvette Wilson
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - David L Field
- School of Science, Edith Cowan University, 270 Joondalup Drive, Joondalup, 6027, Australia
| | - Alex D Twyford
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3FL, UK
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
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10
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Siepielski AM, Gómez-Llano M, McPeek MA. Environmental Conditions during Development Affect Sexual Selection through Trait-Fitness Relationships. Am Nat 2022; 199:34-50. [DOI: 10.1086/717294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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11
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Lichilín N, El Taher A, Böhne A. Sex-biased gene expression and recent sex chromosome turnover. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200107. [PMID: 34304591 PMCID: PMC8310714 DOI: 10.1098/rstb.2020.0107] [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] [Accepted: 12/11/2020] [Indexed: 12/13/2022] Open
Abstract
Cichlids are well known for their propensity to radiate generating arrays of morphologically and ecologically diverse species in short evolutionary time. Following this rapid evolutionary pace, cichlids show high rates of sex chromosome turnover. We here studied the evolution of sex-biased gene (SBG) expression in 14 recently diverged taxa of the Lake Tanganyika Tropheini cichlids, which show different XY sex chromosomes. Across species, sex chromosome sequence divergence predates divergence in expression between the sexes. Only one sex chromosome, the oldest, showed signs of demasculinization in gene expression and potentially contribution to the resolution of sexual conflict. SBGs in general showed high rates of turnovers and evolved mostly under drift. Sexual selection did not shape the rapid evolutionary changes of SBGs. Male-biased genes evolved faster than female-biased genes, which seem to be under more phylogenetic constraint. We found a relationship between the degree of sex bias and sequence evolution driven by sequence differences among the sexes. Consistent with other species, strong sex bias towards sex-limited expression contributes to resolving sexual conflict in cichlids. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)'.
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Affiliation(s)
- Nicolás Lichilín
- Zoological Institute, Department of Environmental Sciences, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
| | - Athimed El Taher
- Zoological Institute, Department of Environmental Sciences, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
| | - Astrid Böhne
- Zoological Institute, Department of Environmental Sciences, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany
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12
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Gorman CE, Hulsey CD. Non-trophic Functional Ecology of Vertebrate Teeth: A Review. Integr Comp Biol 2021; 60:665-675. [PMID: 32573716 DOI: 10.1093/icb/icaa086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Teeth are critical to the functional ecology of vertebrate trophic abilities, but are also used for a diversity of other non-trophic tasks. Teeth can play a substantial role in how animals move, manipulate their environment, positively interact with conspecifics, antagonistically interact with other organisms, and sense the environment. We review these non-trophic functions in an attempt to place the utility of human and all other vertebrate dentitions in a more diverse framework that emphasizes an expanded view of the functional importance and ecological diversity of teeth. In light of the extensive understanding of the developmental genetics, trophic functions, and evolutionary history of teeth, comparative studies of vertebrate dentitions will continue to provide unique insights into multi-functionality, many-to-one mapping, and the evolution of novel abilities.
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Affiliation(s)
- Courtney E Gorman
- Department of Biology, University of Konstanz, Konstanz 78457, Germany
| | - C Darrin Hulsey
- Department of Biology, University of Konstanz, Konstanz 78457, Germany
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13
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Roycroft E, Achmadi A, Callahan CM, Esselstyn JA, Good JM, Moussalli A, Rowe KC. Molecular Evolution of Ecological Specialisation: Genomic Insights from the Diversification of Murine Rodents. Genome Biol Evol 2021; 13:6275684. [PMID: 33988699 PMCID: PMC8258016 DOI: 10.1093/gbe/evab103] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/07/2021] [Indexed: 12/15/2022] Open
Abstract
Adaptive radiations are characterized by the diversification and ecological differentiation of species, and replicated cases of this process provide natural experiments for understanding the repeatability and pace of molecular evolution. During adaptive radiation, genes related to ecological specialization may be subject to recurrent positive directional selection. However, it is not clear to what extent patterns of lineage-specific ecological specialization (including phenotypic convergence) are correlated with shared signatures of molecular evolution. To test this, we sequenced whole exomes from a phylogenetically dispersed sample of 38 murine rodent species, a group characterized by multiple, nested adaptive radiations comprising extensive ecological and phenotypic diversity. We found that genes associated with immunity, reproduction, diet, digestion, and taste have been subject to pervasive positive selection during the diversification of murine rodents. We also found a significant correlation between genome-wide positive selection and dietary specialization, with a higher proportion of positively selected codon sites in derived dietary forms (i.e., carnivores and herbivores) than in ancestral forms (i.e., omnivores). Despite striking convergent evolution of skull morphology and dentition in two distantly related worm-eating specialists, we did not detect more genes with shared signatures of positive or relaxed selection than in a nonconvergent species comparison. Although a small number of the genes we detected can be incidentally linked to craniofacial morphology or diet, protein-coding regions are unlikely to be the primary genetic basis of this complex convergent phenotype. Our results suggest a link between positive selection and derived ecological phenotypes, and highlight specific genes and general functional categories that may have played an integral role in the extensive and rapid diversification of murine rodents.
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Affiliation(s)
- Emily Roycroft
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia.,Sciences Department, Museums Victoria, Melbourne, Victoria, Australia.,Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, Australian Capital Territory, Australia
| | - Anang Achmadi
- Museum Zoologicum Bogoriense, Research Center for Biology, Cibinong, Jawa Barat, Indonesia
| | - Colin M Callahan
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Jacob A Esselstyn
- Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana, USA.,Department of Biological Sciences, Louisiana State University, Baton Rouge, Los Angeles, USA
| | - Jeffrey M Good
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA.,Wildlife Biology Program, University of Montana, Missoula, Montana, USA
| | - Adnan Moussalli
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia.,Sciences Department, Museums Victoria, Melbourne, Victoria, Australia
| | - Kevin C Rowe
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia.,Sciences Department, Museums Victoria, Melbourne, Victoria, Australia
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14
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Gómez-Llano M, Germain RM, Kyogoku D, McPeek MA, Siepielski AM. When Ecology Fails: How Reproductive Interactions Promote Species Coexistence. Trends Ecol Evol 2021; 36:610-622. [PMID: 33785182 DOI: 10.1016/j.tree.2021.03.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 11/19/2022]
Abstract
That species must differ ecologically is often viewed as a fundamental condition for their stable coexistence in biological communities. Yet, recent work has shown that ecologically equivalent species can coexist when reproductive interactions and sexual selection regulate population growth. Here, we review theoretical models and highlight empirical studies supporting a role for reproductive interactions in maintaining species diversity. We place reproductive interactions research within a burgeoning conceptual framework of coexistence theory, identify four key mechanisms in intra- and interspecific interactions within and between sexes, speculate on novel mechanisms, and suggest future research. Given the preponderance of sexual reproduction in nature, our review suggests that this is a neglected path towards explaining species diversity when traditional ecological explanations have failed.
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Affiliation(s)
- Miguel Gómez-Llano
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA.
| | - Rachel M Germain
- Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Daisuke Kyogoku
- The Museum of Nature and Human Activities, Hyogo 669-1546, Japan
| | - Mark A McPeek
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
| | - Adam M Siepielski
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
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15
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Nakamura H, Aibara M, Kajitani R, Mrosso HDJ, Mzighani SI, Toyoda A, Itoh T, Okada N, Nikaido M. Genomic Signatures for Species-Specific Adaptation in Lake Victoria Cichlids Derived from Large-Scale Standing Genetic Variation. Mol Biol Evol 2021; 38:3111-3125. [PMID: 33744961 PMCID: PMC8321545 DOI: 10.1093/molbev/msab084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The cichlids of Lake Victoria are a textbook example of adaptive radiation, as >500 endemic species arose in just 14,600 years. The degree of genetic differentiation among species is very low due to the short period of time after the radiation, which allows us to ascertain highly differentiated genes that are strong candidates for driving speciation and adaptation. Previous studies have revealed the critical contribution of vision to speciation by showing the existence of highly differentiated alleles in the visual opsin gene among species with different habitat depths. In contrast, the processes of species-specific adaptation to different ecological backgrounds remain to be investigated. Here, we used genome-wide comparative analyses of three species of Lake Victoria cichlids that inhabit different environments-Haplochromis chilotes, H. sauvagei, and Lithochromis rufus-to elucidate the processes of adaptation by estimating population history and by searching for candidate genes that contribute to adaptation. The patterns of changes in population size were quite distinct among the species according to their habitats. We identified many novel adaptive candidate genes, some of which had surprisingly long divergent haplotypes between species, thus showing the footprint of selective sweep events. Molecular phylogenetic analyses revealed that a large fraction of the allelic diversity among Lake Victoria cichlids was derived from standing genetic variation that originated before the adaptive radiation. Our analyses uncovered the processes of species-specific adaptation of Lake Victoria cichlids and the complexity of the genomic substrate that facilitated this adaptation.
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Affiliation(s)
- Haruna Nakamura
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Mitsuto Aibara
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Rei Kajitani
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Hillary D J Mrosso
- Tanzania Fisheries Research Institute (TAFIRI), Mwanza Fisheries Research Center, Mwanza, Tanzania
| | - Semvua I Mzighani
- Tanzania Fisheries Research Institute (TAFIRI), Headquarters, Dar es Salaam, Tanzania.,Fisheries Education and Training Agency, Dar es Salaam, Tanzania
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Takehiko Itoh
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Norihiro Okada
- School of Pharmacy, Kitasato University, Kanagawa, Japan
| | - Masato Nikaido
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
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16
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El Taher A, Böhne A, Boileau N, Ronco F, Indermaur A, Widmer L, Salzburger W. Gene expression dynamics during rapid organismal diversification in African cichlid fishes. Nat Ecol Evol 2021; 5:243-250. [PMID: 33230257 PMCID: PMC7610457 DOI: 10.1038/s41559-020-01354-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 10/21/2020] [Indexed: 12/13/2022]
Abstract
Changes in gene expression play a fundamental role in phenotypic evolution. Transcriptome evolutionary dynamics have so far mainly been compared among distantly related species and remain largely unexplored during rapid organismal diversification, in which gene regulatory changes have been suggested as particularly effective drivers of phenotypic divergence. Here we studied gene expression evolution in a model system of adaptive radiation, the cichlid fishes of African Lake Tanganyika. By comparing gene expression profiles of 6 different organs in 74 cichlid species representing all subclades of this radiation, we demonstrate that the rate of gene expression evolution varies among organs, transcriptome parts and the subclades of the radiation, indicating different strengths of selection. We found that the noncoding part of the transcriptome evolved more rapidly than the coding part, and that the gonadal transcriptomes evolved more rapidly than the somatic ones, with the exception of liver. We further show that the rate of gene expression change was not constant over the course of the radiation but accelerated at its later phase. Finally, we show that-at the per-gene level-the evolution of expression patterns is dominated by stabilizing selection.
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Affiliation(s)
- Athimed El Taher
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland.
| | - Astrid Böhne
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Nicolas Boileau
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Fabrizia Ronco
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Adrian Indermaur
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Lukas Widmer
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Walter Salzburger
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland.
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17
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Santos-Santos JH, Audenaert L, Verheyen E, Adriaens D. Ontogenetic divergence generates novel phenotypes in hybrid cichlids. J Anat 2021; 238:1116-1127. [PMID: 33417249 PMCID: PMC8053579 DOI: 10.1111/joa.13375] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 11/10/2020] [Accepted: 11/16/2020] [Indexed: 12/20/2022] Open
Abstract
Hybridization is suggested to contribute to ecomorphological and taxonomic diversity in lacustrine East African cichlids. This is supported by studies demonstrating that genetic diversity within lake radiations has been influenced by hybridization events, leading to extensive phenotypic differentiation of genetically closely related species. Hybrid persistence and speciation in sympatry with gene flow can be explained by pleiotropy in traits involved in reproductive isolation; however, little attention has been given to how trait differentiation is established during hybrid ontogeny, and how this may relate to trophic and locomotor specialization. This study compares body shape changes in a Lake Victoria cichlid hybrid throughout its post-hatch ontogeny to those of its parental species. Across the considered age/size categories, hybrids occupy a distinct and intermediate morphological space, yet where several transgressive traits emerge. A between-group principal component analysis on body shapes across size categories reveals axes of shape variation exclusive to the hybrids in the youngest/smallest size categories. Shape differences in the hybrids involved morphological traits known to be implicated in trophic and locomotor specializations in the parental species. Combined, our findings suggest that phenotypic divergence in the hybrid can lead to functional differences that may potentially release them to some degree from competition with the parental species. These findings agree with recent literature that addresses the potential importance of hybridization for the unusually recent origin of the Lake Victoria cichlid super-species flock.
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Affiliation(s)
- Javier H Santos-Santos
- Evolutionary Morphology of Vertebrates, Ghent University, Gent, Belgium.,Department of Biogeography and Global Change, Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas (MNCN-CSIC), Madrid, Spain
| | - Leen Audenaert
- OD Taxonomy and Phylogeny, Vertebrates, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Erik Verheyen
- OD Taxonomy and Phylogeny, Vertebrates, Royal Belgian Institute of Natural Sciences, Brussels, Belgium.,Evolutionary Ecology Group, Biology Department, University of Antwerp, Antwerp, Belgium
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18
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Puntambekar S, Newhouse R, San-Miguel J, Chauhan R, Vernaz G, Willis T, Wayland MT, Umrania Y, Miska EA, Prabakaran S. Evolutionary divergence of novel open reading frames in cichlids speciation. Sci Rep 2020; 10:21570. [PMID: 33299045 PMCID: PMC7726158 DOI: 10.1038/s41598-020-78555-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 11/26/2020] [Indexed: 01/02/2023] Open
Abstract
Novel open reading frames (nORFs) with coding potential may arise from noncoding DNA. Not much is known about their emergence, functional role, fixation in a population or contribution to adaptive radiation. Cichlids fishes exhibit extensive phenotypic diversification and speciation. Encounters with new environments alone are not sufficient to explain this striking diversity of cichlid radiation because other taxa coexistent with the Cichlidae demonstrate lower species richness. Wagner et al. analyzed cichlid diversification in 46 African lakes and reported that both extrinsic environmental factors and intrinsic lineage-specific traits related to sexual selection have strongly influenced the cichlid radiation, which indicates the existence of unknown molecular mechanisms responsible for rapid phenotypic diversification, such as emergence of novel open reading frames (nORFs). In this study, we integrated transcriptomic and proteomic signatures from two tissues of two cichlids species, identified nORFs and performed evolutionary analysis on these nORF regions. Our results suggest that the time scale of speciation of the two species and evolutionary divergence of these nORF genomic regions are similar and indicate a potential role for these nORFs in speciation of the cichlid fishes.
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Affiliation(s)
- Shraddha Puntambekar
- Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra, 411008, India
| | - Rachel Newhouse
- Department of Genetics, University of Cambridge, Downing Site, Cambridge, CB2 3EH, UK
| | - Jaime San-Miguel
- Department of Genetics, University of Cambridge, Downing Site, Cambridge, CB2 3EH, UK
| | - Ruchi Chauhan
- Department of Genetics, University of Cambridge, Downing Site, Cambridge, CB2 3EH, UK
| | - Grégoire Vernaz
- Department of Genetics, University of Cambridge, Downing Site, Cambridge, CB2 3EH, UK
- The Wellcome Trust/CRUK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Thomas Willis
- Department of Genetics, University of Cambridge, Downing Site, Cambridge, CB2 3EH, UK
| | - Matthew T Wayland
- Department of Zoology, University of Cambridge, Downing Site, Cambridge, CB2 3EH, UK
| | - Yagnesh Umrania
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Eric A Miska
- Department of Genetics, University of Cambridge, Downing Site, Cambridge, CB2 3EH, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Sudhakaran Prabakaran
- Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra, 411008, India.
- Department of Genetics, University of Cambridge, Downing Site, Cambridge, CB2 3EH, UK.
- St. Edmund's College, University of Cambridge, Cambridge, CB3 0BN, UK.
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19
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Drivers and dynamics of a massive adaptive radiation in cichlid fishes. Nature 2020; 589:76-81. [DOI: 10.1038/s41586-020-2930-4] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 08/20/2020] [Indexed: 12/29/2022]
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20
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Svardal H, Salzburger W, Malinsky M. Genetic Variation and Hybridization in Evolutionary Radiations of Cichlid Fishes. Annu Rev Anim Biosci 2020; 9:55-79. [PMID: 33197206 DOI: 10.1146/annurev-animal-061220-023129] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Evolutionary radiations are responsible for much of the variation in biodiversity across taxa. Cichlid fishes are well known for spectacular evolutionary radiations, as they have repeatedly evolved into large and phenotypically diverse arrays of species. Cichlid genomes carry signatures of past events and, at the same time, are the substrate for ongoing evolution. We survey genome-wide data and the available literature covering 438 cichlid populations (412 species) across multiple radiations to synthesize information about patterns and sharing of genetic variation. Nucleotide diversity within species is low in cichlids, with 92% of surveyed populations having less diversity than the median value found in other vertebrates. Divergence within radiations is also low, and a large proportion of variation is shared among species due to incomplete lineage sorting and widespread hybridization. Population genetics therefore provides a suitable conceptual framework for evolutionary genomic studies of cichlid radiations. We focus in detail on the roles of hybridization in shaping the patterns of genetic variation and in promoting cichlid diversification.
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Affiliation(s)
- Hannes Svardal
- Department of Biology, University of Antwerp, 2020 Antwerp, Belgium; .,Naturalis Biodiversity Center, 2333 Leiden, The Netherlands
| | - Walter Salzburger
- Zoological Institute, University of Basel, 4051 Basel, Switzerland; ,
| | - Milan Malinsky
- Zoological Institute, University of Basel, 4051 Basel, Switzerland; ,
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21
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Riera JL, Baldo L. Microbial co-occurrence networks of gut microbiota reveal community conservation and diet-associated shifts in cichlid fishes. Anim Microbiome 2020; 2:36. [PMID: 33499972 PMCID: PMC7807433 DOI: 10.1186/s42523-020-00054-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 09/11/2020] [Indexed: 12/15/2022] Open
Abstract
Background The extent to which deterministic rather than stochastic processes guide gut bacteria co-existence and ultimately their assembling into a community remains largely unknown. Co-occurrence networks of bacterial associations offer a powerful approach to begin exploring gut microbial community structure, maintenance and dynamics, beyond compositional aspects alone. Here we used an iconic model system, the cichlid fishes, with their multiple lake assemblages and extraordinary ecological diversity, to investigate a) patterns of microbial associations that were robust to major phylogeographical variables, and b) changes in microbial network structure along dietary shifts. We tackled these objectives using the large gut microbiota sequencing dataset available (nine lakes from Africa and America), building geographical and diet-specific networks and performing comparative network analyses. Results Major findings indicated that lake and continental microbial networks were highly resembling in global topology and node taxonomic composition, despite the heterogeneity of the samples. A small fraction of the observed co-occurrences among operational taxonomic units (OTUs) was conserved across all lake assemblages. These were all positive associations and involved OTUs within the genera Cetobacterium and Turicibacter and several OTUs belonging to the families of Peptostreptococcaceae and Clostridiaceae (order Clostridiales). Mapping of diet contribution on the African Lake Tanganyika network (therefore excluding the geographic variable) revealed a clear community change from carnivores (C) to omnivores (O) to herbivores (H). Node abundances and effect size for pairwise comparisons between diets supported a strong contrasting pattern between C and H. Moreover, diet-associated nodes in H formed complex modules of positive interactions among taxonomically diverse bacteria (mostly Verrucomicrobia and Proteobacteria). Conclusions Conservation of microbial network topologies and specific bacterial associations across distinct lake assemblages point to a major host-associated effect and potential deterministic processes shaping the cichlid gut microbiota. While the origin and biological relevance of these common associations remain unclear, their persistence suggests an important functional role in the cichlid gut. Among the very diverse cichlids of L. Tanganyika, diet nonetheless represents a major driver of microbial community changes. By intersecting results from predictive network inferences and experimental trials, future studies will be directed to explore the strength of these associations, predict the outcome of community alterations driven by diet and ultimately help understanding the role of gut microbiota in cichlid trophic diversification.
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Affiliation(s)
- Joan Lluís Riera
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, Barcelona, Spain
| | - Laura Baldo
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, Barcelona, Spain. .,Institute for Research on Biodiversity (IRBio), University of Barcelona, Barcelona, Spain.
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22
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Rometsch SJ, Torres-Dowdall J, Meyer A. Evolutionary dynamics of pre- and postzygotic reproductive isolation in cichlid fishes. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190535. [PMID: 32654645 DOI: 10.1098/rstb.2019.0535] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Cichlid fishes are exceptionally species-rich, speciated at explosive rates and, hence, are a model system in speciation research. Yet, their reproductive isolating barriers have, so far, not been comprehensively studied. Here, we review current knowledge on pre- and postzygotic mechanisms in cichlids. While premating isolation is the norm in cichlids, its strength varies across lineages and with the geographical setting. Moreover, manipulations of ambient conditions tended to reduce assortative mating among closely related species, suggesting that premating isolation in cichlids is often fragile and context dependent. The observed lack of complete reproductive isolation is supported by past and present hybridization events that have contributed to diversity by creating novel allelic combinations. On the other hand, our meta-analysis highlights that intrinsic postzygotic isolation might accumulate faster than assumed. Mild forms of genetic incompatibilities, such as sex ratio distortion, can already be observed among closely related species. Therefore, cessation of gene flow by strong reproductive isolation in cichlids requires a combination of premating prezygotic isolation supplemented with intrinsic and extrinsic postzygotic barriers. Further, we suggest crucial next steps to improve our knowledge about reproductive barriers in cichlids to understand the evolutionary dynamics of pre- and postzygotic isolation mechanisms during adaptive radiations. This article is part of the theme issue 'Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.
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Affiliation(s)
- Sina J Rometsch
- Department of Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Julián Torres-Dowdall
- Department of Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Axel Meyer
- Department of Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
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23
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Ali FS, Ismail M, Aly W. DNA barcoding to characterize biodiversity of freshwater fishes of Egypt. Mol Biol Rep 2020; 47:5865-5877. [PMID: 32661870 DOI: 10.1007/s11033-020-05657-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 07/08/2020] [Indexed: 12/16/2022]
Abstract
The current study represents the first molecular characterization of freshwater fish species in Egypt from two major fish resources; the River Nile and Lake Nasser. A total of 160 DNA barcodes using a 655-bp-long fragment of the mitochondrial cytochrome oxidase subunit I (COI) gene were generated from 37 species belonging to 32 genera that represent 15 families from nine orders. The studied species were identified using different molecular-based identification approaches, in addition to the morphological identification, including neighbor-joining (NJ) trees, Barcode Index Number, and Automatic Barcode Gap Discovery (ABGD). The average genetic divergence based on the Kimura two-parameter model (K2P) within orders, families, genera, and species were 0.175, 0.067, 0.02, and 0.008, respectively. The minimum and maximum K2P distance-based genetic divergences were 0.0 and 0.154, respectively. Nucleotide diversity (π) varied among families and ranged between 0.0% for families Malapteruridae, Auchenoglanididae, Schilbeidae, Anguillidae, Centropomidae and Tetraodontidae and 17% for family Cyprinidae. The current study cautions against the lack of species coverage at public databases which limits the accurate identification of newly surveyed species and recommends that multiple methods are encouraged for accurate species identification. The findings of the current study also support that COI barcode enabled effective fish species identification in River Nile and Lake Nasser. Moreover, the results of the current study will establish a comprehensive DNA barcode library for freshwater fishes along the River Nile in Egypt. Egyptian freshwater fish DNA barcodes will contribute substantially to future efforts in monitoring, conservation, and management of fisheries in Egypt.
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Affiliation(s)
- Fawzia S Ali
- Genetics Laboratory, Aquaculture Division, National Institute of Oceanography and Fisheries (NIOF), Cairo, Egypt.
| | - Mohamed Ismail
- Genetics Department, Faculty of Agriculture, Menoufia University, Shibin El-Kom, Egypt
| | - Walid Aly
- Fisheries Division, National Institute of Oceanography and Fisheries (NIOF), Cairo, Egypt
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24
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Resource trait specialisation in an introduced fish population with reduced genetic diversity. Biol Invasions 2020. [DOI: 10.1007/s10530-020-02264-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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25
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Faber-Hammond JJ, Bezault E, Lunt DH, Joyce DA, Renn SCP. The Genomic Substrate for Adaptive Radiation: Copy Number Variation across 12 Tribes of African Cichlid Species. Genome Biol Evol 2020; 11:2856-2874. [PMID: 31504491 DOI: 10.1093/gbe/evz185] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2019] [Indexed: 02/06/2023] Open
Abstract
The initial sequencing of five cichlid genomes revealed an accumulation of genetic variation, including extensive copy number variation in cichlid lineages particularly those that have undergone dramatic evolutionary radiation. Gene duplication has the potential to generate substantial molecular substrate for the origin of evolutionary novelty. We use array-based comparative heterologous genomic hybridization to identify copy number variation events (CNVEs) for 168 samples representing 53 cichlid species including the 5 species for which full genome sequence is available. We identify an average of 50-100 CNVEs per individual. For those species represented by multiple samples, we identify 150-200 total CNVEs suggesting a substantial amount of intraspecific variation. For these species, only ∼10% of the detected CNVEs are fixed. Hierarchical clustering of species according to CNVE data recapitulates phylogenetic relationships fairly well at both the tribe and radiation level. Although CNVEs are detected on all linkage groups, they tend to cluster in "hotspots" and are likely to contain and be flanked by transposable elements. Furthermore, we show that CNVEs impact functional categories of genes with potential roles in adaptive phenotypes that could reasonably promote divergence and speciation in the cichlid clade. These data contribute to a more complete understanding of the molecular basis for adaptive natural selection, speciation, and evolutionary radiation.
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Affiliation(s)
| | - Etienne Bezault
- BOREA Research Unit, MNHN, CNRS 7208, Sorbonne Université, IRD 207, UCN, UA, Paris, France
| | - David H Lunt
- Department of Biological and Marine Sciences, University of Hull, Hull Kingston-Upon-Hull, United Kingdom
| | - Domino A Joyce
- Department of Biological and Marine Sciences, University of Hull, Hull Kingston-Upon-Hull, United Kingdom
| | - Suzy C P Renn
- Department of Biology, Reed College, Portland OR 97202
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26
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Raffini F, Schneider RF, Franchini P, Kautt AF, Meyer A. Diving into divergence: Differentiation in swimming performances, physiology and gene expression between locally‐adapted sympatric cichlid fishes. Mol Ecol 2019; 29:1219-1234. [DOI: 10.1111/mec.15304] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 10/24/2019] [Accepted: 11/08/2019] [Indexed: 12/25/2022]
Affiliation(s)
- Francesca Raffini
- Lehrstuhl für Zoologie und Evolutionsbiologie Department of Biology University of Konstanz Konstanz Germany
- International Max Planck Research School (IMPRS) for Organismal Biology Max‐Planck‐Institut für Ornithologie Radolfzell Germany
- Max Planck Institute for Ornithology Radolfzell Germany
| | - Ralf F. Schneider
- Lehrstuhl für Zoologie und Evolutionsbiologie Department of Biology University of Konstanz Konstanz Germany
- International Max Planck Research School (IMPRS) for Organismal Biology Max‐Planck‐Institut für Ornithologie Radolfzell Germany
| | - Paolo Franchini
- Lehrstuhl für Zoologie und Evolutionsbiologie Department of Biology University of Konstanz Konstanz Germany
| | - Andreas F. Kautt
- Lehrstuhl für Zoologie und Evolutionsbiologie Department of Biology University of Konstanz Konstanz Germany
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie Department of Biology University of Konstanz Konstanz Germany
- International Max Planck Research School (IMPRS) for Organismal Biology Max‐Planck‐Institut für Ornithologie Radolfzell Germany
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27
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Patterson LB, Parichy DM. Zebrafish Pigment Pattern Formation: Insights into the Development and Evolution of Adult Form. Annu Rev Genet 2019; 53:505-530. [DOI: 10.1146/annurev-genet-112618-043741] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Vertebrate pigment patterns are diverse and fascinating adult traits that allow animals to recognize conspecifics, attract mates, and avoid predators. Pigment patterns in fish are among the most amenable traits for studying the cellular basis of adult form, as the cells that produce diverse patterns are readily visible in the skin during development. The genetic basis of pigment pattern development has been most studied in the zebrafish, Danio rerio. Zebrafish adults have alternating dark and light horizontal stripes, resulting from the precise arrangement of three main classes of pigment cells: black melanophores, yellow xanthophores, and iridescent iridophores. The coordination of adult pigment cell lineage specification and differentiation with specific cellular interactions and morphogenetic behaviors is necessary for stripe development. Besides providing a nice example of pattern formation responsible for an adult trait of zebrafish, stripe-forming mechanisms also provide a conceptual framework for posing testable hypotheses about pattern diversification more broadly. Here, we summarize what is known about lineages and molecular interactions required for pattern formation in zebrafish, we review some of what is known about pattern diversification in Danio, and we speculate on how patterns in more distant teleosts may have evolved to produce a stunningly diverse array of patterns in nature.
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Affiliation(s)
| | - David M. Parichy
- Department of Biology and Department of Cell Biology, University of Virginia, Charlottesville, Virginia 22903, USA
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28
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Roycroft EJ, Nations JA, Rowe KC. Environment predicts repeated body size shifts in a recent radiation of Australian mammals. Evolution 2019; 74:671-680. [PMID: 31595503 DOI: 10.1111/evo.13859] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 09/19/2019] [Accepted: 09/19/2019] [Indexed: 12/22/2022]
Abstract
Closely related species that occur across steep environmental gradients often display clear body size differences, and examining this pattern is crucial to understanding how environmental variation shapes diversity. Australian endemic rodents in the Pseudomys Division (Muridae: Murinae) have repeatedly colonized the arid, monsoon, and mesic biomes over the last 5 million years. Using occurrence records, body mass data, and Bayesian phylogenetic models, we test whether body mass of 31 species in the Pseudomys Division can be predicted by their biome association. We also model the effect of eight environmental variables on body mass. Despite high phylogenetic signal in body mass evolution across the phylogeny, we find that mass predictably increases in the mesic biome and decreases in arid and monsoon biomes. As per Bergmann's rule, temperature is strongly correlated with body mass, as well as several other variables. Our results highlight two important findings. First, body size in Australian rodents has tracked with climate through the Pleistocene, likely due to several environmental variables rather than a single factor. Second, support for both Brownian motion and predictable change at different taxonomic levels in the Pseudomys Division phylogeny demonstrates how the level at which we test hypotheses can alter interpretation of evolutionary processes.
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Affiliation(s)
- Emily J Roycroft
- School of BioSciences, The University of Melbourne, Parkville, Victoria, 3010, Australia.,Sciences Department, Museums Victoria, GPO Box 666, Melbourne, Victoria, 3001, Australia
| | - Jonathan A Nations
- Museum of Natural Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803.,Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803
| | - Kevin C Rowe
- School of BioSciences, The University of Melbourne, Parkville, Victoria, 3010, Australia.,Sciences Department, Museums Victoria, GPO Box 666, Melbourne, Victoria, 3001, Australia
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Baldo L, Riera JL, Salzburger W, Barluenga M. Phylogeography and Ecological Niche Shape the Cichlid Fish Gut Microbiota in Central American and African Lakes. Front Microbiol 2019; 10:2372. [PMID: 31681230 PMCID: PMC6803461 DOI: 10.3389/fmicb.2019.02372] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 09/30/2019] [Indexed: 01/01/2023] Open
Abstract
Cichlid fishes, with their repeated colonization of lakes and subsequent radiations at different scales of phylogenetic and ecological diversification, offer an excellent model system to understand the factors shaping the host-gut microbiota association in nature. Here, we characterized the gut microbiota of the Amphilophus species complex from Central America (known as the Midas cichlid complex), encompassing 158 wild specimens (13 species) collected from seven Nicaraguan lakes, and combined these data with previously published data from two African lakes (spanning 29 species). Our aim was to comprehensively explore trends in microbiota variation and persistence along the large spatial and temporal scales of cichlid diversification (from the oldest radiation in L. Tanganyika, 9-12 My old, to young ones in Nicaraguan crater lakes, <0.5 My old), in allopatry and sympatry (within and across lakes), and across the range of dietary niches (from highly specialized to generalist feeders). Despite their extraordinary diversity, cichlids shared a remarkably conserved microbial taxonomic profile, which argues for a primary role of the host genetics in the assembly and maintenance of these microbial communities. Within this partly constrained microbiota profile, geographic isolation (continent and lake) represented the first level of discrimination. For the Midas cichlid, a partial congruency was found between host microbiota and genetic distances, suggesting that microbial communities have partly diversified along their cichlid phylogeographic history of crater lake colonization. In sympatry (within lakes), the young and poorly ecologically diversified cichlid assemblages of Central American lakes display largely unresolved gut microbiotas (in terms of both alpha and beta diversities), whereas the phylogenetically and ecologically diverse species found in African lakes showed greater microbial interspecific diversity. This pattern largely points to the level of habitat segregation, trophic niche overlap, and reproductive barriers as major modulators of the gut microbiota connectivity among sympatric species.
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Affiliation(s)
- Laura Baldo
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, Barcelona, Spain
- Institute for Research on Biodiversity (IRBio), University of Barcelona, Barcelona, Spain
| | - Joan Lluís Riera
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, Barcelona, Spain
| | | | - Marta Barluenga
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
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30
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Penk SBR, Altner M, F Cerwenka A, Schliewen UK, Reichenbacher B. New fossil cichlid from the middle Miocene of East Africa revealed as oldest known member of the Oreochromini. Sci Rep 2019; 9:10198. [PMID: 31308387 PMCID: PMC6629881 DOI: 10.1038/s41598-019-46392-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 06/28/2019] [Indexed: 11/09/2022] Open
Abstract
A new genus and species of fossil cichlid fishes of middle Miocene age (12.5 Ma) is described from the Ngorora fish Lagerstätte (Tugen Hills, Kenya) in the East African Rift Valley. Parsimony analysis of morphological characters using published phylogenetic frameworks for extant cichlids combined with the application of a comprehensive best-fit approach based on morphology was employed to place the new fossil taxon in the phylogenetic context of the African cichlids. The data reveal that the fossil specimens can be assigned to the tribe Oreochromini within the haplotilapiines. †Oreochromimos kabchorensis gen. et sp. nov. shows a mosaic set of characters bearing many similarities to the almost pan-African Oreochromis and the East African lake-endemic Alcolapia. As the striking diversity of present-day African cichlids, with 1100 recognised species, has remained largely invisible in the fossil record, the material described here adds significantly to our knowledge of the Miocene diversity of the group. It effectively doubles the age of a fossil calibration point, which has hitherto been used to calibrate divergence times of the East African cichlids in molecular phylogenetic investigations. Furthermore, the comparative dataset derived from extant cichlids presented here will greatly facilitate the classification of fossil cichlids in future studies.
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Affiliation(s)
- Stefanie B R Penk
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, 80333, Munich, Germany.
| | - Melanie Altner
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, 80333, Munich, Germany
| | - Alexander F Cerwenka
- Section Evertebrata varia, SNSB Bavarian State Collection of Zoology, 81247, Munich, Germany
| | - Ulrich K Schliewen
- GeoBio-Center, Ludwig-Maximilians-Universität München, 80333, Munich, Germany
- Department of Ichthyology, SNSB Bavarian State Collection of Zoology, 81247, Munich, Germany
| | - Bettina Reichenbacher
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, 80333, Munich, Germany.
- GeoBio-Center, Ludwig-Maximilians-Universität München, 80333, Munich, Germany.
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31
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Pinho C, Cardoso V, Hey J. A population genetic assessment of taxonomic species: The case of Lake Malawi cichlid fishes. Mol Ecol Resour 2019; 19:1164-1180. [PMID: 31012255 PMCID: PMC6764894 DOI: 10.1111/1755-0998.13027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 03/20/2019] [Accepted: 04/10/2019] [Indexed: 02/05/2023]
Abstract
Organisms sampled for population‐level research are typically assigned to species by morphological criteria. However, if those criteria are limited to one sex or life stage, or the organisms come from a complex of closely related forms, the species assignments may misdirect analyses. The impact of such sampling can be assessed from the correspondence of genetic clusters, identified only from patterns of genetic variation, to the species identified using only phenotypic criteria. We undertook this protocol with the rock‐dwelling mbuna cichlids of Lake Malawi, for which species within genera are usually identified using adult male coloration patterns. Given high local endemism of male colour patterns, and considerable allele sharing among species, there persists considerable taxonomic uncertainty in these fishes. Over 700 individuals from a single transect were photographed, genotyped and separately assigned: (a) to morphospecies using photographs; and (b) to genetic clusters using five widely used methods. Overall, the correspondence between clustering methods was strong for larger clusters, but methods varied widely in estimated number of clusters. The correspondence between morphospecies and genetic clusters was also strong for larger clusters, as well as some smaller clusters for some methods. These analyses generally affirm (a) adult male‐limited sampling and (b) the taxonomic status of Lake Malawi mbuna, as the species in our study largely appear to be well‐demarcated genetic entities. More generally, our analyses highlight the challenges for clustering methods when the number of populations is unknown, especially in cases of highly uneven sample sizes.
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Affiliation(s)
- Catarina Pinho
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Vera Cardoso
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Jody Hey
- Rutgers, the State University of New Jersey, Piscataway, New Jersey.,CCGG, Center for Computational Genetics and Genomics, Department of Biology, Temple University, Philadelphia, Pennsylvania
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Muschick M, Russell JM, Jemmi E, Walker J, Stewart KM, Murray AM, Dubois N, Stager JC, Johnson TC, Seehausen O. Arrival order and release from competition does not explain why haplochromine cichlids radiated in Lake Victoria. Proc Biol Sci 2019; 285:rspb.2018.0462. [PMID: 29743255 DOI: 10.1098/rspb.2018.0462] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 04/12/2018] [Indexed: 12/31/2022] Open
Abstract
The frequent occurrence of adaptive radiations on oceanic islands and in lakes is often attributed to ecological opportunity resulting from release from competition where arrival order among lineages predicts which lineage radiates. This priority effect occurs when the lineage that arrives first expands its niche breadth and diversifies into a set of ecological specialists with associated monopolization of the resources. Later-arriving species do not experience ecological opportunity and do not radiate. While theoretical support and evidence from microbial experiments for priority effects are strong, empirical evidence in nature is difficult to obtain. Lake Victoria (LV) is home to an exceptional adaptive radiation of haplochromine cichlid fishes, where 20 trophic guilds and several hundred species emerged in just 15 000 years, the age of the modern lake that was preceded by a complete desiccation lasting several thousand years. However, while about 50 other lineages of teleost fish also have established populations in the lake, none of them has produced more than two species and most of them did not speciate at all. Here, we test if the ancestors of the haplochromine radiation indeed arrived prior to the most competent potential competitors, 'tilapias' and cyprinids, both of which have made rapid radiations in other African lakes. We assess LV sediment core intervals from just before the desiccation and just after refilling for the presence of fossil fish teeth. We show that all three lineages were present when modern LV began to fill with water. We conclude that the haplochromines' extraordinary radiation unfolded in the presence of potentially competing lineages and cannot be attributed to a simple priority effect.
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Affiliation(s)
- Moritz Muschick
- 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 for Aquatic Science and Technology, CH-6047 Kastanienbaum, Switzerland
| | - James M Russell
- Department of Earth, Environmental, and Planetary Sciences, Brown University, 324 Brook St, Providence, RI 02912, USA
| | - Eliane Jemmi
- 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 for Aquatic Science and Technology, CH-6047 Kastanienbaum, Switzerland
| | - Jonas Walker
- 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 for Aquatic Science and Technology, CH-6047 Kastanienbaum, Switzerland
| | - Kathlyn M Stewart
- Palaeobiology Section, Canadian Museum of Nature, P.O. Box 3443, Station D, Ottawa, Ontario, Canada K1P 6P4
| | - Alison M Murray
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada T6G 2E9
| | - Nathalie Dubois
- Department of Earth Sciences, ETHZ, CH-8092 Zurich, Switzerland.,Department of Surface Waters-Research and Management, EAWAG, Swiss Federal Institute for Aquatic Science and Technology, CH-8600 Dübendorf, Switzerland
| | - J Curt Stager
- Natural Sciences, Paul Smith's College, 7777 State Route 30, Paul Smiths, NY 12970, USA
| | - Thomas C Johnson
- Large Lakes Observatory, University of Minnesota Duluth, 2205 E. 5th Street, Duluth, MN 55812, USA
| | - Ole Seehausen
- 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 for Aquatic Science and Technology, CH-6047 Kastanienbaum, Switzerland
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33
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Dugo-Cota Á, Vilà C, Rodríguez A, Gonzalez-Voyer A. Ecomorphological convergence in Eleutherodactylus frogs: a case of replicate radiations in the Caribbean. Ecol Lett 2019; 22:884-893. [PMID: 30868693 DOI: 10.1111/ele.13246] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 07/25/2018] [Accepted: 01/16/2019] [Indexed: 11/28/2022]
Abstract
Replicate radiations, the repeated multiplication of species associated with ecological divergence, have attracted much attention and generated as much debate. Due to the few well-studied cases, it remains unclear whether replicate radiations are an exceptional result of evolution or a relatively common example of the power of adaptation by natural selection. We examined the case of Eleutherodactylus frogs, which radiated in the Caribbean islands resulting in more than 160 species that occupy very diverse habitats. A time-calibrated phylogeny revealed that these frogs independently diversified on all larger islands producing species that occupy a broad range of microhabitats in different islands. Using phylogenetic comparative methods, we found an association between morphological traits and particular microhabitats, and for most microhabitats detected significant morphological convergence. Our results indicate Caribbean Eleutherodactylus are a novel example of replicate radiations, and highlight the predictability of evolutionary processes, as similar ecological opportunities can lead to similar outcomes.
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Affiliation(s)
- Álvaro Dugo-Cota
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Av. Américo Vespucio 26, 41092, Sevilla, España
| | - Carles Vilà
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Av. Américo Vespucio 26, 41092, Sevilla, España
| | - Ariel Rodríguez
- Institut für Zoologie, Stiftung Tierärztliche Hochschule Hannover, Bünteweg 17, 30559, Hannover, Germany
| | - Alejandro Gonzalez-Voyer
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Cd. México, 04510, México
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34
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Gu L, Xia C. Cluster expansion of apolipoprotein D (ApoD) genes in teleost fishes. BMC Evol Biol 2019; 19:9. [PMID: 30621595 PMCID: PMC6325677 DOI: 10.1186/s12862-018-1323-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 12/11/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Gene and genome duplication play important roles in the evolution of gene function. Compared to individual duplicated genes, gene clusters attract particular attention considering their frequent associations with innovation and adaptation. Here, we report for the first time the expansion of the apolipoprotein D (ApoD) ligand-transporter genes in a cluster manner specific to teleost fishes. RESULTS Based on comparative genomic and transcriptomic analyses, protein 3D structure comparison, positive selection detection and breakpoints detection, the single ApoD gene in the ancestor expanded into two clusters following a dynamic evolutionary pattern in teleost fishes. Orthologous genes show conserved expression patterns, whereas lineage-specific duplicated genes show tissue-specific expression patterns and even evolve new gene expression profiles. Positive selection occurred in branches before and after gene duplication, especially for lineage-specific duplicated genes. Cluster analyses based on protein 3D structure comparisons, especially comparisons of the four loops at the opening side, show gene duplication-segregating patterns. Duplicated ApoD genes are predicted to be associated with forkhead transcription factors and MAPK genes. ApoD clusters are located next to the breakpoints of genome rearrangements. CONCLUSIONS Here, we report the expansion of ApoD genes specific to teleost fishes in a cluster manner for the first time. Neofunctionalization and subfunctionalization were observed at both the protein and expression levels after duplication. Evidence from different aspects-i.e., abnormal expression-induced disease in humans, fish-specific expansion, predicted associations with forkhead transcription factors and MAPK genes, specific expression patterns in tissues related to sexual selection and adaptation, duplicated genes under positive selection and their location next to the breakpoints of genome rearrangements-suggests the potentially advantageous roles of ApoD genes in teleost fishes. The cluster expansion of ApoD genes specific to teleost fishes provides thus an ideal evo-devo model for studying gene duplication, cluster maintenance and new gene function emergence.
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Affiliation(s)
- Langyu Gu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Canwei Xia
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
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35
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Prazdnikov DV, Shkil FN. The Experimental Heterochronies in a Green Terror Cichlid Andinoacara rivulatus (Teleostei: Cichlidae: Cichlasomatinae) Indicate a Role of Developmental Changes in the Cichlids Coloration Evolution. BIOL BULL+ 2019. [DOI: 10.1134/s1062359019010102] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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36
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Nandamuri SP, Conte MA, Carleton KL. Multiple trans QTL and one cis-regulatory deletion are associated with the differential expression of cone opsins in African cichlids. BMC Genomics 2018; 19:945. [PMID: 30563463 PMCID: PMC6299527 DOI: 10.1186/s12864-018-5328-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 11/28/2018] [Indexed: 01/22/2023] Open
Abstract
Background Dissecting the genetic basis of phenotypic diversity is one of the fundamental goals in evolutionary biology. Despite growing evidence for gene expression divergence being responsible for the evolution of complex traits, knowledge about the proximate genetic causes underlying these traits is still limited. African cichlids have diverse visual systems, with different species expressing different combinations of seven cone opsin genes. Using opsin expression variation in African cichlids as a model for gene expression evolution, this study aims to investigate the genetic architecture of opsin expression divergence in this group. Results Results from a genome-wide linkage mapping on the F2 progeny of an intergeneric cross, between two species with differential opsin expression show that opsins in Lake Malawi cichlids are controlled by multiple quantitative trait loci (QTLs). Most of these QTLs are located in trans to the opsins except for one cis-QTL for SWS1 on LG17. A closer look at this major QTL revealed the presence of a 691 bp deletion in the promoter of the SWS1 opsin (located 751 bp upstream of the start site) that is associated with a decrease in its expression. Phylogenetic footprinting indicates that the region spanning the deletion harbors a microRNA miR-729 and a conserved non-coding element (CNE) that also occurs in zebrafish and other teleosts. This suggests that the deletion might contain ancestrally preserved regulators that have been tuned for SWS1 gene expression in Lake Malawi. While this deletion is not common, it does occur in several other species within the lake. Conclusions Differential expression of cichlid opsins is associated with multiple overlapping QTL, with all but one in trans to the opsins they regulate. The one cis-acting factor is a deletion in the promoter of the SWS1 opsin, suggesting that ancestral polymorphic deletions may contribute to cichlid’s visual diversity. In addition to expanding our understanding of the molecular landscape of opsin expression in African cichlids, this study sheds light on the molecular mechanisms underlying phenotypic variation in natural populations. Electronic supplementary material The online version of this article (10.1186/s12864-018-5328-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sri Pratima Nandamuri
- Department of Biology, University of Maryland, 1210 Biology / Psychology Bldg #144, College Park, MD, 20742, USA
| | - Matthew A Conte
- Department of Biology, University of Maryland, 1210 Biology / Psychology Bldg #144, College Park, MD, 20742, USA
| | - Karen L Carleton
- Department of Biology, University of Maryland, 1210 Biology / Psychology Bldg #144, College Park, MD, 20742, USA.
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37
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Meyer BS, Hablützel PI, Roose AK, Hofmann MJ, Salzburger W, Raeymaekers JAM. An exploration of the links between parasites, trophic ecology, morphology, and immunogenetics in the Lake Tanganyika cichlid radiation. HYDROBIOLOGIA 2018; 832:215-233. [PMID: 30880832 PMCID: PMC6394741 DOI: 10.1007/s10750-018-3798-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 10/02/2018] [Accepted: 10/12/2018] [Indexed: 06/09/2023]
Abstract
Differences in habitat and diet between species are often associated with morphological differences. Habitat and trophic adaptation have therefore been proposed as important drivers of speciation and adaptive radiation. Importantly, habitat and diet shifts likely impose changes in exposure to different parasites and infection risk. As strong selective agents influencing survival and mate choice, parasites might play an important role in host diversification. We explore this possibility for the adaptive radiation of Lake Tanganyika (LT) cichlids. We first compare metazoan macroparasites infection levels between cichlid tribes. We then describe the cichlids' genetic diversity at the major histocompatibility complex (MHC), which plays a key role in vertebrate immunity. Finally, we evaluate to what extent trophic ecology and morphology explain variation in infection levels and MHC, accounting for phylogenetic relationships. We show that different cichlid tribes in LT feature partially non-overlapping parasite communities and partially non-overlapping MHC diversity. While morphology explained 15% of the variation in mean parasite abundance, trophic ecology accounted for 16% and 22% of the MHC variation at the nucleotide and at the amino acid level, respectively. Parasitism and immunogenetic adaptation may thus add additional dimensions to the LT cichlid radiation.
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Affiliation(s)
- Britta S. Meyer
- Zoological Institute, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
- Evolutionary Ecology of Marine Fishes, Helmholtz Centre for Ocean Research Kiel, GEOMAR, Düsternbrooker Weg 20, 24105 Kiel, Germany
- Present Address: Max Planck Institute for Evolutionary Biology, Max Planck Research Group Behavioural Genomics, August-Thienemann-Str. 2, 24306 Plön, Germany
| | - Pascal I. Hablützel
- Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, Ch. Deberiotstraat 32, 3000 Louvain, Belgium
- Present Address: Flanders Marine Institute, Wandelaarkaai 7, 8400 Ostend, Belgium
| | - Anna K. Roose
- Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, Ch. Deberiotstraat 32, 3000 Louvain, Belgium
| | - Melinda J. Hofmann
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, CSIC, Calle José Gutiérrez Abascal 2, 28006 Madrid, Spain
- Present Address: Museo de Zoología, Pontificia Universidad Católica del Ecuador, Av. 12 de Octubre 1076, Quito, Ecuador
| | - Walter Salzburger
- Zoological Institute, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
| | - Joost A. M. Raeymaekers
- Zoological Institute, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
- Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, Ch. Deberiotstraat 32, 3000 Louvain, Belgium
- Present Address: Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
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Prazdnikov DV, Shkil FN. Experimental evidence of the role of heterochrony in evolution of the Mesoamerican cichlids pigment patterns. Evol Dev 2018; 21:3-15. [PMID: 30239104 DOI: 10.1111/ede.12272] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The Mesoamerican cichlids display a spectacular diversity of pigment patterns, which serve a variety of functions and serve as a strong selective trait for this lineage. The development and variation of coloration in the Mesoamerican cichlids have been detailed by several groups. In particular, Říčan, Musilová, Muška, and Novák () and Říčan, Piálek, Dragová, and Novák () determined homology of pattern and revealed four alternative types of coloration and their ontogeny. In this work, this group posed an "ontogenetic timing hypothesis" proposing heterochronic shifts underlying major transitions in the evolution of the Mesoamerican cichlids. Here, we experimentally test this hypothesis by experimentally altering timing of pigment pattern formation in the convict cichlid Amatitlania nigrofasciata, a member of the Mesoamerican cichlids, via manipulations of thyroid hormone (TH) function. The response of different pigment cell lineages to TH-perturbations revealed that the transition from larval to juvenile coloration in the convict cichlid is under the control of TH-signaling. Importantly, hormonally induced changes in the timing of pigment cell lineages' development resulted in shifts of coloration ontogeny type observed between lineages and led to the appearance of phenotypes mimicking those in phylogenetically close and distant species. Thus, our findings support the hypothesis that simple changes in ontogenetic timing underlies species specific patterns in pigmentation and provide new perspectives for studying the role of endocrine signaling in the evolution of cichlids.
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Affiliation(s)
- Denis V Prazdnikov
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Fedor N Shkil
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia.,Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia
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39
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Salzburger W. Understanding explosive diversification through cichlid fish genomics. Nat Rev Genet 2018; 19:705-717. [DOI: 10.1038/s41576-018-0043-9] [Citation(s) in RCA: 138] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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40
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Cahenzli F, Bonetti C, Erhardt A. Divergent strategies in pre- and postzygotic reproductive isolation between two closely related Dianthus species. Evolution 2018; 72:1851-1862. [PMID: 30003537 DOI: 10.1111/evo.13556] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Accepted: 07/02/2018] [Indexed: 10/28/2022]
Abstract
Quantifying the relative contribution of multiple isolation barriers to gene flow between recently diverged species is essential for understanding speciation processes. In parapatric populations, local adaptation is thought to be a major contributor to the evolution of reproductive isolation. However, extrinsic postzygotic barriers assessed in reciprocal transplant experiments are often neglected in empirical assessments of multiple isolation barriers. We analyzed multiple isolation barriers between two closely related species of the plant genus Dianthus, a genus characterized by the most rapid species diversification in plants reported so far. Although D. carthusianorum L. and D. sylvestris Wulf. can easily be hybridized in crossing experiments, natural hybrids are rare. We found that in parapatry, pollinator-mediated prezygotic reproductive isolation barriers are important for both D. carthusianorum (0.761) and D. sylvestris (0.468). In contrast to D. carthusianorum, high hybrid viability in D. sylvestris (-0.491) was counteracted by strong extrinsic postzygotic isolation (0.900). Our study highlights the importance of including reciprocal transplant experiments for documenting extrinsic postzygotic isolation and demonstrates clearly divergent strategies and hence asymmetric pre- and postzygotic reproductive isolation between closely related species. It also suggests that pollinator-mediated and ecological isolation could have interacted in synergistic ways, further stimulating rapid speciation in Dianthus.
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Affiliation(s)
- Fabian Cahenzli
- Forschungsinstitut für biologischen Landbau (FiBL), Department of crop Sciences, Ackerstrasse 113, CH-5070, Frick, Switzerland
| | - Christophe Bonetti
- Department of Environmental Sciences, Section Conservation Biology (NLU), University of Basel, St. Johanns-Vorstadt 10, CH-4056, Basel, Switzerland
| | - Andreas Erhardt
- Department of Environmental Sciences, Botany, University of Basel, Schönbeinstrasse 6, CH-4056, Basel, Switzerland
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41
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Siepielski AM, McPeek SJ, McPeek MA. Female mate preferences on high-dimensional shape variation for male species recognition traits. J Evol Biol 2018; 31:1239-1250. [PMID: 29876989 DOI: 10.1111/jeb.13302] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 05/14/2018] [Accepted: 05/31/2018] [Indexed: 01/01/2023]
Abstract
Females in many animal species must discriminate between conspecific and heterospecific males when choosing mates. Such mating preferences that discriminate against heterospecifics may inadvertently also affect the mating success of conspecific males, particularly those with more extreme phenotypes. From this expectation, we hypothesized that female mate choice should cause Enallagma females (Odonata: Coenagrionidae) to discriminate against conspecific males with more extreme phenotypes of the claspers males use to grasp females while mating - the main feature of species mate recognition in these species. To test this, we compared cerci sizes and shapes between males that were captured while mating with females to males that were captured at the same time but not mating in three Enallagma species. In contrast to our hypothesis, we found only one of forty comparisons of shape variation that was consistent with females discriminating against males with more extreme cerci shapes. Instead, differences in cerci shape between mating and single males suggested that females displayed directional preferences on 1-4 aspects of cerci shape in two of the species in our samples. These results suggest that whereas some directional biases in mating based on cerci shape occur, the intraspecific phenotypic variation in male cerci size and shape is likely not large enough for females to express any significant incidental discrimination among conspecifics with more extreme shapes.
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Affiliation(s)
- Adam M Siepielski
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA
| | - Sarah J McPeek
- Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
| | - Mark A McPeek
- Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
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42
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Pauquet G, Salzburger W, Egger B. The puzzling phylogeography of the haplochromine cichlid fish Astatotilapia burtoni. Ecol Evol 2018; 8:5637-5648. [PMID: 29938080 PMCID: PMC6010872 DOI: 10.1002/ece3.4092] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 03/15/2018] [Accepted: 03/27/2018] [Indexed: 12/14/2022] Open
Abstract
Astatotilapia burtoni is a member of the "modern haplochromines," the most species-rich lineage within the family of cichlid fishes. Although the species has been in use as research model in various fields of research since almost seven decades, including developmental biology, neurobiology, genetics and genomics, and behavioral biology, little is known about its spatial distribution and phylogeography. Here, we examine the population structure and phylogeographic history of A. burtoni throughout its entire distribution range in the Lake Tanganyika basin. In addition, we include several A. burtoni laboratory strains to trace back their origin from wild populations. To this end, we reconstruct phylogenetic relationships based on sequences of the mitochondrial DNA (mtDNA) control region (d-loop) as well as thousands of genomewide single nucleotide polymorphisms (SNPs) derived from restriction-associated DNA sequencing. Our analyses reveal high population structure and deep divergence among several lineages, however, with discordant nuclear and mtDNA phylogenetic inferences. Whereas the SNP-based phylogenetic hypothesis uncovers an unexpectedly deep split in A. burtoni, separating the populations in the southern part of the Lake Tanganyika basin from those in the northern part, analyses of the mtDNA control region suggest deep divergence between populations from the southwestern shoreline and populations from the northern and southeastern shorelines of Lake Tanganyika. This phylogeographic pattern and mitochondrial haplotype sharing between populations from the very North and the very South of Lake Tanganyika can only partly be explained by introgression linked to lake-level fluctuations leading to past contact zones between otherwise isolated populations and large-scale migration events.
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Affiliation(s)
| | | | - Bernd Egger
- Zoological InstituteUniversity of BaselBaselSwitzerland
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43
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The Colorful Sex Chromosomes of Teleost Fish. Genes (Basel) 2018; 9:genes9050233. [PMID: 29751562 PMCID: PMC5977173 DOI: 10.3390/genes9050233] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 04/24/2018] [Accepted: 04/24/2018] [Indexed: 12/14/2022] Open
Abstract
Teleost fish provide some of the most intriguing examples of sexually dimorphic coloration, which is often advantageous for only one of the sexes. Mapping studies demonstrated that the genetic loci underlying such color patterns are frequently in tight linkage to the sex-determining locus of a species, ensuring sex-specific expression of the corresponding trait. Several genes affecting color synthesis and pigment cell development have been previously described, but the color loci on the sex chromosomes have mostly remained elusive as yet. Here, we summarize the current knowledge about the genetics of such color loci in teleosts, mainly from studies on poeciliids and cichlids. Further studies on these color loci will certainly provide important insights into the evolution of sex chromosomes.
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44
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Raffini F, Fruciano C, Meyer A. Morphological and genetic correlates in the left–right asymmetric scale-eating cichlid fish of Lake Tanganyika. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly024] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Francesca Raffini
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse, Konstanz, Germany
- International Max Planck Research School (IMPRS) for Organismal Biology, University of Konstanz, Konstanz, Germany
| | - Carmelo Fruciano
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse, Konstanz, Germany
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, QLD, Australia
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse, Konstanz, Germany
- International Max Planck Research School (IMPRS) for Organismal Biology, University of Konstanz, Konstanz, Germany
- Radcliffe Institute for Advance Study, Harvard University, Cambridge, MA, USA
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45
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Dijkstra PD, Maguire SM, Harris RM, Rodriguez AA, DeAngelis RS, Flores SA, Hofmann HA. The melanocortin system regulates body pigmentation and social behaviour in a colour polymorphic cichlid fish. Proc Biol Sci 2018; 284:rspb.2016.2838. [PMID: 28356453 DOI: 10.1098/rspb.2016.2838] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 03/02/2017] [Indexed: 12/26/2022] Open
Abstract
The melanocortin system is a neuroendocrine system that regulates a range of physiological and behavioural processes. We examined the extent to which the melanocortin system simultaneously regulates colour and behaviour in the cichlid fish Astatotilapia burtoni We found that yellow males are more aggressive than blue males, in line with previous studies. We then found that exogenous α-melanocyte-stimulating hormone (α-MSH) increases yellowness of the body and dispersal of xanthophore pigments in both morphs. However, α-MSH had a morph-specific effect on aggression, with only blue males showing an increase in the rate of aggression. Exogenous agouti signalling peptide (ASIP), a melanocortin antagonist, did not affect coloration but reduced the rate of aggression in both colour morphs. Blue males had higher cortisol levels than yellow males. Neural gene expression of melanocortin receptors (mcr) and ligands was not differentially regulated between colour morphs. In the skin, however, mc1r and pro-opiomelanocortin (pomc) β were upregulated in blue males, while asip 1 was upregulated in yellow males. The effects of α-MSH on behaviour and body coloration, combined with morph-specific regulation of the stress response and the melanocortin system, suggest that the melanocortin system contributes to the polymorphism in behaviour and coloration in A. burtoni.
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Affiliation(s)
- Peter D Dijkstra
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA .,Behavioural Biology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands.,Department of Biology, Central Michigan University, Mount Pleasant, MI 48859, USA
| | - Sean M Maguire
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Rayna M Harris
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA.,Institute for Cellular & Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Agosto A Rodriguez
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Ross S DeAngelis
- Program for Ecology, Evolution and Conservation Biology, Beckman Institute, University of Illinois at Urbana-Champaign, 405 N. Mathews Avenue, Urbana, IL 61801, USA
| | - Stephanie A Flores
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Hans A Hofmann
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA.,Institute for Cellular & Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA.,Institute for Neuroscience, The University of Texas at Austin, Austin, TX 78712, USA
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46
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Meyer BS, Matschiner M, Salzburger W. Disentangling Incomplete Lineage Sorting and Introgression to Refine Species-Tree Estimates for Lake Tanganyika Cichlid Fishes. Syst Biol 2018; 66:531-550. [PMID: 27539485 DOI: 10.1093/sysbio/syw069] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 07/27/2016] [Indexed: 12/19/2022] Open
Abstract
Adaptive radiation is thought to be responsible for the evolution of a great portion of the past and present diversity of life. Instances of adaptive radiation, characterized by the rapid emergence of an array of species as a consequence to their adaptation to distinct ecological niches, are important study systems in evolutionary biology. However, because of the rapid lineage formation in these groups, and occasional gene flow between the participating species, it is often difficult to reconstruct the phylogenetic history of species that underwent an adaptive radiation. In this study, we present a novel approach for species-tree estimation in rapidly diversifying lineages, where introgression is known to occur, and apply it to a multimarker data set containing up to 16 specimens per species for a set of 45 species of East African cichlid fishes (522 individuals in total), with a main focus on the cichlid species flock of Lake Tanganyika. We first identified, using age distributions of most recent common ancestors in individual gene trees, those lineages in our data set that show strong signatures of past introgression. This led us to formulate three hypotheses of introgression between different lineages of Tanganyika cichlids: the ancestor of Boulengerochromini (or of Boulengerochromini and Bathybatini) received genomic material from the derived H-lineage; the common ancestor of Cyprichromini and Perissodini experienced, in turn, introgression from Boulengerochromini and/or Bathybatini; and the Lake Tanganyika Haplochromini and closely related riverine lineages received genetic material from Cyphotilapiini. We then applied the multispecies coalescent model to estimate the species tree of Lake Tanganyika cichlids, but excluded the lineages involved in these introgression events, as the multispecies coalescent model does not incorporate introgression. This resulted in a robust species tree, in which the Lamprologini were placed as sister lineage to the H-lineage (including the Eretmodini), and we identify a series of rapid splitting events at the base of the H-lineage. Divergence ages estimated with the multispecies coalescent model were substantially younger than age estimates based on concatenation, and agree with the geological history of the Great Lakes of East Africa. Finally, we formally tested the three hypotheses of introgression using a likelihood framework, and find strong support for introgression between some of the cichlid tribes of Lake Tanganyika.
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Affiliation(s)
- Britta S Meyer
- Zoological Institute, University of Basel, Basel, Switzerland.,Evolutionary Ecology of Marine Fishes, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Michael Matschiner
- Zoological Institute, University of Basel, Basel, Switzerland.,Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Walter Salzburger
- Zoological Institute, University of Basel, Basel, Switzerland.,Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
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47
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Gunter HM, Schneider RF, Karner I, Sturmbauer C, Meyer A. Molecular investigation of genetic assimilation during the rapid adaptive radiations of East African cichlid fishes. Mol Ecol 2017; 26:6634-6653. [PMID: 29098748 DOI: 10.1111/mec.14405] [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: 02/13/2016] [Revised: 08/06/2017] [Accepted: 08/24/2017] [Indexed: 12/19/2022]
Abstract
Adaptive radiations are characterized by adaptive diversification intertwined with rapid speciation within a lineage resulting in many ecologically specialized, phenotypically diverse species. It has been proposed that adaptive radiations can originate from ancestral lineages with pronounced phenotypic plasticity in adaptive traits, facilitating ecologically driven phenotypic diversification that is ultimately fixed through genetic assimilation of gene regulatory regions. This study aimed to investigate how phenotypic plasticity is reflected in gene expression patterns in the trophic apparatus of several lineages of East African cichlid fishes, and whether the observed patterns support genetic assimilation. This investigation used a split brood experimental design to compare adaptive plasticity in species from within and outside of adaptive radiations. The plastic response was induced in the crushing pharyngeal jaws through feeding individuals either a hard or soft diet. We find that nonradiating, basal lineages show higher levels of adaptive morphological plasticity than the derived, radiated lineages, suggesting that these differences have become partially genetically fixed during the formation of the adaptive radiations. Two candidate genes that may have undergone genetic assimilation, gif and alas1, were identified, in addition to alterations in the wiring of LPJ patterning networks. Taken together, our results suggest that genetic assimilation may have dampened the inducibility of plasticity related genes during the adaptive radiations of East African cichlids, flattening the reaction norms and canalizing their feeding phenotypes, driving adaptation to progressively more narrow ecological niches.
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Affiliation(s)
- Helen M Gunter
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany.,Zukunftskolleg, University of Konstanz, Konstanz, Germany
| | - Ralf F Schneider
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany.,International Max Planck Research School for Organismal Biology, University of Konstanz, Konstanz, Germany
| | | | | | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany.,International Max Planck Research School for Organismal Biology, University of Konstanz, Konstanz, Germany.,Radcliffe Institute for Advanced Study, Harvard University, Cambridge, MA, USA
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48
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Bachmann JC, Cortesi F, Hall MD, Marshall NJ, Salzburger W, Gante HF. Real-time social selection maintains honesty of a dynamic visual signal in cooperative fish. Evol Lett 2017; 1:269-278. [PMID: 30283655 PMCID: PMC6121853 DOI: 10.1002/evl3.24] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 08/21/2017] [Accepted: 09/01/2017] [Indexed: 01/04/2023] Open
Abstract
Our understanding of animal communication has been largely driven by advances in theory since empirical evidence has been difficult to obtain. Costly signaling theory became the dominant paradigm explaining the evolution of honest signals, according to which communication reliability relies on differential costs imposed on signalers to distinguish animals of different quality. On the other hand, mathematical models disagree on the source of costs at the communication equilibrium. Here, we present an empirical framework to study the evolution of honest signals that generates predictions on the form, function, and sources of reliability of visual signals. We test these predictions on the facial color patterns of the cooperatively breeding Princess of Burundi cichlid, Neolamprologus brichardi. Using theoretical visual models and behavioral experiments we show that these patterns possess stable chromatic properties for efficient transmission in the aquatic environment, while dynamic changes in signal luminance are used by the fish to communicate switches in aggressive intent. By manipulating signal into out-of-equilibrium expression and simulating a cheater invasion, we demonstrate that social costs (receiver retaliation) promote the honesty of this dynamic conventional signal. By directly probing the sender of a signal in real time, social selection is likely to be the mechanism of choice shaping the evolution of inexpensive, yet reliable context-dependent social signals in general.
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Affiliation(s)
- Judith C Bachmann
- Zoological Institute, Vesalgasse 1 University of Basel 4051 Basel Switzerland.,Department of Evolutionary Biology and Environmental Studies University of Zurich 8057 Zurich Switzerland
| | - Fabio Cortesi
- Zoological Institute, Vesalgasse 1 University of Basel 4051 Basel Switzerland.,Queensland Brain Institute University of Queensland Brisbane Queensland 4072 Australia
| | - Matthew D Hall
- School of Biological Sciences Monash University Melbourne 3800 Australia
| | - N Justin Marshall
- Queensland Brain Institute University of Queensland Brisbane Queensland 4072 Australia
| | - Walter Salzburger
- Zoological Institute, Vesalgasse 1 University of Basel 4051 Basel Switzerland
| | - Hugo F Gante
- Zoological Institute, Vesalgasse 1 University of Basel 4051 Basel Switzerland
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49
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Ornelas-García CP, Bautista A, Herder F, Doadrio I. Functional modularity in lake-dwelling characin fishes of Mexico. PeerJ 2017; 5:e3851. [PMID: 28951817 PMCID: PMC5611896 DOI: 10.7717/peerj.3851] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Accepted: 09/05/2017] [Indexed: 01/21/2023] Open
Abstract
Modular evolution promotes evolutionary change, allowing independent variation across morphological units. Recent studies have shown that under contrasting ecological pressures, patterns of modularity could be related to divergent evolution. The main goal of the present study was to evaluate the presence of modular evolution in two sister lacustrine species, Astyanax aeneus and A. caballeroi, which are differentiated by their trophic habits. Two different datasets were analyzed: (1) skull X-rays from 73 specimens (35 A. aeneus and 38 A. caballeroi) to characterize skull variation patterns, considering both species and sex effects. For this dataset, three different modularity hypotheses were tested, previously supported in other lacustrine divergent species; (2) a complete body shape dataset was also tested for four modularity hypotheses, which included a total of 196 individuals (110 Astyanax aeneus and 86 A. caballeroi). Skull shape showed significant differences among species and sex (P < 0.001), where Astyanax caballeroi species showed an upwardly projected mandible and larger preorbital region. For the skull dataset, the modularity hypothesis ranked first included three partitioning modules. While for the complete body dataset the best ranked hypothesis included two modules (head vs the rest of the body), being significant only for A. caballeroi.
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Affiliation(s)
- Claudia Patricia Ornelas-García
- Colección Nacional de Peces, Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico
| | - Amando Bautista
- Centro Tlaxcala de Biología de la Conducta, Universidad Autónoma de Tlaxcala, Tlaxcala, Mexico
| | - Fabian Herder
- Sektion Ichthyologie, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Ignacio Doadrio
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, Madrid, Spain
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50
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Nandamuri SP, Dalton BE, Carleton KL. Determination of the Genetic Architecture Underlying Short Wavelength Sensitivity in Lake Malawi Cichlids. J Hered 2017; 108:379-390. [PMID: 28498989 DOI: 10.1093/jhered/esx020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 02/27/2017] [Indexed: 11/13/2022] Open
Abstract
African cichlids are an exemplary system to study organismal diversity and rapid speciation. Species differ in external morphology including jaw shape and body coloration, but also differ in sensory systems including vision. All cichlids have 7 cone opsin genes with species differing broadly in which opsins are expressed. The differential opsin expression results in closely related species with substantial differences in spectral sensitivity of their photoreceptors. In this work, we take a first step in determining the genetic basis of opsin expression in cichlids. Using a second generation cross between 2 species with different opsin expression patterns, we make a conservative estimate that short wavelength opsin expression is regulated by a few loci. Genetic mapping in 96 F2 hybrids provides clear evidence of a cis-regulatory region for SWS1 opsin that explains 34% of the variation in expression between the 2 species. Additionally, in situ hybridization has shown that SWS1 and SWS2B opsins are coexpressed in individual single cones in the retinas of F2 progeny. Results from this work will contribute to a better understanding of the genetic architecture underlying opsin expression. This knowledge will help answer long-standing questions about the evolutionary processes fundamental to opsin expression variation and how this contributes to adaptive cichlid divergence.
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Affiliation(s)
| | - Brian E Dalton
- National & Environmental Sciences Department, Western State Colorado University, Gunnison, CO 81231
| | - Karen L Carleton
- From the Department of Biology, University of Maryland, College Park, MD 20742
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