The distribution of biodiversity richness in the tropics

Science Advances, Год журнала: 2020, Номер 6(37)

Опубликована: Сен. 9, 2020

Latin America has more than twice as many vascular plant species Africa south of the Sahara plus Madagascar, in a smaller area.

Язык: Английский

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Phylogenomic analyses highlight innovation and introgression in the continental radiations of Fagaceae across the Northern Hemisphere

Nature Communications, Год журнала: 2022, Номер 13(1)

Опубликована: Март 14, 2022

Northern Hemisphere forests changed drastically in the early Eocene with diversification of oak family (Fagaceae). Cooling climates over next 20 million years fostered spread temperate biomes that became increasingly dominated by oaks and their chestnut relatives. Here we use phylogenomic analyses nuclear plastid genomes to investigate timing pattern major macroevolutionary events ancient genome-wide signatures hybridization across Fagaceae. Innovation related seed dispersal is implicated triggering waves continental radiations beginning rapid lineages resulting unparalleled transformation forest dynamics within 15 following K-Pg extinction. We detect introgression at multiple time scales, including predating origination genus-level diversity. As moved into newly available habitats Miocene, secondary contact between previously isolated species occurred. This resulted adaptive introgression, which may have further amplified white Eurasia.

Язык: Английский

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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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Target Capture Sequencing Unravels Rubus Evolution

Frontiers in Plant Science, Год журнала: 2019, Номер 10

Опубликована: Дек. 20, 2019

Rubus (Rosaceae) comprises more than 500 species with additional commercially cultivated raspberries and blackberries. The most recent (> 100 years old) global taxonomic treatment of the genus defined 12 subgenera; two subgenera were subsequently described some rearranged. Intra- interspecific ploidy levels hybridization make phylogenetic estimation challenging. Our objectives to estimate phylogeny 94 taxonomically geographically diverse three cultivars using chloroplast DNA sequences target capture approximately 1,000 low copy nuclear genes; divergence times between major clades; examine historical biogeography diversification. Target sequencing identified eight groups within Rubus. Subgenus Orobatus Subg. Anoplobatus monophyletic, while other recognized para- or polyphyletic. Multiple events likely occurred across at subgeneric levels, e.g., (blackberries) × Idaeobatus (raspberries) Cylactis (Arctic berries) hybrids. raspberry heritage known blackberry hybrids was confirmed. common ancestor distributed in North America. distribution during Miocene (about 20 Ma) from America into Asia Europe Bering land bridge southward crossing Panamanian Isthmus. diversified greatly Miocene. taxonomy does not reflect relationships revision is warranted. migrated towards Asia, Europe, Central South early then diversified. Ancestors may have Oceania by long distance bird dispersal. This presents a roadmap for further systematics research. In conclusion, dataset provides high resolution though it also gave evidence gene tree/species tree cytonuclear discordance. Discordance be due incomplete lineage sorting, rather lack signal. study illustrates importance multiple methods when examining complex utility software programs that signal conflict datasets.

Язык: Английский

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Phylogeny and divergence time estimation of the walnut family (Juglandaceae) based on nuclear RAD-Seq and chloroplast genome data

Molecular Phylogenetics and Evolution, Год журнала: 2020, Номер 147, С. 106802 - 106802

Опубликована: Март 23, 2020

Язык: Английский

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A global phylogenetic regionalization of vascular plants reveals a deep split between Gondwanan and Laurasian biotas

New Phytologist, Год журнала: 2021, Номер 233(3), С. 1494 - 1504

Опубликована: Ноя. 10, 2021

Existing global regionalization schemes for plants consider the compositional affinities among biotas, but these have not explicitly considered phylogenetic information. Here, we present first time, a phytogeographical delineation of vascular flora based on species-level evolutionary relationships. We analysed 8737 820 geographical occurrence records together with time-calibrated phylogeny including 67 269 species. constructed by estimating species composition and beta diversity 200 km × grid cells across world. identified de novo 16 units that are deeply split into two clusters: Laurasian Gondwanan. Our broadly matches previous schemes, also highlights separation Gondwanan biota an Holotropical cluster Australian-Neozealandic-Patagonian cluster. In contrast, no clear biotas was retrieved when omitting The integration information provides new insights areas their historical relationships, enabling identification three large, clearly differentiated here referred to as kingdoms: Holarctic, Holotropical, Austral. results provide further evidence delineating transition zones show latitudinal pattern increasing distinctiveness towards poles.

Язык: Английский

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A complete genus-level phylogeny reveals the Cretaceous biogeographic diversification of the poppy family

Molecular Phylogenetics and Evolution, Год журнала: 2023, Номер 181, С. 107712 - 107712

Опубликована: Янв. 21, 2023

Язык: Английский

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Chloroplast phylogenomic data support Eocene amphi‐Pacific early radiation for the Asian Palmate core Araliaceae

Journal of Systematics and Evolution, Год журнала: 2019, Номер 57(6), С. 547 - 560

Опубликована: Июнь 21, 2019

Abstract Traditional phylogenies based on analysis of multiple genes have failed to obtain a well‐resolved evolutionary history for the backbone Asian Palmate group Araliaceae, largest clade family. In this study, we applied genome skimming approach next‐generation sequencing address whether lack resolution at base tree is due molecular sampling error or footprint ancient radiation. Twenty‐nine complete plastid genomes Araliaceae (17 newly sequenced) were analyzed (RAxML, Beast, Lagrange, and BioGeoBears) provide first phylogenomic reconstruction (95% genera included). As result, early divergences been clarified but its core not totally resolved, with short internal branches pointing an radiation scenario. East Asia inferred as most likely ancestral area (from late Paleocene Eocene) from which colonization Neotropics during Eocene. The took place Eocene, in context Boreotropical hypothesis. Recurrent episodes southward migration (to tropics) coupled northern latitude local extinctions (promoting geographic isolation lineages) followed by northward expansion contact lineages that erased trace preceding isolation) are hypothesized linked alternation cold warm periods

Язык: Английский

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Joint Phylogenetic Estimation of Geographic Movements and Biome Shifts during the Global Diversification ofViburnum

Systematic Biology, Год журнала: 2020, Номер 70(1), С. 67 - 85

Опубликована: Апрель 2, 2020

Abstract Phylogeny, molecular sequences, fossils, biogeography, and biome occupancy are all lines of evidence that reflect the singular evolutionary history a clade, but they most often studied separately, by first inferring fossil-dated phylogeny, then mapping on ancestral ranges biomes inferred from extant species. Here we jointly model evolution biogeographic ranges, affinities, while incorporating fossils to estimate dated phylogeny for 163 species woody plant clade Viburnum (Adoxaceae) currently recognize in our ongoing worldwide monographic treatment group. Our analyses indicate major lineages evolved Eocene, majority originated since Miocene. radiated Asia, warm, broad-leaved evergreen (lucidophyllous) forests. Within infer several early shifts into more tropical forests, multiple forests experience prolonged freezing. From two movements New World. These probably occupied warm temperate adapted later spreading cold climates. One these (Porphyrotinus) cloud moved south through mountains Neotropics. Several other North America took place recently, facilitated prior adaptations freezing Old We also four disjunctions between Asia Europe: Tinus lineage is oldest when it spread, whereas three were recent cold-adapted lineages. results variously contradict published accounts, especially view initially and, accordingly, maintained vessel elements with scalariform perforations. explored how location assignments affected inference areas states. sensitive to, not entirely dependent upon, inclusion fossil data. It will be critical take advantage available decipher events distant past. The joint estimation approach developed here provides cautious hope even limited. [Biogeography; biome; combined evidence; pollen; phylogeny; Viburnum.]

Язык: Английский

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Plastid phylogenomics and biogeographic analysis support a trans-Tethyan origin and rapid early radiation of Cornales in the Mid-Cretaceous

Molecular Phylogenetics and Evolution, Год журнала: 2019, Номер 140, С. 106601 - 106601

Опубликована: Авг. 21, 2019

Язык: Английский

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