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Hernan Lopezfernandez - One of the best experts on this subject based on the ideXlab platform.
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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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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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adaptive landscape and functional diversity of neotropical cichlids implications for the ecology and evolution of cichlinae Cichlidae cichliformes
Journal of Evolutionary Biology, 2014Co-Authors: Jessica H Arbour, Hernan LopezfernandezAbstract:Morphological, lineage and ecological diversity can vary substantially even among closely related lineages. Factors that influence morphological diversification, especially in functionally relevant traits, can help to explain the modern distribution of disparity across phylogenies and communities. Multivariate axes of feeding functional morphology from 75 species of Neotropical cichlid and a stepwise-AIC algorithm were used to estimate the adaptive landscape of functional morphospace in Cichlinae. Adaptive landscape complexity and convergence, as well as the functional diversity of Cichlinae, were compared with expectations under null evolutionary models. Neotropical cichlid feeding function varied primarily between traits associated with ram feeding vs. suction feeding/biting and secondarily with oral jaw muscle size and pharyngeal crushing capacity. The number of changes in selective regimes and the amount of convergence between lineages was higher than expected under a null model of evolution, but convergence was not higher than expected under a similarly complex adaptive landscape. Functional disparity was compatible with an adaptive landscape model, whereas the distribution of evolutionary change through morphospace corresponded with a process of evolution towards a single adaptive peak. The continentally distributed Neotropical cichlids have evolved relatively rapidly towards a number of adaptive peaks in functional trait space. Selection in Cichlinae functional morphospace is more complex than expected under null evolutionary models. The complexity of selective constraints in feeding morphology has likely been a significant contributor to the diversity of feeding ecology in this clade.
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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.
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diet morphology correlations in the radiation of south american geophagine cichlids perciformes Cichlidae cichlinae
PLOS ONE, 2012Co-Authors: Hernan Lopezfernandez, Kirk O Winemiller, Carmen G Montana, Rodney L HoneycuttAbstract:Genera within the South American cichlid tribe Geophagini display specialized feeding and reproductive strategies, with some taxa specialized for both substrate-sifting and mouth brooding. Several lineages within the clade also possess an epibranchial lobe (EBL), a unique pharyngeal structure that has been proposed to have a function in feeding and/or mouth brooding. A recently published genus-level phylogeny of Neotropical cichlids was used as the evolutionary framework for investigating the evolution of morphological features presumably correlated with diet and mouth brooding in the tribe Geophagini. We tested for possible associations between the geophagine epibranchial lobe and benthic feeding and mouth brooding. We also addressed whether the EBL may be associated with unique patterns of diversification in certain geophagine clades. Tests of binary character correlations revealed the EBL was significantly associated with mouth brooding. We also tested for a relationship between diet and morphology. We analyzed stomach contents and morphometric variation among 21 species, with data for two additional species obtained from the literature. Principal Components Analysis revealed axes of morphological variation significantly correlated with piscivory and benthivory, and both morphology and diet were significantly associated with phylogeny. These results suggest that the EBL could be an adaptation for either feeding or mouth brooding. The EBL, however, was not associated with species richness or accelerated rates of phyletic diversification.
Mutsumi Nishida - One of the best experts on this subject based on the ideXlab platform.
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Independent evolution of the specialized pharyngeal jaw apparatus in cichlid and labrid fishes
BMC Evolutionary Biology, 2007Co-Authors: Kohji Mabuchi, Masaki Miya, Yoichiro Azuma, Mutsumi NishidaAbstract:Background Fishes in the families Cichlidae and Labridae provide good probable examples of vertebrate adaptive radiations. Their spectacular trophic radiations have been widely assumed to be due to structural key innovation in pharyngeal jaw apparatus (PJA), but this idea has never been tested based on a reliable phylogeny. For the first step of evaluating the hypothesis, we investigated the phylogenetic positions of the components of the suborder Labroidei (including Pomacentridae and Embiotocidae in addition to Cichlidae and Labridae) within the Percomorpha, the most diversified (> 15,000 spp) crown clade of teleosts. We examined those based on 78 whole mitochondrial genome sequences (including 12 newly determined sequences) through partitioned Bayesian analyses with concatenated sequences (13,933 bp). Results The resultant phylogenies indicated that the Labridae and the remaining three labroid families have diverged basally within the Percomorpha, and monophyly of the suborder was confidently rejected by statistical tests using Bayes factors. Conclusion The resultant phylogenies indicated that the specified PJA evolved independently at least twice, once in Labridae and once in the common ancestor of the remaining three labroid families (including the Cichlidae). Because the independent evolution of pharyngeal jaws appears to have been followed by trophic radiations, we consider that our result supports, from the aspect of historical repeatability, the idea that the evolution of the specialized PJA provided these lineages with the morphological potential for their spectacular trophic radiations. The present result will provide a new framework for the study of functional morphology and genetic basis of their PJA.
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Independent evolution of the specialized pharyngeal jaw apparatus in cichlid and labrid fishes
BMC evolutionary biology, 2007Co-Authors: Kohji Mabuchi, Masaki Miya, Yoichiro Azuma, Mutsumi NishidaAbstract:Background Fishes in the families Cichlidae and Labridae provide good probable examples of vertebrate adaptive radiations. Their spectacular trophic radiations have been widely assumed to be due to structural key innovation in pharyngeal jaw apparatus (PJA), but this idea has never been tested based on a reliable phylogeny. For the first step of evaluating the hypothesis, we investigated the phylogenetic positions of the components of the suborder Labroidei (including Pomacentridae and Embiotocidae in addition to Cichlidae and Labridae) within the Percomorpha, the most diversified (> 15,000 spp) crown clade of teleosts. We examined those based on 78 whole mitochondrial genome sequences (including 12 newly determined sequences) through partitioned Bayesian analyses with concatenated sequences (13,933 bp).
Cláudia Portes Santos - One of the best experts on this subject based on the ideXlab platform.
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Parasites of Satanoperca jurupari (Osteichthyes: Cichlidae) from Brazil
Parasitology research, 2011Co-Authors: Marly De Fátima Carvalho De Melo, Everton Gustavo Nunes Dos Santos, Elane Guerreiro Giese, Jeannie Nascimento Dos Santos, Cláudia Portes SantosAbstract:Satanoperca jurupari (Osteichthyes: Cichlidae) is reported for the first time to be parasitized by the nematodes Procamallanus (Spirocamallanus) rarus Travassos, Artigas and Pereira, 1928, Procamallanus (Spirocamallanus) sp., larvae of Raphidascaroides sp. and Anisakidae gen. sp., and by the acanthocephalan Neoechinorhynchus (Neoechinorhynchus) paraguayensis Machado Filho (Rev Bras Biol 19:379-381, 1959).
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Raphidascaris (Sprentascaris) lanfrediae sp. nov. (Nematoda: Anisakidae) from the fish Satanoperca jurupari (Osteichthyes: Cichlidae)
Memorias do Instituto Oswaldo Cruz, 2011Co-Authors: Marly De Fátima Carvalho De Melo, Everton Gustavo Nunes Dos Santos, Elane Guerreiro Giese, Jeannie Nascimento Dos Santos, Cláudia Portes SantosAbstract:Raphidascaris (Sprentascaris) lanfrediae sp. nov. is described from the intestine of the freshwater fish Satanoperca jurupari (Heckel) (Cichlidae) from the Guama River, state of Para, Brazil. The prevalence in fish (n = 59) was 27% with intensity of one-124 (mean 16) nematodes per fish. The new species is characterized mainly by the markedly larger size of ventricular appendix in relation to the oesophagus, presence of short male caudal alae, 14-16 subventral pairs of preanal papillae and six pairs of postanal papillae.
Kohji Mabuchi - One of the best experts on this subject based on the ideXlab platform.
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Independent evolution of the specialized pharyngeal jaw apparatus in cichlid and labrid fishes
BMC Evolutionary Biology, 2007Co-Authors: Kohji Mabuchi, Masaki Miya, Yoichiro Azuma, Mutsumi NishidaAbstract:Background Fishes in the families Cichlidae and Labridae provide good probable examples of vertebrate adaptive radiations. Their spectacular trophic radiations have been widely assumed to be due to structural key innovation in pharyngeal jaw apparatus (PJA), but this idea has never been tested based on a reliable phylogeny. For the first step of evaluating the hypothesis, we investigated the phylogenetic positions of the components of the suborder Labroidei (including Pomacentridae and Embiotocidae in addition to Cichlidae and Labridae) within the Percomorpha, the most diversified (> 15,000 spp) crown clade of teleosts. We examined those based on 78 whole mitochondrial genome sequences (including 12 newly determined sequences) through partitioned Bayesian analyses with concatenated sequences (13,933 bp). Results The resultant phylogenies indicated that the Labridae and the remaining three labroid families have diverged basally within the Percomorpha, and monophyly of the suborder was confidently rejected by statistical tests using Bayes factors. Conclusion The resultant phylogenies indicated that the specified PJA evolved independently at least twice, once in Labridae and once in the common ancestor of the remaining three labroid families (including the Cichlidae). Because the independent evolution of pharyngeal jaws appears to have been followed by trophic radiations, we consider that our result supports, from the aspect of historical repeatability, the idea that the evolution of the specialized PJA provided these lineages with the morphological potential for their spectacular trophic radiations. The present result will provide a new framework for the study of functional morphology and genetic basis of their PJA.
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Independent evolution of the specialized pharyngeal jaw apparatus in cichlid and labrid fishes
BMC evolutionary biology, 2007Co-Authors: Kohji Mabuchi, Masaki Miya, Yoichiro Azuma, Mutsumi NishidaAbstract:Background Fishes in the families Cichlidae and Labridae provide good probable examples of vertebrate adaptive radiations. Their spectacular trophic radiations have been widely assumed to be due to structural key innovation in pharyngeal jaw apparatus (PJA), but this idea has never been tested based on a reliable phylogeny. For the first step of evaluating the hypothesis, we investigated the phylogenetic positions of the components of the suborder Labroidei (including Pomacentridae and Embiotocidae in addition to Cichlidae and Labridae) within the Percomorpha, the most diversified (> 15,000 spp) crown clade of teleosts. We examined those based on 78 whole mitochondrial genome sequences (including 12 newly determined sequences) through partitioned Bayesian analyses with concatenated sequences (13,933 bp).
Marly De Fátima Carvalho De Melo - One of the best experts on this subject based on the ideXlab platform.
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Parasites of Satanoperca jurupari (Osteichthyes: Cichlidae) from Brazil
Parasitology research, 2011Co-Authors: Marly De Fátima Carvalho De Melo, Everton Gustavo Nunes Dos Santos, Elane Guerreiro Giese, Jeannie Nascimento Dos Santos, Cláudia Portes SantosAbstract:Satanoperca jurupari (Osteichthyes: Cichlidae) is reported for the first time to be parasitized by the nematodes Procamallanus (Spirocamallanus) rarus Travassos, Artigas and Pereira, 1928, Procamallanus (Spirocamallanus) sp., larvae of Raphidascaroides sp. and Anisakidae gen. sp., and by the acanthocephalan Neoechinorhynchus (Neoechinorhynchus) paraguayensis Machado Filho (Rev Bras Biol 19:379-381, 1959).
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Raphidascaris (Sprentascaris) lanfrediae sp. nov. (Nematoda: Anisakidae) from the fish Satanoperca jurupari (Osteichthyes: Cichlidae)
Memorias do Instituto Oswaldo Cruz, 2011Co-Authors: Marly De Fátima Carvalho De Melo, Everton Gustavo Nunes Dos Santos, Elane Guerreiro Giese, Jeannie Nascimento Dos Santos, Cláudia Portes SantosAbstract:Raphidascaris (Sprentascaris) lanfrediae sp. nov. is described from the intestine of the freshwater fish Satanoperca jurupari (Heckel) (Cichlidae) from the Guama River, state of Para, Brazil. The prevalence in fish (n = 59) was 27% with intensity of one-124 (mean 16) nematodes per fish. The new species is characterized mainly by the markedly larger size of ventricular appendix in relation to the oesophagus, presence of short male caudal alae, 14-16 subventral pairs of preanal papillae and six pairs of postanal papillae.