Genomic fingerprints of palaeogeographic history: The tempo and mode of rift tectonics across tropical Africa has shaped the diversification of the killifish genus Nothobranchius (Teleostei: Cyprinodontiformes)

Merwe, Pieter de Wet van der; Cotterill, F.P.D.; Kandziora, Martha; Watters, Brian R.; Nagy, Božidar; Genade, Tyrone; Flügel, Tyrel J.; Svendsen, David S.; Bellstedt, Dirk U.

doi:10.1016/j.ympev.2020.106988

Cited by 19 publications

(50 citation statements)

References 92 publications

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“…ca. 14 Mya [41]. Whether the XY sex chromosomes of N. furzeri and N. kadleci share homology with F. thierryi remains to be tested.…”

Section: Discussionmentioning

confidence: 99%

“…The sex chromosome system thus evolved in a common ancestor of N. furzeri and N. kadleci upon their split from N. orthonotus and it is thus 2-5× older than previously assumed (approximately 1.5-4 My; cf. [35,41,46,84]). However, we cannot exclude that the killifish XY sex chromosome system evolved much earlier, as the system could be shared with Fundulosoma thierryi with X1X2Y multiple sex chromosome system formed via sex chromosome-autosome fusion [44] which diverged from Nothobranchius spp.…”

Section: Discussionmentioning

confidence: 99%

“…Most biomedical and genomic research has been addressed using the model species N. furzeri, where the transcriptomic and genomic resources as well as genome editing tools have been established [34][35][36][37][38][39]. Its sister species N. kadleci Reichard, 2010 [40,41] received considerably less attention [42,43].…”

Section: Introductionmentioning

confidence: 99%

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Sex chromosome differentiation via changes in the Y chromosome repeat landscape in African annual killifishes Nothobranchius furzeri and N. kadleci

Štundlová

Kreklova

Lukšíková

et al. 2022

Preprint

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Repetitive DNA represents an important driver of sex chromosome differentiation. Yet, repetitive sequences tend to be misrepresented or overlooked in genomic studies. We analysed repetitive DNA landscape of sex chromosomes in several populations of a turquoise killifish Nothobranchius furzeri and its sister species N. kadleci (Teleostei: Nothobranchiidae), representatives of African annual killifishes with high rate of karyotype and sex chromosome evolution. We combined bioinformatic analyses of repeatome with molecular cytogenetic techniques such as comparative genomic hybridization, fluorescence in situ hybridization with satellite sequences, genes for ribosomal RNAs (rDNA) and bacterial artificial chromosomes (BACs) and immunostaining of SYCP3 and MLH1 proteins, which marked lateral elements of synaptonemal complexes and recombination sites, respectively. We revealed that N. furzeri and N. kadleci share the XY sex chromosome system, which is thus much older than previously assumed. Sex chromosomes are mostly heteromorphic as evidenced by distinct distribution of satellite DNAs and major rDNA. Yet, the heteromorphic XY sex chromosomes pair almost exclusively regularly in meiosis, which implies synaptic adjustment. Physical mapping of BACs identified inversions on Y chromosomes of the N. kadleci populations, akin to the pattern previously reported in N. furzeri. Yet, repetitive DNA landscape of X and Y sex chromosomes either diverged in parallel in populations of both species or it evolved in their common ancestor and thus predates the inversions. The observed differentiation via repeat repatterning thus cannot be explained by the classical sexually antagonistic model. Rather, we hypothesized that relaxed meiotic drive and recombination reduced by neutral processes could drive changes in repeatome and secondary inversions could be maintained by sexually antagonistic regulatory effects resulting from early evolution of dosage compensation.

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“…ca. 14 Mya [41]. Whether the XY sex chromosomes of N. furzeri and N. kadleci share homology with F. thierryi remains to be tested.…”

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Sex chromosome differentiation via changes in the Y chromosome repeat landscape in African annual killifishes Nothobranchius furzeri and N. kadleci

Štundlová

Kreklova

Lukšíková

et al. 2022

Preprint

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“…The present distribution of the fish fauna reflects the complex geomorphological history of river drainages (Skelton, 1994;van der Merwe et al, 2020). Cotterill et al (2016)…”

Section: General Distributionmentioning

confidence: 92%

A review of the conservation status of seasonal Nothobranchius fishes (Teleostei: Cyprinodontiformes), a genus with a high level of threat, inhabiting ephemeral wetland habitats in Africa

Nagy¹,

Watters²

2021

Aquatic Conservation

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1. The small and colourful Nothobranchius fishes inhabit ephemeral habitats in freshwater wetlands of Africa and have extreme life-history adaptations that allow their eggs to survive the periodic drying up of the seasonal natural habitats.They are subject to high levels of threat, with 72% of the 94 assessed species falling into one of the threatened Red List categories, as a consequence of habitat degradation of seasonal wetlands. There is, therefore, a need to conserve ephemeral waters for species that rely on the seasonality of habitats.2. Extinction risk factors for all species of the genus were entirely reworked with IUCN Red List assessments, whereas first-time assessments were established for species that had previously not been evaluated. These fishes complete their

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“…Log-normal river capture curves follow data from Goldberg et al (2021). Musher et al, 2019;Van Steenberge et al, 2020;Albert et al, 2021;Chen et al, 2021;Sun et al, 2021;van der Merwe et al, 2021).…”

Section: The Mega Capture Hypothesisunclassified

Landscape Evolution as a Diversification Driver in Freshwater Fishes

et al. 2022

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The exceptional concentration of vertebrate diversity in continental freshwaters has been termed the “freshwater fish paradox,” with > 15,000 fish species representing more than 20% of all vertebrate species compressed into tiny fractions of the Earth’s land surface area (<0.5%) or total aquatic habitat volume (<0.001%). This study asks if the fish species richness of the world’s river basins is explainable in terms of river captures using topographic metrics as proxies. The River Capture Hypothesis posits that drainage-network rearrangements have accelerated biotic diversification through their combined effects on dispersal, speciation, and extinction. Yet rates of river capture are poorly constrained at the basin scale worldwide. Here we assess correlations between fish species density (data for 14,953 obligate freshwater fish species) and basin-wide metrics of landscape evolution (data for 3,119 river basins), including: topography (elevation, average relief, slope, drainage area) and climate (average rainfall and air temperature). We assess the results in the context of both static landscapes (e.g., species-area and habitat heterogeneity relationships) and transient landscapes (e.g., river capture, tectonic activity, landscape disequilibrium). We also relax assumptions of functional neutrality of basins (tropical vs. extratropical, tectonically stable vs. active terrains). We found a disproportionate number of freshwater species in large, lowland river basins of tropical South America, Africa, and Southeast Asia, under predictable conditions of large geographic area, tropical climate, low topographic relief, and high habitat volume (i.e., high rainfall rates). However, our results show that these conditions are only necessary, but not fully sufficient, to explain the basins with the highest diversity. Basins with highest diversity are all located on tectonically stable regions, places where river capture is predicted to be most conducive to the formation of high fish species richness over evolutionary timescales. Our results are consistent with predictions of several landscape evolution models, including the River Capture Hypothesis, Mega Capture Hypothesis, and Intermediate Capture Rate Hypothesis, and support conclusions of numerical modeling studies indicating landscape transience as a mechanistic driver of net diversification in riverine and riparian organisms with widespread continental distributions.

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Genomic fingerprints of palaeogeographic history: The tempo and mode of rift tectonics across tropical Africa has shaped the diversification of the killifish genus Nothobranchius (Teleostei: Cyprinodontiformes)

Cited by 19 publications

References 92 publications

Sex chromosome differentiation via changes in the Y chromosome repeat landscape in African annual killifishes Nothobranchius furzeri and N. kadleci

Sex chromosome differentiation via changes in the Y chromosome repeat landscape in African annual killifishes Nothobranchius furzeri and N. kadleci

A review of the conservation status of seasonal Nothobranchius fishes (Teleostei: Cyprinodontiformes), a genus with a high level of threat, inhabiting ephemeral wetland habitats in Africa

Landscape Evolution as a Diversification Driver in Freshwater Fishes

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