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Seehausen, O.

Publications and source records attributed to Seehausen, O..

At least 19 recordsLinked to original sources

Heterogeneous evolution of effective recombination landscapes across percomorph fishes

Recombination shapes allelic combinations across the genome and plays a central role in adaptation and speciation. While recombination rates are known to vary and evolve, how recombination landscapes diverge between populations and which processes drive this divergence remains poorly understood. Here, we use the Population Recombination Divergence Index (PRDI) to quantify divergence in effective recombination landscapes between seven pairs of populations and species from four percomorph fish lineages (cichlids, sticklebacks, killifish, and clownfish). While accounting for stochasticity and confounders of linkage disequilibrium (LD) -based recombination rate estimates, we find that recombination landscapes diverged substantially in all comparisons. This divergence generally increases with genetic differentiation and divergence time, but the amount of PRDI accumulated per unit of genetic divergence (FST), net nucleotide divergence (da), or divergence time varies markedly among population and species pairs. Comparisons across systems suggest that PRDI accumulation tends to be faster (per unit of FST, da, or divergence time) in pairs with higher inferred gene flow. We also introduce a local version of PRDI (_l) to better characterize genomic heterogeneity in effective recombination divergence. We find that higher inferred gene flow between populations tends to be associated with stronger intragenomic correlation between local FST and _l. Finally, we propose a conceptual framework for investigating how divergent selection and gene flow may interact to shape effective recombination landscape divergence. Our work highlights the heterogeneous dynamics of effective recombination landscape evolution, and motivates further theoretical and empirical efforts to integrate recombination landscape evolution into studies of adaptation and speciation.

evolutionary biology↗

Anthropogenic-driven loss of an adaptive radiation reduces thermal response diversity

Biodiversity is predicted to stabilize ecosystems if species have different environmental responses. How this response diversity is shaped by ecological and evolutionary processes remains poorly understood. We determine the drivers of thermal response diversity of 16 Swiss peri-alpine lake-fish communities. We report the first evidence that evolutionary diversification of lineages through adaptive radiation can increase the response diversity of an ecosystem. In-situ diversification increases response diversity in the cold-deep lake environment, but non-endemic and non-native species contributed only weakly to response diversity. The loss of endemic species during historical anthropogenic eutrophication led to a negative legacy on present thermal response diversity in cold and deep lake strata. Overall, the interplay of evolutionary diversification, ecological assembly and anthropogenic impacts drives variation in response diversity. Conserving and restoring processes that generate diversity may help maintain ecosystem stability beyond the Anthropocene.

ecology↗

Highly modular genomic architecture underlies combinatorial mechanism of speciation and adaptive radiation

Hybridisation can fuel rapid adaptive radiation, but how it enables the formation of phenotypically highly dimensional species-rich radiations remains unclear. We investigated this by analysing genotype-phenotype associations for 14 ecological (trophic, body patterns) and mating traits (nuptial colour) across 107 species of Lake Victoria cichlid fishes. We find weak trait covariance across the radiation, with many different trait combinations constituting different species. Across the radiation, polygenic, redundant, and lowly pleiotropic genomic architectures of hybrid origin underlie the repeated evolution of key traits. Such independent genomic modules can be reshuffled and recombined like Lego bricks, generating diverse trait combinations from a finite number of elements. During speciation, dispersed oligogenic trait modules become coupled through long-range linkage disequilibrium. We propose that this genomic and phenotypic modularity emerged from repeated cycles of past hybridisation, enabling superfast adaptive radiation through combinatorial speciation.

evolutionary biology↗

Systemic bio-inequity links poverty to biodiversity and induces a conservation paradox

O_LIBiodiversity is declining globally while inequity is growing, and poverty rates are not improving. Global sustainable development and conservation initiatives aim to address biodiversity loss and poverty simultaneously. C_LIO_LIThrough text analysis of global biodiversity policies, we identified a consistent narrative that countries with high biodiversity are expected to use this natural capital to reduce poverty. Theoretically then, should higher biodiversity lead to higher prosperity? Clearly countries with higher biodiversity often experience higher poverty rates, so we explore how this paradox emerges using a path analysis integrating multiple mediating factors represented in biological, historical, and socio-economic data. C_LIO_LIWe find that historical colonial exploitation was directed towards biodiversity rich regions, and through socio-economic legacies, continues to influence present-day poverty. At a country-scale, biodiversity is associated with higher poverty rates through increasing the likelihood of historical colonisation. Colonisation drove colonised countries towards natural resource exportation with weakened governance and increased poverty rates. We find no statistical support that country-scale biodiversity levels directly influence poverty, either positively or negatively. C_LIO_LIMoreover, we find that conservation investments did not align with countries biodiversity or their economic capacity to protect nature, indicating a conservation paradox. Our work uncovers that conservation initiatives to protect biodiversity ignore that biodiversity is strongly associated as a historical catalyst for modern global inequalities. C_LIO_LIOur findings quantitatively support the "systemic bio-inequity" hypothesis proposed here. This hypothesis argues that modern biodiversity-poverty linkages are, at least partly, attributed to historical legacies of unequal exploitation of the natural resources provided by biodiversity. This hypothesis aligns with the theory of ecologically unequal exchange. Our findings highlight the problematics of the narrative that natural wealth, and its conservation, will underpin future economic prosperity of countries. This assumption overlooks systemic, historical and institutional drivers of modern poverty. C_LIO_LIRecognizing that colonial and neoliberal structures have created inverted poverty-biodiversity relationships fundamentally changes how we should approach conservation. A decolonial approach is needed in conservation to address this legacy, whereby conservationists must not only recognise but challenge and replace damaging narratives that overlook past and present inequalities in access to the benefits of biodiversity. C_LI

ecology↗

Hi-reComb: constructing recombination maps from bulk gamete Hi-C sequencing

Recombination is central to genetics and to evolution of sexually reproducing organisms. However, obtaining accurate estimates of recombination rates, and of how they vary along chromosomes, continues to be challenging. To advance our ability to estimate recombination rates, we present Hi-reComb, a new method and software for estimation of recombination maps from bulk gamete chromosome conformation capture sequencing (Hi-C). Simulations show that Hi-reComb produces robust, accurate recombination landscapes. With empirical data from sperm of five fish species we show the advantages of this approach, including joint assessment of recombination maps and large structural variants, map comparisons using bootstrap, and workflows with trio phasing vs. Hi-C phasing. With off-the-shelf library construction and a straightforward rapid workflow, our approach will facilitate routine recombination landscape estimation for a broad range of studies and model organisms in genetics and evolutionary biology. Hi-reComb is open-source and freely available at https://github.com/millanek/Hi-reComb.

genetics↗

Genomes reveal age and demographic consequence of ultrafast adaptive radiation

New species typically evolve over several million years1. However, rates of speciation and ecological diversification vary by orders of magnitude across the tree of life1-3, with the fastest shown by some adaptive radiations. Eight hundred endemic species of cichlid fishes emerged and formed entire food webs in Lake Victoria and nearby lakes in East Africa. According to Victorias paleolimnological history4, five hundred may have arisen within the past 16,700 years, but molecular phylogenies estimated a much older origin5-8. We reconstruct the age and demography of all Lake Victoria region radiations from whole genomes. We show that indeed, in Lake Victoria all trophic guilds diverged <16,700 years ago, corresponding to between 537 and nearly 30000 speciation events per species per million years, the fastest speciation rate in metazoans1,2. Cichlid radiations in lakes Edward, Albert and Kivu too began <20,000 years ago, an order of magnitude faster than previously thought. Evolutionary transitions between trophic levels led to divergence in effective population sizes as predicted by the trophic pyramid of numbers concept9 and replicated across three parallel food web radiations. Our results demonstrate that classical theory of trophic interactions in ecologically assembled food webs applies equally to food webs that assembled through rapid adaptive radiation.

evolutionary biology↗

Admixture and environmental fluctuations shape the evolutionary history of a predator radiation in East Africa's Lake Tanganyika

Top predators have oversized influence on food webs and ecosystem dynamics, and introducing a novel predator to a naive environment can have dramatic consequences for endemic biodiversity. Using genomic data, we find that the colonization of Lake Tanganyika by Lates fishes--the top predators in this ancient lake--occurred more recently than other diverse clades within the lake. Diversification into four endemic Lates species occurred within the lake during a time of dramatic changes in lake levels driven by glacial-interglacial cycles, supporting the hypothesis that these fluctuations were a "species pump" for lacustrine taxa. These lake level fluctuations also likely contributed to multiple admixture events among Lates species during the Pleistocene ([~] 90-500 Kya). Together, our findings suggest a dynamic and environmentally-linked evolutionary history of this predator radiation, and that their colonization of the lake and subsequent diversification likely had dramatic ecosystem consequences for taxa already present in Lake Tanganyika.

evolutionary biology↗

Parallel cases of ring speciation within a rapid adaptive radiation of cichlid fishes

Speciation often emerges from the complex interplay of geography, demography, ecology, and sexual selection, yet disentangling their relative contributions remains a challenge. In this study, we examine two species complexes of rock-dwelling Lake Victoria cichlids in the genera Pundamilia and Neochromis that are distributed along a continuous geographic gradient of rocky shores. Using morphometric analyses and male nuptial coloration data, we reveal clinal craniofacial divergence following an isolation by distance model of evolution, punctuated by strong local effects. While the Pundamilia cline exhibited modular shifts in craniofacial anatomy linked to diet-specific morphology, variation in the Neochromis cline was dominated by allometric constraints, suggesting different evolutionary processes at play. At the single site where the terminal populations of both clines co-occur, each pair of sister species showed pronounced divergence in morphology and male nuptial coloration, consistent with ecological and sexual character displacement facilitating co-existence. Our findings highlight that clinal morphological variation in parapatry and more abrupt shifts in sympatry interact to generate and maintain species. These rocky shore cichlids provide a rare opportunity to investigate the speciation continuum in one of the worlds youngest adaptive radiations.

evolutionary biology↗

Developmental tinkering of gene regulation facilitated super rapid adaptive radiation

Developmental shifts in gene regulation underlying key innovations remain largely uncharacterized over short evolutionary timescales. Here, we investigate the gene regulatory landscape of trophic innovations in the fastest vertebrate adaptive radiation: cichlid fishes from Lake Victoria. By analyzing the whole-transcriptomes of the oral and pharyngeal jaws from two life stages in five species adapted to divergent trophic niches, we find that both gene and isoform expression are developmentally dynamic. Expression signatures are most similar across jaws at the early stage and then diverge into species-specific developmental programs in adults. However, even at the early stage, expression in the oral jaws of species adapted to herbivory is distinct from those of carnivores, a pattern not observed for the pharyngeal jaws. We further show that differentially expressed and spliced genes between herbivorous and carnivorous species regulate different genes and pathways, particularly in adults. Interestingly, we find that splicing-mediated exonization of a craniofacial development gene, kaznb, may have contributed to the evolution of herbivory in Lake Victoria cichlids. Overall, our results contribute to our understanding of how ontogenetic shifts in gene regulation can facilitate rapid adaptive evolution.

evolutionary biology↗

The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

A global genome database of all of Earths species diversity could be a treasure trove of scientific discoveries. However, regardless of the major advances in genome sequencing technologies, only a tiny fraction of species have genomic information available. To contribute to a more complete planetary genomic database, scientists and institutions across the world have united under the Earth BioGenome Project (EBP), which plans to sequence and assemble high-quality reference genomes for all [~]1.5 million recognized eukaryotic species through a stepwise phased approach. As the initiative transitions into Phase II, where 150,000 species are to be sequenced in just four years, worldwide participation in the project will be fundamental to success. As the European node of the EBP, the European Reference Genome Atlas (ERGA) seeks to implement a new decentralised, accessible, equitable and inclusive model for producing high-quality reference genomes, which will inform EBP as it scales. To embark on this mission, ERGA launched a Pilot Project to establish a network across Europe to develop and test the first infrastructure of its kind for the coordinated and distributed reference genome production on 98 European eukaryotic species from sample providers across 33 European countries. Here we outline the process and challenges faced during the development of a pilot infrastructure for the production of reference genome resources, and explore the effectiveness of this approach in terms of high-quality reference genome production, considering also equity and inclusion. The outcomes and lessons learned during this pilot provide a solid foundation for ERGA while offering key learnings to other transnational and national genomic resource projects.

genomics↗

Testing for a role of postzygotic incompatibilities in rapidly speciated Lake Victoria cichlids

Intrinsic postzygotic hybrid incompatibilities are usually due to negative epistatic interactions between alleles from different parental genomes. While such incompatibilities are thought to be uncommon in speciation with gene flow, they may be important if such speciation results from a hybrid population. Here we aimed to test this idea in the endemic cichlid fishes of Lake Victoria. Hundreds of species have evolved within the lake in <15k years from a hybrid progenitor. While the importance of prezygotic barriers to gene flow is well established in this system, the possible relevance of postzygotic genetic incompatibilities is unknown. We inferred the presence of negative epistatic interactions from systematic patterns of genotype ratio distortions in experimental crosses and wild samples. We then compared the positions of putative incompatibility loci to regions of high genetic differentiation between sympatric sister species as well as between members of clades that may have arisen at the start of this radiation, and further determined if the loci showed fixed differences between the closest living relatives of the lineages ancestral to the hybrid progenitor. Overall, we find little evidence for a major role of intrinsic postzygotic incompatibilities in the Lake Victoria radiation. However, we find putative incompatibility loci significantly more often coinciding with islands of genetic differentiation between species that separated early in the radiation than between the youngest sister species, consistent with the hypothesis that such variants segregated in the hybrid swarm and were sorted between species in the early speciation events.

evolutionary biology↗

Microtomographic investigation of a large corpus of cichlids

A large collection of cichlids (N=133) from Lake Victoria in Africa spanning a length range of 6 to 18 cm was nondestructively imaged using micro-computed tomography. We describe our method to efficiently obtain three-dimensional tomographic datasets of the oral and pharyngeal jaws and the whole skull of these fishes for accurately describing their morphology. The tomographic data we acquired (9.8 TB of projection images) yielded 1.5 TB of three-dimensional image stacks used for extracting the relevant features of interest. Herein we present our method and an outlook on analyzing the acquired data; a morphological description of the oral and pharyngeal jaws of the fishes, a three-dimensional geometric morphometrics analysis of landmark features on the fish skulls, and a robust method to automatically extract the otoliths of the fishes from the tomographic data.

ecology↗

Hybridization and a mixture of small and large-effect loci facilitate adaptive radiation

Adaptive radiations represent some of the most remarkable explosions of diversification across the tree of life. However, the constraints to rapid diversification and how they are sometimes overcome, particularly the relative roles of genetic architecture and hybridization, remain unclear. Here, we address these questions in the Alpine whitefish radiation, using a whole-genome dataset that includes multiple individuals of each of the 22 species belonging to six ecologically distinct ecomorph classes across several lake-systems. We reveal that repeated ecological and morphological diversification along a common environmental axis is associated with both genome-wide allele frequency shifts and a specific, larger effect, locus, associated with the gene edar. Additionally, we highlight the role of introgression between species from different lake-systems in facilitating the evolution and persistence of species with unique phenotypic combinations and ecology. These results highlight the role of both genome architecture and secondary contact with hybridization in fuelling adaptive radiation.

evolutionary biology↗

Blue and green food webs respond differently to elevation and land use

While aquatic (blue) and terrestrial (green) food webs are parts of the same landscape, it remains unclear whether they respond similarly to shared environmental gradients. We use empirical community data from hundreds of sites across Switzerland, and show that blue and green food webs have different structural and ecological properties along elevation as a temperature proxy, and among various land-use types. Specifically, in green food webs, their modular structure increases with elevation and the overlap of consumers diet niche decreases, while the opposite pattern is observed in blue food webs. Such differences between blue and green food webs are particularly pronounced in farmland-dominated habitats, indicating that anthropogenic habitat modification moderates the climatic effects on food webs but differently in blue versus green systems. These findings indicate general structural differences between blue and green food webs and suggest their potential divergent future alterations through land use or climatic changes.

ecology↗

The interaction of climate history and evolution impacts alpine biodiversity assembly differently in freshwater and on land

Quaternary climate fluctuations can affect biodiversity assembly through speciation in two non-mutually-exclusive ways: a glacial species pump, where isolation in glacial refugia accelerates allopatric speciation, and adaptive radiation during ice-free periods. Here we detected biogeographic and genetic signatures associated with both mechanisms in the generation of the European Alps biodiversity. Age distributions of endemic and widespread species within aquatic and terrestrial taxa (amphipods, fishes, amphibians, butterflies and flowering plants) revealed that endemic fish evolved only in lakes, are highly sympatric and mainly of Holocene age, consistent with adaptive radiation. Endemic amphipods are ancient, suggesting preglacial radiation with limited range expansion and local Pleistocene survival, perhaps facilitated by a groundwater-dwelling lifestyle. Terrestrial endemics are mostly of Pleistocene age, and are thus more consistent with the glacial species pump. The lack of evidence for Holocene adaptive radiation in the terrestrial biome may be attributable to a faster range expansion of these taxa after glacial retreats, though fewer stable environments may also have contributed to differences between terrestrial areas and lakes. The high proportion of young, endemic species make the Alps vulnerable to climate change, but the mechanisms and consequences of species loss will likely differ between biomes because of their distinct histories.

evolutionary biology↗

Isotopic signatures induced by upwelling tag regional fish populations in Lake Tanganyika

Lake Tanganyikas pelagic fish sustain the second largest inland fishery in Africa and are under pressure from heavy fishing and global warming related increases in stratification. Only little is known about whether basin-scale hydrodynamics - including a more stratified north and an upwelling-driven south - induce ecological and genetic differences among populations of highly mobile, pelagic fish inhabiting these different areas. Here, we examine whether the basin-scale dynamics leave distinct isotopic imprints in the pelagic fish of Lake Tanganyika, which may reveal differences in habitat, diet, or lipid content. We conducted two lake-wide campaigns during different seasons and collected physical, nutrient, chlorophyll, phytoplankton and zooplankton data. Additionally, we analyzed the pelagic fish - the clupeids Stolothrissa tanganicae, Limnothrissa miodon and four Lates species - for their isotopic and elemental carbon (C) and nitrogen (N) compositions. The {delta}13C values were significantly higher in the productive south after the upwelling/mixing period across all trophic levels, implying that the fish have regional foraging grounds, and thus record these latitudinal isotope gradients. By combining our isotope data with genetics, we demonstrate that the fish form regional populations on a seasonal to multiannual time scale. Based on {delta}15N and C:N ratios, we found no strong evidence for varying diets or lipid contents between those regional populations. Additional analyses revealed that isotopic variations between specimens from the same location are not linked to genetic differences. We suggest that the development of basinscale ecological differences in response to the prevailing hydrodynamic regimes may be inhibited by lake-wide gene flow on the long term. Our findings show that the pelagic fish species are genetically adapted to the whole lake, but they form regional populations on short time scales. This implies that sustainable management strategies may adopt basin-scale fishing quotas.

ecology↗

The genetic population structure of Lake Tanganyika's Lates species flock, an endemic radiation of pelagic top predators

Understanding genetic connectivity plays a crucial role in species conservation decisions, and genetic connectivity is an important component of modern fisheries management. In this study, we investigated the population genetics of four endemic Lates species of Lake Tanganyika (Lates stappersii, L. microlepis, L. mariae and L. angustifrons) using reduced-representation genomic sequencing methods. We find the four species to be strongly differentiated from one another (mean interspecific FST = 0.665), with no evidence for contemporary admixture. We also find evidence for strong genetic structure within L. mariae, with the majority of individuals from the most southern sampling site forming a genetic group that is distinct from the individuals at other sampling sites. We find evidence for much weaker structure within the other three species (L. stappersii, L. microlepis, and L. angustifrons). Our ability to detect this weak structure despite small and unbalanced sample sizes and imprecise geographic sampling locations suggests the possibility for further structure undetected in our study. We call for further research into the origins of the genetic differentiation in these four species--particularly that of L. mariae--which may be important for conservation and management of this culturally and economically important clade of fish.

evolutionary biology↗

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

African 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. Resume - Quatre especes nouvelles de Cichlidogyrus (Platyhelminthes, Monogenea, Dactylogyridae) parasites dhaplochromine (Cichlidae) du lac Victoria, avec la redescription de C. bifurcatus and C. longipenisA cause des radiations adaptatives quils ont subies, les cichlides africain sont des systemes modeles pour etudier levolution, mais aussi les relations hotes/parasites, car ils hebergent de nombreuses especes de Monogenes parasites qui presentent une specificite etroite vis-a-vis de leurs hotes. Dans ce travail, nous avons echantillonne cinq localites dans le Sud du lac Victoria, le plus jeune des grands lacs dAfrique de lEst. Nous avons examine les Monogenes presents sur les branchies de 18 especes de Cichlides appartenant a la radiation adaptative << superflock >> du lac Victoria et de deux especes representant deux lignees anciennes et non etroitement apparentees. Nous avons trouve une espece de Gyrodactylus (Gyrodactylidae, Monogenea), Gyrodactylus sturmbaueri Vanhove, Snoeks, Volckaert & Huyse, 2011 et sept especes de Cichlidogyrus (Dactylogyridae, Monogenea). Quatre especes nouvelles sont decrites dans le present travail : Cichlidogyrus pseudodossoui n. sp., C. nyanza n. sp., C. furu n. sp., C. vetusmolendarius n. sp.. Une est signalee mais non decrite formellement (trop peux dindividus recueillis, morphologiquement proche de C. furu n. sp.). Deux autres sont redecrites : Cichlidogyrus bifurcatus Paperna, 1960 and C. longipenis Paperna & Thurston, 1969. Nos resultats confirment que la faune des Monogenes des Cichlides du lac Victoria fait preuve dune richesse specifique et dune specificite moins importante que celle du lac Tanganyika. Chez C. furu n. sp. la paire de crochet V etant nettement plus longue que les autres, il faudra reconsiderer le systeme de classification actuel des types de hapteurs chez les Cichlidogyrus, qui considere que tous les crochets (III a VII) ont la meme taille. Quelques caracteristiques morphologiques de C. bifurcatus, C. longipenis et C. nyanza n. sp. pourraient etre la preuve dune ascendance commune avec des congeneres presents chez dautres Haplochromines. De meme, certains caracteres indiqueraient que des representants des Cichlidogyrus ont colonise les Haplochromines du lac Victoria, ou leurs ancetres, au moins a deux reprises, ce qui est coherent avec une colonisation du lac par deux lignees de cichlides distinctes (Haplochromini and Oreochromini).

zoology↗