The utility of single nucleotide polymorphism (SNP) data in phylogenetics

AD Leaché, JR Oaks - Annual Review of Ecology, Evolution …, 2017 - annualreviews.org
Resolving the genealogy of life—the phylogenetic relationships that describe the
evolutionary history of species—remains one of the great challenges of systematic biology …

High-throughput sequencing for algal systematics

MC Oliveira, SI Repetti, C Iha, CJ Jackson… - European Journal of …, 2018 - Taylor & Francis
In recent years, the use of molecular data in algal systematics has increased as high-
throughput sequencing (HTS) has become more accessible, generating very large datasets …

Rapid Radiation and Rampant Reticulation: Phylogenomics of South American Liolaemus Lizards

D Esquerré, JS Keogh, D Demangel… - Systematic …, 2022 - academic.oup.com
Understanding the factors that cause heterogeneity among gene trees can increase the
accuracy of species trees. Discordant signals across the genome are commonly produced …

Pervasive Introgression During Rapid Diversification of the European Mountain Genus Soldanella (L.) (Primulaceae)

M Slovák, A Melichárková, EG Štubňová… - Systematic …, 2023 - academic.oup.com
Hybridization is a key mechanism involved in lineage diversification and speciation,
especially in ecosystems that experienced repeated environmental oscillations. Recently …

Museomics identifies genetic erosion in two butterfly species across the 20th century in Finland

J Gauthier, M Pajkovic… - Molecular Ecology …, 2020 - Wiley Online Library
Erosion of biodiversity generated by anthropogenic activities has been studied for decades
and in many areas at the species level, using taxa monitoring. In contrast, genetic erosion …

Comparing Pool‐seq, Rapture, and GBS genotyping for inferring weak population structure: The American lobster (Homarus americanus) as a case study

Y Dorant, L Benestan, Q Rougemont… - Ecology and …, 2019 - Wiley Online Library
Unraveling genetic population structure is challenging in species potentially characterized
by large population size and high dispersal rates, often resulting in weak genetic …

Hy RAD‐X, a versatile method combining exome capture and RAD sequencing to extract genomic information from ancient DNA

S Schmid, R Genevest, E Gobet… - Methods in Ecology …, 2017 - Wiley Online Library
Over the last decade, protocols aimed at reproducibly sequencing reduced‐genome subsets
in non‐model organisms have been widely developed. Their use is, however, limited to DNA …

SVDquest: Improving SVDquartets species tree estimation using exact optimization within a constrained search space

P Vachaspati, T Warnow - Molecular phylogenetics and evolution, 2018 - Elsevier
Species tree estimation from multi-locus datasets is complicated by processes such as
incomplete lineage sorting (ILS) that result in different loci having different trees. Summary …

Performance and automation of ancient DNA capture with RNA hyRAD probes

T Suchan, MA Kusliy, N Khan… - Molecular ecology …, 2022 - Wiley Online Library
DNA hybridization‐capture techniques allow researchers to focus their sequencing efforts
on preselected genomic regions. This feature is especially useful when analysing ancient …

Homoplastic versus xenoplastic evolution: exploring the emergence of key intrinsic and extrinsic traits in the montane genus Soldanella (Primulaceae)

I Rurik, A Melichárková, E Gbúrová Štubová… - The Plant …, 2024 - Wiley Online Library
Specific ecological conditions in the high mountain environment exert a selective pressure
that often leads to convergent trait evolution. Reticulations induced by incomplete lineage …