scholarly journals Analysis of structural variants in four African Cichlids highlights an association with developmental and immune related genes

2018 ◽  
Author(s):  
Luca Penso-Dolfin ◽  
Angela Man ◽  
Wilfried Haerty ◽  
Federica Di Palma
Keyword(s):  
Antigen Processing ◽  
Lake Victoria ◽  
Ecological Niches ◽  
Structural Variants ◽  
Evolutionary Potential ◽  
Nucleotide Substitutions ◽  
Comprehensive Overview ◽  
Cichlid Species ◽  
Haplochromis Burtoni ◽  
African Cichlids

ABSTRACTAfrican Lakes Cichlids are one of the most impressive example of adaptive radiation. Independently in Lake Victoria, Tanganyika, and Malawi, several hundreds of species arose within the last 10 million to 100,000 years. Whereas most analyses in Cichlids focused on nucleotide substitutions across species to investigate the genetic bases of this explosive radiation, to date, no study has investigated the contribution of structural variants (SVs) to speciation events (through a reduction of gene flow) and adaptation to different ecological niches. Here, we annotate and characterize the repertoires and evolutionary potential of different SV classes (deletion, duplication, inversion, insertions and translocations) in five Cichlid species (Haplochromis burtoni, Metriaclima zebra, Neolamprologus brichardi, Pundamilia nyererei and Oreochromis niloticus). We investigate the patterns of gain/loss across the phylogeny for each SV type enabling the identification of both lineage specific events and a set of conserved SVs, common to all four species in the radiation. Both deletion and inversion events show a significant overlap with SINE elements, while inversions additionally show a limited, but significant association with DNA transposons. Inverted regions are enriched for genes regulating behaviour, or involved in skeletal and visual system development. We also find that duplicated regions show enrichment for genes associated with “antigen processing and presentation” (GO:0019882) and other immune related categories. Altogether, we provide the first, comprehensive overview of rearrangement evolution in East African Cichlids, and some initial insights into their possible contribution to adaptation.

scholarly journals Analysis of structural variants in four African Cichlids highlights an association with developmental and immune related genes

2019 ◽  
Author(s):  
Luca Penso Dolfin ◽  
Angela Man ◽  
Tarang Mehta ◽  
Wilfried Haerty ◽  
Federica Di Palma
Keyword(s):  
Antigen Processing ◽  
Lake Victoria ◽  
Ecological Niches ◽  
Structural Variants ◽  
Evolutionary Potential ◽  
Nucleotide Substitutions ◽  
Comprehensive Overview ◽  
Cichlid Species ◽  
Haplochromis Burtoni ◽  
African Cichlids

Abstract Background. African Lakes Cichlids are one of the most impressive example of adaptive radiation. Independently in Lake Victoria, Tanganyika, and Malawi, several hundreds of species arose within the last 10 million to 100,000 years. Whereas most analyses in Cichlids focused on nucleotide substitutions across species to investigate the genetic bases of this explosive radiation, to date, no study has investigated the contribution of structural variants (SVs) to speciation events and adaptation to different ecological niches. Results. Here, we annotate and characterize the repertoires and evolutionary potential of different SV classes (deletion, duplication, inversion, insertions and translocations) in four Cichlid species: Haplochromis burtoni, Metriaclima zebra, Neolamprologus brichardi and Pundamilia nyererei. We investigate the patterns of gain and loss evolution for each SV type, enabling the identification of lineage specific events. Both deletions and inversions show a significant overlap with SINE elements, while inversions additionally show a limited, but significant association with DNA transposons. Inverted regions are enriched for genes regulating behaviour, or involved in skeletal and visual system development. We also find that duplicated regions show enrichment for genes associated with “antigen processing and presentation” and other immune related categories. Our pipeline and biological results were further tested by PCR validation of selected deletions and inversions, which confirmed respectively 7 out of 10 and 6 out of 9 events. Conclusions. Altogether, we provide the first, comprehensive overview of rearrangement evolution in East African Cichlids, and some important insights into their likely contribution to adaptation.

scholarly journals Analysis of structural variants in four African Cichlids highlights an association with developmental and immune related genes

2020 ◽  
Author(s):  
Luca Penso Dolfin ◽  
Angela Man ◽  
Tarang Mehta ◽  
Wilfried Haerty ◽  
Federica Di Palma
Keyword(s):  
Antigen Processing ◽  
Lake Victoria ◽  
Structural Variants ◽  
Evolutionary Potential ◽  
East African ◽  
Nucleotide Substitutions ◽  
Comprehensive Overview ◽  
Cichlid Species ◽  
Haplochromis Burtoni ◽  
African Cichlids

Abstract Background . East African lake cichlids are one of the most impressive examples of an adaptive radiation. Independently in Lake Victoria, Tanganyika, and Malawi, several hundreds of species arose within the last 10 million to 100,000 years. Whereas most analyses in cichlids focused on nucleotide substitutions across species to investigate the genetic bases of this explosive radiation, to date, no study has investigated the contribution of structural variants (SVs) in the evolution of adaptive traits across the three Great Lakes of East Africa. Results . Here, we annotate and characterize the repertoires and evolutionary potential of different SV classes (deletion, duplication, inversion, insertions and translocations) in four cichlid species: Haplochromis burtoni, Metriaclima zebra, Neolamprologus brichardi and Pundamilia nyererei . We investigate the patterns of gain and loss evolution for each SV type, enabling the identification of lineage specific events. Both deletions and inversions show a significant overlap with SINE elements, while inversions additionally show a limited, but significant association with DNA transposons. Inverted regions are enriched for genes regulating behaviour, or involved in skeletal and visual system development. We also find that duplicated regions show enrichment for genes associated with “antigen processing and presentation” and other immune related categories. Our pipeline and results were further tested by PCR validation of selected deletions and inversions, which confirmed respectively 7 out of 10 and 6 out of 9 events. Conclusions . Altogether, we provide the first comprehensive overview of rearrangement evolution in East African cichlids, and some important insights into their likely contribution to adaptation.

scholarly journals Four new species of Cichlidogyrus (Platyhelminthes, Monogenea, Dactylogyridae) from Lake Victoria haplochromine cichlid fishes, with the redescription of C. bifurcatus and C. longipenis

2021 ◽  
Author(s):  
Tiziana P Gobbin ◽  
Maarten PM Vanhove ◽  
Ole Seehausen ◽  
Martine E Maan ◽  
Antoine Pariselle
Keyword(s):  
Nous Avons ◽  
Host Specificity ◽  
Lake Victoria ◽  
Model Systems ◽  
Zoological Nomenclature ◽  
Cichlid Species ◽  
African Great Lakes ◽  
Adaptive Radiations ◽  
African Cichlids ◽  
Host Parasite

AbstractAfrican cichlids are model systems for evolutionary studies and for host-parasite interactions, because of their adaptive radiations and because they harbour many species of monogenean parasites with high host-specificity. Here, we sampled five locations in southern Lake Victoria, the youngest of the African Great Lakes. We surveyed gillinfecting monogeneans from 18 cichlid species belonging to the Lake Victoria radiation superflock and two cichlid species representing two older and distantly related lineages. We found one species of Gyrodactylus (Gyrodactylidae, Monogenea), Gyrodactylus sturmbaueri Vanhove, Snoeks, Volckaert & Huyse, 2011, and seven species of Cichlidogyrus (Dactylogyridae, Monogenea). Four species are herein described: Cichlidogyrus pseudodossoui n. sp., C. nyanza n. sp., C. furu n. sp., C. vetusmolendarius n. sp.. Another species is reported but not formally described (because of few specimens and morphological similarity with C. furu n. sp.). Two other species are redescribed: Cichlidogyrus bifurcatus Paperna, 1960 and C. longipenis Paperna & Thurston, 1969. Our results confirm that the monogenean fauna of Victorian littoral cichlids displays lower species richness and lower host-specificity than that of Lake Tanganyika littoral cichlids. In C. furu n. sp., hooks V are clearly longer than the other hooks, highlighting the need to re-evaluate the current classification system of haptoral configurations that considers hook pairs III-VII as rather uniform. Some morphological features of C. bifurcatus, C. longipenis and C. nyanza n. sp. suggest that these are closely related to other congeners that infect haplochromines. We also found morphological indications that representatives of Cichlidogyrus colonised Lake Victoria haplochromines or their ancestors at least twice, which is in line with the Lake Victoria superflock being colonized by two cichlid tribes (Haplochromini and Oreochromini).DisclaimerThis preprint is disclaimed for purposes of Zoological Nomenclature in accordance with the International Code of Zoological Nomenclature, Fourth Edition Articles 8.2 and 8.3 (ICZN 1999). No new names or nomenclatural changes are available from statements in this preprint.Résumé - Quatre espèces nouvelles de Cichlidogyrus (Platyhelminthes, Monogenea, Dactylogyridae) parasites d’haplochrominé (Cichlidae) du lac Victoria, avec la redescription de C. bifurcatus and C. longipenisA cause des radiations adaptatives qu’ils ont subies, les cichlidés africain sont des systèmes modèles pour étudier l’évolution, mais aussi les relations hôtes/parasites, car ils hébergent de nombreuses espèces de Monogènes parasites qui présentent une spécificité étroite vis-à-vis de leurs hôtes. Dans ce travail, nous avons échantillonné cinq localités dans le Sud du lac Victoria, le plus jeune des grands lacs d’Afrique de l’Est. Nous avons examiné les Monogènes présents sur les branchies de 18 espèces de Cichlidés appartenant à la radiation adaptative « superflock » du lac Victoria et de deux espèces représentant deux lignées anciennes et non étroitement apparentées. Nous avons trouvé une espèce de Gyrodactylus (Gyrodactylidae, Monogenea), Gyrodactylus sturmbaueri Vanhove, Snoeks, Volckaert & Huyse, 2011 et sept espèces de Cichlidogyrus (Dactylogyridae, Monogenea). Quatre espèces nouvelles sont décrites dans le présent travail : Cichlidogyrus pseudodossoui n. sp., C. nyanza n. sp., C. furu n. sp., C. vetusmolendarius n. sp.. Une est signalée mais non décrite formellement (trop peux d’individus recueillis, morphologiquement proche de C. furu n. sp.). Deux autres sont redécrites : Cichlidogyrus bifurcatus Paperna, 1960 and C. longipenis Paperna & Thurston, 1969. Nos résultats confirment que la faune des Monogènes des Cichlidés du lac Victoria fait preuve d’une richesse spécifique et d’une spécificité moins importante que celle du lac Tanganyika. Chez C. furu n. sp. la paire de crochet V étant nettement plus longue que les autres, il faudra reconsidérer le système de classification actuel des types de hapteurs chez les Cichlidogyrus, qui considère que tous les crochets (III à VII) ont la même taille. Quelques caractéristiques morphologiques de C. bifurcatus, C. longipenis et C. nyanza n. sp. pourraient être la preuve d’une ascendance commune avec des congénères présents chez d’autres Haplochrominés. De même, certains caractères indiqueraient que des représentants des Cichlidogyrus ont colonisé les Haplochrominés du lac Victoria, ou leurs ancêtres, au moins à deux reprises, ce qui est cohérent avec une colonisation du lac par deux lignées de cichlidés distinctes (Haplochromini and Oreochromini).

Hypoxia Tolerance in Twelve Species of East African Cichlids: Potential for Low Oxygen Refugia in Lake Victoria

1995 ◽  
Vol 9 (5) ◽  
pp. 1274-1288 ◽  
Author(s):  
LAUREN J. CHAPMAN ◽  
LESLIE S. KAUFMAN ◽  
COLIN A. CHAPMAN ◽  
F. ELLIS MCKENZIE
Keyword(s):  
Lake Victoria ◽  
Hypoxia Tolerance ◽  
Low Oxygen ◽  
East African ◽  
East African Cichlids ◽  
African Cichlids

scholarly journals Interspecific hybridization can generate functional novelty in cichlid fish

2019 ◽  
Vol 286 (1913) ◽  
pp. 20191621 ◽  
Author(s):  
O. M. Selz ◽  
O. Seehausen
Keyword(s):  
Interspecific Hybridization ◽  
First Generation ◽  
Parental Species ◽  
Cichlid Fish ◽  
Context Dependency ◽  
Functional Variation ◽  
Generate Functional ◽  
Cichlid Species ◽  
Evolutionary Consequences ◽  
African Cichlids

The role of interspecific hybridization in evolution is still being debated. Interspecific hybridization has been suggested to facilitate the evolution of ecological novelty, and hence the invasion of new niches and adaptive radiation when ecological opportunity is present beyond the parental species niches. On the other hand, hybrids between two ecologically divergent species may perform less well than parental species in their respective niches because hybrids would be intermediate in performance in both niches. The evolutionary consequences of hybridization may hence be context-dependent, depending on whether ecological opportunities, beyond those of the parental species, do or do not exist. Surprisingly, these complementary predictions may never have been tested in the same experiment in animals. To do so, we investigate if hybrids between ecologically distinct cichlid species perform less well than the parental species when feeding on food either parent is adapted to, and if the same hybrids perform better than their parents when feeding on food none of the species are adapted to. We generated two first-generation hybrid crosses between species of African cichlids. In feeding efficiency experiments we measured the performance of hybrids and parental species on food types representing both parental species niches and additional ‘novel’ niches, not used by either of the parental species but by other species in the African cichlid radiations. We found that hybrids can have higher feeding efficiencies on the ‘novel’ food types but typically have lower efficiencies on parental food types when compared to parental species. This suggests that hybridization can generate functional variation that can be of ecological relevance allowing the access to resources outside of either parental species niche. Hence, we provide support for the hypothesis of ecological context-dependency of the evolutionary impact of interspecific hybridization.

scholarly journals Visual adaptation and microhabitat choice in Lake Victoria cichlid fish

2019 ◽  
Vol 6 (3) ◽  
pp. 181876
Author(s):  
Daniel Mameri ◽  
Corina van Kammen ◽  
Ton G. G. Groothuis ◽  
Ole Seehausen ◽  
Martine E. Maan
Keyword(s):  
Broad Spectrum ◽  
Lake Victoria ◽  
Natural Habitat ◽  
Habitat Preferences ◽  
Cichlid Fish ◽  
Visual Sensitivity ◽  
Visual Adaptation ◽  
Repeated Testing ◽  
Cichlid Species ◽  
Habitat Matching

When different genotypes choose different habitats to better match their phenotypes, genetic differentiation within a population may be promoted. Mating within those habitats may subsequently contribute to reproductive isolation. In cichlid fish, visual adaptation to alternative visual environments is hypothesized to contribute to speciation. Here, we investigated whether variation in visual sensitivity causes different visual habitat preferences, using two closely related cichlid species that occur at different but overlapping water depths in Lake Victoria and that differ in visual perception ( Pundamilia spp.). In addition to species differences, we explored potential effects of visual plasticity, by rearing fish in two different light conditions: broad-spectrum (mimicking shallow water) and red-shifted (mimicking deeper waters). Contrary to expectations, fish did not prefer the light environment that mimicked their typical natural habitat. Instead, we found an overall preference for the broad-spectrum environment. We also found a transient influence of the rearing condition, indicating that the assessment of microhabitat preference requires repeated testing to control for familiarity effects. Together, our results show that cichlid fish exert visual habitat preference but do not support straightforward visual habitat matching.

scholarly journals Analysis of structural variants in four African cichlids highlights an association with developmental and immune related genes

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Luca Penso-Dolfin ◽  
Angela Man ◽  
Tarang Mehta ◽  
Wilfried Haerty ◽  
Federica Di Palma
Keyword(s):  
Structural Variants ◽  
Immune Related Genes ◽  
African Cichlids

Two new cichild species Neolamprologus (Teleostei: Cichlidae) from Lake Tanganyika, East Africa

Zootaxa ◽  
2007 ◽  
Vol 1612 (1) ◽  
pp. 25-44 ◽  
Author(s):  
PIET VERBURG ◽  
ROGER BILLS
Keyword(s):  
Lake Tanganyika ◽  
East Coast ◽  
Lake Victoria ◽  
Niche Partitioning ◽  
Sedimentation Rates ◽  
Rocky Shores ◽  
Ecological Differentiation ◽  
Cichlid Species ◽  
Large Numbers ◽  
Rocky Habitat

Two new cichlid species, Neolamprologus walteri sp. nov. and N. chitamwebwai sp. nov., from the Bangwe peninsula (Tanzania), on the east coast of Lake Tanganyika, are described. Both species belong to the N. savoryi species complex, characterised by a lunate tail with long filaments. Neolamprologus chitamwebwai and N. walteri are highly stenotopic species, restricted to rocky habitat. They occur sympatrically with each other and with two other species of the complex but occupy different microhabitats. Neolamprologus walteri lives in large numbers in sheltered areas with rubble substrate whereas N. chitamwebwai occurs in much lower numbers on more exposed parts of the rocky shores, with large boulders, lower sedimentation rates, coarser sediment, and higher visibility. The two new species although closely related, show clear ecological differentiation. Evidence of ecological differentiation between closely related sympatric cichlids is rare in literature. Closely related sympatric cichlids in the large African lakes (with literature mainly referring to Lake Victoria and Lake Malawi) have been suggested to differ little in diet and habitat use, which has encouraged the idea that cichlid species can coexist without niche partitioning. Our paper provides a different perspective with cichlids from Lake Tanganyika.

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