Resolution of the ordinal phylogeny of mosses using targeted exons from organellar and nuclear genomes

Y Liu, MG Johnson, CJ Cox, R Medina, N Devos… - Nature …, 2019 - nature.com
Mosses are a highly diverse lineage of land plants, whose diversification, spanning at least
400 million years, remains phylogenetically ambiguous due to the lack of fossils, massive …

Comparative chloroplast genomics of 34 species in subtribe Swertiinae (Gentianaceae) with implications for its phylogeny

L Yang, S Deng, Y Zhu, Q Da - BMC Plant Biology, 2023 - Springer
Abstract Background Subtribe Swertiinae, a medicinally significant and highly speciose
Subtribe of family Gentianaceae. Despite previous extensive studies based on both …

Hundreds of nuclear and plastid loci yield novel insights into orchid relationships

OA Pérez‐Escobar, S Dodsworth… - American Journal of …, 2021 - Wiley Online Library
PREMISE The inference of evolutionary relationships in the species‐rich family Orchidaceae
has hitherto relied heavily on plastid DNA sequences and limited taxon sampling. Previous …

The multispecies coalescent model outperforms concatenation across diverse phylogenomic data sets

X Jiang, SV Edwards, L Liu - Systematic biology, 2020 - academic.oup.com
A statistical framework of model comparison and model validation is essential to resolving
the debates over concatenation and coalescent models in phylogenomic data analysis. A …

Climate‐influenced boreotropical survival and rampant introgressions explain the thriving of New World grapes in the north temperate zone

ZL Nie, R Hodel, ZY Ma, G Johnson… - Journal of Integrative …, 2023 - Wiley Online Library
The north temperate region was characterized by a warm climate and a rich thermophilic
flora before the Eocene, but early diversifications of the temperate biome under global …

Target sequence capture in orchids: Developing a kit to sequence hundreds of single‐copy loci

LA Eserman, SK Thomas, EED Coffey… - Applications in Plant …, 2021 - Wiley Online Library
Premise Understanding relationships among orchid species and populations is of critical
importance for orchid conservation. Target sequence capture has become a standard …

Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution

MA Serna-Sánchez, OA Pérez-Escobar, D Bogarín… - Scientific reports, 2021 - nature.com
Recent phylogenomic analyses based on the maternally inherited plastid organelle have
enlightened evolutionary relationships between the subfamilies of Orchidaceae and most of …

Orchid phylotranscriptomics: the prospects of repurposing multi-tissue transcriptomes for phylogenetic analysis and beyond

DCJ Wong, R Peakall - Frontiers in Plant Science, 2022 - frontiersin.org
The Orchidaceae is rivaled only by the Asteraceae as the largest plant family, with the
estimated number of species exceeding 25,000 and encompassing more than 700 genera …

An empirical assessment of a single family‐wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae

KE Jones, T Fér, RE Schmickl, RB Dikow… - Applications in Plant …, 2019 - Wiley Online Library
Premise Hybrid capture with high‐throughput sequencing (Hyb‐Seq) is a powerful tool for
evolutionary studies. The applicability of an Asteraceae family‐specific Hyb‐Seq probe set …

Molecular clocks and archeogenomics of a late period Egyptian date palm leaf reveal introgression from wild relatives and add timestamps on the domestication

OA Pérez-Escobar, S Bellot… - Molecular Biology …, 2021 - academic.oup.com
The date palm, Phoenix dactylifera, has been a cornerstone of Middle Eastern and North
African agriculture for millennia. It was first domesticated in the Persian Gulf, and its …