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Parallel decay of vision genes in subterranean water beetles
…an assemblage of independently-evolved water beetle (Dytiscidae) species from a subterranean archipelago in Western Australia, where parallel vision and eye loss have occurred. Using a combination of transcriptomics and exon…
Congruence and Conflict in the Higher-Level Phylogenetics of Squamate Reptiles: An Expanded Phylogenomic Perspective
…conflicting loci, finding that rate and compositional heterogeneity drives discordance between gene trees and species tree and that conflicting loci rarely overlap across contentious nodes. Finally, by comparing our tests…
Population genetic inferences using immune gene SNPs mirror patterns inferred by microsatellites
…data from the gopher tortoise, Gopherus polyphemus—a species with small populations, to compare SNPs and microsatellites to estimate population genetic parameters. Specifically, we compared one SNP data set (16 tortoises…
First mitochondrial genome of the Amazonian marsh rat Holochilus sciureus Wagner 1842 (Rodentia, Cricetidae, Sigmodontinae)
…semiaquatic rodent is distributed in South America and is of great economic and epidemiological importance. In this study, we obtained the first mitochondrial genome of the genus Holochilus obtained from…
Phylogenetic marker development for target enrichment from transcriptome and genome skim data: the pipeline and its application in southern African Oxalis (Oxalidaceae)
…1164 LCN genes greater than 600 bp. Using target enrichment combined with genome skimming (Hyb-Seq), we obtained on average 1141 LCN loci, nearly the whole plastid genome and the nrDNA…
Joining forces in Ochnaceae phylogenomics: a tale of two targeted sequencing probe kits
…were obtained after data filtering. Merging of data obtained with the two kits resulted in a well-supported phylogenetic tree. Conclusions The Angiosperms353 data set improved upon data filtering, and missing…