Instant taxonomy: choosing adequate characters for species delimitation and description through congruence between molecular data and quantitative shape analysis

2018 ◽  
Vol 32 (3) ◽  
pp. 551 ◽  
Author(s):  
Tomislav Karanovic ◽  
Seunghan Lee ◽  
Wonchoel Lee

The lack of university funding is one of the major impediments to taxonomy, partly because traditional taxonomic training takes longer than a PhD course. Understanding ranges of phenotypic variability for different morphological structures, and their use as characters for delimitation and description of taxa, is a tedious task. We argue that the advent of molecular barcoding and quantitative shape analysis makes it unnecessary. As an example, we tackle a problematic species-complex of marine copepods from Korea and Japan, approaching it as a starting taxonomist might. Samples were collected from 14 locations and the mitochondrial COI gene was sequenced from 42 specimens. Our phylogenetic analyses reveal four distinct clades in Korea and Japan, and an additional nine belonging to a closely related complex from other parts of the Northern Pacific. Twenty different morphological structures were analysed for one Japanese and two Korean clades using landmark-based two-dimensional geometric morphometrics. Although there is no single morphological character that can distinguish with absolute certainty all three cryptic species, most show statistically significant interspecific differences in shape and size. We use five characters to describe two new species from Korea and to re-describe Tigriopus japonicus Mori, 1938 from near its type locality.

Author(s):  
Pradya Somboon ◽  
Thanari Phanitchakun ◽  
Jassada Saingamsook ◽  
Rinzin Namgay ◽  
Ralph E Harbach

Abstract A new subgenus, Reinertia Somboon, Namgay & Harbach, of the genus Aedes Meigen and its type species, Ae. suffusus Edwards, are described from specimens reared from larvae and pupae found in a tree hole in Bhutan. The scutum of the adults is mostly covered with narrow pale falcate scales. The proboscis, maxillary palpus, tibiae, and tarsi are dark-scaled. The gonocoxite of the male genitalia bears a unique setose basomesal sclerite. The larva closely resembles larvae of the subgenus Downsiomyia Vargus in having setae 4–6-C with numerous branches and inserted more or less on level with seta 7-C, abdominal seta 12-I is present and the comb is composed of 6–10 spine-like scales arranged in an irregular row. Surprisingly, Reinertia shares features of the adult habitus, male genitalia, and larva with the Palearctic subgenus Dahliana Reinert, Harbach & Kitching. However, in phylogenetic analyses of the mitochondrial COI gene of species representing 38 subgenera of Aedes and six other genera of the tribe Aedini Neveu-Lemaire, Reinertia was not associated with Dahliana or Downsiomyia. In both maximum likelihood and Bayesian analyses of the data, Ae. suffusus was recovered as the weakly supported sister of a clade composed of five species of the subgenus Protomacleaya Theobald. In the absence of strong support, and because Protomacleaya is an unnatural group of species that resemble each other phenetically by virtue of what they lack, Ae. suffusus cannot be placed in the subgenus Protomacleaya. Thus, the morphological and molecular data attest the uniqueness of Ae. suffusus and its recognition as a monobasic subgeneric lineage.


2019 ◽  
Vol 20 (4) ◽  
pp. 1115-1120
Author(s):  
BADRUL MUNIR MD ZAIN ◽  
KHAIRUL SYA’ADAH MOHHOYUA ◽  
NOR RAHMAN AIFAT ◽  
EHWAN NGADI ◽  
NORSHAQINAH AYOB ◽  
...  

Abstract. Md-Zain BM, Mohhoyua KS, Aifat NR, Ngadi E, Ayob N, Rovie-Ryan JJ, Ampeng A, Mohd-Ridwan AR, Blair ME, Abdul-Latiff MAB. 2019. Molecular data confirm the presence of Nycticebus bengalensis on Langkawi Island, Malaysia. Biodiversitas 20: 1115-1120. Recent taxonomic reviews have stated the possibility of Bengal Slow Loris (Nycticebus bengalensis) presence in the Northern part of the Malay Peninsula. This study aims to confirm the presence of the Bengal Slow Loris in Malaysia by sequencing the mitochondrial COI gene from samples collected from Langkawi Island, Peninsular Malaysia, and Borneo. Phylogenetic analyses produced tree topologies that support the grouping of slow loris samples by their localities. The tree topologies further show that slow loris samples from Sarawak and Peninsular Malaysia form two distinct clades. The clade from Peninsular Malaysia was divided into two subclades, Langkawi and Selangor. The Langkawi slow loris subclade includes sequences from GenBank representing N. bengalensis, supported by a high bootstrap value. This mitochondrial DNA finding has a significant contribution to indicate the presence of the Bengal Slow Loris in Malaysia.


2017 ◽  
Vol 22 (4) ◽  
pp. 467
Author(s):  
Mahran Zeity ◽  
Nagappa Srinivas ◽  
Chinnamade Channegowde Gowda

Study of morphological characters of Tetranychus macfarlanei Baker & Pritchard and Tetranychus malaysiensis Ehara revealed high similarity by comparing all the important characters in addition to the characters pointed out by Ehara to separate those two species. Molecular phylogeny of seven Indian populations of T. macfarlanei and one population of T. malaysiensis from Philippines along with few distantly related species of Tetranychus was attempted. High degree of similarity between these two species at mitochondrial COI gene (96%) as well as ITS2 (rDNA) (96–99%) region was evident. Based on both morphological features and molecular data, T. malaysiensis is proposed as a junior synonym of T. macfarlanei based on ICZN’s law of priority. Also more female characters are prompted in this study to distinctly discriminate T. macfarlanei from its most resembling species, Tetranychus ludeni Zacher. Tetranychus macfarlanei has emerged as a pest of several cultivated crop plants in India. 


Zootaxa ◽  
2021 ◽  
Vol 4999 (1) ◽  
pp. 58-76
Author(s):  
Quyen Hanh Do ◽  
TRUNG MY PHUNG ◽  
HANH THI NGO ◽  
MINH DUC LE ◽  
THOMAS ZIEGLER ◽  
...  

A new species of the Cyrtodactylus irregularis group is described from Ninh Thuan Province, southern Vietnam based on molecular divergence and morphological differences. Cyrtodactylus orlovi sp. nov. is distinguished from the remaining Indochinese bent-toed geckos by having the unique combination of the following characters: size medium (SVL 61.0–77.7 mm); dorsal tubercles in 16–20 irregular rows; 36–39 ventral scale rows; precloacal pores absent in females, 5 or 6 in males, in a continuous row; femoral pores absent; 3–8 enlarged femoral scales; postcloacal spurs 1 or 2; lamellae under toe IV 16–19; a continuous neckband; a highly irregular transverse banded dorsal pattern; the absence of transversely enlarged median subcaudal scales. In phylogenetic analyses, the new species was revealed to be the sister taxon to a clade consisting of Cyrtodactylus cattienensis and the most recently described species from Vietnam, C. chungi, with 12.1–12.4% and 11.7 % pairwise genetic divergence from the two species, respectively, based on a fragment of the mitochondrial COI gene.  


2020 ◽  
Vol 89 (2) ◽  
pp. 188-209
Author(s):  
Yutaro Oku ◽  
Kenji Iwao ◽  
Bert W. Hoeksema ◽  
Naoko Dewa ◽  
Hiroyuki Tachikawa ◽  
...  

Recent molecular phylogenetic analyses of scleractinian corals have resulted in the discovery of cryptic lineages. To understand species diversity in corals, these lineages need to be taxonomically defined. In the present study, we report the discovery of a distinct lineage obscured by the traditional morphological variation of Fungia fungites. This taxon exists as two distinct morphs: attached and unattached. Molecular phylogenetic analyses using mitochondrial COI and nuclear ITS markers as well as morphological comparisons were performed to clarify their phylogenetic relationships and taxonomic positions. Molecular data revealed that F. fungites consists of two genetically distinct clades (A and B). Clade A is sister to a lineage including Danafungia scruposa and Halomitra pileus, while clade B formed an independent lineage genetically distant from these three species. The two morphs were also found to be included in both clades, although the attached morph was predominantly found in clade A. Morphologically, both clades were statistically different in density of septal dentation, septal number, and septal teeth shape. These results indicate that F. fungites as presently recognized is actually a species complex including at least two species. After checking type specimens, we conclude that specimens in clade A represent true F. fungites with two morphs (unattached and attached) and that all of those in clade B represent an unknown species and genus comprising an unattached morph with only one exception. These findings suggest that more unrecognized taxa with hitherto unnoticed morphological differences can be present among scleractinian corals.


Zootaxa ◽  
2020 ◽  
Vol 4846 (1) ◽  
pp. 1-93
Author(s):  
GUILHERME S. T. GARBINO ◽  
BURTON K. LIM ◽  
VALÉRIA DA C. TAVARES

We present a revision of the Neotropical bat genus Chiroderma, commonly known as big-eyed bats. Although species of Chiroderma have a wide distribution from western México to southern Brazil, species limits within Chiroderma are not clearly defined, as attested by identification errors in the literature, and there is no comprehensive revision of the genus that includes morphological and molecular data. Our review is based on phylogenetic analyses of two mitochondrial (COI and CYTB) and two nuclear (RAG2 and DBY) genes, coalescence analyses of mitochondrial genes, and morphological analyses including type specimens of all named taxa. We recognize seven species in three clades: the first clade includes (1) C. scopaeum Handley, 1966, endemic to western México and previously considered a subspecies of C. salvini; and (2) C. salvini Dobson, 1878, a taxon associated with montane forests, distributed from México to Bolivia; the second clade includes (3) C. improvisum Baker and Genoways, 1976, endemic to the Lesser Antilles, and (4) C. villosum Peters, 1860, widely distributed on the continental mainland and polytypic, with subspecies C. v. villosum and C. v. jesupi; and the third clade includes (5) the polytypic C. doriae Thomas, 1891, with C. d. doriae distributed in eastern Brazil and Paraguay, and C. d. vizottoi, occurring in northeastern Brazil; (6) C. trinitatum Goodwin, 1958, distributed from Trinidad to Amazonia; and (7) C. gorgasi Handley, 1960, distributed from Honduras to trans-Andean South America, previously considered a subspecies of C. trinitatum. 


Zootaxa ◽  
2020 ◽  
Vol 4896 (1) ◽  
pp. 85-95
Author(s):  
ROMAN V. YAKOVLEV ◽  
NAZAR A. SHAPOVAL ◽  
VADIM V. IVONIN ◽  
SVYATOSLAV A. KNYAZEV ◽  
GALINA N. KUFTINA ◽  
...  

We described a new cossid species, Dyspessa ulgen sp. nov. from the Tarbagatai and Altai Mountains and compared it to other taxa of Dyspessa reported from the region (D. tristis, D. saldaitisi, D. saissanica), as well as to morphologically similar D. ulula. The new species is most closely related to D. ulula but differs from the latter in the characteristics of the male genitalia, wing pattern, and molecular data (a 658 bp fragment of the mitochondrial COI gene). 


2012 ◽  
Vol 60 (3) ◽  
pp. 152 ◽  
Author(s):  
B. D. Cook ◽  
K. M. Abrams ◽  
J. Marshall ◽  
C. N. Perna ◽  
S. Choy ◽  
...  

Recent research suggests that alluvial aquifers in southern and eastern Australia may contain a diverse subterranean aquatic fauna (i.e. stygofauna). However, to date only a limited number of alluvial aquifers have been studied and little molecular data are available to assess species-level diversity and spatial patterns of genetic variation within stygofaunal species. In this paper, we present the initial results of a stygofaunal survey of the Burdekin River alluvial aquifer in Queensland, extending the northern range of alluvial aquifers along the east coast of Australia that have been investigated. The survey resulted in the collection of bathynellid stygofauna (Syncarida: Bathynellacea) and genetic analyses were conducted to determine species level diversity using the mitochondrial cytochrome oxidase subunit I (COI) gene. We further investigated the phylogenetic relationships of the species with bathynellids from western and southern Australia to assess the generic status of species. Four highly divergent COI lineages within the Parabathynellidae and one lineage within the Bathynellidae were found. These lineages did not group within any described genera, and phylogenetic analyses indicated that both local radiations and the retention of a lineage that was more apical in the genealogy account for the diversity within the Parabathynellidae in the Burdekin River alluvial aquifer. Most COI lineages were sampled from only a single bore, although one taxon within the Parabathynellidae was found to be more widespread in the aquifer. Haplotypes within this taxon were not shared among bores (ΦST = 0.603, P < 0.001). Overall, the high species diversity for bathynellaceans from an alluvial aquifer reported here, and surveys of bathynellaceans in several other alluvial systems in south-eastern Australia, suggests that groundwater ecosystems of eastern Australia may contain high stygofaunal diversity by Australian and world standards, particularly at the generic level for parabathynellids.


Zootaxa ◽  
2012 ◽  
Vol 3465 (1) ◽  
pp. 1 ◽  
Author(s):  
NIKOLAY A. POYARKOV, JR. ◽  
JING CHE ◽  
MI-SOOK MIN ◽  
MASAKI KURO-O ◽  
FANG YAN ◽  
...  

We describe four new species of Asian Clawed salamanders of the genus Onychodactylus (Caudata: Hynobiidae), basedon fresh material collected during fieldwork in Japan, Korea, the Russian Far East and northeastern China between 2003and 2010, as well as older voucher specimens deposited in several museums. Our analyses comprise all species currentlyrecognized within this genus across its entire distribution range. We follow an integrative taxonomic approach bycombining detailed morphological comparative analyses with molecular phylogenetic analyses. We find significantdifferences among species in this genus, based on morphological and molecular data, which resulted in the recognitionand description of four new species within this genus. The new species have uncorrected molecular divergences of over4.5–7.4% and 1.9–4.1% to their closest relatives in the mitochondrial COI and 16S rRNA genes respectively. In themolecular analyses, we found two very divergent lineages in Korea and Japan that need further investigation, as detailedmorphological data are not available for them. We also discuss our approach to delimit species on salamanders. For thenew species described in this group we evaluate their threat status according to IUCN criteria: O. koreanus sp. nov. Min,Poyarkov & Vieites and O. nipponoborealis sp. nov. Kuro-o, Poyarkov & Vieites are classified as Least Concern, whileO. zhaoermii sp. nov. Che, Poyarkov & Yan and O. zhangyapingi sp. nov. Che, Poyarkov, Li & Yan are classified as Vulnerable (Vu2a).


2021 ◽  
Vol 22 (3) ◽  
Author(s):  
Sri Riani ◽  
ROMANUS EDY PRABOWO ◽  
Agus Nuryanto

Abstract. Riani S, Prabowo RE, Nuryanto A. 2021. Molecular characteristics and taxonomic status of morphologically similar barnacles (Amphibalanus) assessed using the cytochrome c oxidase 1 gene. Biodiversitas 22: 1456-1466. Amphibalanus variegatus and A. reticulatus have similar external morphology. Morphological similarities can be a severe problem for direct species-level identification. The problem can be overcome through anatomy-based identification and validated through molecular barcoding. Molecular characterization using the cytochrome c oxidase 1 (COI) gene provides a useful tool for precise species identification. This study attempted to assess the molecular characteristics of morphologically similar barnacle (Amphibalanus) specimens collected at five localities in Indonesia to validate their taxonomic status. Forty-five barnacle specimens were collected during the field trips in Lampung, Jakarta, Semarang, Bali, and Lombok. The COI gene was amplified using LCO1490 and HCO2198 primers. The gene was sequenced using bidirectional sequencing at 1st base Asia. The specimens' taxonomic status was determined based on sequence identity, genetic distance, monophyly, nucleotide compositions, and nucleotides in a particular position. Shell shapes-based identification placed barnacle specimens into A. reticulatus. However, anatomical-based identification placed barnacle samples into two different anatomic groups, which was further validated by molecular data that two anatomic groups of Amphibalanus samples have significant differences in their COI gene. Based on the molecular characteristics, 43 samples were identified as A. reticulatus, while the two remaining samples were identified as A. variegatus.


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