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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Phylogenomics shed light on the complex evolutionary history of a gymnosperm genus showing East Asian–Tethyan disjunction

Journal of Systematics and Evolution, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 3, 2025

Abstract When and how disjunct distributions of biological taxa arose has long attracted interest in biogeography, yet the East Asian–Tethyan disjunction is understudied. Cupressus (Cupressaceae) shows this disjunction, with 10 species Asia three Mediterranean region. Here we used target‐capture sequencing obtained 1991 single‐copy nuclear genes, plus complete plastomes, to infer evolutionary history . Our phylogenomic reconstruction resolved four well supported clades , but revealed significant phylogenetic conflicts, inter‐lineage gene flow, incomplete lineage sorting tree estimation error all making important contributions. The Chengiana clade most likely originated by hybridization between ancestors Himalayan–Hengduan Mountains subtropical clades, whereas orogenic climatic changes may have facilitated flow within clade. Molecular dating suggested that recent common ancestor appeared around middle Eocene period then became continuously distributed across Eurasia. when diverged, been driven Eocene/Oligocene declines global temperature, reinforced ecogeographic barrier created uplift Qinghai–Tibet Plateau. Niche shifts clade, signatures selection genes for drought salt tolerance, probably indicate adaptation local conditions. Overall, our study in‐depth analyses are powerful tools deciphering complex origin organisms, especially gymnosperms.

Language: Английский

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Evolutionary origin of species diversity on the Qinghai–Tibet Plateau

Journal of Systematics and Evolution, Journal Year: 2021, Volume and Issue: 59(6), P. 1142 - 1158

Published: Aug. 25, 2021

Abstract The Qinghai–Tibet Plateau (QTP) sensu lato ( sl ) houses an exceptional species diversity in Asia. To develop a comprehensive understanding of this fascinating region, we reviewed recent progress from biogeographic, paleogeographic, paleontological and genomic research both plants animals the QTP . Numerous studies have been conducted to examine whether uplift triggered production rich there, Quaternary “unified ice sheet” eliminated on central plateau how high‐altitude developed extreme environment adaptations. Major disputes arose about first issue, mainly different circumscriptions related uplift, inaccurate dating molecular phylogenetic trees, non‐causal correlations between diversification. is spatially temporally heterogeneous, abundant fossils reported recently similarly support such asynchronous upheaval model across entire region. Available phylogeographic alpine suggested their glacial refugia , rejecting unified sheet during Last Glacial Maximum. Genomic evidence limited number has identified numerous candidate genes for adaptation. In future, more should be focused speciation adaptation mechanisms based cutting‐edge methods.

Language: Английский

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Rapid parallel adaptation despite gene flow in silent crickets

Nature Communications, Journal Year: 2021, Volume and Issue: 12(1)

Published: Jan. 4, 2021

Abstract Gene flow is predicted to impede parallel adaptation via de novo mutation, because it can introduce pre-existing adaptive alleles from population population. We test this using Hawaiian crickets ( Teleogryllus oceanicus ) in which ‘flatwing’ males that lack sound-producing wing structures recently arose and spread under selection an acoustically-orienting parasitoid. Morphometric genetic comparisons identify distinct flatwing phenotypes populations on three islands, localized different loci. Nevertheless, we detect strong, recent ongoing gene among the populations. Using genome scans expression analysis find evolution of islands associated with shared genomic hotspots contain doublesex , but form differs corresponds known demographics wild. thus show how occur contemporary timescales despite flow, indicating could be less constrained than previously appreciated.

Language: Английский

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Genome sequences and population genomics reveal climatic adaptation and genomic divergence between two closely related sweetgum species

The Plant Journal, Journal Year: 2024, Volume and Issue: 118(5), P. 1372 - 1387

Published: Feb. 11, 2024

SUMMARY Understanding the genetic basis of population divergence and adaptation is an important goal in genetics evolutionary biology. However, relative roles demographic history, gene flow, and/or selective regime driving genomic divergence, climatic adaptation, speciation non‐model tree species are not yet fully understood. To address this issue, we generated whole‐genome resequencing data Liquidambar formosana L. acalycina , which broadly sympatric but altitudinally segregated Tertiary relict forests subtropical China. We integrated environmental to investigate these two sister species. inferred a scenario allopatric during late Miocene, followed by secondary contact Holocene. identified multiple islands elevated that mainly evolved through hitchhiking recombination rate variation, likely fostered long‐term refugial isolation recent differential introgression low‐recombination regions. also found some candidate genes with divergent selection signatures potentially involved reproductive isolation. Our results contribute better understanding how Tertiary/Quaternary change influenced speciation, introgressive hybridization East Asia's flora. In addition, they should facilitate future evolutionary, conservation genomics, molecular breeding studies genus medicinal ornamental values.

Language: Английский

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Genomic insights into adaptation to heterogeneous environments for the ancient relictual Circaeaster agrestis (Circaeasteraceae, Ranunculales)

New Phytologist, Journal Year: 2020, Volume and Issue: 228(1), P. 285 - 301

Published: May 19, 2020

Summary Investigating the interaction between environmental heterogeneity and local adaptation is critical for understanding evolutionary history of a species, providing premise studying response organisms to rapid climate change. However, most species how exactly spatial promotes population divergence genomic variations contribute adaptive evolution remain poorly understood. We examine contributions geographical variables relictual, alpine herb Circaeaster agrestis , as well genetic basis using RAD‐seq plastome data. detected significant structure with an extraordinary disequilibrium diversity among regions, signals isolation‐by‐distance along isolation‐by‐resistance. The populations were estimated begin diverging in late Miocene, possible ancestral distribution Hengduan Mountains adjacent regions. Both gradient redundancy analyses revealed association variation temperature variables. Genome–environment identified 16 putatively loci related mainly biotic abiotic stress resistance. Our genome‐wide data provide new insights into important role shaping structure, access footprints ancient relictual informing future conservation efforts.

Language: Английский

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Unlocking the Hidden Genetic Diversity of Varicosaviruses, the Neglected Plant Rhabdoviruses

Pathogens, Journal Year: 2022, Volume and Issue: 11(10), P. 1127 - 1127

Published: Sept. 29, 2022

The genus Varicosavirus is one of six genera plant-infecting rhabdoviruses. Varicosaviruses have non-enveloped, flexuous, rod-shaped virions and a negative-sense, single-stranded RNA genome. A distinguishing feature varicosaviruses, which shared with dichorhaviruses, bi-segmented Before 2017, sole varicosavirus was known characterized, then two more varicosaviruses were identified through high-throughput sequencing in 2017 2018. More recently, the number has substantially increased concert extensive use platforms data mining approaches. novel revealed not only sequence diversity, but also plasticity terms genome architecture, including virus tentatively unsegmented Here, we report discovery 45 genomes publicly available metatranscriptomic data. identification, assembly, curation raw Sequence Read Archive reads resulted 39 viral sequences full-length coding regions 6 nearly complete regions. highlights obtained include eight genomes, are linked to phylogenetic clade associated gymnosperms. These findings most phylogeny date shed new light on relationships evolutionary landscape this group plant Thus, for allowed us unlock hidden genetic diversity largely neglected

Language: Английский

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Species discrimination in Schima (Theaceae): Next‐generation super‐barcodes meet evolutionary complexity

Molecular Ecology Resources, Journal Year: 2022, Volume and Issue: 22(8), P. 3161 - 3175

Published: July 5, 2022

Plastid genome and nuclear ribosomal DNA (nrDNA) arrays, proposed recently as "super-barcodes," might provide additional discriminatory power overcome the limitations of traditional barcoding loci, yet super-barcodes need to be tested for their effectiveness in more plant groups. Morphological homoplasy among Schima species makes genus a model testing efficacy super-barcodes. In this study, we generated multiple data sets comprising standard barcodes (matK, rbcL, trnH-psbA, nrITS) (plastid genome, nrDNA arrays) across 58 individuals from 12 out 13 China. No samples were correctly assigned using while only 27.27% with accessions distinguished plastid its partitioned sets-the lowest estimated rate super-barcode success literature so far. For other taxa similarly divergence low levels genetic variation, incomplete lineage sorting, hybridization or taxonomic oversplitting are all possible causes failure. Taken together, our study suggests that by no means immune challenges imposed evolutionary complexity. We therefore call developing multilocus markers discrimination

Language: Английский

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Integrated phylogenomic analyses unveil reticulate evolution inParthenocissus(Vitaceae), highlighting speciation dynamics in theHimalayan–HengduanMountains

New Phytologist, Journal Year: 2022, Volume and Issue: 238(2), P. 888 - 903

Published: Oct. 28, 2022

Summary Hybridization caused by frequent environmental changes can lead both to species diversification (speciation) and speciation reversal (despeciation), but the latter has rarely been demonstrated. Parthenocissus , a genus with its trifoliolate lineage in Himalayan–Hengduan Mountains (HHM) region showing perplexing phylogenetic relationships, provides an opportunity for investigating dynamics based on integrated evidence. We investigated discordance reticulate evolution rigorous analyses of plastome transcriptome data. focused reticulations HHM using population‐level genome resequencing dataset, incorporating evidence from morphology, distribution, elevation. Comprehensive confirmed multiple introgressions within robust temporal–spatial framework. Around region, at least three hybridization hot spots were identified, one which showed ongoing reversal. present solid case study integrative methodological approach investigate evolutionary history underlying mechanisms plants. It demonstrates example through hybridizations new perspectives mountainous areas strong topographic heterogeneity.

Language: Английский

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Seeing through the hedge: Phylogenomics of Thuja (Cupressaceae) reveals prominent incomplete lineage sorting and ancient introgression for Tertiary relict flora

Cladistics, Journal Year: 2021, Volume and Issue: 38(2), P. 187 - 203

Published: Sept. 22, 2021

The Eastern Asia (EA) - North America (NA) disjunction is a well-known biogeographic pattern of the Tertiary relict flora; however, few studies have investigated evolutionary history this using phylogenomic approach. Here, we used 2369 single copy nuclear genes and nearly full plastomes to reconstruct small genus Thuja, which consists five disjunctly distributed species. species tree strongly supported an EA clade Thuja standishii-Thuja sutchuenensis "disjunct clade", where western NA T. plicata sister EA-eastern disjunct occidentalis-Thuja koraiensis group. Our results suggested that observed topological discordance among gene trees as well cytonuclear mainly due incomplete lineage sorting, probably facilitated by fast diversification around Early Miocene large effective population sizes ancestral lineages. Furthermore, approximately 20% genome derived from unknown might explain close resemblance its cone morphology ancient fossil Overall, our study demonstrates may not resolve interspecific relationships for taxa, more reliable will come hundreds or thousands loci, revealing complex history. This steadily improve understanding their origin evolution.

Language: Английский

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