The molecularisation of taxonomy

2004 ◽  
Vol 18 (1) ◽  
pp. 1 ◽  
Author(s):  
Michael S. Y. Lee
Keyword(s):  
Dna Sequences ◽  
Sequence Divergence ◽  
Biological Information ◽  
Morphological Data ◽  
Single Type ◽  
Species Boundaries ◽  
Character State ◽  
State Identity ◽  
Test Species ◽  
Taxonomic Framework

The recent proposal for a new system of biological taxonomy based primarily on DNA sequences from one or a few chosen ('standard') genes sequenced across all taxa appears inadvisable for both practical and theoretical reasons. While nucleotide sequences are more objective than traditional (e.g. morphological) data in some respects (character choice, character delineation, character state identity), in other respects both are inherently subjective (homology/alignment, divergence metrics). Sequence divergence in standard gene(s) is an extremely crude method for determining species limits; more appropriate markers (potentially directly linked to species criteria such as reproductive isolation) should be and often are used. It is thus worth persisting with the plurality of genetic, anatomical and ethological criteria currently used to hypothesise ('identify') and test species boundaries. However, once species boundaries have been thus discerned, use of sequences from standard genes to diagnose those boundaries (and place individuals with respect to those boundaries) is highly feasible, though subject to error like any single type of marker. In many cases this approach might have advantages over morphological diagnoses. However, unless an appropriate taxonomic framework constructed using all appropriate biological information is already in place, such molecular diagnoses will be premature.

scholarly journals Boolean logic and character state identity: pitfalls of character coding in metazoan cladistics

2002 ◽  
Vol 71 (1-3) ◽  
pp. 67-91 ◽  
Author(s):  
Ronald A. Jenner
Keyword(s):  
Cladistic Analysis ◽  
Comparative Morphology ◽  
Boolean Logic ◽  
Morphological Data ◽  
Critical Study ◽  
Published Data ◽  
Character State ◽  
Data Sets ◽  
State Identity ◽  
Character Coding

A critical study of the morphological data sets used for the most recent analyses of metazoan cladistics exposes a rather cavalier attitude towards character coding. Binary absence/presence coding is ubiquitous, but without any explicit justification. This uncompromising application of Boolean logic in character coding is remarkable since several recent investigations have nominated absence/presence coding as the most problematic coding method available for standard cladistic analysis. Moreover, the prevalence of unspecified “absence” character states in the published data sets introduces a discrepancy between the theoretical foundations of phylogenetic parsimony and current practices in metazoan cladistics. Because phylogenetic parsimony assumes transformation of character states, its effective operation breaks down when not all character states are carefully delimited. Examples of resulting meaningless character state transformations are discussed in two categories: 1) when unspecified “absence” states are plesiomorphic; and 2) when unspecified “absence” states are apomorphic (character reversals). To facilitate future progress in metazoan cladistics, the mandatory link between comparative morphology and character coding needs to be reestablished through a more explicit study of morphological variation prior to character coding, and through a more explicitly experimental approach to character coding.

scholarly journals A morphometric assessment of species boundaries in a widespread anole lizard (Squamata: Dactyloidae)

2020 ◽  
Vol 130 (4) ◽  
pp. 813-825
Author(s):  
Tanner C Myers ◽  
Pietro L H de Mello ◽  
Richard E Glor
Keyword(s):  
Cryptic Species ◽  
Model Fitting ◽  
Taxonomic Revision ◽  
Genetic Data ◽  
Morphological Data ◽  
Species Boundaries ◽  
Morphometric Data ◽  
Normal Mixture ◽  
Test Species ◽  
Candidate Species

Abstract Cryptic species – genetically distinct species that are morphologically difficult to distinguish – present challenges to systematists. Operationally, cryptic species are very difficult to identify and sole use of genetic data or morphological data can fail to recognize evolutionarily isolated lineages. We use morphometric data to test species boundaries hypothesized with genetic data in the North Caribbean bark anole (Anolis distichus), a suspected species complex. We use univariate and multivariate analyses to test if candidate species based on genetic data can be accurately diagnosed. We also test alternative species delimitation scenarios with a model fitting approach that evaluates normal mixture models capable of identifying morphological clusters. Our analyses reject the hypothesis that the candidate species are diagnosable. Neither uni- nor multivariate morphometric data distinguish candidate species. The best-supported model included two morphological clusters; however, these clusters were uneven and did not align with a plausible species divergence scenario. After removing two related traits driving this result, only one cluster was supported. Despite substantial differentiation revealed by genetic data, we recover no new evidence to delimit species and refrain from taxonomic revision. This study highlights the importance of considering other types of data along with molecular data when delimiting species.

scholarly journals A new species of Leptobrachella (Anura, Megophryidae) from Guizhou Province, China

ZooKeys ◽  
2020 ◽  
Vol 923 ◽  
pp. 115-140 ◽  
Author(s):  
Tao Luo ◽  
Ning Xiao ◽  
Kai Gao ◽  
Jiang Zhou
Keyword(s):  
New Species ◽  
16S Rrna ◽  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
Sequence Divergence ◽  
Guizhou Province ◽  
Morphological Data ◽  
Rrna Gene ◽  
Habitat Variation ◽  
A New Species

This study describes a new species of the genus Leptobrachella, Leptobrachella suiyangensissp. nov. from the Huoqiuba Nature Reserve, Suiyang County, Guizhou Province, China, based on morphological data and phylogenetic analyses (16S rRNA mtDNA). The new species can be distinguished from other congeners by the molecular divergence and by a combination of morphological characters, including body size, dorsal and ventral patterns, dorsal skin texture, size of the pectoral and femoral glands, degree of webbing and fringing on the toes and fingers, dorsum coloration, and iris coloration in life. Currently, the genus Leptobrachella contains 75 species, 21 of which are found in China, including seven species reported from Guizhou Province. The uncorrected sequence divergence percentage between Leptobrachella suiyangensissp. nov. and all homologous DNA sequences available for the 16S rRNA gene was found to be >4.7%. The new record of the species and its relationships with others in the same genus imply that species distribution, habitat variation, environmental adaptation, and diversity of the genus Leptobrachella in southwest China need to be further investigated.

The evolutionary history and molecular systematics of the Musteloidea

2018 ◽  
Author(s):  
Klaus-Peter Koepfli ◽  
Jerry W. Dragoo ◽  
Xiaoming Wang
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Evolutionary History ◽  
Molecular Data ◽  
Morphological Data ◽  
Species Boundaries ◽  
Extant Species ◽  
Taxonomic History ◽  
History Of ◽  
A New Species

This chapter provides a review of the evolutionary and taxonomic history of the Musteloidea, which is the most species-rich superfamily of the Carnivora, containing approximately 30% of the extant species in the order. An up-to-date summary of knowledge on the evolutionary and taxonomic history and phylogenetic relationships of the Mephitidae, Ailuridae, Procyonidae and Mustelidae is provided. Multilocus DNA sequences have made a large impact on the understanding of phylogenetic relationships among the Musteloidea. Molecular data have revealed distinct families (Ailuridae and Mephitidae) within the Musteloidea and have illuminated new relationships based on tempo and patterns of evolution within the Procyonidae. Morphological data in conjunction with molecular data have been used to elucidate species boundaries within certain musteloid genera and have led to the discovery of a new species. Research studies published during the last 30 years have enriched and transformed our understanding of the evolution of musteloid biodiversity.

The endemic New Guinean genus Murexia (Dasyuromorphia : Dasyuridae). How many species? An analysis based on morphological, distributional and molecular data

2019 ◽  
Vol 67 (3) ◽  
pp. 134
Author(s):  
Patricia A. Woolley ◽  
Carey Krajewski ◽  
Michael Westerman
Keyword(s):  
Mitochondrial Dna ◽  
Dna Sequences ◽  
Molecular Data ◽  
Morphological Data ◽  
Species Boundaries ◽  
Individual Species ◽  
External Appearance ◽  
Multiple Exemplars ◽  
Species Groups

Five species are currently recognised in the dasyurid genus Murexia, i.e. longicaudata, naso, habbema, melanurus and rothschildi. Morphological data, including spacing of premolar teeth, the footpads and aspects of external appearance, together with nuclear and mitochondrial DNA sequences from multiple exemplars from across the range of each species, suggest that at least three of these represent species groups rather than individual species. Some of the taxa currently synonymised in the five species may warrant reinstatement, including M. murex, M. aspera, M. maxima in the ‘M. longicaudata’ group, M. tafa in the ‘M. naso’ group and M. wilhelmina in the ‘M. melanurus’ group. Our data also suggest the presence of other, synonymised or undescribed taxa within the ‘longicaudata’, ‘naso’, ‘melanurus’ and ‘habbema’ species groups whose species boundaries require clarification by further collections and study.

scholarly journals Confirming the identity of newly recorded Nymphaea rubra Roxb. ex Andrews discerning from Nymphaea pubescens Willd. using morphometrics and molecular sequence analyses

2016 ◽  
Vol 23 (2) ◽  
pp. 107-117
Author(s):  
D.P.G. Shashika K. Guruge ◽  
Deepthi Yakandawala ◽  
Kapila Yakandawala
Keyword(s):  
Dna Sequences ◽  
Sequence Divergence ◽  
Morphological Data ◽  
Gene Region ◽  
Multivariate Statistical ◽  
Molecular Sequence ◽  
Query Coverage ◽  
Matk Gene ◽  
Plant Taxon ◽  
Additional Reference

A multivariate statistical analysis was carried out to evaluate the morphological variation between Nymphaea pubescens Willd., and a deep purplish red flowered Nymphaea that occur in Sri Lanka. The plant resembles N. rubra Roxb. ex Andrews, a species that had been sometimes circumscribed as a variety under N. pubescens Willd. DNA sequences data of matK and psbA-trnH regions were used to obtain further support. Morphological data were scored from collected samples and analyzed using PAST software. Extracted DNA were amplified for matK and psbA-trnH gene regions. Obtained sequences were matched with the related accessions deposited in the GenBank. Multivariate analysis supported the recognition of deep purplish red flowered Nymphaea as a different species from N. pubescens, and was identified as N. rubra based on literature. GenBank accessions for the matK region of N. rubra showed 99% similarity while it gave only a 96% similarity for N. pubescens with query coverage of 97% and 96% respectively, corroborating with the morphological analysis. Comparison of the sequence divergence between N. pubescens and N. rubra sequences indicated a 95% similarity for matK gene region while 92% similarity for psbA-trnH gene region. The sequences generated during the present study would provide additional reference sequences for the two taxa.Bangladesh J. Plant Taxon. 23(2): 107-117, 2016 (December)

Inferring species boundaries using acoustic and morphological data in the ground cricket genus Gymnogryllus (Orthoptera: Grylloidea: Gryllinae)

2018 ◽  
Vol 16 (8) ◽  
pp. 731-742 ◽  
Author(s):  
Ming Kai Tan ◽  
Crystal Yun Han Yong ◽  
Sigfrid Ingrisch ◽  
Hanyrol H. Ahmad Sah ◽  
Rodzay bin Haji Abdul Wahab ◽  
...  
Keyword(s):  
Morphological Data ◽  
Species Boundaries

scholarly journals Characterization of an unusually conserved AluI highly reiterated DNA sequence family from the honeybee, Apis mellifera.

Genetics ◽  
1993 ◽  
Vol 134 (4) ◽  
pp. 1195-1204
Author(s):  
S Tarès ◽  
J M Cornuet ◽  
P Abad
Keyword(s):  
Apis Mellifera ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Sequence Data ◽  
Sequence Divergence ◽  
Repeated Sequence ◽  
Consensus Sequences ◽  
Dna Sequence Data ◽  
Repeat Class ◽  
Honeybee Subspecies

Abstract An AluI family of highly reiterated nontranscribed sequences has been found in the genome of the honeybee Apis mellifera. This repeated sequence is shown to be present at approximately 23,000 copies per haploid genome constituting about 2% of the total genomic DNA. The nucleotide sequence of 10 monomers was determined. The consensus sequences is 176 nucleotides long and has an A + T content of 58%. There are clusters of both direct and inverted repeats. Internal subrepeating units ranging from 11 to 17 nucleotides are observed, suggesting that it could have evolved from a shorter sequence. DNA sequence data reveal that this repeat class is unusually homogeneous compared to the other class of invertebrate highly reiterated DNA sequences. The average pairwise sequence divergence between the repeats is 2.5%. In spite of this unusual homogeneity, divergence has been found in the repeated sequence hybridization ladder between four different honeybee subspecies. Therefore, the AluI highly reiterated sequences provide a new probe for fingerprinting in A. m. mellifera.

A mushroom-inducing DNA sequence isolated from the Basidiomycete, Schizophyllum commune.

Genetics ◽  
1991 ◽  
Vol 129 (3) ◽  
pp. 707-716 ◽  
Author(s):  
J S Horton ◽  
C A Raper
Keyword(s):  
Dna Sequence ◽  
Dna Sequences ◽  
De Novo ◽  
Schizophyllum Commune ◽  
Sequence Divergence ◽  
Fruiting Bodies ◽  
Genomic Dnas ◽  
Different Strains ◽  
Mating Interaction ◽  
Normal Requirement

Abstract A DNA sequence capable of inducing the de novo development of fruiting bodies (mushrooms) when integrated into the genome of unmated, nonfruiting strains of the Basidiomycete Schizophyllum commune has been isolated and partially characterized. This sequence, designated FRT1, overrides the normal requirement of a mating interaction for fruiting in this organism. It has been shown to integrate stably in different chromosome locations and appears to be trans-acting. It also enhances the normal process of fruiting that occurs after mating. Additional DNA sequences with similarity to FRT1 were detected within the genome of the strain of origin by hybridization of labeled FRT1 DNA to blots of digested genomic DNAs. FRT1 and the genomic sequences similar to it were shown to be genetically linked. Southern hybridization experiments suggested sequence divergence at the FRT1 locus between different strains of S. commune. A testable model for how FRT1 may act as a key element in the pathway for the differentiation of fruiting bodies is presented as a working hypothesis for further investigation.

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