Phylogenomics Of Boraginaceae and Boraginales Using Lineage-Specific and Angiosperms353 Loci

Systematic Botany, Год журнала: 2025, Номер 49(4), С. 749 - 767

Опубликована: Янв. 6, 2025

Abstract— During the past 20 yr, phylogenetics of Boraginaceae has taken shape using plastid DNA regions and nuclear ribosomal internal transcribed spacer (ITS), but these only reflect a limited understanding evolutionary history family. Using hybridization-enrichment sequencing, 531 from lineage-specific Angiosperms353 loci were sequenced aligned for 49 species across Boraginaceae. Additionally, incorporated with broader dataset same 115 accessions Boraginales relatives. Based on multiple phylogenetic approaches datasets, resolved phylogenies quite similar to our current understanding, yet taxa recognized in different positions. These included: 1) Echiochiloideae as sister Cynoglossoideae instead rest entire family, 2) Moritzinae nested within Boragininae, 3) Lasiocaryeae Trichodesmeae not sisters. positions recovered, via methods, hundreds suggest that incomplete lineage sorting, hybridization, shifts substitution rates may have occurred during early origin In analyses Boraginales, Namaceae was non-monophyletic, providing evidence Hydrophyllaceae again be appropriate, Lennoaceae Ehretiaceae. While both sets allowed well-resolved well-supported phylogeny reconstructed, recovered some more intriguing relationships part because appear less conserved than those Angiosperms353. The two provide an interesting complement patterns evolution family order.

Язык: Английский

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American amphitropical disjuncts: Perspectives from vascular plant analyses and prospects for future research

American Journal of Botany, Год журнала: 2017, Номер 104(11), С. 1600 - 1650

Опубликована: Ноя. 1, 2017

PREMISE OF THE STUDY: Historical patterns and processes of plants with an American amphitropical disjunct (AAD) distribution have long interested botanists biogeographers. Here we update examples AAD vascular plants, their biogeographic history, aspects biology elucidated by recent studies to make inferences about common formulate future research questions. METHODS: All known were tabulated, along data on plant duration habit, chromosome number, dispersal direction, divergence time. The then compared regard taxonomic categories, bioregions, character evolution. KEY RESULTS: We clarify the definition summarize features plants. identify 237 events. Timing these events generally corresponds category. Plant habit are associated bioregions. Increases in number mostly occurred members recipient area. bipolar or temperate bioregions entirely largely dispersed from North South America, whereas almost half desert America. CONCLUSIONS: Tabulating group bioregion yields insight into evolution divergence. Phylogenetic provide information timing direction dispersal. However, more is needed draw regarding general processes, especially those at clade level. Our Working Group website provides current aid workers doing this field.

Язык: Английский

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Plastome phylogenomics, biogeography, and clade diversification of Paris (Melanthiaceae)

BMC Plant Biology, Год журнала: 2019, Номер 19(1)

Опубликована: Дек. 1, 2019

Abstract Background Paris (Melanthiaceae) is an economically important but taxonomically difficult genus, which unique in angiosperms because some species have extremely large nuclear genomes. Phylogenetic relationships within long been controversial. Based on complete plastomes and ribosomal DNA (nrDNA) sequences, this study aims to reconstruct a robust phylogenetic tree explore historical biogeography clade diversification the genus. Results All 29 currently recognized were sampled. Whole nrDNA sequences generated by genome skimming approach. reconstructed using maximum likelihood Bayesian inference methods. framework molecular dating, biogeographic scenarios of explored. Significant conflicts between plastid datasets identified, plastome highly congruent with past interpretations morphology. Ancestral area reconstruction indicated that may originated northeastern Asia northern China, has experienced multiple dispersal vicariance events during its diversification. The rate sharply accelerated since Miocene/Pliocene boundary. Conclusions Our results provide insights for clarifying long-standing taxonomic debates . Cytonuclear discordance caused ancient recent hybridizations climatic geological changes late Miocene, such as intensification Asian monsoon rapid uplift Qinghai-Tibet Plateau, well fluctuations Pleistocene, played essential roles driving range expansion radiative findings challenge theoretical prediction sizes limit speciation.

Язык: Английский

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Vascular plant extinction in the continental United States and Canada

Conservation Biology, Год журнала: 2020, Номер 35(1), С. 360 - 368

Опубликована: Авг. 29, 2020

Extinction rates are expected to increase during the Anthropocene. Current extinction of plants and many animals remain unknown. We quantified extinctions among vascular flora continental United States Canada since European settlement. compiled data on apparently extinct species by querying plant conservation databases, searching literature, vetting resulting list with botanical experts. Because taxonomic opinion varies widely, we developed an index uncertainty (ITU). The ITU ranges from A F, indicating unanimous recognition F only a single author. allowed us rigorously evaluate rates. Our suggest that 51 14 infraspecific taxa, representing 33 families 49 genera plants, have become in our study area Seven these taxa exist cultivation but wild. Most occurred west, this outcome may reflect timing exploration relative Sixty-four percent were single-site endemics, outside recognized biodiversity hotspots. Given paucity surveys areas, particularly prior settlement, actual rate is undoubtedly much higher than indicated here.

Язык: Английский

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A revised subfamilial classification of Polypodiaceae based on plastome, nuclear ribosomal, and morphological evidence

Taxon, Год журнала: 2022, Номер 71(2), С. 288 - 306

Опубликована: Янв. 19, 2022

Abstract The polygrammoid fern family Polypodiaceae represents one of the most diversified epiphytic groups, with more than 1600 species distributed on all continents except Antarctica, highest diversity in tropical and subtropical regions. Despite progress recent phylogenetic studies Polypodiaceae, infrafamilial classification this group ferns is still problematic. Here, we explore relationship within using plastid genome (plastome) nuclear ribosomal cistron data obtained from high‐throughput sequencing. Although skimming strongly support monophyly many genera clades relationships some along backbone phylogeny remain incongruent between plastome data. explanation possibly a factor complex evolutionary history found these clades, such as rapid radiation, incomplete lineage sorting, ancient hybridization, introgression. Based concatenated dataset, our analyses nine major which merit recognition subfamilies, Crypsinoideae, Grammitidoideae, Loxogrammoideae, Microsoroideae, Platycerioideae, Polypodioideae, Adetogrammoideae, Campyloneuroideae, Serpocauloideae, while latter three are separated Polypodioideae new subfamilies. All divisions, identified molecular data, further supported by non‐molecular features including leaf dissection, venation, scales paraphyses, soral features, geographical distributions. Systematic taxonomic discussions subfamilial treatment also provided.

Язык: Английский

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Genome Skimming Reveals Widespread Hybridization in a Neotropical Flowering Plant Radiation

Frontiers in Ecology and Evolution, Год журнала: 2021, Номер 9

Опубликована: Май 28, 2021

The tropics hold at least an order of magnitude greater plant diversity than the temperate zone, yet reasons for this difference are still subject to debate. Much tropical is in highly speciose genera and understanding drivers such high species richness will help solve enigma. Hybridization has recently been shown underlie many adaptive radiations, but its role evolution received little attention. Here, we address topic hyperdiverse Bromeliaceae genus Vriesea using genome skimming data covering three genomic compartments. We find evidence hybridization ca. 11% our dataset, both within between other genera, which commensurate with underlying hyperdiversity , potentially Tillandsioideae. While additional research be needed further clarify contribution rapid diversification study provides important first point suggesting importance diversity.

Язык: Английский

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When the sand blossoms: Phylogeny, trait evolution, and geography of speciation in Linanthus

American Journal of Botany, Год журнала: 2025, Номер unknown

Опубликована: Фев. 25, 2025

Abstract Premise Understanding how plants successfully diversified in novel environments is a central question evolutionary biology. Linanthus occurs arid areas of western North America and exhibits extensive floral trait variation, multiple color polymorphisms, differences blooming time, variation life history strategies. We reconstructed the this genus. Methods generated restriction‐site associated (ddRAD) sequences for 180 individuals target capture (TC) 63 individuals, with complete species sampling. Using maximum likelihood pseudo‐coalescent approaches, we inferred phylogenies used them to model evolution phenotypic traits investigate genus's geographic speciation history. Results Relationships are consistent well supported both ddRAD TC data. Most monophyletic despite local sympatry range overlap, suggesting strong isolating barriers. The non‐monophyly night‐blooming perennial may be due rapid or cryptic diversity. Perenniality likely evolved from annuality, rare shift angiosperms. Night‐blooming three times independently. Flower polymorphism an evolutionarily labile that ancestral. No single mode characterizes diversification, but most overlap range, which suggests they parapatry. Conclusions Our results illustrate complexity phylogenetic inference recent radiations, even sources genomic data This analysis provides foundation understanding aridity adaptations, such as flower night‐blooming, perenniality, mechanisms.

Язык: Английский

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Chromosome‐scale reference genome of Pectocarya recurvata, the species with the smallest reported genome size in Boraginaceae

Applications in Plant Sciences, Год журнала: 2025, Номер unknown

Опубликована: Май 21, 2025

Abstract Premise Pectocarya recurvata (Boraginaceae, subfamily Cynoglossoideae), a species native to the Sonoran Desert (North America), has served as model system for suite of ecological and evolutionary studies. However, no reference genomes are currently available in Cynoglossoideae. A high‐quality genome P. would be valuable addressing questions this across broader taxonomic scales. Methods Using PacBio HiFi sequencing, we assembled annotated coding regions with full‐length transcripts from an Iso‐Seq library. We assessed completeness BUSCO k ‐mer analysis, estimated size six individuals using flow cytometry. Results The chromosome‐scale assembly was 216.0 Mbp long (N50 = 12.1 Mbp). Previous observations indicated is 2 n 24. Our included 12 primary contigs (158.3 Mbp) containing 30,655 genes telomeres at 23 out 24 ends. Flow cytometry measurements same population two plants 1C 196.9 Mbp, smallest measured Boraginaceae, four 385.8 which consistent tetraploidy population. Discussion annotation provide genomic resource sparsely represented area angiosperm phylogeny. This new will facilitate answering open ecophysiology, biogeography, systematics.

Язык: Английский

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Evaluating the Monophyly and Biogeography of Cryptantha (Boraginaceae)

Systematic Botany, Год журнала: 2018, Номер 43(1), С. 53 - 76

Опубликована: Март 18, 2018

Cryptantha, an herbaceous plant genus of the Boraginaceae, subtribe Amsinckiinae, has American amphitropical disjunct distribution, found in western North America and South America, but not intervening tropics. In a previous study, Cryptantha was to be polyphyletic split into five genera, including weakly supported, potentially non-monophyletic s. this subsequent studies interrelationshipswithin were generally strongly supported sample size low. Here we analyze greatly increased sampling taxa using high-throughput, genome skimming data, which obtained complete ribosomal cistron, nearly chloroplast genome, twenty-three mitochondrial genes. Our analyses have allowed for inference clades within complex with strong support. The occurrence is confirmed, three major obtained, termed here Johnstonella/Albidae clade, Maritimae large core each as monophyletic. From these phylogenomic analyses, assess classification, character evolution, phylogeographic history that elucidates current distribution group. Revealing timing, direction, number times dispersal between gives insight origin great biodiversity regions.

Язык: Английский

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Genome skimming provides well resolved plastid and nuclear phylogenies, showing patterns of deep reticulate evolution in the tropical carnivorous plant genus Nepenthes (Caryophyllales)

Australian Systematic Botany, Год журнала: 2019, Номер unknown

Опубликована: Янв. 1, 2019

Nepenthes is a genus of carnivorous plants consisting ~160 species that are distributed in the paleotropics. Molecular systematics has so far not been able to resolve evolutionary relationships most because limited genetic divergence previous studies. In present study, we used genome-skimming approach infer phylogenetic on basis 81 plastid genes and highly repetitive rRNA (external transcribed spacer (ETS)–26S) for 39 accessions representing 34 from eight sections. Maximum-likelihood analysis Bayesian inference were performed separately nuclear datasets. Divergence-time estimations conducted relaxed molecular-clock model, using secondary calibration points. The analyses datasets yielded well resolved supported phylogenies. Incongruences between two detected, suggesting multiple hybridisation events or incomplete lineage sorting deeper more recent history genus. inclusion several known suspected hybrids provided insights into their parentage. placed crown diversification early Miocene, c. 20 million years ago. This study showed genome skimming provides phylogenies provide valuable complex Nepenthes.

Язык: Английский

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