Genomic landscape of the global oak phylogeny

New Phytologist, Journal Year: 2019, Volume and Issue: 226(4), P. 1198 - 1212

Published: Oct. 14, 2019

Summary The tree of life is highly reticulate, with the history population divergence emerging from populations gene phylogenies that reflect histories introgression, lineage sorting and divergence. In this study, we investigate global patterns oak diversity test hypothesis there are regions genome broadly informative about phylogeny. We utilize fossil data restriction‐site associated DNA sequencing ( RAD ‐seq) for 632 individuals representing nearly 250 Quercus species to infer a time‐calibrated phylogeny world's oaks. use reversible‐jump Markov chain Monte Carlo method reconstruct shifts in diversification rates, accounting among‐clade sampling biases. then map > 20 000 ‐seq loci back an annotated genomic distribution introgression phylogenetic support across Oak lineages have diversified among geographic regions, followed by ecological within Americas Eurasia. Roughly 60% traces four clades experienced increases net diversification, probably response climatic transitions or opportunity. strong contrasts high heterogeneity signal introgression. Oaks phylogenomic mosaics, their may fact depend on flow shapes genome.

Language: Английский

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Genome evolution and diversity of wild and cultivated potatoes

Nature, Journal Year: 2022, Volume and Issue: 606(7914), P. 535 - 541

Published: June 8, 2022

Potato (Solanum tuberosum L.) is the world's most important non-cereal food crop, and vast majority of commercially grown cultivars are highly heterozygous tetraploids. Advances in diploid hybrid breeding based on true seeds have potential to revolutionize future potato production1-4. So far, relatively few studies examined genome evolution diversity wild cultivated landrace potatoes, which limits application their breeding. Here we assemble 44 high-quality genomes from 24 20 accessions that representative Solanum section Petota, tuber-bearing clade, as well 2 neighbouring section, Etuberosum. Extensive discordance phylogenomic relationships suggests complexity evolution. We find substantially expanded its repertoire disease-resistance genes when compared with closely related seed-propagated solanaceous crops, indicative effect tuber-based propagation strategies genome. discover a transcription factor determines tuber identity interacts mobile tuberization inductive signal SP6A. also identify 561,433 high-confidence structural variants construct map large inversions, provides insights for improving inbred lines precluding linkage drag, exemplified by 5.8-Mb inversion associated carotenoid content tubers. This study will accelerate enrich our understanding biology global staple crop.

Language: Английский

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Widespread introgression across a phylogeny of 155 Drosophila genomes

Current Biology, Journal Year: 2021, Volume and Issue: 32(1), P. 111 - 123.e5

Published: Nov. 16, 2021

Language: Английский

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Prevalence and Adaptive Impact of Introgression

Annual Review of Genetics, Journal Year: 2021, Volume and Issue: 55(1), P. 265 - 283

Published: Sept. 28, 2021

Alleles that introgress between species can influence the evolutionary and ecological fate of exposed to novel environments. Hybrid offspring different are often unfit, yet it has long been argued introgression be a potent force in evolution, especially plants. Over last two decades, genomic data have increasingly provided evidence is critically important source genetic variation this additional useful adaptive evolution both animals Here, we review factors probability foreign variants provide long-term benefits (so-called introgression) discuss their potential benefits. We find plays an role particularly when far from its fitness optimum, such as they expand range or subject changing

Language: Английский

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Phylogenomic approaches to detecting and characterizing introgression

Genetics, Journal Year: 2021, Volume and Issue: 220(2)

Published: Nov. 11, 2021

Abstract Phylogenomics has revealed the remarkable frequency with which introgression occurs across tree of life. These discoveries have been enabled by rapid growth methods designed to detect and characterize from whole-genome sequencing data. A large class phylogenomic makes use data species infer based on expectations multispecies coalescent. range simple tests, such as D-statistic, model-based approaches for inferring phylogenetic networks. Here, we provide a detailed overview various signals that different modes are expected leave in genome, how current them. We discuss strengths pitfalls these identify areas future development, highlighting introgression, power each method conclude discussion challenges they could potentially be addressed.

Language: Английский

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Species divergence with gene flow and hybrid speciation on the Qinghai–Tibet Plateau

New Phytologist, Journal Year: 2022, Volume and Issue: 234(2), P. 392 - 404

Published: Jan. 12, 2022

Summary The Qinghai–Tibet Plateau (QTP) sensu lato ( sl ), comprising the platform, Himalaya and Hengduan Mountains, is characterized by a large number of endemic plant species. This evolutionary cradle may have arisen from explosive species diversification because geographic isolation. However, gene flow has been widely detected during speciation processes all groups examined, suggesting that natural selection also played an important role divergence in this region. In addition, hybrids recovered almost species‐rich genera. suggests numerous region are still ‘on pathway to complete reproductive isolation (RI)’. Such could directly develop into new through hybrid polyploidization homoploid (HHS). HHS take place more easily than previously thought alternate inheritance alleles parents at multiple RI loci. Therefore, isolation, hybridization together promoted genera on QTP . We emphasize need for identification functional analysis major genes speciation, especially encourage investigations parallel adaptive causing across different lineages within similar but specific habitats

Language: Английский

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Why sequence all eukaryotes?

Proceedings of the National Academy of Sciences, Journal Year: 2022, Volume and Issue: 119(4)

Published: Jan. 18, 2022

Life on Earth has evolved from initial simplicity to the astounding complexity we experience today. Bacteria and archaea have largely excelled in metabolic diversification, but eukaryotes additionally display abundant morphological innovation. How these innovations come about what constraints are there origins of novelty continuing maintenance biodiversity Earth? The history life code for working parts cells systems written genome. BioGenome Project proposed that genomes all extant, named eukaryotes—about 2 million species—should be sequenced high quality produce a digital library Earth, beginning with strategic phylogenetic, ecological, high-impact priorities. Here discuss why should sequence eukaryotic species, not just representative few scattered across many branches tree life. We suggest questions evolutionary ecological significance will only addressable when whole-genome data representing divergences at branchings or species natural ecosystems available. envisage genomic foster understanding ongoing processes speciation, adaptation, organismal dependencies within entire ecosystems. These explorations resolve long-standing problems phylogenetics, evolution, ecology, conservation, agriculture, bioindustry, medicine.

Language: Английский

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A genomic timescale for placental mammal evolution

Science, Journal Year: 2023, Volume and Issue: 380(6643)

Published: April 27, 2023

The precise pattern and timing of speciation events that gave rise to all living placental mammals remain controversial. We provide a comprehensive phylogenetic analysis genetic variation across an alignment 241 mammal genome assemblies, addressing prior concerns regarding limited genomic sampling species. compared neutral genome-wide phylogenomic signals using concatenation coalescent-based approaches, interrogated chromosomes, analyzed extensive catalogs structural variants. Interordinal relationships exhibit relatively low rates conflict diverse datasets analytical methods. Conversely, X-chromosome versus autosome conflicts characterize multiple independent clades radiated during the Cenozoic. Genomic time trees reveal accumulation cladogenic before immediately after Cretaceous-Paleogene (K-Pg) boundary, implying important roles for Cretaceous continental vicariance K-Pg extinction in radiation.

Language: Английский

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Incomplete lineage sorting and phenotypic evolution in marsupials

Cell, Journal Year: 2022, Volume and Issue: 185(10), P. 1646 - 1660.e18

Published: April 20, 2022

Incomplete lineage sorting (ILS) makes ancestral genetic polymorphisms persist during rapid speciation events, inducing incongruences between gene trees and species trees. ILS has complicated phylogenetic inference in many lineages, including hominids. However, we lack empirical evidence that leads to incongruent phenotypic variation. Here, performed phylogenomic analyses show the South American monito del monte is sister of all Australian marsupials, although over 31% its genome closer Diprotodontia than other groups due ancient radiation. Pervasive conflicting signals across whole are consistent with some morphological variation among extant marsupials. We detected hundreds genes experienced stochastic fixation ILS, encoding same amino acids non-sister species. Using functional experiments, confirm how may have directly contributed hemiplasy traits were established marsupial ca. 60 mya.

Language: Английский

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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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