Taxonomy and DNA sequence databases: A perfect match?

AbstractDespite the declining number of traditional taxonomists, our knowledge of Earth's biodiversity continues to grow in the form of DNA sequence data. Freely available through online databases, analyses of sequence datasets are increasingly used as an alternative for the traditional taxonomic process. Species identifications have become “DNA barcoding,” new species discoveries are characterised by genetic divergences, and traditional classification has been supplanted by molecular phylogenetics. These developments are illustrated through a case study investigating the identities of Taygetis butterflies of Costa Rica. Here I review prospects and problems with the molecularization of taxonomy and the key role of publicly available nucleotide sequence databases in efforts to catalogue diversity of life.

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Molecular phylogeny and systematics of the centipede genus Ethmostigmus Pocock (Chilopoda : Scolopendromorpha) from peninsular India

Invertebrate Systematics ◽

10.1071/is18030 ◽

2018 ◽

Vol 32 (6) ◽

pp. 1316 ◽

Cited By ~ 3

Author(s):

Jahnavi Joshi ◽

Gregory D. Edgecombe

Keyword(s):

Dna Sequence ◽

Molecular Phylogenetics ◽

Sequence Data ◽

Indian Plate ◽

Eastern Ghats ◽

Integrative Approach ◽

Phylogenetic Position ◽

Ecological Data ◽

Peninsular India ◽

Dna Sequence Data

Integrative taxonomy assesses the congruence between different lines of evidence for delimiting species, such as morphological, molecular or ecological data. Herein molecular phylogenetics is used to test monophyly and determine the phylogenetic position of the Old World tropical centipede genus Ethmostigmus Pocock, 1898, and to define species boundaries for Ethmostigmus in peninsular India. A phylogeny of the family Scolopendridae based on DNA sequence data for three markers from 427 specimens sampling in all major lineages (144 individuals generated in this study) recovers Ethmostigmus as a monophyletic group, but relationships among the genera in its subfamily Otostigminae are poorly supported. Two species delimitation methods for DNA sequence data and phylogeny are integrated with morphology and geographic data to propose a well-supported species hypothesis for Ethmostigmus on the peninsular Indian plate. Five species of Ethmostigmus are recognised in peninsular India, of which E. coonooranus Chamberlin, 1920 and three new species, namely, E. agasthyamalaiensis, sp. nov., E. sahyadrensis, sp. nov. and E. praveeni, sp. nov., occur in the Western Ghats, a biodiversity hotspot. The lesser-known Eastern Ghats harbour one species, E. tristis (Meinert, 1886), which has been nearly unreported for 130 years. This study highlights the value of an integrative approach to systematics, especially in underexplored, high biodiversity regions and where morphological variation is limited among closely related species.

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Phylogeny, taxonomy, and zoogeography of the genus Gekko Laurenti, 1768 with the revalidation of G. reevesii Gray, 1831 (Sauria: Gekkonidae)

Zootaxa ◽

10.11646/zootaxa.2989.1.1 ◽

2011 ◽

Vol 2989 (1) ◽

pp. 1 ◽

Cited By ~ 26

Author(s):

HERBERT RÖSLER ◽

AARON M. BAUER ◽

MATTHEW P. HEINICKE ◽

ELI GREENBAUM ◽

TODD JACKMAN ◽

...

Keyword(s):

Dna Sequence ◽

Molecular Phylogenetics ◽

Nuclear Dna ◽

Sequence Data ◽

Identification Key ◽

Dna Sequence Data ◽

Preliminary Identification ◽

Specific Rank ◽

Species Groups

A review of the taxonomy, phylogeny, and zoogeography of all currently recognized Gekko species is provided based on morphology (including size, scalation, color, and pattern) and mitochondrial and nuclear DNA sequence data. We distinguish six morphological (phenotypic) species groups within the gekkonid genus Gekko: the G. gecko, G. japonicus, G. monarchus, G. petricolus, G. porosus, and G. vittatus groups, all of which receive support from molecular phylogenetics. The taxon G. reevesii, formerly evaluated as a synonym of G. gekko, is revalidated herein at specific rank. Furthermore, a preliminary identification key of all currently recognized Gekko taxa is provided.

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Molecular phylogenetics of the Onobrychis genus (Fabaceae: Papilionoideae) using ITS and trnL–trnF DNA sequence data

Australian Journal of Botany ◽

10.1071/bt13279 ◽

2014 ◽

Vol 62 (3) ◽

pp. 235 ◽

Cited By ~ 2

Author(s):

S. Safaei Chaei Kar ◽

F. Ghanavati ◽

M. R. Naghavi ◽

H. Amirabadi-zade ◽

R. Rabiee

Keyword(s):

Dna Sequence ◽

Molecular Phylogenetics ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Dna Sequence Data ◽

Group I ◽

Molecular Phylogenetic ◽

Nuclear Its ◽

Cultivated Species ◽

Relationship Of

Onobrychis, comprising more than 130 species, is a genus of the family Fabaceae. At this time, the interspecies relationship of this biologically important genus is still a subject of great discussion and debate. To help resolve this disagreement, we used molecular phylogeny to analyse internal transcribed spacer (ITS) and trnL–trnF sequences of 76 species of Onobrychis. Bayesian interference, maximum parsimony and maximum likelihood analyses of nuclear ITS and plastid trnL–trnF DNA sequence data generated trees with strong posterior probability for two groups: Onobrychis subgen. Sisyrosema (including: Heliobrychis, Hymenobrychis, Afghanicae and Anthyllium sections) along with Laxiflorae section in Group I and Onobrychis subgen. Onobrychis (except Laxiflorae section) in the other (Group II). The Laxiflorae section roots back to the ancestral node for Sisyrosema subgen. O. viciifolia (cultivated species), which is closely associated with O. cyri var. cyri, suggesting that the latter may be a wild progenitor of O. viciifolia. The present study supported the paraphyly of subgenera Onobrychis and Sisyrosema. The study proposed the paraphyletic nature of the sections Onobrychis, Dendrobrychis, Heliobrychis and Hymenobrychis. Together with our molecular phylogenetic analyses we present a review of Onobrychis morphology and discuss and compare our results with those of earlier morphological and molecular phylogenetic analyses.

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