Data from: Estimating and mitigating amplification bias in qualitative and quantitative arthropod metabarcodingHenrik Krehenwinkel, Madeline Wolf, Jun Ying Lim, Andrew J. Rominger, Warren B. Simison & Rosemary G. Gillespie
Amplicon based metabarcoding promises rapid and cost-efficient analyses of species composition. However, it is disputed whether abundance estimates can be derived from metabarcoding due to taxon specific PCR amplification biases. PCR-free approaches have been suggested to mitigate this problem, but come with considerable increases in workload and cost. Here, we analyze multilocus datasets of diverse arthropod communities, to evaluate whether amplification bias can be countered by (1) targeting loci with highly degenerate primers or conserved...
Data from: The effect of DNA degradation bias in passive sampling devices on metabarcoding studies of arthropod communities and their associated microbiotaHenrik Krehenwinkel, Marisa Fong, Susan Kennedy, Edward Greg Huang, Suzuki Noriyuki, Luis Cayetano & Rosemary Gillespie
PCR amplification bias is a well-known problem in metagenomic analysis of arthropod communities. In contrast, variation of DNA degradation rates is a largely neglected source of bias. Differential degradation of DNA molecules could cause underrepresentation of taxa in a community sequencing sample. Arthropods are often collected by passive sampling devices, like malaise traps. Specimens in such a trap are exposed to varying periods of suboptimal storage and possibly different rates of DNA degradation. Degradation bias...
Data from: Evaluating hybridization capture with RAD probes as a tool for museum genomics with historical bird specimensEthan B. Linck, Zachary R. Hanna, Anna Sellas & John P. Dumbacher
Laboratory techniques for high-throughput sequencing have enhanced our ability to generate DNA sequence data from millions of natural history specimens collected prior to the molecular era, but remain poorly tested at shallower evolutionary time scales. Hybridization capture using restriction site-associated DNA probes (hyRAD) is a recently developed method for population genomics with museum specimens. The hyRAD method employs fragments produced in a restriction site-associated double digestion as the basis for probes that capture orthologous loci...
Data from: Idiosyncratic responses to climate-driven forest fragmentation and marine incursions in reed frogs from Central Africa and the Gulf of Guinea IslandsRayna C. Bell, Juan L. Parra, Gabriel Badjedjea, Michael F. Barej, David C. Blackburn, Marius Burger, Alan Channing, J. Maximilian Dehling, Eli Greenbaum, Václav Gvoždík, Jos Kielgast, Chifundera Kusamba, Stefan Lötters, Patrick J. McLaughlin, Zoltán T. Nagy, Mark-Oliver Rödel, Daniel M. Portik, Bryan L. Stuart, Jeremy VanDerWal, Ange-Ghislain Zassi Boulou & Kelly R. Zamudio
Organismal traits interact with environmental variation to mediate how species respond to shared landscapes. Thus, differences in traits related to dispersal ability or physiological tolerance may result in phylogeographic discordance among co-distributed taxa, even when they are responding to common barriers. We quantified climatic suitability and stability, and phylogeographic divergence within three reed frog species complexes across the Guineo-Congolian forests and Gulf of Guinea archipelago of Central Africa to investigate how they responded to a...
Data from: X-ray microtomography for ant taxonomy: an exploration and case study with two new Terataner (Hymenoptera, Formicidae, Myrmicinae) species from MadagascarFrancisco Hita Garcia, Georg Fischer, Cong Liu, Tracy L. Audisio, Gary D. Alpert, Brian L. Fisher & Evan P. Economo
We explore the potential of x-ray micro computed tomography (μCT) for the field of ant taxonomy by using it to enhance the descriptions of two remarkable new species of the ant genus Terataner: T. balrog sp. n. and T. nymeria sp. n.. We provide an illustrated worker-based species identification key for all species found on Madagascar, as well as detailed taxonomic descriptions, which include diagnoses, discussions, measurements, natural history data, high-quality montage images and distribution...
Data from: Taxonomic revision of imitating carpenter ants, Camponotus subgenus Myrmopytia (Hymenoptera, Formicidae) of Madagascar, using morphometry and qualitative traitsNicole Rasoamanana, Sándor Csősz & Brian L. Fisher
The ant genus Camponotus (Mayr, 1861) is one of the most abundant and species rich ant genera in the Malagasy zoogeographical region. Although this group is commonly encountered, its taxonomy is far from complete. Here, we clarify the taxonomy of the Malagasy-endemic Camponotus subgenus Myrmopytia (Emery, 1920). Species delimitation was based on traditional morphological characters and multivariate morphometric analyses, including exploratory Nest Centroid clustering and confirmatory cross-validated Linear Discriminant Analysis. Four species are recognized: Camponotus...
Data from: Widespread hybridization and bidirectional introgression in sympatric species of coral reef fishHugo B. Harrison, Michael L. Berumen, Pablo Saenz-Agudelo, Eva Salas, David H. Williamson & Geoffrey P. Jones
Coral reefs are highly diverse ecosystems, where numerous closely related species often coexist. How new species arise and are maintained in these high geneflow environments have been long-standing conundrums. Hybridization and patterns of introgression between sympatric species provide a unique insight into the mechanisms of speciation and the maintenance of species boundaries. In this study, we investigate the extent of hybridization between two closely related species of coral reef fish: the common coral trout (Plectropomus...
Data from: Taxon sampling to address an ancient rapid radiation: a supermatrix phylogeny of early brachyceran flies (Diptera)Seunggwan Shin, Keith M. Bayless, Shaun L. Winterton, Torsten Dikow, Bryan D. Lessard, David K. Yeates, Brian M. Wiegmann & Michelle D. Trautwein
Early diverging brachyceran fly lineages underwent a rapid radiation approximately 180 million years ago, coincident in part with the origin of flowering plants. This region of the fly tree includes 25,000 described extant species with diverse ecological roles such as blood feeding (haematophagy), parasitoidism, predation, pollination, and wood feeding (xylophagy). Early diverging brachyceran lineages were once considered a monophyletic group of families called Orthorrhapha, based on the shared character of a longitudinal break in the...
California Academy of Sciences8
University of California, Berkeley3
James Cook University2
University of Washington1
University of the Western Cape1
The University of Texas at Austin1
University of California System1
North Carolina Museum of Natural Sciences1