Genomic phylogeography illuminates deep cyto-nuclear discordances in midwife toads (Alytes)

Molecular Phylogenetics and Evolution, Год журнала: 2023, Номер 183, С. 107783 - 107783

Опубликована: Апрель 11, 2023

Язык: Английский

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The phylogeny and global biogeography of Primulaceae based on high-throughput DNA sequence data

Molecular Phylogenetics and Evolution, Год журнала: 2023, Номер 182, С. 107702 - 107702

Опубликована: Фев. 11, 2023

The angiosperm family Primulaceae is morphologically diverse and distributed nearly worldwide. However, phylogenetic uncertainty has obstructed the identification of major morphological biogeographic transitions within clade. We used target capture sequencing with Angiosperms353 probes, taxon-sampling encompassing all genera family, tree-based sequence curation, multiple approaches to investigate clades their relationship other Ericales. generated dated trees conducted broad-scale analyses as well stochastic character mapping growth habit. show that Ardisia, a pantropical genus largest in not monophyletic, at least 19 smaller nested it. Neotropical members Ardisia several form clade, an ancestor which arrived Neotropics began diversifying about 20 Ma. This clade most closely related Elingamita Tapeinosperma, are on islands Pacific. Both Androsace Primula non-monophyletic by inclusion genera. Ancestral state reconstructions revealed there have either been parallel herbaceous habit Primuloideae, Samolus, three lineages Myrsinoideae, or common was herbaceous. Our results provide robust estimate relationships across revised classification Myrsinoideae necessary render monophyletic.

Язык: Английский

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Molecular phylogeny and inflorescence evolution of Prunus (Rosaceae) based on RAD-seq and genome skimming analyses

Plant Diversity, Год журнала: 2023, Номер 45(4), С. 397 - 408

Опубликована: Апрель 6, 2023

is an economically important genus widely distributed in the temperate Northern Hemisphere. Previous studies on using a variety of loci yielded conflicting phylogenetic hypotheses. Here, we generated nuclear reduced representation sequencing data and plastid genomes for 36

Язык: Английский

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Time-calibrated phylogenies reveal mediterranean and pre-mediterranean origin of the thermophilous vegetation of the Canary Islands

Annals of Botany, Год журнала: 2023, Номер 131(4), С. 667 - 684

Опубликована: Янв. 3, 2023

Abstract Background and Aims The Canary Islands have strong floristic affinities with the Mediterranean Basin. One of most characteristic diverse vegetation belts archipelago is thermophilous woodland (between 200 900 m.a.s.l.). This plant community consists many non-endemic species shared Floristic Region together Canarian endemic species. Consequently, phytogeographic studies historically proposed hypothesis an origin following establishment summer-dry mediterranean climate in Basin around 2.8 million years ago. Methods Time-calibrated phylogenies for 39 groups including were primarily analysed to infer colonization times. In particular, we used 26 previously published 13 new time-calibrated (including newly generated plastid nuclear DNA sequence data) assess whether time interval between stem crown ages lineages postdates Ma. For postdating this threshold, additionally conducted ancestral area reconstructions potential source colonization. Key Results A total 43 identified from groups. Both (16) pre-mediterranean (9) found. However, failed determine temporal 18 because a stem–crown overlaps 2.8-Ma threshold. spatial was also heterogeneous, areas (nine) other regions (six). Conclusions Our findings reveal unexpectedly heterogeneous terms times mainland areas. substantial proportion arrived Canaries before established complex geographic challenges view (and Madeira) as subregion within Region.

Язык: Английский

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Ancestral state reconstruction sheds new light on the loss of divarication hypothesis on New Zealand's outlying islands

Journal of Ecology, Год журнала: 2025, Номер unknown

Опубликована: Апрель 2, 2025

Abstract The New Zealand flora is remarkable in many respects, but one of its most notable features the convergent evolution plant lineages towards a divaricate habit. adaptive significance divarication remains controversial, it has usually been considered response to harsh climates or defence mechanism against diverse array Ratites (large browsing birds) that once populated Zealand. loss hypothesis posits divaricate‐related traits should be lost on Zealand's outlying islands, as these islands were never reached by Ratites. Like evolutionary components island syndrome, this was tested through pairwise comparison method, is, comparing endemics those their closest relative(s) mainland, assuming recent common ancestor (MRCA) divaricate. This assumption challenged results tested. Here, we test assumption. We collated data for all genus comprising at least species and endemic region. used ancestral range reconstruction determine which colonised from then state whether each MRCA quantify degree morphological leaf size branching angle (i.e. significant traits) islands. Twenty‐one out 29 MRCAs estimated likely non‐divaricate, meaning cases evolved mainland present Island also larger leaves smaller angles regardless not. Synthesis . These findings show how advance our understanding In addition, they have broader implications field biogeography, highlight limits method provide way overcome them.

Язык: Английский

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Phylogenomics of the tetraploid Hawaiian lobeliads: Implications for their origin, dispersal history, and adaptive radiation

Proceedings of the National Academy of Sciences, Год журнала: 2025, Номер 122(19)

Опубликована: Май 5, 2025

Hawaiian lobeliads exhibit extensive adaptive radiations and are considered the largest plant clade (143 species) endemic to any oceanic archipelago. Rapid insular prone reticulate evolution, yet detecting hybridization is often limited by inadequate sampling of taxa or independent loci. We analyzed 633 nuclear loci (including tetraploid duplications) whole plastomes for 89% extant species derive phylogenies lobeliads. Nuclear data provide strong support nine major clades in both likelihood ASTRAL analyses. All genera/sections monophyletic except Clermontia Cyanea . plastome conflict on short, deep branches; tree resolves a fleshy-fruited Clermontia/Cyanea-Brighamia/Delissea , sister Polynesian Sclerotheca with capsular-fruited clade. Incomplete lineage sorting rapid radiation starting 8.5–11.3 Ma sufficient explain uncertainty cytonuclear discordance along backbone. Sequence reticulation within especially identify 42 interisland dispersal events: accord strict progression rule, involving movement next younger island hotspot chain, consistent theory. Plastid overestimate such events 17%. have undergone parallel elevational distribution flower length all islands, multiple founders some differences. lobeliad diversification was driven an early intergeneric divergence habitat, followed ecological speciation Clermontia/Cyanea combined widespread single-island endemism, frequent dispersal, occasional hybridization.

Язык: Английский

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Conservation in the face of hybridisation: genome-wide study to evaluate taxonomic delimitation and conservation status of a threatened orchid species

Conservation Genetics, Год журнала: 2021, Номер 22(1), С. 151 - 168

Опубликована: Янв. 29, 2021

Язык: Английский

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Molecular phylogeny of Asian Ardisia (Myrsinoideae, Primulaceae) and their leaf-nodulated endosymbionts, Burkholderia s.l. (Burkholderiaceae)

PLoS ONE, Год журнала: 2022, Номер 17(1), С. e0261188 - e0261188

Опубликована: Янв. 19, 2022

The genus Ardisia (Myrsinoideae, Primulaceae) has 16 subgenera and over 700 accepted names, mainly distributed in tropical Asia America. circumscription of is not well-defined sometimes confounded with the separation some small genera. A taxonomic revision focusing on allies necessary. In subgenus Crispardisia , symbiotic association leaf-nodule bacteria a unique character within genus. endosymbionts are vertically transmitted, highly specific dependent hosts, suggesting strict cospeciation may have occurred evolutionary history. present study, we aimed to establish phylogenetic framework for further revision. We also test hypothesis leaf-nodulate their endosymbiotic bacteria. Nuclear ITS two chloroplast intergenic spaces were used reconstruct phylogeny Asian relatives Myrsinoideae, Primulaceae. 16S-23S rRNA bacterial symbionts’ phylogeny. To understand symbionts, topology tests cophylogenetic analyses conducted. molecular suggested monophyletic, unless Sardiria Hymenandra Badula Oncostemum included. results suggest generic limit Myrsinoideae (Primulaceae) needs be revised. Pimelandra Stylardisia supported as monophyly, while Bladhia was separated into distant clades. proposed divide s . str Odontophylla Both rejected between hosts Burkholderia Cophylogenetic showed general concordance events, host-switching events loss all inferred.

Язык: Английский

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Phylogenomic analyses reveal a history of hybridisation and introgression between Sophora sect. Edwardsia (Fabaceae) species in New Zealand

New Zealand Journal of Botany, Год журнала: 2021, Номер 60(2), С. 113 - 133

Опубликована: Авг. 4, 2021

Past studies of Sophora sect. Edwardsia using traditional phylogenetic and population genetic markers have been unable to produce a resolved species phylogeny this recent radiation shrubs trees. Here we examined the relationships within between New Zealand next-generation sequencing. We generated genome-wide SNP data with double-digest restriction site-associated DNA sequencing (ddRADseq). prostrata was as sister remaining in all analyses. Relationships taxa exhibited high level conflict many clusters reflecting geography rather than boundaries. This result contrasts previous study, which able differentiate most genotype from nine microsatellite loci. Overall our ddRADseq results indicate interspecific hybridisation introgression group, blurs taxonomic boundaries throughout distributional ranges species. Hybridisation among regional metapopulations comprising closely related may increase adaptive potential respond changing local conditions, at same time selection acts maintain their identity face ongoing gene flow.

Язык: Английский

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Collections‐based systematics and biogeography in the 21st century: A tribute to Dr. Vicki Funk

Journal of Systematics and Evolution, Год журнала: 2020, Номер 58(6), С. 743 - 750

Опубликована: Ноя. 1, 2020

This special issue honors Dr. Vicki Ann Funk (26 November 1947–22 October 2019), who passed away after a battle with an aggressive cancer (Fig. 1). was Botanist at the Smithsonian Institution in 1981–2019. inspirational evolutionary biologist and champion for collections-based systematics biogeography (Funk, 2018). She quite literally changed way we perform our today, she consistently driving force positive change botany beyond. one of most active, enthusiastic, passionate professional botanists time. combined these qualities quick mind glowing wit, always new ideas or opinions that eager to share anyone would listen be willing enter engaging dialog. During her distinguished career, achieved pre-eminence fields phylogenetic methods, systematics, biogeography, biodiversity conservation. very active member leader several societies biogeography. Her vision leadership as well passion mentoring next generation have had strong influence on direction botanical research career development many colleagues. A detailed biography published recently by Wagner & Specht (2020), contributions can also found works et al. (2019) Gillespie Whittaker (2020). pioneered use cladistics theory plant late 1970s early 1980s (e.g., Stuessy, 1978; Funk, 1982, 1985a). few time actively collaborated leading zoologists advocating approaches Brooks, 1981; Platnick 1983; Wiley al., 1991). innovatively developed guidelines detect hybridization events, which are common plants, using patterns extensive case studies 1985b). continued extensively study diversification classification Compositae phylogenetics 2005, 2009; Nie 2013), added next-generation phylogenomics tool box last years Mandel 2015, 2017, 2019). world's experts sunflower family, Compositae, largest family flowering plants more than 27 000 species, accounting 10% all angiosperm species. started Ohio State University dissertation Montanoa Cerv. 1982) under Tod Stuessy. In 1981, spent postdoctoral year New York Botanical Garden, where studied Art Cronquist. time, 1 day week American Museum Natural History develop expertise intellectual among community. subsequent 35 years, large network collaborators across globe generated numerous important evolution this large, diverse, ecologically important, taxonomically difficult family. The spectacular book (Systematics, Evolution, Biogeography Compositae) (Funk 2009) is outstanding example Vicki's organizational skills, represents synthesis plants. work won prestigious Stebbins Medal from International Association Plant Taxonomy (IAPT) 2010 2). office Smithsonian, surrounded favorite objects 3). founding members Society (IBS), served President IBS (Gillespie Whittaker, 2020). Early advocated innovative cladistic biogeographic analyses 1982; 1983). 1990s, teamed Warren organize symposium Honolulu meetings explored utility understand Hawaiian archipelago. proceedings were highly influential Biogeography: Evolution Hot Spot Archipelago (Wagner 1995). volume, (1995) articulated famous progression rule hotspot archipelagos: clades tend inhabit older islands first disperse younger order appear. collection papers set foundation inspired archipelago, Pacific, island systems general (Appelhans 2018a, 2018b). On expedition Tibet 2006 4), often discussed young participants island-like vast Qinghai–Tibetan Plateau Asia region Baird 2010; Wen 2013, 2014; 2016; Zhang exceptionally advocate 1999; Richardson, 2002; 2004, 2006, 2018; 2015). Director Biological Diversity Guiana Shield Biodiversity Program (BDG) over 30 supported diverse organisms birds, mammals, insects region. BDG program fundamental document, understand, conserve biological diversity area northeastern South America. made 60,000 collections databased those plus nearly 100,000 previously collected specimens (Kelloff database extremely valuable systematic conservation efforts biodiversity-rich 15,000 number brought back worldwide, especially legendarily remote areas Death Valley Roof World targeted taxa like Bidens orofenensis M.L.Grant Tahiti via helicopter (see cover image, issue). genomic era, instrumental establishing Global Genome Initiative Gardens (GGI-Gardens) 2015 goal fulfilling GGI mission: preserve life Earth—for tree 5). about biologists, mentored 40 undergraduate graduate students fellows, interns, students, visiting scientists through Botany Department National Smithsonian. various other roles. Systematic Biologists 1998–1999, Taxonomists 2006–2007, 2007–2009, Washington 2014, 2011 2017. received awards recognizing achievements biology, For example, addition IAPT, awarded Rolf Dahlgren Prize 2014 2018, Asa Gray Award, highest honor bestowed individual (ASPT). ASPT established named Graduate Student Research Award 2019 Meetings Tucson, Arizona. Also, 2019, Linnean London recognized its lifetime service natural sciences. issue, invited broad group explore advances 21st century, pay tribute true field. We emphasize four major significant contributions: Pacific statistical (Asteraceae), systematics. Three oceanic islands. Stuessy (2020) has reviewed processes (ontogeny islands, population divergence, speciation, hybridization) argues present distribution ecology species within endemic groups may little do when originated. Thus, understanding environmental changes infer such founder effect modes Juan Fernández Lord Howe Island. Knope radiation genus Pacific. Although confirmed polyphyletic Coreopsis, Polynesian inferred monophyletic, morphologically clade likely radiated ancestor initial colonization either Marquesas (43% probability) Islands (39% probability). crown estimated occurred ~1.63 million ago (Ma), youngest rapid events documented Within each Marquesan radiations result single being monophyletic paraphyletic respect radiation. From Marquesas, dispersed then Austral Islands. showcases relatively rare long-distance dispersal event coupled loss potential within-island lead repeated, complex, explosive adaptive archipelagoes Polynesia. basis RADseq data, Appelhans reconstructed Myrsine L. primrose (Primulaceae), only ten species-rich lineages never been analysis. monotypic Macaronesian genera Heberdenia Pleiomeris nested it, monophyletic. includes three main lineages: contains majority mainly Kauaʻi two widespread Quartet Sampling HyDe further suggest incongruence throughout phylogeny provide evidence lineage (also see Kleinkopf Four showcase power inferring classical patterns. Echeverría-Londoño another megadiverse Solanum (c. 1200 Solanaceae). Despite Neotropics, Old diversified rapidly, recent increase coinciding Neotropics regions climatic changes. Two migrated Australia independently, arid-adapted experiencing increases rate, they adapted long-term trend toward seasonally dry arid biomes there. excellent showing how successful niches drive diversifications. Zhu conducted analysis Celastrus Celastraceae) wide disjunct five continents both hemispheres. suggested linked global warming during Miocene. originated tropical Central America, North Oceania, Madagascar different periods dispersals. Birds facilitated transoceanic migrations Celastrus, due bicolored fruits, contain red fleshy arils, highlighting importance key morphological innovations animal-mediated dispersals distributional ranges. constructed origin Saxifraga sect. Irregulares Haw. 15–20 Saxifragaceae), early-diverged genus. results corroborate monophyly sister relationship Heterisia Divergence estimates ancestral western migration into eastern Bering land bridge (Graham, 2018) middle Oligocene. desert belt Miocene hypothesized divergence north south Asia, supporting emerging pattern Asia. Wang tackled Asia—the Sino-Japanese disjunctions Diabelia Landrein (four Caprifoliaceae; Linnaeoideae). dated Oligocene, phylogenomic plastomes independent vicariance disjunction between Japan Korea middle-to-late China (Zhejiang) Five included memory evolution. Watson analyzed closely related tribes (Anthemideae, Astereae, Calenduleae, Gnaphalieae, Senecioneae), represent 10 These form subfamily Asteroideae. nuclear plastid genomes HybSeq approach (Zimmer Wen, 2015), concordance conflicting support data sets ancient events. With timing five-tribe shortly before Eocene–Oligocene extinction 34 Ma), lost, hence obscuring details their history. Ackerfield thistle (Cirsium L.), challenging attempt thistles suggests messy difficulties Cirsium (i) undescribed taxa, (ii) inadequate representation herbarium specimens, (iii) phenotypic convergence, (iv) hybridization, (v) incipient speciation. Using approach, Lichter-Marck rock daisy tribe Perityleae, consisting seven genera, c. 84 narrowly cliffs southwest United States northern Mexico. Discordance sources molecular supports Perityleae. Phylogenies reject Perityle Benth. sections. Pappus elements show high level homoplasy, flower color conserved. base chromosome x = 18 give rise lower numbers subtribe Peritylinae (x 12, 13, 16, 17, 19) descending dysploidization. Most constitute but polyploidization inferred. progenitor-specific amplicon sequencing method, Wan tested hypothesis allopolyploidization same parental led yarrow Achillea alpina A. wilsoniana Heimerl ex Hand.-Mazz., diploid progenitor pair, acuminata (Ledeb.) Sch. Bip. asiatica Serg. sequences 17 genes 21 wild populations investigated, allopolyploidy gave genetically distinct taxa. Approximate Bayesian computation tetraploid Last Glacial Maximum went declines Ma origins cultivated chrysanthemums chloroplast LEAFY gene. Several Chrysanthemum L., C. indicum zawadskii Herbich, dichrum (C.Shih) H.Ohashi Yonek., nankingense argyrophyllum Ling, vestitum (Hemsl.) Stapl, directly indirectly involved paternal chrysanthemum cultivars examined study. Yet, maternal extinct cultivars, accessions sampled formed strongly clade, plastome tree. multiple hybridizations involving rather serving parents. Phylogenetic progressed tremendously decade additional sampling characters DiMichele Bateman updated reconstruction Carboniferous tree-clubmoss Paralycopodites Morey disarticulated, anatomically preserved fossils determine position developmental biology dictated remarkable architecture. Their taxonomic conclusions phylogenetically basalmost stigmarian lycopsids expanded encompass compression mode preservation. Considering Pteridophyte Phylogeny Group (PPG I, 2016) did not include intergeneric hybrids (nothogenera), Liu provided evaluation proposed nothogenera context current phylogeny-based pteridophyte classification. They nothospecies phylogeny. future better report ferns lycophytes, areas. Spooner compared carrot Daucus regions: entire genome, 47 mitochondrial genes, 94 conserved orthologs, 564 895 SNPs. Extensive discordance detected maximum parsimony, likelihood, trees coalescent well. results, thus, raise questions concerning best analytical methods reconstruct "true" Thode evaluated character partitioning models Amphilophium Kunth (Bignoniaceae) incongruences recovered relationships located short internodes. selection appropriate partition strategies accuracy relationships, even sets. Welker grass Andropogoneae Dumort. (14 subtribes, 92 1224 species), crops maize, sugarcane, sorghum, dominates grasslands world. diverged Arundinelleae Miocene, "core Andropogoneae" Africa World. Soreng presented ribosomal DNA Poa characterized breeding morphology Nivicolae (Roshev.) Prob., assessed taxonomy poorly understood section. Rabarijaona revisited divergences Cayratia Juss. Vitaceae close relatives Cayratieae J.Wen L.M.Lu (Wen 2018), broadly Madagascar. evidence, authors genus, Afrocayratia J.Wen, L.M.Lu, Z.D.Chen revision untimely passing big science dear friend us, organizing emotional process us. hope will help inspire colleagues carrying spirit promote Century

Язык: Английский

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