Phylogeny and molecular species delimitation of long-nosed armadillos (Dasypus: Cingulata) supports morphology-based taxonomy

AbstractThe armadillo genus Dasypus is the most species-rich and widely distributed genus of the order Cingulata and it has a dynamic taxonomic history. Recent morphology-based studies have proposed new taxonomic arrangements, but these were not yet assessed with molecular data. The two comprehensive phylogenetic hypotheses available for the genus are conflicting and were each based on a subset of taxa, hampering a proper evaluation of species boundaries. Using a multilocus molecular dataset, based on the broadest geographic sampling of Dasypus to date, we inferred the phylogenetic relationships of all species of the genus, including the recently reinstated D. beniensis and D. pastasae. We tested recent taxonomic hypotheses using several species-delimitation approaches. Our phylogeny recovered three main lineages of long-nosed armadillos that we treat as subgenera (Hyperoambon, Muletia and Dasypus) and identified the majority of its diversification as having occurred during the Pliocene. Molecular species delimitation supported morphological evidence in assigning D. hybridus as a subspecies of D. septemcinctus and confirming the split of the D. kappleri complex into three species. Our results strongly support the recognition of Guiana Shield populations formerly assigned to D. novemcinctus as a distinct species. The phylogenetic positions of D. mazzai and D. sabanicola remain uncertain. Further investigation using faster-evolving genes and additional samples may help to clarify the relationships of these young species.

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Molecular species delimitation in the primitively segmented spider genus Heptathela endemic to Japanese islands

10.1101/812214 ◽

2019 ◽

Cited By ~ 1

Author(s):

Xin Xu ◽

Matjaž Kuntner ◽

Jason E. Bond ◽

Hirotsugu Ono ◽

Simon Y. W. Ho ◽

...

Keyword(s):

Molecular Species ◽

Species Delimitation ◽

Computational Time ◽

Species Boundaries ◽

Biological Research ◽

Morphological Evidence ◽

Data Sets ◽

Bayesian Approaches ◽

Multispecies Coalescent ◽

Japanese Islands

ABSTRACTDetermining species boundaries forms an important foundation for biological research. However, the results of molecular species delimitation can vary with the data sets and methods that are used. Here we use a two-step approach to delimit species in the genus Heptathela, a group of primitively segmented trapdoor spiders that are endemic to Japanese islands. Morphological evidence suggests the existence of 19 species in the genus. We tested this initial species hypothesis by using six molecular species-delimitation methods to analyse 180 mitochondrial COI sequences of Heptathela sampled from across the known range of the genus. We then conducted a set of more focused analyses by sampling additional genetic markers from the subset of taxa that were inconsistently delimited by the single-locus analyses of mitochondrial DNA. Multilocus species delimitation was performed using two Bayesian approaches based on the multispecies coalescent. Our approach identified 20 putative species among the 180 sampled individuals of Heptathela. We suggest that our two-step approach provides an efficient strategy for delimiting species while minimizing costs and computational time.

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The hidden anatomy of paranasal sinuses reveals biogeographically distinct morphotypes in the nine-banded armadillo (Dasypus novemcinctus)

PeerJ ◽

10.7717/peerj.3593 ◽

2017 ◽

Vol 5 ◽

pp. e3593 ◽

Cited By ~ 8

Author(s):

Guillaume Billet ◽

Lionel Hautier ◽

Benoit de Thoisy ◽

Frédéric Delsuc

Keyword(s):

South America ◽

Paranasal Sinuses ◽

Morphological Diversity ◽

Distinct Species ◽

Molecular Data ◽

Morphological Data ◽

Diagnostic Feature ◽

Guiana Shield ◽

Diagnostic Features ◽

Continental Scale

BackgroundWith their Pan-American distribution, long-nosed armadillos (genusDasypus) constitute an understudied model for Neotropical biogeography. This genus currently comprises seven recognized species, the nine-banded armadillo (D. novemcinctus) having the widest distribution ranging from Northern Argentina to the South-Eastern US. With their broad diversity of habitats, nine-banded armadillos provide a useful model to explore the effects of climatic and biogeographic events on morphological diversity at a continental scale.MethodsBased on a sample of 136 skulls ofDasypusspp. belonging to six species, including 112 specimens identified asD. novemcinctus, we studied the diversity and pattern of variation of paranasal cavities, which were reconstructed virtually using µCT-scanning or observed through bone transparency.ResultsOur qualitative analyses of paranasal sinuses and recesses successfully retrieved a taxonomic differentiation between the traditional speciesD. kappleri,D. pilosusandD. novemcinctusbut failed to recover diagnostic features between the disputed and morphologically similarD. septemcinctusandD. hybridus. Most interestingly, the high variation detected in our large sample ofD. novemcinctusshowed a clear geographical patterning, with the recognition of three well-separated morphotypes: one ranging from North and Central America and parts of northern South America west of the Andes, one distributed across the Amazonian Basin and central South America, and one restricted to the Guiana Shield.DiscussionThe question as to whether these paranasal morphotypes may represent previously unrecognized species is to be evaluated through a thorough revision of theDasypusspecies complex integrating molecular and morphological data. Remarkably, our recognition of a distinct morphotype in the Guiana Shield area is congruent with the recent discovery of a divergent mitogenomic lineage in French Guiana. The inflation of the second medialmost pair of caudal frontal sinuses constitutes an unexpected morphological diagnostic feature for this potentially distinct species. Our results demonstrate the benefits of studying overlooked internal morphological structures in supposedly cryptic species revealed by molecular data. It also illustrates the under-exploited potential of the highly variable paranasal sinuses of armadillos for systematic studies.

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Beyond the carapace: skull shape variation and morphological systematics of long-nosed armadillos (genus Dasypus)

10.7287/peerj.preprints.2924 ◽

2017 ◽

Author(s):

Lionel Hautier ◽

Guillaume Billet ◽

Benoit De Thoisy ◽

Frédéric Delsuc

Keyword(s):

Morphological Variation ◽

Distinct Species ◽

Morphological Characters ◽

Molecular Data ◽

Guiana Shield ◽

Shape Variation ◽

Skull Morphology ◽

Geometric Morphometric ◽

Skull Shape ◽

Shape And Size

Background. The systematics of long-nosed armadillos (genus Dasypus) has been mainly based on a handful of external morphological characters and classical measurements. Here, we studied the pattern of morphological variation in the skull of long-nosed armadillos species, with a focus on the systematics of the widely distributed nine-banded armadillo (D. novemcinctus). Methods. We present the first exhaustive 3D comparison of the skull morphology within the genus Dasypus, based on µCT-scans. We used geometric morphometric approaches to explore the patterns of the intra- and interspecific morphological variation of the skull with regard to several factors such as taxonomy, geography, allometry, and sexual dimorphism. Results. We show that the shape and size of the skull vary greatly between Dasypus species, with D. pilosus representing a clear outlier compared to other long-nosed armadillos. The study of the cranial intraspecific variation in D. novemcinctus evidences clear links to the geographic distribution and argue in favour of a revision of past taxonomic delimitations. Our detailed morphometric comparisons detected previously overlooked morphotypes of nine-banded armadillo, especially a very distinctive unit circumscribed to the Guiana Shield. Discussion. As our results are congruent with recent molecular data and analyses of the structure of paranasal sinuses, we propose that D. novemcinctus should be regarded either as a polytypic species (with three to four subspecies) or as a complex of several distinct species.

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Species delimitation of the praying mantis Hierodula patellifera (Audinet-Serville) based on morphological and molecular characters (Mantodea: Mantidae)

Zootaxa ◽

10.11646/zootaxa.4951.1.7 ◽

2021 ◽

Vol 4951 (1) ◽

pp. 147-158

Author(s):

JAEIL SHIM ◽

HAECHUL PARK ◽

SEONGHYUN KIM ◽

HO-JONG JU ◽

JEONG-HUN SONG

Keyword(s):

Species Delimitation ◽

Male Genitalia ◽

Gene Tree ◽

Distinct Species ◽

Morphological Characters ◽

Molecular Data ◽

Neighbor Joining ◽

Praying Mantis ◽

Taxonomic Analysis ◽

Molecular Characters

An integrative taxonomic analysis of Hierodula patellifera (Audinet-Serville) is presented based on morphological and molecular characters (COI, 28S rDNA). During repeated trips to the Korean peninsula, we collected unusual specimens from Wanju-gun. They were similar to H. patellifera, but can be distinguished by a larger body size, the number and shape of spines on foreleg, and the shape of male genitalia. To examine the phenotypes and delimit H. patellifera from fourteen sampled populations, we used forecoxal spines and male genitalia as key morphological characters, as well as molecular data including gene tree monophyly and genetic divergence data. The molecular analyses (p-distance, neighbor-joining, and parsimony analyses) did not separate the specimens as two distinct species. The diagnostic characters of H. patellifera are illustrated with habitus images.

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Niviventer confucianus sacer (Rodentia, Muridae) is a distinct species based on molecular, karyotyping, and morphological evidence

ZooKeys ◽

10.3897/zookeys.959.53426 ◽

2020 ◽

Vol 959 ◽

pp. 137-159

Author(s):

Yaoyao Li ◽

Yiqiao Li ◽

Haotian Li ◽

Jing Wang ◽

Xiaoxiao Rong ◽

...

Keyword(s):

Species Delimitation ◽

Mitochondrial Gene ◽

Morphological Characteristics ◽

Tail Length ◽

Distinct Species ◽

Molecular Karyotyping ◽

Morphological Evidence ◽

Integrated Analysis ◽

Incisive Foramen ◽

Tail Tip

Niviventer confucianus sacer Thomas, 1908, which has been regarded as a subspecies of N. confucianus, was found to be a distinct species from N. confucianus based on molecular, karyotyping, and morphological characteristics in this study. Niviventer c. sacer was found to belong to a distinct phylogenetic clade in phylogenetic tree constructed using the mitochondrial gene Cytb, it clustered with N. bukit (Bonhote, 1903) from Vietnam and N. confucianus (Milne-Edwards, 1871) from Yunnan, but showed a distant relationship with N. confucianus from adjacent areas. The genetic distance between N. c. sacer and N. confucianus was more than 5.8%, reaching the level of interspecific differentiation. The species delimitation indicates that N. c. sacer is a monophyletic group. The karyotype of N. c. sacer (FN = 55, 8m+4st+32t+X(sm)Y(t)) differed from that of N. confucianus (FN = 59, 6m+4sm+2st+32t+X(sm)Y(t)). In terms of morphological features, the length of incisive foramen (LIF) and length of auditory bulla (LAB) of N. c. sacer is significantly larger than that of N. confucianus and N. bukit (P < 0.05) and the proportion of white tail tip to total tail length is significantly longer at N. c. sacer (≥ 1/3) than that at N. confucianus (≤ 1/3). Therefore, integrated analysis confirmed that N. c. sacer is a distinct species of genus Niviventer rather than a subspecies of N. confucianus or N. bukit, namely N. sacer, which is only distributed in Shandong.

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The hidden anatomy of paranasal sinuses reveals biogeographically distinct morphotypes in the nine-banded armadillos (Dasypus novemcinctus)

10.7287/peerj.preprints.2923v1 ◽

2017 ◽

Cited By ~ 1

Author(s):

Guillaume Billet ◽

Lionel Hautier ◽

Benoit de Thoisy ◽

Frédéric Delsuc

Keyword(s):

South America ◽

Paranasal Sinuses ◽

Morphological Diversity ◽

Distinct Species ◽

Molecular Data ◽

Morphological Data ◽

Diagnostic Feature ◽

Guiana Shield ◽

Diagnostic Features ◽

Continental Scale

Background. With their Pan-American distribution, long-nosed armadillos (genus Dasypus) constitute an understudied model for Neotropical biogeography. This genus currently comprises seven recognized species, the nine-banded armadillo (D. novemcinctus) having the widest distribution ranging from Northern Argentina to the South-Eastern US. With their broad diversity of habitats, nine-banded armadillos provide a useful model to explore the effects of climatic and biogeographic events on morphological diversity at a continental scale. Methods. Based on a sample of 136 skulls of Dasypus spp., including 112 specimens identified as D. novemcinctus, we studied the diversity and pattern of variation of internal paranasal cavities, which were reconstructed virtually using µCT-scanning or observed through bone transparency. Results. Our qualitative analyses of paranasal sinuses and recesses successfully retrieved a taxonomic differentiation between the traditional species D. kappleri, D. pilosus and D. novemcinctus but failed to recover diagnostic features between the disputed and morphologically similar D. septemcinctus and D. hybridus. Most interestingly, the high variation detected in our large sample of D. novemcinctus showed a clear geographical patterning, with the recognition of three well-separated morphotypes: one ranging from North and Central America and parts of northern South America west of the Andes, one distributed across the Amazonian Basin and central South America, and one restricted to the Guiana Shield. Discussion. The question as to whether these paranasal morphotypes may represent previously unrecognized species is to be evaluated through a thorough revision of the Dasypus species complex integrating molecular and morphological data. Remarkably, our recognition of a distinct morphotype in the Guiana Shield area is congruent with the recent discovery of a divergent mitogenomic lineage in French Guiana. The inflation of the second medialmost pair of caudal frontal sinuses constitutes an unexpected morphological diagnostic feature for this potentially distinct species. Our results demonstrate the benefits of studying overlooked internal morphological structures in supposedly cryptic species revealed by molecular data. It also illustrates the under-exploited potential of the highly variable paranasal sinuses of armadillos for systematic studies.

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A new Epeorus (Caucasiron) (Ephemeroptera: Heptageniidae) species from Turkey based on molecular and morphological evidence

Zootaxa ◽

10.11646/zootaxa.4550.1.2 ◽

2019 ◽

Vol 4550 (1) ◽

pp. 58 ◽

Cited By ~ 4

Author(s):

ĽUBOŠ HRIVNIAK ◽

PAVEL SROKA ◽

GENCER TÜRKMEN ◽

ROMAN J. GODUNKO ◽

NİLGÜN KAZANCI

Keyword(s):

New Species ◽

Morphological Analysis ◽

Distinct Species ◽

Individual Species ◽

Morphological Evidence ◽

Fine Hair ◽

The Caucasus ◽

Molecular Dataset ◽

Coi Sequences ◽

Analytical Approaches

Epeorus (Caucasiron) turcicus sp. nov. is described based on larvae from NE Turkey. The new species can be distinguished from other Caucasiron by a unique combination of several diagnostic characters: the presence of a rounded hypodermal medial femur spot, colouration of abdominal terga and sterna, narrow gill plate VII, fine hair-like setae on the surface of abdominal terga, and absence of postero-lateral projections on tergum X. In addition to morphological analysis, two single-locus analytical approaches are employed for delimiting the new species using COI sequences (Automatic Barcode Gap Discovery, ABGD; and General Mixed Yule Coalescent Model, GMYC). Both approaches unambiguously recognized E. (C.) turcicus sp. nov. as a distinct species. Our molecular dataset contains all Caucasiron species occurring in the Caucasus and the delimitation of individual species mostly follows the morphologically defined species. This study confirms the suitability of the GMYC approach for species delimitation within Caucasiron.

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Resurrection of Pomphorhynchus tereticollis (Rudolphi, 1809) (Acanthocephala: Pomphorhynchidae) based on new morphological and molecular data

Helminthologia ◽

10.2478/s11687-011-0038-y ◽

2011 ◽

Vol 48 (4) ◽

pp. 268-277 ◽

Cited By ~ 35

Author(s):

M. Špakulová ◽

M. Perrot-Minnot ◽

B. Neuhaus

Keyword(s):

Anterior Part ◽

Genetic Data ◽

Distinct Species ◽

Molecular Data ◽

Fish Host ◽

Morphological Evidence ◽

Baltic Coast ◽

Morphological And Molecular Data ◽

The Baltic ◽

Fish Hosts

AbstractPomphorhynchus tereticollis (Rudolphi, 1809) is here redescribed on the basis of Rudolphi’s material, deposited in the Museum für Naturkunde Berlin, and on acanthocephalans recently collected from the type host Platichthys flessus (L.) and the region embodying the type locality. Out of the paratypes of P. tereticollis, the lectotype and paralectotypes have been designated. Their morphology fits well with that of newly collected material of P. tereticollis dissected from the type fish host from the Baltic coast near Stralsund. The resurrection of P. tereticollis, previously considered a synonym of Pomphorhynchus laevis (Zoega in Müller, 1779), is supported by several morphological features distinguishing the two Pomphorhynchus species: 1. The basal parts of the proboscis hooks located on the posterior proboscis half possess proximal projections in P. tereticollis but not in P. laevis. This shape of the hook bases is clearly visible only in unfixed fresh worms; 2. The last hooks are situated at the anterior part of the bulbus or rarely at the posterior-most end of the proboscis in P. tereticollis, while they lie anterior to the end of the proboscis in P. laevis; 3. The proboscis hooks No. 5 or 6 are markedly stout (robust) and clearly distinct in comparison with the surrounding hooks in P. tereticollis, while less robust and more similar to the hooks in P. laevis. In addition, genetic divergence between P. tereticollis and P. laevis based on ITS1, ITS2 and COI sequencing supports the existence of two distinct species and reveals that some isolates previously identified as P. laevis were actually P. tereticollis. Previous and present morphological and genetic data show that both Pomphorhynchus species occur in freshwaters throughout Europe and may infect the same fish hosts, such as chub and barbel, and also several species of isopods (Gammaridae). This study also provides morphological evidence that Pomphorhynchus intermedius Engelbrecht, 1957 is a synonym of P. tereticollis, because the only discrimination character of the former species, the “existing but small proximal projections of basal parts of the proboscis hooks located on the posterior proboscis half” are present also in P. tereticollis.

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Morphological and Molecular Assessments of Bobtail Squids (Cephalopoda: Sepiolidae) Reveal a Hidden History of Biodiversity

Frontiers in Marine Science ◽

10.3389/fmars.2020.632261 ◽

2021 ◽

Vol 7 ◽

Author(s):

Fernando Á. Fernández-Álvarez ◽

Pilar Sánchez ◽

Roger Villanueva

Keyword(s):

Molecular Species ◽

Species Delimitation ◽

Sequence Data ◽

Morphological Evolution ◽

Morphological Characters ◽

Molecular Data ◽

Medium Size ◽

Nominal Species ◽

Cryptic Biodiversity ◽

New Research

Molecular species delimitation assists taxonomic decisions for challenging species, like cryptic species complexes. Bobtail squids (Family Sepiolidae Leach, 1817) are a very diverse group of benthic and nektonic small to medium size cephalopods with many taxonomic questions to solve. In this study we provided new sequence data for 12 out 17 Mediterranean bobtail squid species including all the genera present i n the area. Other relevant species from other parts of the world were used as comparison. The combined use of several molecular species delimitation methods consistently showed a picture of hidden biodiversity within this family which hinders the use of molecular data isolated from morphological characters. On the one hand, those methods provided contrasting results for the number of recognized species of some morphologically well-defined species. We suggest this can be an effect of recent speciation phenomena followed by an intense morphological drift. On the other hand, cryptic biodiversity was detected among members of several monophyletic clades assigned to the same nominal species, pointing to recent speciation phenomena without a parallel morphological evolution. Although Mediterranean bobtail diversity has been extensively studied for more than a century, a new species of Stoloteuthis Verrill (1881) was discovered and described here, both using molecular and morphological methods. This new research stresses the necessity of combined morphological and molecular studies to correctly assess cephalopod diversity. urn:lsid:zoobank.org:act:57AFBB38-18EA-4F80-B1D4-73519C12694F.

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DNA-based species delimitation reveals cryptic and incipient species in synchronous flashing fireflies (Coleoptera: Lampyridae) of Southeast Asia

Biological Journal of the Linnean Society ◽

10.1093/biolinnean/blaa072 ◽

2020 ◽

Vol 130 (3) ◽

pp. 520-532

Author(s):

Wan F A Jusoh ◽

Lesley Ballantyne ◽

Kin Onn Chan

Keyword(s):

Southeast Asia ◽

Species Delimitation ◽

East Coast ◽

Morphological Differentiation ◽

Population Level ◽

Distinct Species ◽

Peninsular Malaysia ◽

Species Boundaries ◽

Incipient Species ◽

Genetic Sampling

Abstract Synchronous flashing fireflies of the genus Pteroptyx are ubiquitous throughout Southeast Asia, yet fundamental knowledge about their biodiversity is lacking. Recent studies have revealed notable population-level phylogeographical structure within the Pteroptyx tener and P. bearni groups in Malaysia, suggesting that cryptic species may exist. Additionally, morphological and genetic similarities between P. balingiana and P. malaccae have raised questions about the former’s validity as a distinct species. We collected samples from previously unsampled populations and assembled the most comprehensive genetic dataset for Pteroptyx to date, to characterize species boundaries within the P. tener, P. bearni and P. malaccae groups. Using a suite of species delimitation analyses, we show that P. tener along the west coast of Peninsular Malaysia (PM) is distinct from populations from the east coast and Borneo despite the absence of morphological differentiation. However, analyses could not conclusively differentiate P. bearni from Borneo and eastern PM, nor identify P. balingiana and P. malaccae as distinct species, indicating that these populations may be conspecific or represent incipient species. This study underlines the need to increase geographical, taxonomic and genetic sampling of Southeast Asian fireflies to provide a better understanding of their biodiversity.

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