Movement of transposable elements contributes to cichlid diversity

Carleton, Karen L.; Conte, Matthew A.; Malinsky, Milan; Nandamuri, Sri Pratima; Sandkam, Benjamin A.; Meier, Joana I.; Mwaiko, Salome; Seehausen, Ole; Kocher, Thomas D.

doi:10.1101/2020.02.26.961987

Cited by 6 publications

(7 citation statements)

References 87 publications

(88 reference statements)

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“…In conclusion, our discovery that at least three different alleles control sex and segregate differentially within an isolated population of A. calliptera provides evidence that genetic sex determination in nature can be extremely fluid even at very small demographic scales. All of the alleles we identified involved structural genetic variants, with two of the three generated by transposable element insertions, highlighting a potentially important role for TEs in the rapidly evolving sex systems of African cichlids, similar to their role in adaptive variation in opsin regulation (Carleton et al . 2020).…”

Section: Discussionmentioning

confidence: 94%

Differential use of multiple genetic sex determination systems in divergent ecomorphs of an African crater lake cichlid

Munby

Linderoth

Fischer

et al. 2021

Preprint

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African cichlid fishes not only exhibit remarkably high rates of speciation but also have some of the fastest evolving sex determination systems in vertebrates. However, little is known empirically in cichlids about the genetic mechanisms generating new sex-determining variants, what forces dictate their fate, the demographic scales at which they evolve, and whether they are related to speciation. To address these questions, we looked for sex-associated loci in full genome data from 647 individuals of Astatotilapia calliptera from Lake Masoko, a small isolated crater lake in Tanzania, which contains two distinct ecomorphs of the species. We identified three separate XY systems on recombining chromosomes. Two Y alleles derive from mutations that increase expression of the gonadal soma-derived factor gene (gsdf) on chromosome 7; the first is a tandem duplication of the entire gene observed throughout much of the Lake Malawi haplochromine cichlid radiation to which A. calliptera belongs, and the second is a 5 kb insertion directly upstream of gsdf. Both the latter variant and another 700 bp insertion on chromosome 19 responsible for the third Y allele arose from transposable element insertions. Males belonging to the Masoko deep-water benthic ecomorph are determined exclusively by the gsdf duplication, whereas all three Y alleles are used in the Masoko littoral ecomorph, in which they appear to act antagonistically among males with different amounts of benthic admixture. This antagonism in the face of ongoing admixture may be important for sustaining multifactorial sex determination in Lake Masoko. In addition to identifying the molecular basis of three coexisting sex determining alleles, these results demonstrate that genetic interactions between Y alleles and genetic background can potentially affect fitness and adaptive evolution.

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Section: Discussionmentioning

confidence: 94%

Differential use of multiple genetic sex determination systems in divergent ecomorphs of an African crater lake cichlid

Munby

Linderoth

Fischer

et al. 2021

Preprint

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“…( 138)], perhaps because of mismatches between the TE sequences and the host mechanisms repressing TE activity in the germ line. Therefore, hybridisation in cichlids may contribute to increased TE activity (90).…”

Section: Discussionmentioning

confidence: 99%

Genetic Variation and Hybridization in Evolutionary Radiations of Cichlid Fishes

Svardal

Salzburger

Malinsky

2021

Annu. Rev. Anim. Biosci.

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Evolutionary radiations are responsible for much of the variation in biodiversity. 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. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 9 is February 16, 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

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“…2019; Carleton et al. 2020), there is extensive TE mobilization and proliferation, indicating that these defects might be common among hybrids. In Drosophila , TEs are often overexpressed in Drosophila hybrids (Kelleher et al.…”

Section: Discussionmentioning

confidence: 99%

P ‐elements strengthen reproductive isolation within the Drosophila simulans species complex

et al. 2021

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Determining mechanisms that underlie reproductive isolation (RI) is key to understanding how species boundaries are maintained in nature. Transposable elements (TEs) are ubiquitous across eukaryotic genomes. However, the role of TEs in modulating the strength of RI between species is poorly understood. Several species of Drosophila have been found to harbor P‐elements (PEs), yet only D. simulans is known to be currently polymorphic for their presence in wild populations. PEs can cause RI between PE‐containing (P) and PE‐lacking (M) lineages of the same species. However, it is unclear whether they also contribute to the magnitude of RI between species. Here, we use the simulans species complex to assess whether differences in PE status between D. simulans and its sister species, which do not harbor PEs, contribute to multiple barriers to gene flow between species. We show that crosses involving a P D. simulans father and an M mother from a sister species exhibit lower F1 female fecundity than crosses involving an M D. simulans father and an M sister‐species mother. We also find that another TE, I‐element, might play a minor role in determining the frequency of dysgenesis between species. Our results suggest that the presence of PEs in a species can strengthen isolation from its sister species, providing evidence that TEs can play a role in RI.

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Movement of transposable elements contributes to cichlid diversity

Cited by 6 publications

References 87 publications

Differential use of multiple genetic sex determination systems in divergent ecomorphs of an African crater lake cichlid

Differential use of multiple genetic sex determination systems in divergent ecomorphs of an African crater lake cichlid

Genetic Variation and Hybridization in Evolutionary Radiations of Cichlid Fishes

P ‐elements strengthen reproductive isolation within the Drosophila simulans species complex

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