Rarity and incomplete sampling in DNA-based species delimitation
File(s)
Accepted version
Author(s)
Type
Journal Article
Abstract
DNA-based species delimitation may be compromised by limited sampling effort and species rarity, including “singleton” representatives of species, which hampers estimates of intra- versus interspecies evolutionary processes. In a case study of southern African chafers (beetles in the family Scarabaeidae), many species and subclades were poorly represented and 48.5% of species were singletons. Using cox1 sequences from >500 specimens and ∼100 species, the Generalized Mixed Yule Coalescent (GMYC) analysis as well as various other approaches for DNA-based species delimitation (Automatic Barcode Gap Discovery (ABGD), Poisson tree processes (PTP), Species Identifier, Statistical Parsimony), frequently produced poor results if analyzing a narrow target group only, but the performance improved when several subclades were combined. Hence, low sampling may be compensated for by “clade addition” of lineages outside of the focal group. Similar findings were obtained in reanalysis of published data sets of taxonomically poorly known species assemblages of insects from Madagascar. The low performance of undersampled trees is not due to high proportions of singletons per se, as shown in simulations (with 13%, 40% and 52% singletons). However, the GMYC method was highly sensitive to variable effective population size (NeNe), which was exacerbated by variable species abundances in the simulations. Hence, low sampling success and rarity of species affect the power of the GMYC method only if they reflect great differences in NeNe among species. Potential negative effects of skewed species abundances and prevalence of singletons are ultimately an issue about the variation in NeNe and the degree to which this is correlated with the census population size and sampling success. Clade addition beyond a limited study group can overcome poor sampling for the GMYC method in particular under variable NeNe. This effect was less pronounced for methods of species delimitation not based on coalescent models.
Date Issued
2016-05-01
Date Acceptance
2016-01-13
Citation
Systematic Biology, 2016, 65 (3), pp.478-494
ISSN
1076-836X
Publisher
Oxford University Press (OUP)
Start Page
478
End Page
494
Journal / Book Title
Systematic Biology
Volume
65
Issue
3
Copyright Statement
This is a pre-copyedited, author-produced PDF of an article accepted for publication in Systematic Biology following peer review. The version of record Dirk Ahrens, Tomochika Fujisawa, Hans-Joachim Krammer, Jonas Eberle, Silvia Fabrizi, Alfried P. Vogler; Rarity and Incomplete Sampling in DNA-Based Species Delimitation, Systematic Biology, Volume 65, Issue 3, 1 May 2016, Pages 478–494, https://doi.org/10.1093/sysbio/syw002
Identifier
https://academic.oup.com/sysbio/article/65/3/478/2468954
Subjects
Science & Technology
Life Sciences & Biomedicine
Evolutionary Biology
Coleoptera
effective population size
Sericini
singletons
southern Africa
EFFECTIVE POPULATION-SIZE
YULE-COALESCENT MODEL
SINGLE-LOCUS DATA
SEQUENCE DATA
PHYLOGENETIC SIGNAL
COMPARATIVE BIOLOGY
EVOLUTION
COLEOPTERA
TAXONOMY
TREES
Publication Status
Published
Date Publish Online
2016-01-21