Between a Rock and a Hard Polytomy: Phylogenomics of the Rock-Dwelling Mbuna Cichlids of Lake Malaŵi

Systematic Biology, Journal Year: 2022, Volume and Issue: 71(3), P. 741 - 757

Published: Jan. 31, 2022

Whole genome sequences are beginning to revolutionize our understanding of phylogenetic relationships. Yet, even whole can fail resolve the evolutionary history most rapidly radiating lineages, where incomplete lineage sorting, standing genetic variation, introgression, and other factors obscure group. To overcome such challenges, one emerging strategy is integrate results across different methods. Most approaches have been implemented on reduced representation genomic data sets, but genomes should provide maximum possible evidence approach. Here, we test ability single nucleotide polymorphisms extracted from resequencing data, in an integrative approach, key nodes phylogeny mbuna, rock-dwelling cichlid fishes Lake Malaŵi, which epitomize intractability that often accompanies explosive diversification. This monophyletic radiation has diversified at unparalleled rate into several hundred species less than 2 million years. Using array phylogenomic methods, consistently recovered four major clades a large basal polytomy among them. Although introgression between apparently contributed challenge reconstruction, reduction set nonintrogressed sites still did not help polytomy. On hand, relationships six congeneric pairs were resolved without ambiguity, case existing led us predict resolution would be difficult. We conclude bursts diversification earliest stages mbuna may phylogenetically unresolvable, regions tree clearly supported. Integration multiple will continue increase confidence inferred these whole-genome sets. [Incomplete sorting; introgression; linkage disequilibrium; multispecies coalescence; rapid radiation; soft polytomy.].

Language: Английский

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An updated classification for the hyper‐diverse genusCorydalis(Papaveraceae: Fumarioideae) based on phylogenomic and morphological evidence

Journal of Integrative Plant Biology, Journal Year: 2023, Volume and Issue: 65(9), P. 2138 - 2156

Published: April 29, 2023

Abstract The genus Corydalis , with ca. 530 species, has long been considered taxonomically challenging because of its great variability. Previous molecular analyses, based on a few markers and incomplete taxonomic sampling, were clearly inadequate to delimit sections subgenera. We have performed phylogenetic analyses related taxa, using 65 shared protein‐coding plastid genes from 313 accessions (including 280 samples 226 species ) 152 universal low‐copy nuclear 296 271 covering all 42 previously recognized five independent “series”. Phylogenetic trees inferred Bayesian Inference Maximum Likelihood. Eight selected morphological characters estimated ancestral state reconstructions. Results include: (i) the three subgenera two are fully supported by both data; third, subg. Cremnocapnos is weakly DNA only, whereas in data included form successive outgroups rest genus; (ii) among “series”, 25 one “series” resolved as monophyletic sets; (iii) common ancestor likely be perennial plant taproot, yellow flowers short saccate spur, linear fruits recurved fruiting pedicels, seeds elaiosomes; (iv) we provide new classification four (of which Bipapillatae here newly described), 39 sections, 16 consistent previous classification, recircumscribed, section reinstated six established. Characters associated lifespan, underground structures, floral fruit elaiosomes important for recognition sections. These combined character reconstructions uncovered unrecognized relationships, greatly improved our understanding evolution genus.

Language: Английский

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Phylogenomics and morphological evolution of the mega-diverse genus Artemisia (Asteraceae: Anthemideae): implications for its circumscription and infrageneric taxonomy

Annals of Botany, Journal Year: 2023, Volume and Issue: 131(5), P. 867 - 883

Published: March 28, 2023

Abstract Background and Aims Artemisia is a mega-diverse genus consisting of ~400 species. Despite its medicinal importance ecological significance, well-resolved phylogeny for global Artemisia, natural generic delimitation infrageneric taxonomy remain missing, owing to the obstructions from limited taxon sampling insufficient information on DNA markers. Its morphological characters, such as capitulum, life form leaf, show marked variations are widely used in taxonomy. However, their evolution within poorly understood. Here, we aimed reconstruct via phylogenomic approach, infer evolutionary patterns key characters update circumscription Methods We sampled 228 species (258 samples) allies both fresh herbarium collections, covering all subgenera main geographical areas, conducted analysis based nuclear single nucleotide polymorphisms (SNPs) obtained genome skimming data. Based phylogenetic framework, inferred possible six previous Key Results The Kaschgaria was revealed be nested with strong support. A eight highly supported clades recovered, two which were identified first time. Most previously recognized not monophyletic. Evolutionary inferences showed that different states these originated independently more than once. Conclusions enlarged include Kaschgaria. traditionally do match new tree. They experienced complex history thought. propose revised newly circumscribed accommodate results.

Language: Английский

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Phylogenomics reveals extreme gene tree discordance in a lineage of dominant trees: hybridization, introgression, and incomplete lineage sorting blur deep evolutionary relationships despite clear species groupings in Eucalyptus subgenus Eudesmia

Molecular Phylogenetics and Evolution, Journal Year: 2023, Volume and Issue: 187, P. 107869 - 107869

Published: July 8, 2023

Language: Английский

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Morphological trait evolution in Solanum (Solanaceae): Evolutionary lability of key taxonomic characters

Taxon, Journal Year: 2023, Volume and Issue: 72(4), P. 811 - 847

Published: July 4, 2023

Abstract Solanum is one of the world's largest and economically most important plant genera, including 1245 currently accepted species several major minor crops (e.g., tomato, potato, brinjal eggplant, scarlet Gboma lulo, pepino). Here we provide an overview evolution 25 key morphological traits for clades this giant genus based on stochastic mapping using a well‐sampled recently published phylogeny . The evolutionarily labile (showing >100 transitions across genus) relate to structure (growth form sympodial unit structure), herbivore defence (glandular trichomes), pollination (corolla shape colour), dispersal (fruit colour). Ten further show evolutionary lability with 50–100 specialised underground organs, trichome structure, leaf type, inflorescence position branching, stamen heteromorphism). Our results reveal number highly convergent in , tubers, rhizomes, simple leaves, yellow corollas, heteromorphic anthers, dioecy, dry fruits, some unexpected pathways trait that could be explored future studies. We informally named can morphologically defined by combinations providing tool identification enabling predictive phylogenetic placement unsampled species.

Language: Английский

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Nuclear phylogenomics of angiosperms and insights into their relationships and evolution

Journal of Integrative Plant Biology, Journal Year: 2024, Volume and Issue: 66(3), P. 546 - 578

Published: Jan. 30, 2024

Angiosperms (flowering plants) are by far the most diverse land plant group with over 300,000 species. The sudden appearance of angiosperms in fossil record was referred to Darwin as "abominable mystery," hence contributing heightened interest angiosperm evolution. display wide ranges morphological, physiological, and ecological characters, some which have probably influenced their species richness. evolutionary analyses these characteristics help address questions diversification require well resolved phylogeny. Following great successes phylogenetic using plastid sequences, dozens thousands nuclear genes from next-generation sequencing been used phylogenomic analyses, providing phylogenies new insights into evolution angiosperms. In this review we focus on recent large clades, orders, families, subdivisions families provide a summarized Nuclear Phylogenetic Tree Angiosperm Families. newly established relationships highlighted compared previous results. sequenced genomes Amborella, Nymphaea, Chloranthus, Ceratophyllum, monocots, Magnoliids, basal eudicots, facilitated phylogenomics among five major clades. All but one 64 orders were included except placements several orders. Most robust highly supported placements, especially for within important families. Additionally, examine divergence time estimation biogeographic basis frameworks discuss differences analyses. Furthermore, implications ancestral reconstruction characters groups, limitations current studies, taxa that future attention.

Language: Английский

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Fruity, sticky, stinky, spicy, bitter, addictive, and deadly: evolutionary signatures of metabolic complexity in the Solanaceae

Natural Product Reports, Journal Year: 2022, Volume and Issue: 39(7), P. 1438 - 1464

Published: Jan. 1, 2022

Covering: 2000-2022Plants collectively synthesize a huge repertoire of metabolites. General metabolites, also referred to as primary are conserved across the plant kingdom and required for processes essential growth development. These include amino acids, sugars, lipids, organic acids. In contrast, specialized historically termed secondary structurally diverse, exhibit lineage-specific distribution provide selective advantage host species facilitate reproduction environmental adaptation. Due their potent bioactivities, metabolites attract considerable attention use flavorings, fragrances, pharmaceuticals, bio-pesticides. The Solanaceae (Nightshade family) consists approximately 2700 includes crops significant economic, cultural, scientific importance: these potato, tomato, pepper, eggplant, tobacco, petunia. has emerged model family studying biochemical evolution metabolism multiple examples exist that influence senses physiology commensal harmful organisms, including humans. include, alcohols, phenylpropanoids, carotenoids contribute fruit aroma color in tomato (

Language: Английский

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The challenges of classifying big genera such asIpomoea

Taxon, Journal Year: 2023, Volume and Issue: 72(6), P. 1201 - 1215

Published: March 6, 2023

Abstract Big genera represent a significant proportion of the world's plants. However, comprehensive taxonomic and evolutionary studies these are often complicated by their size geographic spread. This paper explores challenges faced in classifying megadiverse plant groups consequent to existing tension between diagnosability increasing levels resolution from molecular sequence data. We use recent examples across angiosperms illustrate how monophyly, completeness interplay with each other attempts classify several big and, specifically, genus Ipomoea (Convolvulaceae). tribe Ipomoeeae have been object phylogenetic that highlight limitations previous group, show smaller segregate traditionally recognised nested within neither monophyletic nor diagnosable. argue classifications must be abandoned, recognising an expanded incorporates all is most appropriate solution as it reconciles properties completeness, favours nomenclatural stability.

Language: Английский

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Convergent evolution of plant prickles is driven by repeated gene co-option over deep time

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Feb. 22, 2024

Abstract An enduring question in evolutionary biology concerns the degree to which episodes of convergent trait evolution depend on same genetic programs, particularly over long timescales. Here we genetically dissected repeated origins and losses prickles, sharp epidermal projections, that convergently evolved numerous plant lineages. Mutations a cytokinin hormone biosynthetic gene caused at least 16 independent prickles eggplants wild relatives genus Solanum . Strikingly, homologs promote prickle formation across angiosperms collectively diverged 150 million years ago. By developing new systems, leveraged this discovery eliminate species an indigenously foraged berry. Our findings implicate shared hormone-activation program underlying evolutionarily widespread recurrent instances morphological innovation.

Language: Английский

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Trading acyls and swapping sugars: metabolic innovations in Solanum trichomes

PLANT PHYSIOLOGY, Journal Year: 2024, Volume and Issue: 196(2), P. 1231 - 1253

Published: May 15, 2024

Abstract Solanaceae (nightshade family) species synthesize a remarkable array of clade- and tissue-specific specialized metabolites. Protective acylsugars, one such class structurally diverse metabolites, are produced by ACYLSUGAR ACYLTRANSFERASE (ASAT) enzymes from sugars acyl-coenzyme A esters. Published research has revealed trichome acylsugars composed glucose sucrose cores in across the family. In addition, have been analyzed small fraction >1,200 phenotypically megadiverse Solanum genus, with handful containing inositol glycosylated cores. The current study sampled several dozen subclades to get more detailed view acylsugar chemodiversity. depth characterization clade II brinjal eggplant (Solanum melongena) led identification eight unusual structures or glycoside hydroxyacyl chains. Liquid chromatography-mass spectrometry analysis 31 additional genus striking diversity, some traits restricted specific clades species. Acylinositols inositol-based acyldisaccharides were detected throughout much genus. contrast, acylglucoses acylsucroses distribution. Analysis transcriptomes interspecific acetylation differences ASAT 3-LIKE 1 (SmASAT3-L1; SMEL4.1_12g015780) enzyme. This enzyme is distinct previously characterized acetyltransferases, which ASAT4 clade, appears be functionally divergent ASAT3. provides foundation for investigating evolution function harnessing this diversity breeding synthetic biology.

Language: Английский

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