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Axel Meyer - One of the best experts on this subject based on the ideXlab platform.
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A: The species flocks of East African Cichlid fishes: recent advances in molecular phylogenetics and population genetics. Naturwissenschaften 2004
2020Co-Authors: Walter Salzburger, Axel MeyerAbstract:Abstract With more than 3,000 species, the fish family Cichlidae is one of the most species-rich families of vertebrates. Cichlids occur in southern and central America, Africa, Madagascar, and India. The hotspot of their biodiversity is East Africa, where they form adaptive radiations composed of hundreds of endemic species in several lakes of various sizes and ages. The unparalleled species richness of East African Cichlids has been something of a conundrum for evolutionary biologists and ecologists, since it has been in doubt whether these hundreds of species arose by allopatric speciation or whether it is necessary to invoke somewhat less traditional models of speciation, such as micro-allopatric, peripatric, or even sympatric speciation or evolution through sexual selection mediated by female choice. Ernst Mayr's analyses of these evolutionary uniquely diverse species assemblages have contributed to a more direct approach to this problem and have led to a deeper understanding of the patterns and processes that caused the formation of these huge groups of species. We review here recent molecular data on population differentiation and phylogenetics, which have helped to unravel, to some extent, the patterns and processes that led to the formation and ecological maintenance of Cichlid species flocks. It is becoming apparent that sexually selected traits do play an important role in speciation in micro-allopatric or even sympatric settings. Species richness seems to be roughly correlated with the surface area, but not the age, of the lakes. We observe that the oldest lineages of a species flock of Cichlids are often less species-rich and live in the open water or deepwater habitats. While the species flocks of the Lake Malawai and the Lake Victoria areas were shown to be monophyletic, the Cichlid assemblage of Lake Tanganyika seems to consist of several independent species flocks. Cichlids emerge as an evolutionary model system in which many fundamental questions in evolution and ecology can be tested successfully, yet for other fish species flocks the relative importance of alternative mechanisms of speciation is likely to differ from that in Cichlid fish
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success of cuckoo catfish brood parasitism reflects coevolutionary history and individual experience of their Cichlid hosts
Science Advances, 2018Co-Authors: Radim Blažek, Axel Meyer, Matej Polacik, Carl Smith, Marcel Honza, Martin ReichardAbstract:Obligate brood parasites manipulate other species into raising their offspring. Avian and insect brood parasitic systems demonstrate how interacting species engage in reciprocal coevolutionary arms races through behavioral and morphological adaptations and counteradaptations. Mouthbrooding Cichlid fishes are renowned for their remarkable evolutionary radiations and complex behaviors. In Lake Tanganyika, mouthbrooding Cichlids are exploited by the only obligate nonavian vertebrate brood parasite, the cuckoo catfish Synodontis multipunctatus. We show that coevolutionary history and individual learning both have a major impact on the success of cuckoo catfish parasitism between coevolved sympatric and evolutionarily naive allopatric Cichlid species. The rate of cuckoo catfish parasitism in coevolved Tanganyikan hosts was 3 to 11 times lower than in evolutionarily naive Cichlids. Moreover, using experimental infections, we demonstrate that parasite egg rejection in sympatric hosts was much higher, leading to seven times greater parasite survival in evolutionarily naive than sympatric hosts. However, a high rejection frequency of parasitic catfish eggs by coevolved sympatric hosts came at a cost of increased rejection of their own eggs. A significant cost of catfish parasitism was universal, except for coevolved sympatric Cichlid species with previous experience of catfish parasitism, demonstrating that learning and individual experience both contribute to a successful host response.
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tol2 transposon mediated transgenesis in the midas Cichlid amphilophus citrinellus towards understanding gene function and regulatory evolution in an ecological model system for rapid phenotypic diversification
BMC Developmental Biology, 2017Co-Authors: Axel Meyer, Claudius F Kratochwil, Maggie M Sefton, Yipeng LiangAbstract:The Midas Cichlid species complex (Amphilophus spp.) is widely known among evolutionary biologists as a model system for sympatric speciation and adaptive phenotypic divergence within extremely short periods of time (a few hundred generations). The repeated parallel evolution of adaptive phenotypes in this radiation, combined with their near genetic identity, makes them an excellent model for studying phenotypic diversification. While many ecological and evolutionary studies have been performed on Midas Cichlids, the molecular basis of specific phenotypes, particularly adaptations, and their underlying coding and cis-regulatory changes have not yet been studied thoroughly. For the first time in any New World Cichlid, we use Tol2 transposon-mediated transgenesis in the Midas Cichlid (Amphilophus citrinellus). By adapting existing microinjection protocols, we established an effective protocol for transgenesis in Midas Cichlids. Embryos were injected with a Tol2 plasmid construct that drives enhanced green fluorescent protein (eGFP) expression under the control of the ubiquitin promoter. The transgene was successfully integrated into the germline, driving strong ubiquitous expression of eGFP in the first transgenic Midas Cichlid line. Additionally, we show transient expression of two further transgenic constructs, ubiquitin::tdTomato and mitfa::eGFP. Transgenesis in Midas Cichlids will facilitate further investigation of the genetic basis of species-specific traits, many of which are adaptations. Transgenesis is a versatile tool not only for studying regulatory elements such as promoters and enhancers, but also for testing gene function through overexpression of allelic gene variants. As such, it is an important first step in establishing the Midas Cichlid as a powerful model for studying adaptive coding and non-coding changes in an ecological and evolutionary context.
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The Integrated Genomic Architecture and Evolution of Dental Divergence in East African Cichlid Fishes (Haplochromis chilotes x H. nyererei).
G3: Genes|Genomes|Genetics, 2017Co-Authors: C. Darrin Hulsey, Gonzalo Machado-schiaffino, Lara Keicher, Diego Ellis-soto, Frederico Henning, Axel MeyerAbstract:The independent evolution of the two toothed jaws of Cichlid fishes is thought to have promoted their unparalleled ecological divergence and species richness. However, dental divergence in Cichlids could exhibit substantial genetic covariance and this could dictate how traits like tooth numbers evolve in different African Lakes and on their two jaws. To test this hypothesis, we used a hybrid mapping cross of two trophically divergent Lake Victoria species (Haplochromis chilotes × Haplochromis nyererei) to examine genomic regions associated with Cichlid tooth diversity. Surprisingly, a similar genomic region was found to be associated with oral jaw tooth numbers in Cichlids from both Lake Malawi and Lake Victoria. Likewise, this same genomic location was associated with variation in pharyngeal jaw tooth numbers. Similar relationships between tooth numbers on the two jaws in both our Victoria hybrid population and across the phylogenetic diversity of Malawi Cichlids additionally suggests that tooth numbers on the two jaws of haplochromine Cichlids might generally coevolve owing to shared genetic underpinnings. Integrated, rather than independent, genomic architectures could be key to the incomparable evolutionary divergence and convergence in Cichlid tooth numbers.
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embryonic and larval development in the midas Cichlid fish species flock amphilophus spp a new evo devo model for the investigation of adaptive novelties and species differences
BMC Developmental Biology, 2015Co-Authors: Claudius F Kratochwil, Maggie M Sefton, Axel MeyerAbstract:Central American crater lake Cichlid fish of the Midas species complex (Amphilophus spp.) are a model system for sympatric speciation and fast ecological diversification and specialization. Midas Cichlids have been intensively analyzed from an ecological and morphological perspective. Genomic resources such as transcriptomic and genomic data sets, and a high-quality draft genome are available now. Many ecologically relevant species-specific traits and differences such as pigmentation and cranial morphology arise during development. Detailed descriptions of the early development of the Midas Cichlid in particular, will help to investigate the ontogeny of species differences and adaptations. We describe the embryonic and larval development of the crater lake Cichlid, Amphilophus xiloaensis, until seven days after fertilization. Similar to previous studies on teleost development, we describe six periods of embryogenesis - the zygote, cleavage, blastula, gastrula, segmentation, and post-hatching period. Furthermore, we define homologous stages to well-described teleost models such as medaka and zebrafish, as well as other Cichlid species such as the Nile tilapia and the South American Cichlid Cichlasoma dimerus. Key morphological differences between the embryos of Midas Cichlids and other teleosts are highlighted and discussed, including the presence of adhesive glands and different early chromatophore patterns, as well as variation in developmental timing. The developmental staging of the Midas Cichlid will aid researchers in the comparative investigation of teleost ontogenies. It will facilitate comparative developmental biological studies of Neotropical and African Cichlid fish in particular. In the past, the species flocks of the African Great Lakes have received the most attention from researchers, but some lineages of the 300–400 species of Central American lakes are fascinating model systems for adaptive radiation and rapid phenotypic evolution. The availability of genetic resources, their status as a model system for evolutionary research, and the possibility to perform functional experiments including transgenesis makes the Midas Cichlid complex a very attractive model for evolutionary-developmental research.
Walter Salzburger - One of the best experts on this subject based on the ideXlab platform.
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ancestral hybridization facilitated species diversification in the lake malawi Cichlid fish adaptive radiation
Molecular Biology and Evolution, 2020Co-Authors: Hannes Svardal, Walter Salzburger, Eric A. Miska, Milan Malinsky, Martin J. Genner, George F. Turner, Fu Xiang Quah, Benjamin P Ngatunga, Richard DurbinAbstract:The adaptive radiation of Cichlid fishes in East African Lake Malawi encompasses over 500 species that are believed to have evolved within the last 800,000 years from a common founder population. It has been proposed that hybridization between ancestral lineages can provide the genetic raw material to fuel such exceptionally high diversification rates, and evidence for this has recently been presented for the Lake Victoria region Cichlid superflock. Here, we report that Lake Malawi Cichlid genomes also show evidence of hybridization between two lineages that split 3-4 Ma, today represented by Lake Victoria Cichlids and the riverine Astatotilapia sp. "ruaha blue." The two ancestries in Malawi Cichlid genomes are present in large blocks of several kilobases, but there is little variation in this pattern between Malawi Cichlid species, suggesting that the large-scale mosaic structure of the genomes was largely established prior to the radiation. Nevertheless, tens of thousands of polymorphic variants apparently derived from the hybridization are interspersed in the genomes. These loci show a striking excess of differentiation across ecological subgroups in the Lake Malawi Cichlid assemblage, and parental alleles sort differentially into benthic and pelagic Malawi Cichlid lineages, consistent with strong differential selection on these loci during species divergence. Furthermore, these loci are enriched for genes involved in immune response and vision, including opsin genes previously identified as important for speciation. Our results reinforce the role of ancestral hybridization in explosive diversification by demonstrating its significance in one of the largest recent vertebrate adaptive radiations.
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A: The species flocks of East African Cichlid fishes: recent advances in molecular phylogenetics and population genetics. Naturwissenschaften 2004
2020Co-Authors: Walter Salzburger, Axel MeyerAbstract:Abstract With more than 3,000 species, the fish family Cichlidae is one of the most species-rich families of vertebrates. Cichlids occur in southern and central America, Africa, Madagascar, and India. The hotspot of their biodiversity is East Africa, where they form adaptive radiations composed of hundreds of endemic species in several lakes of various sizes and ages. The unparalleled species richness of East African Cichlids has been something of a conundrum for evolutionary biologists and ecologists, since it has been in doubt whether these hundreds of species arose by allopatric speciation or whether it is necessary to invoke somewhat less traditional models of speciation, such as micro-allopatric, peripatric, or even sympatric speciation or evolution through sexual selection mediated by female choice. Ernst Mayr's analyses of these evolutionary uniquely diverse species assemblages have contributed to a more direct approach to this problem and have led to a deeper understanding of the patterns and processes that caused the formation of these huge groups of species. We review here recent molecular data on population differentiation and phylogenetics, which have helped to unravel, to some extent, the patterns and processes that led to the formation and ecological maintenance of Cichlid species flocks. It is becoming apparent that sexually selected traits do play an important role in speciation in micro-allopatric or even sympatric settings. Species richness seems to be roughly correlated with the surface area, but not the age, of the lakes. We observe that the oldest lineages of a species flock of Cichlids are often less species-rich and live in the open water or deepwater habitats. While the species flocks of the Lake Malawai and the Lake Victoria areas were shown to be monophyletic, the Cichlid assemblage of Lake Tanganyika seems to consist of several independent species flocks. Cichlids emerge as an evolutionary model system in which many fundamental questions in evolution and ecology can be tested successfully, yet for other fish species flocks the relative importance of alternative mechanisms of speciation is likely to differ from that in Cichlid fish
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ancestral hybridisation facilitated species diversification in the lake malawi Cichlid fish adaptive radiation
bioRxiv, 2019Co-Authors: Hannes Svardal, Walter Salzburger, Eric A. Miska, Milan Malinsky, Martin J. Genner, George F. Turner, Fu Xiang Quah, Benjamin P Ngatunga, Richard DurbinAbstract:Abstract The adaptive radiation of Cichlid fishes in East Afrian Lake Malawi encompasses over 500 species that are believed to have evolved within the last 800 thousand years from a common founder population. It has been proposed that hybridisation between ancestral lineages can provide the genetic raw material to fuel such exceptionally high diversification rates, and evidence for this has recently been presented for the Lake Victoria Region Cichlid superflock. Here we report that Lake Malawi Cichlid genomes also show evidence of hybridisation between two lineages that split 3-4 million years ago, today represented by Lake Victoria Cichlids and the riverine Astatotilapia sp. ‘ruaha blue’. The two ancestries in Malawi Cichlid genomes are present in large blocks of several kilobases, but there is little variation in this pattern between Malawi Cichlid species, suggesting that the large-scale mosaic structure of the genomes was largely established prior to the radiation. Nevertheless, tens of thousands of polymorphic variants apparently derived from the hybridisation are interspersed in the genomes. These loci show a striking excess of differentiation across ecological subgroups in the Lake Malawi Cichlid assemblage, and parental alleles sort differentially into benthic and pelagic Malawi Cichlid lineages, consistent with strong differential selection on these loci during species divergence. Furthermore, these loci are enriched for genes involved in immune response and vision, including opsin genes previously identified as important for speciation. Our results reinforce the role of ancestral hybridisation in explosive diversification by demonstrating its significance in one of the largest recent vertebrate adaptive radiations.
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an exploration of the links between parasites trophic ecology morphology and immunogenetics in the lake tanganyika Cichlid radiation
Hydrobiologia, 2019Co-Authors: Britta S. Meyer, Walter Salzburger, Pascal I Hablutzel, Anna K Roose, Melinda J Hofmann, Joost A M RaeymaekersAbstract: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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Variations on a theme: Genomics of sex determination in the Cichlid fish Astatotilapia burtoni.
BMC genomics, 2016Co-Authors: Astrid Böhne, Catherine Wilson, John H. Postlethwait, Walter SalzburgerAbstract:Sex chromosomes change more frequently in fish than in mammals or birds. However, certain chromosomes or genes are repeatedly used as sex determinants in different members of the teleostean lineage. East African Cichlids are an enigmatic model system in evolutionary biology representing some of the most diverse extant vertebrate adaptive radiations. How sex is determined and if different sex-determining mechanisms contribute to speciation is unknown for almost all of the over 1,500 Cichlid species of the Great Lakes. Here, we investigated the genetic basis of sex determination in a Cichlid from Lake Tanganyika, Astatotilapia burtoni, a member of the most species-rich Cichlid lineage, the haplochromines. We used RAD-sequencing of crosses for two populations of A. burtoni, a lab strain and fish caught at the south of Lake Tanganyika. Using association mapping and comparative genomics, we confirmed male heterogamety in A. burtoni and identified different sex chromosomes (LG5 and LG18) in the two populations of the same species. LG5, the sex chromosome of the lab strain, is a fusion chromosome in A. burtoni. Wnt4 is located on this chromosome, representing the best candidate identified so far for the master sex-determining gene in our lab strain of A. burtoni. Cichlids exemplify the high turnover rate of sex chromosomes in fish with two different chromosomes, LG5 and LG18, containing major sex-determining loci in the two populations of A. burtoni examined here. However, they also illustrate that particular chromosomes are more likely to be used as sex chromosomes. Chromosome 5 is such a chromosome, which has evolved several times as a sex chromosome, both in haplochromine Cichlids from all Great Lakes and also in other teleost fishes.
Frederico Henning - One of the best experts on this subject based on the ideXlab platform.
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phylogenomics uncovers early hybridization and adaptive loci shaping the radiation of lake tanganyika Cichlid fishes
Nature Communications, 2018Co-Authors: Iker Irisarri, Stephan Koblmüller, Frederico Henning, Paolo Franchini, Pooja Singh, Julian Torresdowdall, Christoph Fischer, Alan R LemmonAbstract:Lake Tanganyika is the oldest and phenotypically most diverse of the three East African Cichlid fish adaptive radiations. It is also the cradle for the younger parallel haplochromine Cichlid radiations in Lakes Malawi and Victoria. Despite its evolutionary significance, the relationships among the main Lake Tanganyika lineages remained unresolved, as did the general timescale of Cichlid evolution. Here, we disentangle the deep phylogenetic structure of the Lake Tanganyika radiation using anchored phylogenomics and uncover hybridization at its base, as well as early in the haplochromine radiation. This suggests that hybridization might have facilitated these speciation bursts. Time-calibrated trees support that the radiation of Tanganyika Cichlids coincided with lake formation and that Gondwanan vicariance concurred with the earliest splits in the Cichlid family tree. Genes linked to key innovations show signals of introgression or positive selection following colonization of lake habitats and species’ dietary adaptations are revealed as major drivers of colour vision evolution. These findings shed light onto the processes shaping the evolution of adaptive radiations. Lake Tanganyika’s Cichlid radiation is the main source of East African Cichlid diversity. Irisarri et al. resolve its phylogenetic backbone using anchored phylogenomics and identify trans-lineage hybridization prior to major speciation bursts and adaptive loci underlying ecological innovations.
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The Integrated Genomic Architecture and Evolution of Dental Divergence in East African Cichlid Fishes (Haplochromis chilotes x H. nyererei).
G3: Genes|Genomes|Genetics, 2017Co-Authors: C. Darrin Hulsey, Gonzalo Machado-schiaffino, Lara Keicher, Diego Ellis-soto, Frederico Henning, Axel MeyerAbstract:The independent evolution of the two toothed jaws of Cichlid fishes is thought to have promoted their unparalleled ecological divergence and species richness. However, dental divergence in Cichlids could exhibit substantial genetic covariance and this could dictate how traits like tooth numbers evolve in different African Lakes and on their two jaws. To test this hypothesis, we used a hybrid mapping cross of two trophically divergent Lake Victoria species (Haplochromis chilotes × Haplochromis nyererei) to examine genomic regions associated with Cichlid tooth diversity. Surprisingly, a similar genomic region was found to be associated with oral jaw tooth numbers in Cichlids from both Lake Malawi and Lake Victoria. Likewise, this same genomic location was associated with variation in pharyngeal jaw tooth numbers. Similar relationships between tooth numbers on the two jaws in both our Victoria hybrid population and across the phylogenetic diversity of Malawi Cichlids additionally suggests that tooth numbers on the two jaws of haplochromine Cichlids might generally coevolve owing to shared genetic underpinnings. Integrated, rather than independent, genomic architectures could be key to the incomparable evolutionary divergence and convergence in Cichlid tooth numbers.
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The evolutionary genomics of Cichlid fishes: explosive speciation and adaptation in the postgenomic era.
Annual review of genomics and human genetics, 2014Co-Authors: Frederico Henning, Axel MeyerAbstract:With more than 1,500 species, Cichlid fishes provide textbook examples of recent and diverse adaptive radiations, rapid rates of speciation, and the parallel evolution of adaptive phenotypes among both recently and distantly related lineages. This extraordinary diversity has attracted considerable interest from researchers across several biological disciplines. Their broad phenotypic variation coupled with recent divergence makes Cichlids an ideal model system for understanding speciation, adaptation, and phenotypic diversification. Genetic mapping, genome-wide analyses, and genome projects have flourished in the past decade and have added new insights on the question of why there are so many Cichlids. These recent findings also show that the sharing of older DNA polymorphisms is extensive and suggest that linage sorting is incomplete and that adaptive introgression played a role in the African radiation. Here, we review the results of genetic and genomic research on Cichlids in the past decade and suggest some potential avenues to further exploit the potential of the Cichlid model system to provide a better understanding of the genomics of adaptation and speciation.
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A microsatellite-based genetic linkage map of the Cichlid fish, Astatotilapia burtoni (Teleostei): a comparison of genomic architectures among rapidly speciating Cichlids.
Genetics, 2008Co-Authors: Matthias Sanetra, Axel Meyer, Frederico Henning, Shoji FukamachiAbstract:Cichlid fishes compose an astonishingly large number of species and formed species flocks in record-breaking time. To facilitate efficient genome scans and comparisons of Cichlid genomes, we constructed a medium-density genetic linkage map of microsatellite markers of Astatotilapia burtoni. The mapping cross was derived from two inbred laboratory lines to obtain F2 progeny by intercrossing. The map revealed 25 linkage groups spanning 1249.3 cM of the genome (size ∼950 Mb) with an average marker spacing of 6.12 cM. The seven Hox clusters, ParaHox C1, and two paralogs of Pdgfrβ were mapped to different linkage groups, thus supporting the hypothesis of a teleost-specific genome duplication. The A. burtoni linkage map was compared to the other two available maps for Cichlids using shared markers that showed conservation and synteny among East African Cichlid genomes. Interesting candidate genes for Cichlid speciation were mapped using SNP markers.
Claudius F Kratochwil - One of the best experts on this subject based on the ideXlab platform.
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tol2 transposon mediated transgenesis in the midas Cichlid amphilophus citrinellus towards understanding gene function and regulatory evolution in an ecological model system for rapid phenotypic diversification
BMC Developmental Biology, 2017Co-Authors: Axel Meyer, Claudius F Kratochwil, Maggie M Sefton, Yipeng LiangAbstract:The Midas Cichlid species complex (Amphilophus spp.) is widely known among evolutionary biologists as a model system for sympatric speciation and adaptive phenotypic divergence within extremely short periods of time (a few hundred generations). The repeated parallel evolution of adaptive phenotypes in this radiation, combined with their near genetic identity, makes them an excellent model for studying phenotypic diversification. While many ecological and evolutionary studies have been performed on Midas Cichlids, the molecular basis of specific phenotypes, particularly adaptations, and their underlying coding and cis-regulatory changes have not yet been studied thoroughly. For the first time in any New World Cichlid, we use Tol2 transposon-mediated transgenesis in the Midas Cichlid (Amphilophus citrinellus). By adapting existing microinjection protocols, we established an effective protocol for transgenesis in Midas Cichlids. Embryos were injected with a Tol2 plasmid construct that drives enhanced green fluorescent protein (eGFP) expression under the control of the ubiquitin promoter. The transgene was successfully integrated into the germline, driving strong ubiquitous expression of eGFP in the first transgenic Midas Cichlid line. Additionally, we show transient expression of two further transgenic constructs, ubiquitin::tdTomato and mitfa::eGFP. Transgenesis in Midas Cichlids will facilitate further investigation of the genetic basis of species-specific traits, many of which are adaptations. Transgenesis is a versatile tool not only for studying regulatory elements such as promoters and enhancers, but also for testing gene function through overexpression of allelic gene variants. As such, it is an important first step in establishing the Midas Cichlid as a powerful model for studying adaptive coding and non-coding changes in an ecological and evolutionary context.
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embryonic and larval development in the midas Cichlid fish species flock amphilophus spp a new evo devo model for the investigation of adaptive novelties and species differences
BMC Developmental Biology, 2015Co-Authors: Claudius F Kratochwil, Maggie M Sefton, Axel MeyerAbstract:Background Central American crater lake Cichlid fish of the Midas species complex (Amphilophus spp.) are a model system for sympatric speciation and fast ecological diversification and specialization. Midas Cichlids have been intensively analyzed from an ecological and morphological perspective. Genomic resources such as transcriptomic and genomic data sets, and a high-quality draft genome are available now. Many ecologically relevant species-specific traits and differences such as pigmentation and cranial morphology arise during development. Detailed descriptions of the early development of the Midas Cichlid in particular, will help to investigate the ontogeny of species differences and adaptations.
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embryonic and larval development in the midas Cichlid fish species flock amphilophus spp a new evo devo model for the investigation of adaptive novelties and species differences
BMC Developmental Biology, 2015Co-Authors: Claudius F Kratochwil, Maggie M Sefton, Axel MeyerAbstract:Central American crater lake Cichlid fish of the Midas species complex (Amphilophus spp.) are a model system for sympatric speciation and fast ecological diversification and specialization. Midas Cichlids have been intensively analyzed from an ecological and morphological perspective. Genomic resources such as transcriptomic and genomic data sets, and a high-quality draft genome are available now. Many ecologically relevant species-specific traits and differences such as pigmentation and cranial morphology arise during development. Detailed descriptions of the early development of the Midas Cichlid in particular, will help to investigate the ontogeny of species differences and adaptations. We describe the embryonic and larval development of the crater lake Cichlid, Amphilophus xiloaensis, until seven days after fertilization. Similar to previous studies on teleost development, we describe six periods of embryogenesis - the zygote, cleavage, blastula, gastrula, segmentation, and post-hatching period. Furthermore, we define homologous stages to well-described teleost models such as medaka and zebrafish, as well as other Cichlid species such as the Nile tilapia and the South American Cichlid Cichlasoma dimerus. Key morphological differences between the embryos of Midas Cichlids and other teleosts are highlighted and discussed, including the presence of adhesive glands and different early chromatophore patterns, as well as variation in developmental timing. The developmental staging of the Midas Cichlid will aid researchers in the comparative investigation of teleost ontogenies. It will facilitate comparative developmental biological studies of Neotropical and African Cichlid fish in particular. In the past, the species flocks of the African Great Lakes have received the most attention from researchers, but some lineages of the 300–400 species of Central American lakes are fascinating model systems for adaptive radiation and rapid phenotypic evolution. The availability of genetic resources, their status as a model system for evolutionary research, and the possibility to perform functional experiments including transgenesis makes the Midas Cichlid complex a very attractive model for evolutionary-developmental research.
Hernan Lopezfernandez - One of the best experts on this subject based on the ideXlab platform.
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evolution inactivation and loss of short wavelength sensitive opsin genes during the diversification of neotropical Cichlids
Molecular Ecology, 2021Co-Authors: Frances E Hauser, Katriina L Ilves, Hernan Lopezfernandez, Ryan K Schott, Erin Alvi, Belinda S. W. ChangAbstract:Natural variation in the number, expression and function of sensory genes in an organism's genome is often tightly linked to different ecological and evolutionary forces. Opsin genes, which code for the first step in visual transduction, are ideal models for testing how ecological factors such as light environment may influence visual system adaptation. Neotropical Cichlid fishes are a highly ecologically diverse group that evolved in a variety of aquatic habitats, including black (stained), white (opaque) and clear waters. We used cross-species exon capture to sequence Neotropical Cichlid short wavelength-sensitive (SWS) opsins, which mediate ultraviolet (UV) to blue visual sensitivity. Neotropical Cichlid SWS1 opsin (UV-sensitive) underwent a relaxation of selective constraint during the early phases of Cichlid diversification in South America, leading to pseudogenization and loss. Conversely, SWS2a (blue-sensitive) experienced a burst of episodic positive selection at the base of the South American Cichlid radiation. This burst coincides with SWS1 relaxation and loss, and is consistent with findings in ecomorphological studies characterizing a period of extensive ecological divergence in Neotropical Cichlids. We use ancestral sequence reconstruction and protein modelling to investigate mutations along this ancestral branch that probably modified SWS2a function. Together, our results suggest that variable light environments played a prominent early role in shaping SWS opsin diversity during the Neotropical Cichlid radiation. Our results also illustrate that long-term evolution under light-limited conditions in South America may have reduced visual system plasticity; specifically, early losses of UV sensitivity may have constrained the evolutionary trajectory of Neotropical Cichlid vision.
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exon based phylogenomics strengthens the phylogeny of neotropical Cichlids and identifies remaining conflicting clades cichliformes Cichlidae cichlinae
Molecular Phylogenetics and Evolution, 2018Co-Authors: Katriina L Ilves, Dax Torti, Hernan LopezfernandezAbstract:Abstract The phenotypic, geographic, and species diversity of Cichlid fishes have made them a group of great interest for studying evolutionary processes. Here we present a targeted-exon next-generation sequencing approach for investigating the evolutionary relationships of Cichlid fishes (Cichlidae), with focus on the Neotropical subfamily Cichlinae using a set of 923 primarily single-copy exons designed through mining of the Nile tilapia ( Oreochromis niloticus ) genome. Sequence capture and assembly were robust, leading to a complete dataset of 415 exons for 139 species (147 terminals) that consisted of 128 Neotropical species, six African taxa, and five Indo-Malagasy Cichlids. Gene and species trees were calculated using alternative partitioning schemes and reconstruction methods. In general, all methods yielded similar topologies to previously hypothesized relationships within the Cichlinae and clarified several relationships that were previously poorly supported or in conflict. Additional work will be needed to fully resolve all aspects of Cichlinae phylogeny. Overall, this approach yielded a well-resolved phylogeny of Neotropical Cichlids that will be of utility for future assessments of the evolutionary and ecological processes within this diverse group of fishes. Furthermore, the general methodology employed here of exon targeting and capture should be applicable to any group of organisms with the availability of a reference genome.
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accelerated evolution and functional divergence of the dim light visual pigment accompanies Cichlid colonization of central america
Molecular Biology and Evolution, 2017Co-Authors: Frances E Hauser, Katriina L Ilves, Hernan Lopezfernandez, Ryan K Schott, Gianni M Castiglione, Belinda S. W. ChangAbstract:Cichlids encompass one of the most diverse groups of fishes in South and Central America, and show extensive variation in life history, morphology, and colouration. While studies of visual system evolution in Cichlids have focussed largely on the African rift lake species flocks, Neotropical Cichlids offer a unique opportunity to investigate visual system evolution at broader temporal and geographic scales. South American Cichlid colonization of Central America has likely promoted accelerated rates of morphological evolution in Central American lineages as they encountered reduced competition, renewed ecological opportunity, and novel aquatic habitats. To investigate whether such transitions have influenced molecular evolution of vision in Central American Cichlids, we sequenced the dim-light rhodopsin gene in 101 Neotropical Cichlid species, spanning the diversity of the clade. We find strong evidence for increased rates of evolution in Central American Cichlid rhodopsin relative to South American lineages, and identify several sites under positive selection in rhodopsin that likely contribute to adaptation to different photic environments. We expressed a Neotropical Cichlid rhodopsin protein invitro for the first time, and found that while its spectral tuning properties were characteristic of typical vertebrate rhodopsin pigments, the rate of decay of its active signalling form was much slower, consistent with dim light adaptation in other vertebrate rhodopsins. Using site-directed mutagenesis combined with spectroscopic assays, we found that a key amino acid substitution present in some Central American Cichlids accelerates the rate of decay of active rhodopsin, which may mediate adaptation to clear water habitats.
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exon based phylogenomics strengthens the phylogeny of neotropical Cichlids and identifies remaining conflicting clades cichlomorphae Cichlidae cichlinae
bioRxiv, 2017Co-Authors: Katriina L Ilves, Dax Torti, Hernan LopezfernandezAbstract:The phenotypic, geographic, and species diversity of Cichlid fishes have made them a group of great interest for studying evolutionary processes. Here we present a targeted-exon next-generation sequencing approach for investigating the evolutionary relationships of Cichlid fishes (Cichlidae), with a particular focus on the Neotropical subfamily Cichlinae using a set of 923 primarily single-copy exons designed through mining of the Nile tilapia ( Oreochromis niloticus ) genome. Sequence capture and assembly were robust, leading to a complete dataset of 415 exons for 139 species (147 terminals) that consisted of 128 Neotropical species, six African taxa, and five Indo-Malagasy Cichlids. Gene and species trees were calculated using alternative partitioning schemes and reconstruction methods. In general, all methods yielded similar topologies to previously hypothesized relationships within the Cichlinae and clarified several relationships that were previously poorly supported or in conflict. Additional work will be needed to fully resolve all aspects of Cichlinae phylogeny. Overall, this approach yielded a well-resolved phylogeny of Neotropical Cichlids that will be of utility for future assessments of the evolutionary and ecological processes within this diverse group of fishes. Furthermore, the general methodology employed here of exon targeting and capture should be applicable to any group of organisms with the availability of a reference genome.
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body size diversity and frequency distributions of neotropical Cichlid fishes cichliformes Cichlidae cichlinae
PLOS ONE, 2014Co-Authors: Sarah E Steele, Hernan LopezfernandezAbstract:Body size is an important correlate of life history, ecology and distribution of species. Despite this, very little is known about body size evolution in fishes, particularly freshwater fishes of the Neotropics where species and body size diversity are relatively high. Phylogenetic history and body size data were used to explore body size frequency distributions in Neotropical Cichlids, a broadly distributed and ecologically diverse group of fishes that is highly representative of body size diversity in Neotropical freshwater fishes. We test for divergence, phylogenetic autocorrelation and among-clade partitioning of body size space. Neotropical Cichlids show low phylogenetic autocorrelation and divergence within and among taxonomic levels. Three distinct regions of body size space were identified from body size frequency distributions at various taxonomic levels corresponding to subclades of the most diverse tribe, Geophagini. These regions suggest that lineages may be evolving towards particular size optima that may be tied to specific ecological roles. The diversification of Geophagini appears to constrain the evolution of body size among other Neotropical Cichlid lineages; non-Geophagini clades show lower species-richness in body size regions shared with Geophagini. Neotropical Cichlid genera show less divergence and extreme body size than expected within and among tribes. Body size divergence among species may instead be present or linked to ecology at the community assembly scale.