Phylogenomics and the flowering plant tree of life

Journal of Integrative Plant Biology, Journal Year: 2022, Volume and Issue: 65(2), P. 299 - 323

Published: Nov. 23, 2022

Abstract The advances accelerated by next‐generation sequencing and long‐read technologies continue to provide an impetus for plant phylogenetic study. In the past decade, a large number of studies adopting hundreds thousands genes across wealth clades have emerged ushered phylogenetics evolution into new era. meantime, roadmap researchers when making decisions different approaches their phylogenomic research design is imminent. This review focuses on utility genomic data (from organelle genomes, both reduced representation whole‐genome sequencing) in evolutionary investigations, describes baseline methodology experimental analytical procedures, summarizes recent progress flowering phylogenomics at ordinal, familial, tribal, lower levels. We also discuss challenges, such as adverse impact orthology inference reconstruction raised from systematic errors, underlying biological factors, duplication, hybridization/introgression, incomplete lineage sorting, together suggesting that bifurcating tree may not be best model life. Finally, we promising avenues future studies.

Language: Английский

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The genomic consequences of hybridization

eLife, Journal Year: 2021, Volume and Issue: 10

Published: Aug. 4, 2021

In the past decade, advances in genome sequencing have allowed researchers to uncover history of hybridization diverse groups species, including our own. Although field has made impressive progress documenting extent natural hybridization, both historical and recent, there are still many unanswered questions about its genetic evolutionary consequences. Recent work suggested that outcomes may be part predictable, but open nature selection on hybrids biological variables shape such hampered this area. We synthesize what is known mechanisms drive changes ancestry after highlight major unresolved questions, discuss their implications for predictability evolution hybridization.

Language: Английский

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Stable species boundaries despite ten million years of hybridization in tropical eels

Nature Communications, Journal Year: 2020, Volume and Issue: 11(1)

Published: March 18, 2020

Abstract Genomic evidence is increasingly underpinning that hybridization between taxa commonplace, challenging our views on the mechanisms maintain their boundaries. Here, we focus seven catadromous eel species (genus Anguilla ) and use genome-wide sequence data from more than 450 individuals sampled across tropical Indo-Pacific, morphological information, three newly assembled draft genomes to compare contemporary patterns of with signatures past introgression a time-calibrated phylogeny. We show have remained distinct for up 10 million years find current frequencies pairs contrast genomic introgression. Based near-complete asymmetry in directionality decreasing later-generation hybrids, suggest cytonuclear incompatibilities, hybrid breakdown, purifying selection as can support cohesion even when has been pervasive throughout evolutionary history clades.

Language: Английский

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Rapid adaptive radiation of Darwin’s finches depends on ancestral genetic modules

Science Advances, Journal Year: 2022, Volume and Issue: 8(27)

Published: July 8, 2022

Recent adaptive radiations are models for investigating mechanisms contributing to the evolution of biodiversity. An unresolved question is relative importance new mutations, ancestral variants, and introgressive hybridization phenotypic speciation. Here, we address this issue using Darwin’s finches investigate genomic architecture underlying their diversity. Admixture mapping beak body size in small, medium, large ground revealed 28 loci showing strong genetic differentiation. These represent haplotype blocks with origins predating speciation events during finch radiation. Genes expressed developing overrepresented these regions. Ancestral haplotypes constitute modules selection act as key determinants unusual diversity finches. Such can be critical how species adapt environmental variability change.

Language: Английский

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Genetic resources of Nile tilapia (Oreochromis niloticus Linnaeus, 1758) in its native range and aquaculture

Hydrobiologia, Journal Year: 2022, Volume and Issue: 850(10-11), P. 2425 - 2445

Published: Sept. 22, 2022

Language: Английский

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Unraveling the extensive phylogenetic discordance and evolutionary history of spurless taxa within the Aquilegia ecalcarata complex

New Phytologist, Journal Year: 2025, Volume and Issue: unknown

Published: March 7, 2025

Parallel evolution of the same, or at least very similar, phenotype(s) in different lineages is often interpreted as evidence for action natural selection. However, caution required when inferring parallel based on uncertain potentially incorrect phylogenetic frameworks. Here, by conducting extensive phylogenomic and population genetic analyses, we aim to clarify evolutionary history spurless taxa within Aquilegia ecalcarata complex. We observed substantial discordance patterns across entire genome, primarily attributed ancient introgression incomplete lineage sorting. Additionally, identified several whose positions were distorted admixture events. Using a backbone tree demographic modeling, determined that these independently originated twice this group. Intriguingly, our investigation revealed experienced expansion during global cooling, while their spurred sister groups underwent contraction. The losses petal spurs, therefore, may be linked adaptations low-temperature conditions. These findings emphasize importance comprehensive population-level analyses inference provide valuable insights into dynamics trait loss its implications adaptive strategies.

Language: Английский

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The Legacy of Recurrent Introgression during the Radiation of Hares

Systematic Biology, Journal Year: 2020, Volume and Issue: 70(3), P. 593 - 607

Published: Nov. 19, 2020

Hybridization may often be an important source of adaptive variation, but the extent and long-term impacts introgression have seldom been evaluated in phylogenetic context a radiation. Hares (Lepus) represent widespread mammalian radiation 32 extant species characterized by striking ecological adaptations recurrent admixture. To understand relevance introgressive hybridization during diversification Lepus, we analyzed whole exome sequences (61.7 Mb) from 15 hares (1-4 individuals per species), spanning global distribution genus, two outgroups. We used coalescent framework to infer relationships divergence times, despite extensive genealogical discordance. found high levels allele sharing among show that this reflects incomplete lineage sorting temporally layered hybridization. Our results revealed at all stages along Lepus radiation, including recent gene flow between since last glacial maximum also pervasive ancient occurring near origin hare lineages. northern hemisphere has resulted shared variation potential highly seasonal environments, genes involved circadian rhythm regulation, pigmentation, thermoregulation. illustrate how genetic legacy ancestral persist across leaving long-lasting signature contribute adaptation. [Adaptation; introgression; hybridization; Lepus; phylogenomics.].

Language: Английский

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Genomic variation from an extinct species is retained in the extant radiation following speciation reversal

Nature Ecology & Evolution, Journal Year: 2022, Volume and Issue: 6(4), P. 461 - 468

Published: Feb. 24, 2022

Language: Английский

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On the fast track: hybrids adapt more rapidly than parental populations in a novel environment

Evolution Letters, Journal Year: 2023, Volume and Issue: 8(1), P. 128 - 136

Published: March 1, 2023

Rates of hybridization are predicted to increase due climate change and human activity that cause redistribution species bring previously isolated populations into contact. At the same time leads rapid changes in environment, requiring adapt rapidly order survive. A few empirical cases suggest can facilitate adaptation despite its potential for incompatibilities deleterious fitness consequences. Here we use simulations Fisher's Geometric model evaluate conditions frame via both diploids haplodiploids. We find hybrids faster new environments compared parental nearly all simulated scenarios, generating a advantage offset intrinsic last tens generations, regardless whether population was diploid or haplodiploid. Our results highlight creative role may help contemporary changing climate. However, by well happen at cost reduced biodiversity, if lineages collapse one.

Language: Английский

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Hybridization mediated range expansion and climate change resilience in two keystone tree species of boreal forests

Global Change Biology, Journal Year: 2024, Volume and Issue: 30(4)

Published: March 28, 2024

Current global climate change is expected to affect biodiversity negatively at all scales leading mass loss. Many studies have shown that the distribution of allele frequencies across a species' range often influenced by specific genetic loci associated with local environmental variables. This association reflects adaptation and changes those could thereby contribute evolutionary response change. However, predicting how species will adapt from this type data alone remains challenging. In present study, we combined exome capture sequences niche reconstruction, test multiple methods for assessing resilience in two widely distributed conifers, Norway spruce Siberian spruce. Both are keystone boreal forest share vast hybrid zone. We show conifers can be detected through frequency variation, population-level ecological preferences, historical movement. Moreover, integrated information into offset predictive models hybridization plays central role expanding breadth conifer may help both cope better future changing climates. joint analysis also identified populations risk under current

Language: Английский

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