Rapid dissemination of taxonomic discoveries based on DNA barcoding and morphology
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OPEN
Rapid dissemination of taxonomic
discoveries based on DNA
barcoding and morphology
received: 02 April 2016
Xiaowei Cao1,*, Jie Liu1,*, Jian Chen1, Guo Zheng2, Matjaž Kuntner1,3,4 & Ingi Agnarsson4,5
accepted: 25 October 2016
Published: 19 December 2016
The taxonomic impediment is characterized by dwindling classical taxonomic expertise, and slow
pace of revisionary work, thus more rapid taxonomic assessments are needed. Here we pair rapid
DNA barcoding methods with swift assessment of morphology in an effort to gauge diversity,
establish species limits, and rapidly disseminate taxonomic information prior to completion of formal
taxonomic revisions. We focus on a poorly studied, but diverse spider genus, Pseudopoda, from East
Asia. We augmented the standard barcoding locus (COI) with nuclear DNA sequence data (ITS2) and
analyzed congruence among datasets and species delimitation methods for a total of 572 individuals
representing 23 described species and many potentially new species. Our results suggest that a
combination of CO1 + ITS2 fragments identify and diagnose species better than the mitochondrial
barcodes alone, and that certain tree based methods yield considerably higher diversity estimates
than the distance-based approaches and morphology. Combined, through an extensive field survey,
we detect a twofold increase in species diversity in the surveyed area, at 42–45, with most species
representing short range endemics. Our study demonstrates the power of biodiversity assessments
and swift dissemination of taxonomic data through rapid inventory, and through a combination of
morphological and multi-locus DNA barcoding diagnoses of diverse arthropod lineages.
The turn of the millennium saw a reinforced emphasis on the “taxonomic impediment”1,2, characterized by dwindling classical taxonomic expertise. The typical slow pace of formal taxonomic revisions, combined with limited
funding and lack of taxonomic jobs, translates to a significant lag between species discovery and taxonomic
dissemination3. While notable effort and funds have been devoted to overcome this problem2, the taxonomic
impediment persists4 in spite of recent deluge of modern approaches to taxonomy that relate to DNA barcoding5–8
and cyber-dissemination9,10. The problem of formal taxonomic speed of progress is furthermore exacerbated by
increasing global climate changes and habitat destruction, both amplifying extinction speed11–13. Species-level
taxa are the basic currency for most biological research and underlie conservation decisions, but for these purposes taxonomic information, no matter how great, is useless until it is published. The field urgently needs rapid
taxonomic inventories that allow dissemination of taxonomic information—species delimitation, DNA barcodes,
and morphological diagnosis—and avoid the typical taxonomic time-lag.
For hyperdiverse organisms such as many arthropods, the number of species described to date represents only
a fraction of their estimated actual diversity10,14. The rate of discovery and taxonomic description of species is
typically constrained by limited expertise and relatively slow pace of classical monographic research. For example,
collection, examination, and description of specimens is usually challenged by deciphering taxonomic legacy
including type searching, examination and interpretation, and reviewing scattered and often obscure literature.
Thus, available information is withheld for years and sometimes decades before publication, a time during which
this information is of little or no use to taxonomy’s end users. Truly integrative taxonomic revisions that combine
genetic/genomic data with classical full blown taxonomic treatments continue to be published, but usually at
slow pace, and thus more rapid taxonomic approaches may also be useful15. Some studies thus rely heavily on
1
Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Centre for Behavioural Ecology and
Evolution, College of Life Sciences, Hubei University, Wuhan 430062, Hubei, China. 2College of Life Sciences, Shenyang
Normal University, Shenyang 110034, Liaoning, China. 3Institute of Biology, Scientific Research Centre of the Slovenian
Academy of Sciences and Arts, Novi Trg 2, 1000 Ljubljana, Slovenia. 4Department of Entomology, National Museum
of Natural History, Smithsonian Institution, Washington, DC, USA. 5Department of Biology, University of Vermont,
Burlington, VT, USA. *These authors contributed equally to this work. Correspondence and requests for materials
should be addressed to J.L. (email: ) or I.A. (email: )
Scientific Reports | 6:37066 | DOI: 10.1038/srep37066
1
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COI
ITS2
COI + ITS2
Species
BI
ML
BI
ML
BI
ML
P. bibulba
√(1)
√(100)
√(0.32)
√(68)
√(1)
√(99)
P. bicruris
√(1)
√(100)
√(0.30)
√(47)
√(1)
√(100)
P. cangschana
√(1)
√(100)
√(0.95)
√(96)
√(1)
√(100)
P. confusa
√(1)
√(100)
n/a
n/a
n/a
n/a
P. daliensis
√(1)
√(100)
√(0.35)
√(53)
√(1)
√(100)
P. digitata
√(1)
√(100)
√(0.78)
√(88)
√(1)
√(100)
P. gibberosa
√(1)
√(99)
√(1)
√(99)
√(1)
√(100)
P. interposita
√(1)
√(96)
√(0.95)
√(96)
√(1)
√(96)
P. kunmingensis
√(1)
√(100)
√(0.93)
√(81)
√(1)
√(100)
P. lushanensis
√(1)
√(100)
√(1)
√(100)
√(1)
√(100)
P. mediana
√(1)
√(100)
√(1)
√(100)
√(1)
√(100)
√(0.98)
√(96)
√(1)
√(100)
P. namkhan
√(1)
√(1)
P. recta
√(1)
√(99)
P. rivicola
√(1)
√(100)
√(0.83)
√(96)
√(1)
√(88)
√(1)
√(100)
P. roganda
√(1)
√(100)
√(1)
√(100)
√(1)
√(100)
P. semiannulata
√(0.75)
√(100)
√(0.57)
√(62)
√(0.53)
√(100)
P. signata
√(1)
√(100)
√(1)
√(100)
√(1)
√(100)
P. sinapophysis
√(1)
√(99)
√(1)
√(100)
√(1)
√(100)
P. sp1
√(1)
√(100)
√(0.97)
√(98)
√(1)
√(100)
P. sp2
√(1)
√(100)
√(1)
√(98)
√(1)
√(100)
P. sp3
√(1)
√(100)
√(1)
√(98)
√(1)
√(100)
P. sp4
√(1)
√(100)
√(1)
√(95)
√(1)
√(100)
P. sp6
√(1)
√(100)
√(1)
√(99)
√(1)
√(100)
P. sp7
√(1)
√(100)
√(0.86)
√(84)
√(1)
√(100)
P. sp8
√(1)
√(94)
√(0.68)
√(88)
√(1)
√(97)
P. sp9
√(1)
√(95)
√(1)
√(98)
√(1)
√(99)
P. sp11
√(1)
√(89)
√(1)
√(99)
√(1)
√(100)
P. sp12
√(1)
√(99)
√(1)
√(100)
√(1)
√(100)
P. sp14
√(1)
√(100)
√(1)
√(100)
√(1)
√(100)
P. sp15
√(1)
√(99)
√(1)
√(85)
√(1)
√(100)
P. sp16
√(1)
√(100)
√(1)
√(100)
√(1)
√(100)
P. sp18
√(0.9)
√(81)
√(1)
√(100)
√(1)
√(99)
P. sp19
√(1)
√(100)
√(0.71)
√(1)
√(95)
P. spiculata
√(1)
√(97)
√(0.33)
√(74)
√(1)
√(100)
P. tiantangensis
√(1)
√(100)
√(1)
√(90)
√(1)
√(100)
√(0.99)
√(96)
√(0.87)
√(37)
P. yunnanensis
Table 1. Summary of congruence among partitions (COI, ITS2, COI + ITS2) and methods (Bayes, ML).
Check marks indicate support for monophyly of indicated clades, blanks indicate lack of support, n/a signifies
that the clade was not tested in the given analysis, due to taxon sampling. Va (...truncated)
