Compositae-ParaLoss-1272: Complementary sunflower specific probe-set reduces issues with paralogs in complex systems DOI Open Access
Erika R. Moore‐Pollard, Daniel S. Jones, Jennifer R. Mandel

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: July 21, 2023

ABSTRACT Premise The sunflower family specific probe set, Compositae-1061, has enabled family-wide phylogenomic studies and investigations at lower-taxonomic levels by targeting 1,000+ genes. However, it generally lacks resolution the genus to species level, especially in groups with complex evolutionary histories including polyploidy hybridization. Methods In this study, we developed a new Hyb-Seq Compositae-ParaLoss-1272, designed target orthologous loci Asteraceae members. We tested its efficiency across simulating target-enrichment sequencing silico. Additionally, effectiveness lower taxonomic Packera which history. performed Compositae-ParaLoss-1272 for 19 taxa were previously studied using Compositae-1061 set. Sequences from both sets used generate phylogenies, compare topologies, assess node support. Results report that captured all had less gene tree discordance, recovered considerably fewer paralogous sequences, retained longer than Compositae-1061. Discussion Given complexity of plant histories, assigning orthology analyses will continue be challenging. anticipate set provide improved utility family.

Language: Английский

Macroevolution of the plant–hummingbird pollination system DOI Creative Commons
Elisa Barreto, Mannfred M. A. Boehm, Ezgi Ogutcen

et al.

Biological reviews/Biological reviews of the Cambridge Philosophical Society, Journal Year: 2024, Volume and Issue: 99(5), P. 1831 - 1847

Published: May 5, 2024

ABSTRACT Plant–hummingbird interactions are considered a classic example of coevolution, process in which mutually dependent species influence each other's evolution. Plants depend on hummingbirds for pollination, whereas rely nectar food. As step towards understanding this review focuses the macroevolutionary consequences plant–hummingbird interactions, relatively underexplored area current literature. We synthesize prior studies, illustrating origins and dynamics hummingbird pollination across different angiosperm clades previously pollinated by insects (mostly bees), bats, passerine birds. In some cases, crown age pre‐dates plants they pollinate. other plant groups transitioned to early establishment bird group Americas, with build‐up both diversities coinciding temporally, hence suggesting co‐diversification. Determining what triggers shifts away from remains major open challenge. The impact diversification is complex, many tropical lineages experiencing increased after acquiring flowers that attract hummingbirds, others no change or even decrease rates. This mixed evidence suggests extrinsic intrinsic factors, such as local climate isolation, important covariables driving adapted pollination. To guide future we discuss mechanisms contexts under clade individual (e.g. traits, foraging behaviour, degree specialization), could conclude commenting how signals mutualism relate highlighting unbalanced focus side interaction, advocating use species‐level interaction data studies.

Language: Английский

Citations

9
Compositae‐ParaLoss‐1272: A complementary sunflower‐specific probe set reduces paralogs in phylogenomic analyses of complex systems DOI Creative Commons
Erika R. Moore‐Pollard, Daniel S. Jones, Jennifer R. Mandel

et al.

Applications in Plant Sciences, Journal Year: 2024, Volume and Issue: 12(1)

Published: Jan. 1, 2024

A family-specific probe set for sunflowers, Compositae-1061, enables family-wide phylogenomic studies and investigations at lower taxonomic levels, but may lack resolution genus to species especially in groups complicated by polyploidy hybridization.

Language: Английский

Citations

6
African Mountain Thistles: Three New Genera in the Carduus-Cirsium Group DOI Creative Commons
Lucía D. Moreyra, Núria Garcia‐Jacas, Cristina Roquet

et al.

Plants, Journal Year: 2023, Volume and Issue: 12(17), P. 3083 - 3083

Published: Aug. 28, 2023

The floras on the highest mountains in tropical eastern Africa are among most unique world. Despite exceptionally high concentration of endemic species, these remain understudied from an evolutionary point view. In this study, we focus Carduus-Cirsium group (subtribe Carduinae) to unravel relationships species Afromontane and Afroalpine floras, aiming improve systematics group. We applied Hyb-Seq approach using Compositae1061 probe set 190 samples (159 species), encompassing representatives all genera Carduinae. used two recently developed pipelines that enabled processing raw sequence reads, identification paralogous sequences segregation into orthologous alignments. After implementation a missing data filter, retained 986 nuclear loci 177 plastid regions. Phylogenomic analyses were conducted both concatenated summary-coalescence methods. resulting phylogenies highly resolved revealed three distinct lineages consisting African traditionally referred as Carduus Cirsium. Consequently, propose new Afrocarduus, Afrocirsium Nuriaea; latter did notably not belong detected some incongruences between based concatenation vs. coalescence datasets, likely attributable incomplete lineage sorting and/or hybridization.

Language: Английский

Citations

10
A thorny tale: The origin and diversification of Cirsium (Compositae) DOI
Lucía D. Moreyra, Alfonso Susanna, Juan Antonio Calleja

et al.

Molecular Phylogenetics and Evolution, Journal Year: 2025, Volume and Issue: 204, P. 108285 - 108285

Published: Jan. 11, 2025

Language: Английский

Citations

0
Phylogenetic and DNA barcoding study on Dehaasia pugerensis Koord. & Valeton, an endemic and critically endangered species from East Java, Indonesia DOI Creative Commons
Aulia Hasan Widjaya, Andi Salamah, Tety Maryenti

et al.

Beni-Suef University Journal of Basic and Applied Sciences, Journal Year: 2025, Volume and Issue: 14(1)

Published: June 2, 2025

Abstract Background Dehaasia pugerensis Koord. & Valeton is an endemic plant species classified as critically endangered (CR) in Jember, Java. It thrives arid, rocky forest regions, making it a significant genetic resource for conservation initiatives. This study aimed to analyze the genetics of through molecular approach utilizing DNA (deoxyribonucleic acid) barcoding technique. experiment utilized three accessions from populations Puger East Java: Igir Pletes (IP), Watu Susu (WS), and Undak Sebanen (US), along with Klatakan (KT). Notably, samples WS accession were excluded internal transcribed spacer (ITS) primers due poor sequencing results substituted US accession. A single sample each population underwent markers chloroplast genes: ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit ( rbc L), maturase K mat K), transfer RNA-histidine photosystem II protein D1 trn H- psb A) intergenic spacer, well one nuclear ITS region. Results Sequence analysis demonstrated identical base composition plastid genes L K, minor variation demonstrates that evolutionary rate genome lower than genome. The genomes exhibit differences rates, influenced by various external factors such inheritance mode, mutation rate, pressures. Phylogenetic indicated clustered together within same group, determined close relationship hainanensis incrassata , distance observed on phylogenetic tree. Conclusions L, confirmed identity revealed key diversity. grouped (KT450, IP42, WS152) into clade, closely related indicating shared traits. While genetically stable, showed notable variability, particularly ITS, which important differences. These findings highlight value data shaping strategies pugerensis, propagation, reintroduction, seed banking.

Language: Английский

Citations

0
Cirsium tukuhnikivatzicum, A New Species of Thistle Endemic to the La Sal Mountains of Utah DOI
Jennifer R. Ackerfield

Systematic Botany, Journal Year: 2023, Volume and Issue: 48(2), P. 354 - 362

Published: June 23, 2023

Abstract— Cirsium (thistles) have long been considered one of the most taxonomically challenging groups plants in western North America. However, relationships among thistles become clearer thanks to recent molecular phylogenetic work. The results this work revealed that eatonii var. eriocephalum was polyphyletic, consisting three distinct evolutionary lineages. Each these lineages also found be morphologically as well geographically. Multiple lines evidence thus indicated consisted at least species. first species recognized previously named C. scopulorum . second lineage recently and described funkiae third is here a new species, tukuhnikivatzicum Mount Tukuhnikivatz prominent backdrop against thistle. Southern Paiute word for “place where sun shines longest” Ute “where sets last.” specific epithet therefore used indicate distribution while acknowledging paying tribute legacy use La Sal Mountains. There taxonomic lag time 112 yr between specimen collection description presented here.

Language: Английский

Citations

0
Compositae-ParaLoss-1272: Complementary sunflower specific probe-set reduces issues with paralogs in complex systems DOI Open Access
Erika R. Moore‐Pollard, Daniel S. Jones, Jennifer R. Mandel

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: July 21, 2023

ABSTRACT Premise The sunflower family specific probe set, Compositae-1061, has enabled family-wide phylogenomic studies and investigations at lower-taxonomic levels by targeting 1,000+ genes. However, it generally lacks resolution the genus to species level, especially in groups with complex evolutionary histories including polyploidy hybridization. Methods In this study, we developed a new Hyb-Seq Compositae-ParaLoss-1272, designed target orthologous loci Asteraceae members. We tested its efficiency across simulating target-enrichment sequencing silico. Additionally, effectiveness lower taxonomic Packera which history. performed Compositae-ParaLoss-1272 for 19 taxa were previously studied using Compositae-1061 set. Sequences from both sets used generate phylogenies, compare topologies, assess node support. Results report that captured all had less gene tree discordance, recovered considerably fewer paralogous sequences, retained longer than Compositae-1061. Discussion Given complexity of plant histories, assigning orthology analyses will continue be challenging. anticipate set provide improved utility family.

Language: Английский

Citations

0