Phylogenomic conflict analyses in the apple genus Malus s.l. reveal widespread hybridization and allopolyploidy driving diversification, with insights into the complex biogeographic history in the Northern Hemisphere

Journal of Integrative Plant Biology, Год журнала: 2022, Номер 64(5), С. 1020 - 1043

Опубликована: Март 11, 2022

Phylogenomic evidence from an increasing number of studies has demonstrated that different data sets and analytical approaches often reconstruct strongly supported but conflicting relationships. In this study, 785 single-copy nuclear genes 75 complete plastomes were used to infer the phylogenetic relationships estimate historical biogeography apple genus Malus sensu lato, economically important lineage disjunctly distributed in Northern Hemisphere involved known suspected hybridization allopolyploidy events. The phylogeny recovered monophyly s.l. (including Docynia); however, was be biphyletic plastid phylogeny. An ancient chloroplast capture event Eocene western North America best explains cytonuclear discordance. Our conflict analysis ILS, hybridization, could explain widespread gene tree One deep (Malus doumeri) one recent coronaria) detected Furthermore, our biogeographic integrating living fossil a East Asian-western American origin Eocene, followed by several extinction dispersal events Hemisphere. We also propose general workflow for assessing phylogenomic discordance using genome skimming sets.

Язык: Английский

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A New Pipeline for Removing Paralogs in Target Enrichment Data

Systematic Biology, Год журнала: 2021, Номер 71(2), С. 410 - 425

Опубликована: Июнь 13, 2021

Target enrichment (such as Hyb-Seq) is a well-established high throughput sequencing method that has been increasingly used for phylogenomic studies. Unfortunately, current widely pipelines analysis of target data do not have vigorous procedure to remove paralogs in data. In this study, we develop pipeline call Putative Paralogs Detection (PPD) better address putative from The new an add-on the existing HybPiper pipeline, and entire applies criteria both sequence similarity heterozygous sites at each locus identification paralogs. Users may adjust thresholds identity identify according level phylogenetic divergence their group interest. also removes highly polymorphic attributed errors assembly gappy regions alignment. We demonstrated value using empirical generated Hyb-Seq Angiosperms353 kit two woody genera Castanea (Fagaceae, Fagales) Hamamelis (Hamamelidaceae, Saxifragales). Comparisons sets showed PPD identified many more than popular HybPiper. tree topologies times evident differences between our pipeline. further evaluated accuracy error rates by BLAST mapping paralogous orthologous sequences reference genome mollissima. Compared alone, substantially gene mapped multiple (31 genes compared with 4 alone). conjunction HybPiper, can be removed resulting construction robust time analyses. Our study demonstrates derived probe set elucidating species relationships within genus, argues importance additional steps filter poorly aligned (e.g., occur through errors), such described study. [Angiosperms353; Castanea; time; Hamamelis; Hyb-Seq, paralogs, phylogenomics.].

Язык: Английский

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Phylogenomics of Aralia sect. Aralia (Araliaceae): Signals of hybridization and insights into its species delimitations and intercontinental biogeography

Molecular Phylogenetics and Evolution, Год журнала: 2023, Номер 181, С. 107727 - 107727

Опубликована: Фев. 7, 2023

Язык: 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, Год журнала: 2021, Номер 38(2), С. 187 - 203

Опубликована: Сен. 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.

Язык: Английский

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Adiantum japonicum, a new species of the Adiantum pedatum complex (Pteridaceae) from Japan

Phytotaxa, Год журнала: 2021, Номер 525(1), С. 1 - 14

Опубликована: Ноя. 11, 2021

The Adiantum pedatum complex is disjunctly distributed in North America and eastern Asia. In this study, we carried out a detailed morphological study based on 137 specimens representing the biogeographic diversity of complex. sequences eight chloroplast markers 35 samples were analyzed with maximum likelihood Bayesian inference. phylogenetic analyses support recognition new species A. from Japan. We propose as japonicum examinations Japan comparative whole This can be distinguished by erect rhizome shows significant molecular differences other A taxonomic description characters presented.

Язык: Английский

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RAD‐seq data provide new insights into biogeography, diversity anomaly, and species delimitation in eastern Asian–North American disjunct clade Benthamidia of Cornus (Cornaceae)

Journal of Systematics and Evolution, Год журнала: 2023, Номер 62(1), С. 1 - 19

Опубликована: Дек. 13, 2023

Abstract The big‐bracted dogwood clade Benthamidia of Cornus is a typical example the well‐known eastern Asia (EA) and North America (NA) floristic disjunction, with greater species diversity in EA than NA. lineage provides an opportunity to explore factors contributing plant unevenness between NA test hypotheses on origin disjunct distribution from phylogenetic perspective. We generated RAD‐seq data, conducted phylogenomic biogeographic analyses for sampling all (9) subspecies (10) currently recognized floras. also assessed delineation calculated evaluate Finally, we examined variation diversification rates ecological niches phylogeny potential causes underlying observed pattern. Our results revealed relationships congruent previous studies suggested trans‐Beringian ancestral mid‐Oligocene, dispersal Mexico United States mid‐Miocene, early SW China. confirmed rate clade. Species delimitation analysis 17 , including subspecies. By integrating molecular data morphology, proposed retain without changing their ranks. increased as intrinsic factor explaining region driven mainly by isolation partially niche divergence.

Язык: Английский

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A roadmap of phylogenomic methods for studying polyploid plant genera

Applications in Plant Sciences, Год журнала: 2024, Номер 12(4)

Опубликована: Апрель 22, 2024

Phylogenetic inference of polyploid species is the first step towards understanding their patterns diversification. In this paper, we review challenges and limitations inferring relationships plants using traditional phylogenetic sequencing approaches, as well mischaracterization tree from single or multiple gene trees. We provide a roadmap to infer interspecific among lineages by comparing evaluating application current phylogenetic, phylogenomic, transcriptomic, whole-genome approaches different platforms. For reconstruction, assess following criteria: (1) amount prior information tools required capture genetic region(s) interest; (2) probability recovering homeologs for species; (3) time efficiency downstream data analysis. Moreover, discuss bioinformatic pipelines that can reconstruct networks relationships. summary, although phylogenomic have improved our reticulate in polyploid-rich genera, difficulties reliable orthologous genes sorting all homeologous copies allopolyploids remain challenge. future, assembled long-read will assist recovery identification copies, which be particularly useful reconstructing independent origins polyploids.

Язык: Английский

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Phylogenomics and diversification drivers of the Eastern Asian – Eastern North American disjunct Podophylloideae

Molecular Phylogenetics and Evolution, Год журнала: 2022, Номер 169, С. 107427 - 107427

Опубликована: Фев. 4, 2022

Язык: Английский

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Phylogenomics, biogeography, and evolution of the blue‐ or white‐fruited dogwoods (Cornus)—Insights into morphological and ecological niche divergence following intercontinental geographic isolation

Journal of Systematics and Evolution, Год журнала: 2020, Номер 58(5), С. 604 - 645

Опубликована: Авг. 27, 2020

Abstract The eastern Asian (EA)–eastern North American (ENA) floristic disjunction represents a major pattern of phytogeography the Northern Hemisphere. Despite 20 years studies dedicated to identification taxa that display this disjunct pattern, its origin and evolution remain an open question, especially regarding post‐isolation evolution. blue‐ or white‐fruited dogwoods (BW) are most species‐rich among four clades Cornus L., consisting ~35 species divided into three subgenera (subg. Yinquania , subg. Mesomora Kraniopsis ). BW group provides excellent example EA–ENA for biogeographic study due diversity distribution centered in Asia America, yet relationships delineation have remained poorly understood. In study, we combined genome‐wide markers from RAD‐seq, morphology, fossils, climate data understand relationships, history, ecological niche morphological Our phylogenomic analyses with RAxML MrBayes recovered strongly supported well‐resolved phylogeny intercontinental EA ENA Eurasia which two newly identified within . These also potential new but failed resolve C. hemsleyi – schindleri complex. effort develop approach reduce computation time, analysis different nodal age settings treePL suggests setting node's minimum constraint lower bound fossil's range obtain similar ages BEAST. Divergence time BEAST dated stem back very Late Cretaceous divergence Paleogene. By integrating fossil total evidence‐based dating was used conjunction time‐slice probabilities dispersal under DEC model ancestral ranges each Miocene: (disjunct 1), western America 2), 3). history supports via Atlantic Land Bridge late Paleogene 1 Bering Miocene disjuncts 2 3. Character mapping stochastic phytools comparison niche, morphospace, rate indicated differential patterns molecules between sisters. Although stasis observed characters, evolutionary changes growth habit some features leaf, flower, fruit morphology occurred one both sister clades. A significant differentiation habitats temperature, precipitation, elevation sisters observed, suggesting role post‐isolation. varied were not always congruent molecules, cases non‐neutral driven by selection. phylogenetic evidence comparisons lineages lend insights formation anomaly ENA, particular support early diversification EA. findings, previous studies, again suggest floras assembly descended Mesophytic Forests evolved “boreotropical flora” through pathways across lineages.

Язык: Английский

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Phylogenomics and biogeography of Torreya (Taxaceae)—Integrating data from three organelle genomes, morphology, and fossils and a practical method for reducing missing data from RAD‐seq

Journal of Systematics and Evolution, Год журнала: 2022, Номер 60(6), С. 1241 - 1262

Опубликована: Фев. 12, 2022

Abstract Restriction site‐associated DNA sequencing (RAD‐seq) enables obtaining thousands of genetic markers for phylogenomic studies. However, RAD‐seq data are subject to allele dropout (ADO) due polymorphisms at enzyme cutting sites. We developed a new pipeline, Allele Dropout Remedy in our study the gymnosperm genus, Torreya , mitigate ADO outgroups by recovering missing loci from previously published transcriptomes. By using RADADOR supplement Rad‐seq combination with plastome and mitochondrial gene sequences, morphology, fossil records, we reconstructed phylogenetic biogeographic histories genus tested hypotheses on anomalies biodiversity eastern Asian‐North American floristic disjunction. Our results showed that pipeline recovered many outgroup, improved yielded more robust phylogeny . Using fossilized birth–death model divergence–extinction–cladogenesis method, resolved detailed history suggested Jurassic origin spanning Laurasia differential speciation extinction among continents accounting modern diversity, which is biased toward Asia (EA). The also supported vicariance widespread ancestor EA North America (NA) mid‐Eocene, cross Beringian exchange early Paleogene before vicariant isolation, contrast “out NA” pattern common gymnosperms EA” hypothesis proposed genus. Furthermore, observed discordance between nuclear plastid phylogenies jackii suggesting lineage sorting genomes species or genome capture T.

Язык: Английский

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