scholarly journals Different Sources of Allelic Variation Drove Repeated Color Pattern Divergence in Cichlid Fishes

2020 ◽  
Author(s):  
Sabine Urban ◽  
Alexander Nater ◽  
Axel Meyer ◽  
Claudius F Kratochwil
Keyword(s):  
Genetic Variation ◽  
De Novo ◽  
Allelic Variation ◽  
Lake Victoria ◽  
Cichlid Fish ◽  
Lake Malawi ◽  
Color Pattern ◽  
Species Flock ◽  
De Novo Mutations ◽  
Phenotypic Divergence

Abstract The adaptive radiations of East African cichlid fish in the Great Lakes Victoria, Malawi, and Tanganyika are well known for their diversity and repeatedly evolved phenotypes. Convergent evolution of melanic horizontal stripes has been linked to a single locus harboring the gene agouti-related peptide 2 (agrp2). However, where and when the causal variants underlying this trait evolved and how they drove phenotypic divergence remained unknown. To test the alternative hypotheses of standing genetic variation versus de novo mutations (independently originating in each radiation), we searched for shared signals of genomic divergence at the agrp2 locus. Although we discovered similar signatures of differentiation at the locus level, the haplotypes associated with stripe patterns are surprisingly different. In Lake Malawi, the highest associated alleles are located within and close to the 5′ untranslated region of agrp2 and likely evolved through recent de novo mutations. In the younger Lake Victoria radiation, stripes are associated with two intronic regions overlapping with a previously reported cis-regulatory interval. The origin of these segregating haplotypes predates the Lake Victoria radiation because they are also found in more basal riverine and Lake Kivu species. This suggests that both segregating haplotypes were present as standing genetic variation at the onset of the Lake Victoria adaptive radiation with its more than 500 species and drove phenotypic divergence within the species flock. Therefore, both new (Lake Malawi) and ancient (Lake Victoria) allelic variation at the same locus fueled rapid and convergent phenotypic evolution.

scholarly journals Continuous 1.3-million-year record of East African hydroclimate, and implications for patterns of evolution and biodiversity

2015 ◽  
Vol 112 (51) ◽  
pp. 15568-15573 ◽  
Author(s):  
Robert P. Lyons ◽  
Christopher A. Scholz ◽  
Andrew S. Cohen ◽  
John W. King ◽  
Erik T. Brown ◽  
...  
Keyword(s):  
Lake Level ◽  
Large Scale ◽  
Late Quaternary ◽  
Cichlid Fish ◽  
Biological Evolution ◽  
Distinct Species ◽  
Lake Malawi ◽  
Freshwater Ecosystems ◽  
Water Levels ◽  
Species Flock

The transport of moisture in the tropics is a critical process for the global energy budget and on geologic timescales, has markedly influenced continental landscapes, migratory pathways, and biological evolution. Here we present a continuous, first-of-its-kind 1.3-My record of continental hydroclimate and lake-level variability derived from drill core data from Lake Malawi, East Africa (9–15° S). Over the Quaternary, we observe dramatic shifts in effective moisture, resulting in large-scale changes in one of the world’s largest lakes and most diverse freshwater ecosystems. Results show evidence for 24 lake level drops of more than 200 m during the Late Quaternary, including 15 lowstands when water levels were more than 400 m lower than modern. A dramatic shift is observed at the Mid-Pleistocene Transition (MPT), consistent with far-field climate forcing, which separates vastly different hydroclimate regimes before and after ∼800,000 years ago. Before 800 ka, lake levels were lower, indicating a climate drier than today, and water levels changed frequently. Following the MPT high-amplitude lake level variations dominate the record. From 800 to 100 ka, a deep, often overfilled lake occupied the basin, indicating a wetter climate, but these highstands were interrupted by prolonged intervals of extreme drought. Periods of high lake level are observed during times of high eccentricity. The extreme hydroclimate variability exerted a profound influence on the Lake Malawi endemic cichlid fish species flock; the geographically extensive habitat reconfiguration provided novel ecological opportunities, enabling new populations to differentiate rapidly to distinct species.

De-novo mutations and genetic variation in the SCN1A gene in Malaysian patients with generalized epilepsy with febrile seizures plus (GEFS+)

2012 ◽  
Vol 102 (3) ◽  
pp. 210-215
Author(s):  
Emmilia Husni Tan ◽  
Salmi Abdul Razak ◽  
Jafri Malin Abdullah ◽  
Abdul Aziz Mohamed Yusoff
Keyword(s):  
Genetic Variation ◽  
De Novo ◽  
Febrile Seizures ◽  
De Novo Mutations ◽  
Generalized Epilepsy ◽  
Febrile Seizures Plus ◽  
Scn1a Gene

scholarly journals Nuclear markers reveal unexpected genetic variation and a Congolese-Nilotic origin of the Lake Victoria cichlid species flock

2003 ◽  
Vol 270 (1511) ◽  
pp. 129-137 ◽  
Author(s):  
Ole Seehausen ◽  
Egbert Koetsier ◽  
Maria Victoria Schneider ◽  
Lauren J. Chapman ◽  
Colin A. Chapman ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Lake Victoria ◽  
Species Flock ◽  
Nuclear Markers ◽  
Cichlid Species

scholarly journals Genetic Variation and De Novo Mutations in the Parthenogenetic Caucasian Rock Lizard Darevskia unisexualis

PLoS ONE ◽  
2008 ◽  
Vol 3 (7) ◽  
pp. e2730 ◽  
Author(s):  
Tatiana N. Badaeva ◽  
Daria N. Malysheva ◽  
Vitaly I. Korchagin ◽  
Alexei P. Ryskov
Keyword(s):  
Genetic Variation ◽  
De Novo ◽  
De Novo Mutations ◽  
Rock Lizard

scholarly journals Ancestral Hybridization Facilitated Species Diversification in the Lake Malawi Cichlid Fish Adaptive Radiation

2019 ◽  
Vol 37 (4) ◽  
pp. 1100-1113 ◽  
Author(s):  
Hannes Svardal ◽  
Fu Xiang Quah ◽  
Milan Malinsky ◽  
Benjamin P Ngatunga ◽  
Eric A Miska ◽  
...  
Keyword(s):  
Adaptive Radiation ◽  
Large Scale ◽  
Lake Victoria ◽  
Cichlid Fish ◽  
Lake Malawi ◽  
Raw Material ◽  
Founder Population ◽  
East African ◽  
Cichlid Species ◽  
Show Evidence

Abstract The adaptive radiation of cichlid fishes in East African Lake Malawi encompasses over 500 species that are believed to have evolved within the last 800,000 years from a common founder population. It has been proposed that hybridization between ancestral lineages can provide the genetic raw material to fuel such exceptionally high diversification rates, and evidence for this has recently been presented for the Lake Victoria region cichlid superflock. Here, we report that Lake Malawi cichlid genomes also show evidence of hybridization between two lineages that split 3–4 Ma, today represented by Lake Victoria cichlids and the riverine Astatotilapia sp. “ruaha blue.” The two ancestries in Malawi cichlid genomes are present in large blocks of several kilobases, but there is little variation in this pattern between Malawi cichlid species, suggesting that the large-scale mosaic structure of the genomes was largely established prior to the radiation. Nevertheless, tens of thousands of polymorphic variants apparently derived from the hybridization are interspersed in the genomes. These loci show a striking excess of differentiation across ecological subgroups in the Lake Malawi cichlid assemblage, and parental alleles sort differentially into benthic and pelagic Malawi cichlid lineages, consistent with strong differential selection on these loci during species divergence. Furthermore, these loci are enriched for genes involved in immune response and vision, including opsin genes previously identified as important for speciation. Our results reinforce the role of ancestral hybridization in explosive diversification by demonstrating its significance in one of the largest recent vertebrate adaptive radiations.

scholarly journals Ancestral hybridisation facilitated species diversification in the Lake Malawi cichlid fish adaptive radiation

2019 ◽  
Author(s):  
Hannes Svardal ◽  
Fu Xiang Quah ◽  
Milan Malinsky ◽  
Benjamin P Ngatunga ◽  
Eric A Miska ◽  
...  
Keyword(s):  
Adaptive Radiation ◽  
Large Scale ◽  
Lake Victoria ◽  
Cichlid Fish ◽  
Lake Malawi ◽  
Raw Material ◽  
Founder Population ◽  
Cichlid Species ◽  
Show Evidence ◽  
Adaptive Radiations

AbstractThe adaptive radiation of cichlid fishes in East Afrian Lake Malawi encompasses over 500 species that are believed to have evolved within the last 800 thousand years from a common founder population. It has been proposed that hybridisation between ancestral lineages can provide the genetic raw material to fuel such exceptionally high diversification rates, and evidence for this has recently been presented for the Lake Victoria Region cichlid superflock. Here we report that Lake Malawi cichlid genomes also show evidence of hybridisation between two lineages that split 3-4 million years ago, today represented by Lake Victoria cichlids and the riverine Astatotilapia sp. ‘ruaha blue’. The two ancestries in Malawi cichlid genomes are present in large blocks of several kilobases, but there is little variation in this pattern between Malawi cichlid species, suggesting that the large-scale mosaic structure of the genomes was largely established prior to the radiation. Nevertheless, tens of thousands of polymorphic variants apparently derived from the hybridisation are interspersed in the genomes. These loci show a striking excess of differentiation across ecological subgroups in the Lake Malawi cichlid assemblage, and parental alleles sort differentially into benthic and pelagic Malawi cichlid lineages, consistent with strong differential selection on these loci during species divergence. Furthermore, these loci are enriched for genes involved in immune response and vision, including opsin genes previously identified as important for speciation. Our results reinforce the role of ancestral hybridisation in explosive diversification by demonstrating its significance in one of the largest recent vertebrate adaptive radiations.

scholarly journals Catch me if you can: Adaptation from standing genetic variation to a moving phenotypic optimum

2015 ◽  
Author(s):  
Sebastian Matuszewski ◽  
Joachim Hermisson ◽  
Michael Kopp
Keyword(s):  
Genetic Variation ◽  
De Novo ◽  
Darwinian Evolution ◽  
De Novo Mutations ◽  
Population Means ◽  
Standing Variation ◽  
Analytical Approximations ◽  
Formal Framework ◽  
Phenotype Space ◽  
Effect Size Distribution

Adaptation lies at the heart of Darwinian evolution. Accordingly, numerous studies have tried to provide a formal framework for the description of the adaptive process. Out of these, two complementary modelling approaches have emerged: While so-called adaptive-walk models consider adaptation from the successive fixation of de-novo mutations only, quantitative genetic models assume that adaptation proceeds exclusively from pre-existing standing genetic variation. The latter approach, however, has focused on short-term evolution of population means and variances rather than on the statistical properties of adaptive substitutions. Our aim is to combine these two approaches by describing the ecological and genetic factors that determine the genetic basis of adaptation from standing genetic variation in terms of the effect-size distribution of individual alleles. Specifically, we consider the evolution of a quantitative trait to a gradually changing environment. By means of analytical approximations, we derive the distribution of adaptive substitutions from standing genetic variation, that is, the distribution of the phenotypic effects of those alleles from the standing variation that become fixed during adaptation. Our results are checked against individual-based simulations. We find that, compared to adaptation from de-novo mutations, (i) adaptation from standing variation proceeds by the fixation of more alleles of small effect; (ii) populations that adapt from standing genetic variation can traverse larger distances in phenotype space and, thus, have a higher potential for adaptation if the rate of environmental change is fast rather than slow.

scholarly journals De novo mutations across 1,465 diverse genomes reveal mutational insights and reductions in the Amish founder population

2020 ◽  
Vol 117 (5) ◽  
pp. 2560-2569 ◽  
Author(s):  
Michael D. Kessler ◽  
Douglas P. Loesch ◽  
James A. Perry ◽  
Nancy L. Heard-Costa ◽  
Daniel Taliun ◽  
...  
Keyword(s):  
Genetic Variation ◽  
De Novo ◽  
Whole Genome Sequencing Data ◽  
Human Populations ◽  
Founder Population ◽  
Sequencing Data ◽  
De Novo Mutations ◽  
Narrow Sense Heritability ◽  
High Coverage ◽  
Genome Wide

De novo mutations (DNMs), or mutations that appear in an individual despite not being seen in their parents, are an important source of genetic variation whose impact is relevant to studies of human evolution, genetics, and disease. Utilizing high-coverage whole-genome sequencing data as part of the Trans-Omics for Precision Medicine (TOPMed) Program, we called 93,325 single-nucleotide DNMs across 1,465 trios from an array of diverse human populations, and used them to directly estimate and analyze DNM counts, rates, and spectra. We find a significant positive correlation between local recombination rate and local DNM rate, and that DNM rate explains a substantial portion (8.98 to 34.92%, depending on the model) of the genome-wide variation in population-level genetic variation from 41K unrelated TOPMed samples. Genome-wide heterozygosity does correlate with DNM rate, but only explains <1% of variation. While we are underpowered to see small differences, we do not find significant differences in DNM rate between individuals of European, African, and Latino ancestry, nor across ancestrally distinct segments within admixed individuals. However, we did find significantly fewer DNMs in Amish individuals, even when compared with other Europeans, and even after accounting for parental age and sequencing center. Specifically, we found significant reductions in the number of C→A and T→C mutations in the Amish, which seem to underpin their overall reduction in DNMs. Finally, we calculated near-zero estimates of narrow sense heritability (h2), which suggest that variation in DNM rate is significantly shaped by nonadditive genetic effects and the environment.

scholarly journals Female preference for conspecific males based on olfactory cues in a Lake Malawi cichlid fish

2005 ◽  
Vol 1 (4) ◽  
pp. 411-414 ◽  
Author(s):  
Martin Plenderleith ◽  
Cock van Oosterhout ◽  
Rosanna L Robinson ◽  
George F Turner
Keyword(s):  
Cichlid Fish ◽  
Mate Recognition ◽  
Lake Malawi ◽  
Olfactory Cues ◽  
Species Flock ◽  
East African ◽  
Significant Preference ◽  
African Species ◽  
Cichlid Species

Research on reproductive isolation in African cichlid fishes has largely focused on the role of nuptial colours, but other sensory modes may play an important role in mate choice. Here, we compare the relative importance of visual and olfactory cues in mate recognition by females of a Lake Malawi cichlid species. Female Pseudotropheus emmiltos were given a choice of spawning next to a conspecific male or a male of the closely-related sympatric Pseudotropheus fainzilberi . Significant preference for conspecific males only occurred when olfactory cues were present. This suggests that divergence of olfactory signals may have been an important influence on the explosive radiation of the East African species flock.

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