Population Genomics of Adaptive Radiation DOI

Lucia L. Combrink,

Jimena Golcher‐Benavides, Alexander L. Lewanski

et al.

Molecular Ecology, Journal Year: 2024, Volume and Issue: 34(2)

Published: Dec. 24, 2024

Adaptive radiations are rich laboratories for exploring, testing, and understanding key theories in evolution ecology because they offer spectacular displays of speciation ecological adaptation. Particular challenges to the study adaptive radiation include high levels species richness, rapid speciation, gene flow between species. Over last decade, high-throughput sequencing technologies access population genomic data have lessened these by enabling analysis samples from many individual organisms at whole-genome scales. Here we review how facilitated our knowledge five areas: (1) phylogenetics, (2) hybridization, (3) timing rates diversification, (4) basis trait evolution, (5) role genome structure divergence. We current each area, highlight outstanding questions, focus on methods that facilitate detection complex patterns divergence demography populations through time. It is clear revolutionising ability reconstruct evolutionary history rapidly diversifying clades. Additionally, studies increasingly emphasising central flow, re-use standing genetic variation during adaptation, structural elements as facilitators process radiations. hybridization-and hypothesized processes which it shapes diversification-and questions seeking bridge divide microevolutionary macroevolutionary areas future study. Overall, has an exciting era research, with implications deeper fundamental across tree life.

Language: Английский

Large inversions in Lake Malawi cichlids are associated with habitat preference, lineage, and sex determination DOI Open Access
Narendra Kumar, Taylor L. Cooper, Thomas D. Kocher

et al.

Published: Jan. 31, 2025

Chromosomal inversions are an important class of genetic variation that link multiple alleles together into a single inherited block can have effects on fitness. To study the role large in massive evolutionary radiation Lake Malawi cichlids, we used long-read technologies to identify four and two tandem span half each respective chromosome, which encompass over 10% genome. Each inversion is fixed one states within seven major ecogroups, suggesting they played separation lake lineages specific habitats. One exception benthic sub-radiation, where both inverted non-inverted continue segregate group. The histories three six suggest transferred from pelagic Diplotaxodon group ancestors at time sub-radiation was seeded. remaining found subset species living deep waters. We show some these as XY sex-determination systems but also likely limited total species. Our work suggests been under sexual natural selection cichlids will be understanding how this adaptive evolved.

Language: Английский

Citations

1
Evolutionary lability of a key innovation spurs rapid diversification DOI
Nick Peoples, Michael D. Burns, Michalis Mihalitsis

et al.

Nature, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 26, 2025

Language: Английский

Citations

1
A pangenomic perspective of the Lake Malawi cichlid radiation reveals extensive structural variation driven by transposable elements DOI
Fu Xiang Quah, Miguel Vasconcelos Almeida, Moritz Blumer

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: March 31, 2024

Abstract The East African Rift Lakes, namely Lake Malawi, Victoria, and Tanganyika, host a remarkable diversity of cichlid fishes, representing one nature’s most striking vertebrate radiations. Despite rich phenotypic diversity, single nucleotide polymorphism (SNP)-based sequencing studies have revealed little sequence divergence between cichlids, with 0.1 to 0.25% pairwise within Malawi. These were based on aligning short reads linear reference genome, which ignores the contribution larger scale structural variants (SVs). To complement existing SNP-based studies, we adopted pangenomic approach by constructing multiassembly graph haplochromine cichlids in We produced six new long read genome assemblies, alongside two publicly available ones, span major eco-morphological clades lake. This not only identifies longer SVs, but also visually represents complex nested variation. Strikingly, SV landscape is dominated large insertions, many exclusive individual assemblies. From perspective, observed an exceptional amount extra sequence, totaling up 33.1% additional bases respect genome. Approximately 4.73 9.86% assemblies estimated be interspecies variation, suggesting substantial genomic underappreciated previous studies. While coding regions remain highly conserved, our analysis uncovers significant SVs from transposable element (TE) especially DNA, LINE, LTR transposons. findings underscore intricate interplay evolutionary forces shaping including both small mutations TE-derived alterations.

Language: Английский

Citations

6
From microcosm to macrocosm: adaptive radiation of Darwin’s finches DOI Creative Commons
Peter R. Grant,

B. Rosemary Grant

Evolutionary Journal of the Linnean Society, Journal Year: 2024, Volume and Issue: 3(1)

Published: Jan. 1, 2024

Abstract In this Perspective we show the value of studying living organisms in field to understand their history. Darwin’s finches are an iconic example early stages speciation a young adaptive radiation that produced 18 species little more than million years. The question they pose is how and why so many originated diversified rapidly. A long-term study four on small island Daphne Major, combined with genomic investigations, provide some answers terms extrinsic intrinsic factors. Beak size shape, as well body size, key heritable features involved both ecological reproductive isolation, evolution by natural selection was caused competitor during prolonged droughts. Introgressive hybridization related rare but recurring, apparently widespread, increases genetic variation, does not incur fitness cost. Hybridization can produce new species. We use phylogeny based whole genome sequences infer morphological transitions radiation. Several lines evidence indicate missing from phase due extinction. Combining these results, re-cast classical allopatry-then-sympatry theory competition-selection-hybridization process generates diversity

Language: Английский

Citations

5
Genome of the early spider-orchid Ophrys sphegodes provides insights into sexual deception and pollinator adaptation DOI Creative Commons
Alessia Russo,

Mattia Alessandrini,

Moaïne El Baidouri

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: July 26, 2024

Abstract Pollinator-driven evolution of floral traits is thought to be a major driver angiosperm speciation and diversification. Ophrys orchids mimic female insects lure male pollinators into pseudocopulation. This strategy, called sexual deception, species-specific, thereby providing strong premating reproductive isolation. Identifying the genomic architecture underlying pollinator adaptation may shed light on mechanisms Here, we report 5.2 Gb chromosome-scale genome sequence sphegodes . We find evidence for transposable element expansion that preceded radiation O. group, gene duplication having contributed chemical mimicry. highly differentiated candidate region pollinator-mediated chromosome 2. The will prove useful investigations repeated architectures facilitate evolutionary radiations.

Language: Английский

Citations

5
Cladistic species definitions can lead to under-representation of biodiversity from adaptive radiations DOI Creative Commons
George F. Turner

Evolutionary Journal of the Linnean Society, Journal Year: 2024, Volume and Issue: 3(1)

Published: Jan. 1, 2024

Abstract Many species are paraphyletic, but current taxonomic practices often do not recognize this, and attempts made to apply a monophyletic concept. While allowing the recognition of ecomorphologically equivalent, or even phenotypically indistinguishable allopatric, taxa as species, this leads combining distinctive local forms (such cave-adapted populations) whole adaptive radiations (often in lakes) with widespread paraphyletic force monophyly. It is suggested that has negative consequences for our documentation understanding biodiversity, well conservation, through issues such lack IUCN red-listing.

Language: Английский

Citations

5
Recurrent gene flow events occurred during the diversification of clownfishes of the skunk complex DOI Creative Commons
Anna Marcionetti, Joris A. M. Bertrand, Fabio Cortesi

et al.

Molecular Ecology, Journal Year: 2024, Volume and Issue: 33(11)

Published: April 16, 2024

Clownfish (subfamily Amphiprioninae) are an iconic group of coral reef fish that evolved a mutualistic interaction with sea anemones, which triggered the adaptive radiation clade. Within clownfishes, "skunk complex" is particularly interesting. Besides ecological speciation, interspecific gene flow and hybrid speciation thought to have shaped evolution group. We investigated mechanisms characterizing diversification this complex. By taking advantage their disjunct geographical distribution, we obtained whole-genome data sympatric allopatric populations three main species complex (Amphiprion akallopisos, A. perideraion sandaracinos). examined population structure, genomic divergence introgression signals performed demographic modelling identify most realistic scenario. excluded scenarios strict isolation or origin sandaracinos. discovered moderate from ancestor akallopisos + sandaracinos weak between in Indo-Australian Archipelago throughout identified introgressed regions detected two large high other species. While found has occurred species' diversification, also observed recent admixture was less pervasive than initially thought, suggesting role host repartition behavioural barriers maintaining genetic identity sympatry.

Language: Английский

Citations

4
Dynamic co-evolution of transposable elements and the piRNA pathway in African cichlid fishes DOI Creative Commons
Miguel Vasconcelos Almeida, Moritz Blumer, Chengwei Ulrika Yuan

et al.

Genome biology, Journal Year: 2025, Volume and Issue: 26(1)

Published: Jan. 22, 2025

Abstract Background East African cichlid fishes have diversified in an explosive fashion, but the (epi)genetic basis of phenotypic diversity these remains largely unknown. Although transposable elements (TEs) been associated with variation cichlids, little is known about their transcriptional activity and epigenetic silencing. We set out to bridge this gap understand interactions between TEs hosts. Results Here, we describe dynamic patterns TE expression gonads during early development. Orthology inference revealed strong conservation silencing factors expansion piwil1 genes Lake Malawi likely driven by PiggyBac TEs. The expanded copies signatures positive selection retain amino acid residues essential for catalytic activity. Furthermore, cichlids express a Piwi-interacting RNA (piRNA) pathway that targets define genomic sites piRNA production find divergence closely related species, line fast evolution piRNA-producing loci. Conclusions Our findings suggest co-evolution host pathways radiations. propose has contributed diversity.

Language: Английский

Citations

0
Large inversions in Lake Malawi cichlids are associated with habitat preference, lineage, and sex determination DOI Open Access
Narendra Kumar, Taylor L. Cooper, Thomas D. Kocher

et al.

Published: Jan. 31, 2025

Chromosomal inversions are an important class of genetic variation that link multiple alleles together into a single inherited block can have effects on fitness. To study the role large in massive evolutionary radiation Lake Malawi cichlids, we used long-read technologies to identify four and two tandem span half each respective chromosome, which encompass over 10% genome. Each inversion is fixed one states within seven major ecogroups, suggesting they played separation lake lineages specific habitats. One exception benthic sub-radiation, where both inverted non-inverted continue segregate group. The histories three six suggest transferred from pelagic Diplotaxodon group ancestors at time sub-radiation was seeded. remaining found subset species living deep waters. We show some these as XY sex-determination systems but also likely limited total species. Our work suggests been under sexual natural selection cichlids will be understanding how this adaptive evolved.

Language: Английский

Citations

0
Museomic analyses clarify species diversity in the icefish genus Channichthys DOI Creative Commons
Benedicte Garmann-Aarhus, Е. А. Николаева, Thomas Desvignes

et al.

Polar Biology, Journal Year: 2025, Volume and Issue: 48(1)

Published: Jan. 31, 2025

Language: Английский

Citations

0