Genome-Based Taxa Delimitation (GBTD): A New Approach

Abstract

Proper taxonomic identification is essential for biological research. Unfortunately, there are no clear guidelines for taxonomic assignment above the species level. Here, we present a novel approach—GBTD—to the use of genetic divergence to evaluate the taxonomic position of certain samples with simultaneous estimation of the current systematics correctness. This approach includes measuring the raw and model-adjusted distances between DNA sequences and attributing them to the lowest taxonomic levels that are common in sample pairs to reveal distance distributions matching different taxonomic levels (species, genus, family etc.). GBTD facilitated the reassessment of the taxonomic position of the samples, whose genetic distances relative to other samples in the dataset did not match their taxonomic divergence. A data set of complete mitochondrial genome sequences of segmented worms was chosen to test this approach. As a result, numerous inconsistencies in the systematics of samples from GenBank were pointed out. These inconsistencies included both the oversplitting and overlumping of individuals into taxa of different levels and clear cases of misidentification. Our approach sparks re-evaluation of the current systematics where traditional methods fail to provide sufficient resolution.

Taxonomy and Melanism Patterns of Freshwater Leeches in the Genus Glossiphonia (Hirudinea: Glossiphoniidae) from Northeast Asia

“…Our new results together with a review of the body of literature [5,7,8,28,32] indicate that the genus Glossiphonia represents a rather species-rich clade of freshwater leeches, which currently contains no less than 16 valid species (Table 2). The taxonomic status of these species was already confirmed by means of a DNA-based approach, except for Glossiphonia paludosa, G. pulchella, and G. slovaca, whose sequences are unavailable.…”

“…Comments: It was found that the type species of both glossiphoniid genera, which were thought to be endemic to Lake Baikal (Baicaloclepsis and Paratorix), belong to the Glossiphonia clade [27,28]. Hence, these genus-group names are junior synonyms of Glossiphonia, and the species they contain must be transferred to the latter genus as follows: G. baicalensis (Stschegolev, 1922) Comments: It was found that the type species of both glossiphoniid genera, which were thought to be endemic to Lake Baikal (Baicaloclepsis and Paratorix), belong to the Glossiphonia clade [27,28]. Hence, these genus-group names are junior synonyms of Glossiphonia, and the species they contain must be transferred to the latter genus as follows: G. baicalensis (Stschegolev, 1922), G. echinulata (Grube, 1871) comb.…”

“…nov. In total, this genus contains 16 species ( Not stated [37] Continental Europe (Austria, France, Germany, Slovenia, Balkans, and European Russia) north to the Moscow Region of Russia, the British Isles, and Morocco [7,8] Sequenced representatives of this species from Germany (COI) [7] Russia: Lake Baikal [12] Endemic to Lake Baikal [1] Sequenced topotype (complete mitogenome) [28] G. elegans (Verrill, 1872) = Clepsine elegans Verrill (1872):…”

“…132 [43] USA: West River, New Haven County, CT [43] Canada and the USA [5] Sequenced topotypes (COI) [5,44] G. grubei (Lukin & Epshtein, 1959) comb. nov. = Baicaloclepsis grubei Lukin & Epshtein (1959): 189 [33] Russia: Lake Baikal [33] Endemic to Lake Baikal [1] Sequenced topotype (complete mitogenome) [28] G. nebulosa Kalbe, 1964 = G. complanata nebulosa Kalbe (1964): 141 [45] Germany: Nieplitz River near Treuenbrietzen, 52.0911 Figures 4a-c, 7a-c,g, 8a,b, 10a and 11a, Table S2. LSID: https://zoobank.org/urn:lsid:zoobank.org:act:692335BB-C17F-47AD-8E98-AB CACF5E11E8 (accessed on 27 May 2023).…”

“…It was thought that the ancient Lake Baikal housed two endemic genera of the glossiphoniid leeches [1,61]. However, a body of recent phylogenetic research [27,28] clearly indicates that the level of endemism of this family in Baikal should be downgraded to the species level, with three endemic species: Glossiphonia baicalensis, G. echinulata, and G. grubei. Epshtein [61] assumed that all the three species may have originated from a common ancestor.…”