Estimating phylogenies from genomes: A beginners review of commonly used genomic data in vertebrate phylogenomics

Carter, Javan K.; Kimball, Rebecca T.; Funk, Erik R.; Kane, Nolan C.; Schield, Drew R.; Spellman, Garth M.; Safran, Rebecca J.

doi:10.1093/jhered/esac061

Cited by 9 publications

(1 citation statement)

References 131 publications

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“…UCE has been used for phylogenetic analysis to recover the relationships of many groups, such as fish (Faircloth et al, 2013), arachnids (Starrett et al, 2017), birds (Stiller et al, 2024), wasps (Cooper et al, 2020), and scale insects (Liu et al, 2022). All these marker sets rely on homology searching in predefined databases or probe sets to identify target loci from genomes (Dietrich et al, 2017;Faircloth, 2017;Breinholt et al, 2018), and have proved useful for inferring phylogenetic relationships at both shallow and deep levels (Zhang and Lai, 2020c;Carter et al, 2023).…”

Section: Introductionmentioning

confidence: 99%

Phylogenomic analysis and molecular identification of true fruit flies

He,

Wang,

et al. 2024

Front. Genet.

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The family Tephritidae in the order Diptera, known as true fruit flies, are agriculturally important insect pests. However, the phylogenetic relationships of true fruit flies, remain controversial. Moreover, rapid identification of important invasive true fruit flies is essential for plant quarantine but is still challenging. To this end, we sequenced the genome of 16 true fruit fly species at coverage of 47–228×. Together with the previously reported genomes of nine species, we reconstructed phylogenetic trees of the Tephritidae using benchmarking universal single-copy ortholog (BUSCO), ultraconserved element (UCE) and anchored hybrid enrichment (AHE) gene sets, respectively. The resulting trees of 50% taxon-occupancy dataset for each marker type were generally congruent at 88% nodes for both concatenation and coalescent analyses. At the subfamily level, both Dacinae and Trypetinae are monophyletic. At the species level, Bactrocera dorsalis is more closely related to Bactrocera latifrons than Bactrocera tryoni. This is inconsistent with previous conclusions based on mitochondrial genes but consistent with recent studies based on nuclear data. By analyzing these genome data, we screened ten pairs of species-specific primers for molecular identification of ten invasive fruit flies, which PCR validated. In summary, our work provides draft genome data of 16 true fruit fly species, addressing the long-standing taxonomic controversies and providing species-specific primers for molecular identification of invasive fruit flies.

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