scholarly journals The onset of ecological diversification 50 years after colonization of a crater lake by haplochromine cichlid fishes

2018 ◽  
Vol 285 (1884) ◽  
pp. 20180171 ◽  
Author(s):  
Florian N. Moser ◽  
Jacco C. van Rijssel ◽  
Salome Mwaiko ◽  
Joana I. Meier ◽  
Benjamin Ngatunga ◽  
...  
Keyword(s):  
Adaptive Radiation ◽  
Lake Victoria ◽  
Demographic History ◽  
Genomic Diversity ◽  
Radiation Process ◽  
Haplochromine Cichlids ◽  
Ecological Diversification ◽  
Cichlid Fishes ◽  
Wide Range ◽  
Phenotypic Fitness

Adaptive radiation research typically relies on the study of evolution in retrospective, leaving the predictive value of the concept hard to evaluate. Several radiations, including the cichlid fishes in the East African Great Lakes, have been studied extensively, yet no study has investigated the onset of the intraspecific processes of niche expansion and differentiation shortly after colonization of an adaptive zone by cichlids. Haplochromine cichlids of one of the two lineages that seeded the Lake Victoria radiation recently arrived in Lake Chala, a lake perfectly suited for within-lake cichlid speciation. Here, we infer the colonization and demographic history, quantify phenotypic, ecological and genomic diversity and diversification, and investigate the selection regime to ask if the population shows signs of diversification resembling the onset of adaptive radiation. We find that since their arrival in the lake, haplochromines have colonized a wide range of depth habitats associated with ecological and morphological expansion and the beginning of phenotypic differentiation and potentially nascent speciation, consistent with the very early onset of an adaptive radiation process. Moreover, we demonstrate evidence of rugged phenotypic fitness surfaces, indicating that current ecological selection may contribute to the phenotypic diversification.

Adaptive Radiation Genomics of Two Ecologically Divergent Hawai‘ian Honeycreepers: The ‘akiapōlā‘au and the Hawai‘i ‘amakihi

2019 ◽  
Author(s):  
Michael G Campana ◽  
André Corvelo ◽  
Jennifer Shelton ◽  
Taylor E Callicrate ◽  
Karen L Bunting ◽  
...  
Keyword(s):  
Adaptive Radiation ◽  
De Novo ◽  
Demographic History ◽  
Genomic Islands ◽  
Genomic Diversity ◽  
Morphology Evolution ◽  
Effective Population ◽  
Island Endemic ◽  
Wide Range ◽  
Bill Morphology

Abstract The Hawai‘ian honeycreepers (drepanids) are a classic example of adaptive radiation: they adapted to a variety of novel dietary niches, evolving a wide range of bill morphologies. Here we investigated genomic diversity, demographic history, and genes involved in bill morphology phenotypes in 2 honeycreepers: the ‘akiapōlā‘au (Hemignathus wilsoni) and the Hawai‘i ‘amakihi (Chlorodrepanis virens). The ‘akiapōlā‘au is an endangered island endemic, filling the “woodpecker” niche by using a unique bill morphology, while the Hawai‘i ‘amakihi is a dietary generalist common on the islands of Hawai‘i and Maui. We de novo sequenced the ‘akiapōlā‘au genome and compared it to the previously sequenced ‘amakihi genome. The ‘akiapōlā‘au is far less heterozygous and has a smaller effective population size than the ‘amakihi, which matches expectations due to its smaller census population and restricted ecological niche. Our investigation revealed genomic islands of divergence, which may be involved in the honeycreeper radiation. Within these islands of divergence, we identified candidate genes (including DLK1, FOXB1, KIF6, MAML3, PHF20, RBP1, and TIMM17A) that may play a role in honeycreeper adaptations. The gene DLK1, previously shown to influence Darwin’s finch bill size, may be related to honeycreeper bill morphology evolution, while the functions of the other candidates remain unknown.

scholarly journals Adaptation limits ecological diversification and promotes ecological tinkering during the competition for substitutable resources

2018 ◽  
Vol 115 (44) ◽  
pp. E10407-E10416 ◽  
Author(s):  
Benjamin H. Good ◽  
Stephen Martis ◽  
Oskar Hallatschek
Keyword(s):  
Evolutionary Dynamics ◽  
Competitive Exclusion ◽  
Directional Selection ◽  
Ecological Niches ◽  
Ecological Diversification ◽  
Effective Competition ◽  
Uptake Rates ◽  
Wide Range ◽  
Dynamical Features ◽  
Adaptation Limits

Microbial communities can evade competitive exclusion by diversifying into distinct ecological niches. This spontaneous diversification often occurs amid a backdrop of directional selection on other microbial traits, where competitive exclusion would normally apply. Yet despite their empirical relevance, little is known about how diversification and directional selection combine to determine the ecological and evolutionary dynamics within a community. To address this gap, we introduce a simple, empirically motivated model of eco-evolutionary feedback based on the competition for substitutable resources. Individuals acquire heritable mutations that alter resource uptake rates, either by shifting metabolic effort between resources or by increasing the overall growth rate. While these constitutively beneficial mutations are trivially favored to invade, we show that the accumulated fitness differences can dramatically influence the ecological structure and evolutionary dynamics that emerge within the community. Competition between ecological diversification and ongoing fitness evolution leads to a state of diversification–selection balance, in which the number of extant ecotypes can be pinned below the maximum capacity of the ecosystem, while the ecotype frequencies and genealogies are constantly in flux. Interestingly, we find that fitness differences generate emergent selection pressures to shift metabolic effort toward resources with lower effective competition, even in saturated ecosystems. We argue that similar dynamical features should emerge in a wide range of models with a mixture of directional and diversifying selection.

scholarly journals Characterizing the genomic variation and population dynamics of Plasmodium falciparum malaria parasites in and around Lake Victoria, Kenya

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ashley Osborne ◽  
Emilia Manko ◽  
Mika Takeda ◽  
Akira Kaneko ◽  
Wataru Kagaya ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Population Dynamics ◽  
Malaria Elimination ◽  
Lake Victoria ◽  
Genomic Variation ◽  
Genomic Diversity ◽  
Sub Saharan Africa ◽  
Lake Victoria Basin ◽  
East African ◽  
Lake Region

AbstractCharacterising the genomic variation and population dynamics of Plasmodium falciparum parasites in high transmission regions of Sub-Saharan Africa is crucial to the long-term efficacy of regional malaria elimination campaigns and eradication. Whole-genome sequencing (WGS) technologies can contribute towards understanding the epidemiology and structural variation landscape of P. falciparum populations, including those within the Lake Victoria basin, a region of intense transmission. Here we provide a baseline assessment of the genomic diversity of P. falciparum isolates in the Lake region of Kenya, which has sparse genetic data. Lake region isolates are placed within the context of African-wide populations using Illumina WGS data and population genomic analyses. Our analysis revealed that P. falciparum isolates from Lake Victoria form a cluster within the East African parasite population. These isolates also appear to have distinct ancestral origins, containing genome-wide signatures from both Central and East African lineages. Known drug resistance biomarkers were observed at similar frequencies to those of East African parasite populations, including the S160N/T mutation in the pfap2mu gene, which has been associated with delayed clearance by artemisinin-based combination therapy. Overall, our work provides a first assessment of P. falciparum genetic diversity within the Lake Victoria basin, a region targeting malaria elimination.

scholarly journals The great tit HapMap project: a continental-scale analysis of genomic variation in a songbird

2019 ◽  
Author(s):  
Lewis G. Spurgin ◽  
Mirte Bosse ◽  
Frank Adriaensen ◽  
Tamer Albayrak ◽  
Christos Barboutis ◽  
...  
Keyword(s):  
Positive Selection ◽  
Recombination Rate ◽  
Demographic History ◽  
Great Tit ◽  
Genomic Variation ◽  
Genomic Diversity ◽  
Hapmap Project ◽  
Widespread Species ◽  
Continental Scale ◽  
Genome Wide

AbstractA major aim of evolutionary biology is to understand why patterns of genomic diversity vary among populations and species. Large-scale genomic studies of widespread species are useful for studying how the environment and demographic history shape patterns of genomic divergence, and with the continually decreasing cost of sequencing and genotyping, such studies are now becoming feasible. Here, we carry out one of the most geographically comprehensive surveys of genomic variation in a wild vertebrate to date; the great tit (Parus major) HapMap project. We screened ca 500,000 SNP markers across 647 individuals from 29 populations, spanning almost the entire geographic range of the European great tit subspecies. We found that genome-wide variation was consistent with a recent colonisation across Europe from a single refugium in South-East Europe, with bottlenecks and reduced genetic diversity in island populations. Differentiation across the genome was highly heterogeneous, with clear “islands of differentiation” even among populations with very low levels of genome-wide differentiation. Low local recombination rate in the genome was a strong predictor of high local genomic differentiation (FST), especially in island and peripheral mainland populations, suggesting that the interplay between genetic drift and recombination is a key driver of highly heterogeneous differentiation landscapes. We also detected genomic outlier regions that were confined to one or more peripheral great tit populations, most likely as a result of recent directional selection at the range edges of this species. Haplotype-based measures of selection were also related to recombination rate, albeit less strongly, and highlighted population-specific sweeps that likely resulted from positive selection. These regions under positive selection contained candidate genes associated with morphology, thermal adaptation and colouration, providing promising avenues for future investigation. Our study highlights how comprehensive screens of genomic variation in wild organisms can provide unique insights into evolution.

Explosive Speciation and Adaptive Radiation of East African Cichlid Fishes

2011 ◽  
pp. 333-362 ◽  
Author(s):  
Christian Sturmbauer ◽  
Martin Husemann ◽  
Patrick D. Danley
Keyword(s):  
Adaptive Radiation ◽  
East African ◽  
Cichlid Fishes ◽  
African Cichlid ◽  
Explosive Speciation

Genomic diversity and Demographic History of the Dromiciops genus (Marsupialia: Microbiotheriidae)

2022 ◽  
pp. 107405
Author(s):  
Julian F. Quintero-Galvis ◽  
Pablo Saenz-Agudelo ◽  
Guillermo C. Amico ◽  
Soledad Vazquez ◽  
Aaron B.A. Shafer ◽  
...  
Keyword(s):  
Demographic History ◽  
Genomic Diversity ◽  
History Of

scholarly journals Genome-wide diversity and global migration patterns in dromedaries follow ancient caravan routes

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Sara Lado ◽  
Jean Pierre Elbers ◽  
Angela Doskocil ◽  
Davide Scaglione ◽  
Emiliano Trucchi ◽  
...  
Keyword(s):  
Demographic History ◽  
Genomic Diversity ◽  
Phylogeographic Structure ◽  
Arid Environments ◽  
Migration Patterns ◽  
Migration Rates ◽  
Global Migration ◽  
Genome Wide ◽  
A Genome ◽  
Scale Population

AbstractDromedaries have been essential for the prosperity of civilizations in arid environments and the dispersal of humans, goods and cultures along ancient, cross-continental trading routes. With increasing desertification their importance as livestock species is rising rapidly, but little is known about their genome-wide diversity and demographic history. As previous studies using few nuclear markers found weak phylogeographic structure, here we detected fine-scale population differentiation in dromedaries across Asia and Africa by adopting a genome-wide approach. Global patterns of effective migration rates revealed pathways of dispersal after domestication, following historic caravan routes like the Silk and Incense Roads. Our results show that a Pleistocene bottleneck and Medieval expansions during the rise of the Ottoman empire have shaped genome-wide diversity in modern dromedaries. By understanding subtle population structure we recognize the value of small, locally adapted populations and appeal for securing genomic diversity for a sustainable utilization of this key desert species.

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