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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Detection of Ghost Introgression Requires Exploiting Topological and Branch Length Information

Systematic Biology, Journal Year: 2024, Volume and Issue: 73(1), P. 207 - 222

Published: Jan. 1, 2024

Abstract In recent years, the study of hybridization and introgression has made significant progress, with ghost introgression—the transfer genetic material from extinct or unsampled lineages to extant species—emerging as a key area for research. Accurately identifying introgression, however, presents challenge. To address this issue, we focused on simple cases involving 3 species known phylogenetic tree. Using mathematical analyses simulations, evaluated performance popular methods, including HyDe PhyloNet/MPL, full-likelihood method, Bayesian Phylogenetics Phylogeography (BPP), in detecting introgression. Our findings suggest that heuristic approaches relying site-pattern counts gene-tree topologies struggle differentiate between sampled non-sister species, frequently leading incorrect identification donor recipient species. The method BPP uses multilocus sequence alignments directly—hence taking into account both branch lengths, by contrast, is capable phylogenomic datasets. We analyzed real-world dataset 14 Jaltomata (Solanaceae) showcase potential methods accurate inference

Language: Английский

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Target capture and genome skimming for plant diversity studies

Applications in Plant Sciences, Journal Year: 2023, Volume and Issue: 11(4)

Published: July 1, 2023

Recent technological advances in long-read high-throughput sequencing and assembly methods have facilitated the generation of annotated chromosome-scale whole-genome sequence data for evolutionary studies; however, generating such can still be difficult many plant species. For example, obtaining high-molecular-weight DNA is typically impossible samples historical herbarium collections, which often degraded DNA. The need to fast-freeze newly collected living conserve high-quality complicated when plants are only found remote areas. Therefore, short-read reduced-genome representations, as target capture genome skimming, remain important studies. Here, we review pros cons each technique non-model taxa. We provide guidance related logistics, budget, genomic resources previously available clade, nature study. Furthermore, assess bioinformatic analyses, detailing best practices pitfalls, suggest pathways combine generated with legacy data. Finally, explore possible downstream analyses allowed by type using technique. a practical guide help researchers make best-informed choice regarding reduced representation studies cases where remains impractical.

Language: Английский

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Testing plastomes and nuclear ribosomal DNA sequences as the next-generation DNA barcodes for species identification and phylogenetic analysis in Acer

BMC Plant Biology, Journal Year: 2024, Volume and Issue: 24(1)

Published: May 23, 2024

Abstract Background Acer is a taxonomically intractable and speciose genus that contains over 150 species. It challenging to distinguish species only by morphological method due their abundant variations. Plastome nuclear ribosomal DNA (nrDNA) sequences are recommended as powerful next-generation barcodes for discrimination. However, efficacies were still poorly studied. The current study will evaluate the application of plastome nrDNA in identification perform phylogenetic analyses . Result Based on collection 83 individuals representing 55 (c. 55% Chinese species) from 13 sections, our barcoding demonstrated plastomes exhibited highest (90.47%) discriminatory power among all plastid markers, such standard matK + rbcL trnH - psbA (61.90%) ycf1 (76.19%). And (80.95%) revealed higher resolution than ITS (71.43%). show interspecific variations, however, failure may be incomplete lineage sorting (ILS) chloroplast capture resulting hybridization. We found usage contributed identifying those unidentified plastomes, implying its capability some extent mitigate impact hybridization ILS combining not given cytonuclear conflict caused potential Our analysis covering 19 sections (95% ) 128 (over 80% this genus) pervasive inter- intra-section discordances, hinting has played an important role evolution Conclusion Plastomes can significantly improve uncovered scope depth , providing insights into evolution.

Language: Английский

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Uncovering ghost introgression through genomic analysis of a distinct eastern Asian hickory species

The Plant Journal, Journal Year: 2024, Volume and Issue: 119(3), P. 1386 - 1399

Published: June 6, 2024

SUMMARY Ghost introgression, or the transfer of genetic material from extinct unsampled lineages to sampled species, has attracted much attention. However, conclusive evidence for ghost especially in plant remains scarce. Here, we newly assembled chromosome‐level genomes both Carya sinensis and cathayensis , additionally re‐sequenced whole 43 C. individuals as well 11 representing diploid hickory species. These genomic datasets were used investigate reticulation bifurcation patterns within genus (Juglandaceae), with a particular focus on beaked . By combining D ‐statistic BPP methods, obtained compelling that supports occurrence introgression an ancestral lineage. This conclusion was reinforced through phylogenetic network analysis genome scan method VolcanoFinder, latter which can detect signatures adaptive unknown donors. Our results not only dispel certain misconceptions about history but also further refine our understanding 's biogeography via divergence estimates. Moreover, successful integration methods demonstrates their efficacy facilitating more precise identification types.

Language: Английский

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Deciphering complex reticulate evolution of Asian Buddleja (Scrophulariaceae): insights into the taxonomy and speciation of polyploid taxa in the Sino-Himalayan region

Annals of Botany, Journal Year: 2023, Volume and Issue: 132(1), P. 15 - 28

Published: Jan. 31, 2023

Species of the genus Buddleja in Asia are mainly distributed Sino-Himalayan region and form a challenging taxonomic group, with extensive hybridization polyploidization. A phylogenetic approach to unravelling history reticulation this lineage will deepen our understanding speciation biodiversity hotspots.

Language: Английский

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Transcriptome-Based Study on the Phylogeny and Hybridization of Marattialean Ferns (Marattiaceae)

Plants, Journal Year: 2023, Volume and Issue: 12(12), P. 2237 - 2237

Published: June 7, 2023

Marattiaceae is a phylogenetically isolated family of tropical eusporangiate ferns including six genera with more than one-hundred species. In Marattiaceae, monophyly has been well-supported phylogenetically. However, the phylogenetic relationships among them were elusive and controversial. Here, dataset 26 transcriptomes (including 11 newly generated) used to assess single-copy nuclear genes obtain organelle gene sequences. Through phylotranscriptomic analysis, phylogeny hybridization events explored robust phylogenomic framework for evolution was provided. Using both concatenation- coalescent-based phylogenies, gene-tree discordance, incomplete lineage sorting (ILS) simulations, network inference examined. Except low support mitochondrial chloroplast strongly supported sister relationship between leptosporangiate ferns. At genus level, all analysis based on datasets recovered five in as monophyletic strong support. Danaea Ptisana first two diverged clades turn. Christensenia clade Marattia + Angiopteris s.l. s.l., three (Angiopteris s.s., Archangiopteris group, An. sparsisora) well identified maximum The group derived from s.s. at ca. 18 Ma. putative hybrid species sparsisora verified by analyses maternal plastid genes. This study will improve our understanding using method explore investigate difficult taxa

Language: Английский

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Phylogeny and evolution of Asparagaceae subfamily Nolinoideae: new insights from plastid phylogenomics

Annals of Botany, Journal Year: 2022, Volume and Issue: 131(2), P. 301 - 312

Published: Nov. 26, 2022

Abstract Background and aims Asparagaceae subfamily Nolinoideae is an economically important plant group, but the deep relationships evolutionary history of lineage remain poorly understood. Based on a large data set including 37 newly sequenced samples publicly available plastomes, this study to better resolve inter-tribal Nolinoideae, rigorously examine tribe-level monophyly Convallarieae, Ophiopogoneae Polygonateae. Methods Maximum likelihood (ML) Bayesian inference (BI) methods were used infer phylogenetic at genus level above. The diversification was explored using molecular dating. Key results Both ML BI analyses identically recovered five clades within respectively corresponding Dracaeneae + Rusceae, Polygonateae Theropogon, Ophiopogoneae, Nolineae, Convallarieae excluding most nodes well supported. As Theropogon embedded in Polygonateae, plastome phylogeny failed as reciprocally monophyletic. Divergence time estimation showed that origins genera dated Miocene Pliocene. youthfulness represented three herbaceous tribes (Convallarieae, Polygonateae) chiefly distributed temperate areas Northern Hemisphere, median stem ages all 14 currently belonging them estimated <12.37 Ma. Conclusions This robust backbone phylogeny, providing new insights for understanding evolution classification Nolinoideae. Compared with by previous based transcriptomic data, our suggest ancient hybridization or incomplete sorting may have occurred early Our findings will provide reference further complexity nuclear genomic data. recent origin these provides evidence support hypothesis global expansion habitats caused climate cooling over past 15 million years dramatically driven speciation Hemisphere flora.

Language: Английский

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Conservation genomic investigation of an endangered conifer, Thuja sutchuenensis, reveals low genetic diversity but also low genetic load

Plant Diversity, Journal Year: 2023, Volume and Issue: 46(1), P. 78 - 90

Published: June 16, 2023

Endangered species generally have small populations with low genetic diversity and a high load.

Language: Английский

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Genomic vulnerability and local adaptation of an arid tolerant tree species on the Qinghai–Tibet Plateau

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

Published: April 29, 2025

Abstract Coping with increasing global temperatures due to climate change may be especially challenging for trees long generation times as changes might happen too quickly successful adaptation. Juniperus przewalskii Komarov is an arid tolerant key species of forest ecosystems on the northeastern Qinghai–Tibet Plateau. Target capture sequencing was utilized survey genetic variation and population structure, infer evolutionary history this by analyzing 170 individuals from 23 populations. This approach provided valuable information how local adaptation influences background species, well potential predictions regarding species' response change. Our results revealed a new fine‐scale structure high levels diversity adaptations despite gene flow. Redundancy analysis showed that contributed most J. . Analysis gradient risk nonadaptedness indicated that, variables examined majority locations sampled, it improbable will need significant alterations in allele frequencies endure forecasted shifts. We also identified at‐risk populations preservation numerous candidate genes upcoming The significance combining environmental forecast resilience tree warming underscored our results, particularly areas susceptible fluctuations.

Language: Английский

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