Integrative taxonomy of two thrush complexes (Aves: Turdidae) reveals introgression across sister species

The classification of some Turdus species, such as the Naumann’s and dusky thrush complexes and the red-throated and black-throated thrush complexes, is controversial. Herein, we used molecular data (mitochondrial genes and microsatellite loci) and morphological characters to review the taxonomy of these thrush complexes and analyze the genetic differentiation between them. Our phylogenetic analysis based on mitochondrial genes indicated that all haplotypes could be divided into two reciprocally monophyletic sister clades corresponding to these two thrush complexes. The same results were revealed by coalescence-based species delimitation. Therefore, these two thrush complexes should be divided into two separate species (T. naumanni and T. ruficollis) and include two subspecies per species according to combined characters from morphological analyses and multilocus approaches. The above classifications were also supported by an analysis of genetic differentiation between T. naumanni and T. ruficollis and within each species. Moreover, there was significant mixing between these two thrush species in the neighbor-joining (NJ) tree and the cluster analysis of microsatellite loci. This led to a pattern of nuclear-mitochondrial discordance between the two species. This could be the result of extensive nuclear introgression between these two sister species. We also provide a potential explanation for the mechanism of gene introgression and nuclear-mitochondrial discordance between the two bird species.

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Systematics and phylogeography of the Australasian mangrove crabs Parasesarma semperi and P. longicristatum (Decapoda : Brachyura : Sesarmidae) based on morphological and molecular data

Invertebrate Systematics ◽

10.1071/is17040 ◽

2018 ◽

Vol 32 (1) ◽

pp. 196 ◽

Cited By ~ 2

Author(s):

Adnan Shahdadi ◽

Peter J. F. Davie ◽

Christoph D. Schubart

Keyword(s):

Genetic Data ◽

Morphological Characters ◽

Molecular Data ◽

Geographic Range ◽

The Philippines ◽

Mitochondrial Genes ◽

Width Ratio ◽

Sister Relationship ◽

Mangrove Crabs ◽

Morphological And Molecular Data

Parasesarma semperi (Bürger, 1893) was first described from Bohol in the Philippines and is considered to be widely distributed in Southeast Asia. Parasesarma longicristatum (Campbell, 1967) was originally described as a subspecies of P. semperi from Queensland, Australia, and later recognised as a full species. In this study, we re-examine specimens of the two species from across their entire geographic range using genetic markers, a morphometric analysis, and traditional morphological characters. Previous taxonomic species diagnoses were found to be unreliable, but morphometric principle component analyses consistently separate the two species, with the length to width ratio of the propodus of the fourth pereiopod being of particular importance. Genetic data corresponding to the mitochondrial genes COI, ND1 and 16S confirmed a close sister relationship between the two species, forming reciprocally monophyletic groups. Both species have high haplotype diversities and high intraspecific gene flow.

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Description of two new species of Rhamphus related to R. oxyacanthae (Curculionidae, Curculioninae, Rhamphini) from Italy based on a morphological study supported by molecular data

Zootaxa ◽

10.11646/zootaxa.4995.1.6 ◽

2021 ◽

Vol 4995 (1) ◽

pp. 111-128

Author(s):

LUCIANO DIOTTI ◽

ROBERTO CALDARA ◽

IVO TOŠEVSKI

Keyword(s):

New Species ◽

Morphological Study ◽

Host Plants ◽

Molecular Study ◽

Morphological Characters ◽

Molecular Data ◽

Integrative Taxonomy ◽

The Other ◽

Distribution Data ◽

Two New Species

Two new species of the weevil genus Rhamphus from Italy are herein described: R. bavierai n. sp. (Sicily) and R. hampsicora n. sp. (Sardinia). Both are morphologically and from a molecular perspective close to R. oxyacanthae (Marsham, 1802) and R. monzinii Pesarini & Diotti, 2012. Aside from a diagnostic description and a synoptic key, distribution data and notes on the host plants of the four species are reported. Whereas R. monzinii can be distinguished by several morphological characters, the other three species are morphologically very similar to each other and separable only by the combination of a few subtle characters. On the contrary, a preliminary molecular study revealed substantial divergences of mtCOI from 6.2 to 14.9% between the species, confirming the importance of an integrative taxonomy.

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An example of problems associated with DNA barcoding in tardigrades: a novel method for obtaining voucher specimens

Zootaxa ◽

10.11646/zootaxa.3104.1.3 ◽

2011 ◽

Vol 3104 (1) ◽

pp. 42 ◽

Cited By ~ 15

Author(s):

MICHELE CESARI ◽

ILARIA GIOVANNINI ◽

ROBERTO BERTOLANI ◽

LORENA REBECCHI

Keyword(s):

Dna Barcoding ◽

Dna Barcode ◽

Intraspecific Variability ◽

Original Description ◽

Morphological Characters ◽

Molecular Data ◽

Integrative Taxonomy ◽

Type Locality ◽

Moss Sample ◽

Voucher Specimens

We have in recent papers revealed that an integrative taxonomy approach helps to solve taxonomic problems in tardigrades. However, whole tardigrades are required for DNA work, which leaves no hologenophore voucher specimens with adult morphology. Using a novel methodology for the Tardigrada, we introduce the practice of collecting high quality maximum magnification light microscopy images of recently thawed animals to act as hologenophore voucher specimens of animals later used for DNA barcode sequencing. Within the framework of a DNA barcoding project on tardigrades, we collected a moss sample from the type locality of Macrobiotus terminalis Bertolani & Rebecchi, 1993 (Castelsantangelo, Central Apennines, Italy), a species of the “Macrobiotus hufelandi group”. Within the moss sample we found several animals and eggs with a morphology that corresponded to the original description of M. terminalis, while others were attributable to Macrobiotus macrocalix Bertolani & Rebecchi, 1993. In this study, molecular (cox1 mtDNA) analyses demonstrated no intraspecific variability in M. terminalis from the type locality but very large interspecific differences when compared with M. macrocalix and GenBank data for other species within the M. “hufelandi group”. There was also a large difference between our M. terminalis sequences and the GenBank data of a specimen attributed to the same species. The GenBank sequence originated from a population in the Northern Apennines, whose morphology appeared to be like that of the specimens of the locus typicus. This confirmed the importance in utilising material from the type locality for linking molecular data to the species’ morphological characters. Our paper underlines the importance of an integrative taxonomy in species diagnoses and demonstrates a scenario where morphological observations alone are not always sufficient. Lastly, this work adds reliable information to the sequence reference library that provides a useful building block for further studies on similar and related tardigrade taxa.

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Integrative taxonomy reveals two new cryptic species of Hyphessobrycon Durbin, 1908 (Teleostei: Characidae) from the Maracaçumé and middle Tocantins River basins, Eastern Amazon region

European Journal of Taxonomy ◽

10.5852/ejt.2020.723.1145 ◽

2020 ◽

Vol 723 ◽

pp. 77-107

Author(s):

Erick Cristofore Guimarães ◽

Pâmella Silva De Brito ◽

Pedro Henrique Negreiros Bragança ◽

Jadson Pinheiro Santos ◽

Axel Makay Katz ◽

...

Keyword(s):

New Species ◽

Mitochondrial Gene ◽

Morphological Characters ◽

Molecular Data ◽

Color Pattern ◽

Integrative Taxonomy ◽

The Body ◽

Dorsal Fin ◽

Two New Species ◽

Molecular Phylogenetic

Two new species, Hyphessobrycon frickei Guimarães, Brito, Bragança, Katz & Ottoni sp. nov. and H. geryi Guimarães, Brito, Bragança, Katz & Ottoni sp. nov., are herein described, based on seven different and independent species delimitation methods, and on molecular and morphological characters, making the hypothesis of these new species supported from an integrative taxonomy perspective. They belong to the “Rosy tetra” clade, which is mainly characterized by the presence of a dark brown or black blotch on the dorsal fin and the absence of a midlateral stripe on the body. These two new species are distinguished from the other members of this clade mainly by the arrangement, shape and color pattern of humeral and dorsal-fin spots, as well as by other characters related to scale counts and body pigmentation. The placement of the new species within the “Rosy tetra” clade was based on the combination of morphological character states mentioned above and corroborated by a molecular phylogenetic analysis using the mitochondrial gene cytochrome oxidase subunit 1. In addition, a new clade (here termed Hyphessobrycon copelandi clade) within the “Rosy tetra” clade is proposed based on molecular data, comprising H. copelandi, H. frickei sp. nov., H. geryi sp. nov. and a still undescribed species. Our results corroborate the occurrence of hidden species within the “Rosy tetra” clade, as suggested by previous studies.

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Morphology and phylogeny of Reticulitermes sp. (Isoptera, Rhinotermitidae) from Cyprus

Bulletin of Entomological Research ◽

10.1017/s0007485312000260 ◽

2012 ◽

Vol 102 (6) ◽

pp. 672-681 ◽

Cited By ~ 3

Author(s):

S. Ghesini ◽

M. Marini

Keyword(s):

Eastern Mediterranean ◽

Morphological Characters ◽

Molecular Data ◽

Mitochondrial Genes ◽

East Mediterranean ◽

European Species ◽

Qualitative And Quantitative ◽

North Eastern ◽

Size Groups ◽

Morphological And Molecular Data

AbstractTaxonomy and phylogeny of termites of the genus Reticulitermes in central and eastern Mediterranean lands are poorly understood, partly due to insufficient sampling. This study aims to contribute to the knowledge of east Mediterranean termites by presenting morphological and molecular data on Reticulitermes from Cyprus. Samples from 15 colonies were collected throughout the island. Qualitative and quantitative morphological characters were analyzed for alate and soldier castes. Partial sequences of the mitochondrial genes COII and 16S were used to evaluate genetic diversity of Cypriot colonies and to determine their phylogenetic relationships with taxa from central and eastern Mediterranean areas.Cypriot alates have some morphological features in common with the Israeli R. clypeatus: an enlarged postclypeus and a wide unpigmented margin of the eye. They are larger than R. clypeatus but smaller than western European species, such as R. banyulensis, R. lucifugus corsicus and R. grassei. For Cypriot soldiers, two size groups were identified, possibly in relation with the age of their mother colonies.Phylogenetic analysis shows that, contrary to what might be expected, the samples with the highest affinity with Cypriot samples are not those from the nearby mainland (south Turkey, Israel), but from north-eastern Greece. Comprehensive sampling in the nearby mainland is lacking, so the possibility that populations exist it that region with an affinity towards Cypriot Reticulitermes sp. cannot be ruled out. Together with samples from the Halkidiki peninsula, north-eastern Greece, northern Turkey and Crete, Cypriot Reticulitermes form a well-supported north-eastern Mediterranean clade.

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Integrative Taxonomy, Phylogeny, and New Species of the Weevil GenusOnyxacallesStüben (Coleoptera: Curculionidae: Cryptorhynchinae)

Psyche A Journal of Entomology ◽

10.1155/2012/654948 ◽

2012 ◽

Vol 2012 ◽

pp. 1-22

Author(s):

Peter E. Stüben ◽

Jonas J. Astrin

Keyword(s):

New Species ◽

Molecular Phylogeny ◽

Related Species ◽

Mediterranean Area ◽

Molecular Data ◽

Integrative Taxonomy ◽

Mitochondrial Genes ◽

Western Palearctic ◽

Species Groups ◽

Three New Species

A molecular phylogeny of the western Palearctic weevil genusOnyxacallesStüben, 1999 is presented, combining two mitochondrial genes (COI and 16S) in a Bayesian analysis. Based on molecular data,Onyxacalles pyrenaeusBoheman, 1844 is transferred into the genusKyklioacallesStüben 1999 (K. faustigroup) and—in an integrative taxonomy framework—the interaction between morphology and molecular analysis is illustrated. The species ofOnyxacalless. str. are assigned to three new species groups,O. henoni,O. luigionii, andO. portusvenerisgroups. The distribution of the related species in the Mediterranean area is illustrated with values of COI and 16S p-distances. Three new species are described and distinguished from their related species:Onyxacalles nuraghiStüben sp.n. from Italy (Sardinia),Onyxacalles torreStüben and Astrin sp. n. from France (Corsica) andOnyxacalles vilaeStüben sp. n. from Croatia (Velebit Mts.). A catalogue of all 20 species ofOnyxacallesis given, and a key is finally presented combined with image stacking of the habitus and aedeagus for all species.

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A Great Difference Between Sedentary Subspecies of Laniarius atroflavus Shelley, 1887 Suggests on the Base of Molecular Data that Laniarius atroflavus and Laniarius craterum are Two Separate Species

The Open Ornithology Journal ◽

10.2174/1874453201407010030 ◽

2014 ◽

Vol 7 (1) ◽

pp. 30-39

Author(s):

Billy Nguembock

Keyword(s):

Genetic Variation ◽

West Africa ◽

Size Variation ◽

Molecular Data ◽

Genetic Distances ◽

Mitochondrial Genes ◽

Secondary Contact ◽

Separate Species ◽

Quaternary Period ◽

Molecular Characters

Laniarius atroflavus is a sedentary member of the bush-shrike radiation (family Malaconotidae) and in our first paper, it appeared with strong divergence between its two subspecies. To confirm this divergence and leaning partially on our first obtained results, we investigated a genetic variation of the individuals of Laniarius atroflavus atroflavus (West Africa) and Laniarius atroflavus craterum (West Africa). For the genetic variation, we use two mitochondrial genes (ATPase6 and ND2) to calculate their genetic distances within the Laniarius ingroup and to explore their mutational differentiation. With our ATPase6 and ND2, a genetic distance of 1.66% and 2.14% has been respectively estimated between individuals of Laniarius atroflavus atroflavus (Cameroon Mountain) and Laniarius atroflavus craterum (Manenguba Mountain) whereas it was, for the same markers, of 0% and 0.57% respectively between specimens of Laniarius atroflavus craterum only caught in diverse parts of the Manenguba Mountain. For the mutational differentiation, a total of 34 different molecular characters have been observed with the two markers investigated between these two subspecies. Leaning on some dating results, it appears that Laniarius atroflavus atroflavus diverged from Laniarius atroflavus craterum during the Quaternary period and these dates correspond remarkably with those suggested for several polyphased volcanic activities noted in the Cameroon Volcanic Line. For these separate sedentary birds which are marked by their clinal size variation, measures of their wings as well as the variation of the color of their breast and belly, a possible secondary contact will certainly lead to reinforcement. Thus, we suggest resurrecting names Laniarius atroflavus Shelley, 1887 and Laniarius craterum Bates, 1926 for individuals of the populations hitherto referred as Laniarius atroflavus atroflavus and Laniarius atroflavus craterum respectively.

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Integrative taxonomy of the genus Pseudostegana (Diptera, Drosophilidae) from China, with descriptions of eleven new species

PeerJ ◽

10.7717/peerj.5160 ◽

2018 ◽

Vol 6 ◽

pp. e5160 ◽

Cited By ~ 3

Author(s):

Jinming Lu ◽

Yuan Zhang ◽

Hongwei Chen

Keyword(s):

New Species ◽

Species Delimitation ◽

Morphological Characteristics ◽

Morphological Characters ◽

Molecular Data ◽

Integrative Taxonomy ◽

Southwestern China ◽

28S Rrna ◽

Nuclear Locus ◽

Barcode Gap

The genus Pseudostegana (Okada, 1978) currently contains thirty-nine described species. A number of Pseudostegana were collected from the fieldwork in southwestern China from 2010 to 2017. Eleven new species were discovered and are described from southwestern China: Pseudostegana alpina Zhang & Chen, sp. nov.; Pseudostegana amnicola Zhang & Chen, sp. nov.; Pseudostegana amoena Zhang & Chen, sp. nov.; Pseudostegana mailangang Zhang & Chen, sp. nov.; Pseudostegana meiduo Zhang & Chen, sp. nov.; Pseudostegana meiji Zhang & Chen, sp. nov.; Pseudostegana mystica Zhang & Chen, sp. nov.; Pseudostegana stictiptrata Zhang & Chen, sp. nov.; Pseudostegana stigmatptera Zhang & Chen, sp. nov.; Pseudostegana ximalaya Zhang & Chen, sp. nov. and Pseudostegana zhuoma Zhang & Chen, sp. nov. A key to all Chinese Pseudostegana species based on morphological characters is provided. Two mitochondrial loci (COI and ND2) and one nuclear locus (28S rRNA) were sequenced for the Pseudostegana specimens, and Bayesian and RAxML concatenated analyses were run. Molecular species delimitation is performed using the distance-based automatic barcode gap discovery (ABGD) method. Molecular data support the morphological characteristics observed among these Chinese species and confirm the new species as being distinctly different.

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Endangered Rough Pigtoe Pearlymussel: Assessment of Phylogenetic Status and Genetic Differentiation of Two Disjunct Populations

Journal of Fish and Wildlife Management ◽

10.3996/052013-jfwm-036 ◽

2015 ◽

Vol 6 (2) ◽

pp. 338-349 ◽

Cited By ~ 2

Author(s):

Jess W. Jones ◽

Nathan Johnson ◽

Paul Grobler ◽

Daniel Schilling ◽

Richard J Neves ◽

...

Keyword(s):

Genetic Differentiation ◽

River Basin ◽

Dna Sequences ◽

Microsatellite Loci ◽

Nuclear Dna ◽

Fish Host ◽

Shell Morphology ◽

Ohio River ◽

Separate Species ◽

Phylogenetic Status

Abstract We conducted a genetic characterization of two extant populations of an endangered freshwater mussel, the rough pigtoe Pleurobema plenum, in the Clinch River, Tennessee of the Tennessee River basin, and the Green River, Kentucky, of the Ohio River basin for purposes of conservation recovery planning. First, phylogenetic status of this species within the Pleurobema cordatum species complex (P. cordatum, plenum, rubrum, sintoxia) was assessed using mitochondrial ND1 deoxyribonucleic acid (DNA) sequences, which showed that all investigated species of Pleurobema are genetically distinct. Our results indicated that P. cordatum, P. plenum, P. rubrum, and P. sintoxia each represent monophyletic clades; however, the latter two species were closely related, separated by only one to three nucleotide differences. Further, DNA sequence haplotypes from both populations of P. plenum grouped together into one monophyletic clade and did not support characterizing the populations as separate species. Thus, our phylogenetic analysis confirms that populations of P. plenum in the Clinch and Green rivers are the same species. Second, we assessed genetic differentiation between P. plenum populations in each river by analyzing variation at eight nuclear DNA microsatellite loci, where FST (=0.023) and Jost’s D (=0.175) indicated genetically differentiated populations. Because these populations are geographically and demographically independent, and differentiated at nuclear microsatellite loci, recognition as management units is recommended. Additional studies are needed to determine whether there are differences at adaptive or life-history traits, such as fish host usage, shell morphology, and soft anatomy between populations, and to further investigate the phylogenetic relationship of P. rubrum and P. sintoxia.

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Genetic and morphometric categorization ofTaenia ovisfrom Sheep in Iran

Parasitology ◽

10.1017/s0031182018001907 ◽

2018 ◽

Vol 146 (5) ◽

pp. 563-568 ◽

Cited By ~ 1

Author(s):

Sima Rostami ◽

Reza Salavati ◽

Robin N. Beech ◽

Zahra Babaei ◽

Mitra Sharbatkhori ◽

...

Keyword(s):

Sequence Analysis ◽

Correlation Coefficients ◽

Morphological Characters ◽

Mitochondrial Genes ◽

Rrna Genes ◽

12S Rrna ◽

Length Variation ◽

Rostellar Hook ◽

Separate Species ◽

Interclass Correlation

AbstractLittle is known about the genetic and morphological characters ofTaenia ovis. The purpose of the present study was to characterize sheep isolates ofT. ovisusing rostellar hook morphometry as well as mitochondrial genes sequence analysis. Ninety sheep specimens ofCysticercus oviswere collected from 18 slaughterhouses in Iran. The mean ±s.d.for total length of large and small hooks were 174.1 ± 6.4 and 116.7 ± 5.4µm, respectively. CO1 and 12S rRNA sequence analysis showed 11 and nine haplotypes, respectively. The level of pairwise nucleotide variations between individual haplotypes of CO1 and 12S rRNA genes were 0.3–1.1 and 0.2–1.0%, respectively. Level of nucleotide variation in CO1 and 12S rRNA betweenT. ovishaplotypes from present study and eight otherTaeniaspecies was found to be 11.3–17.8 and 5.3–16.3%, respectively. Phylogenetic analysis clustered allT. ovisisolates into a single clade comprised of the all CO1 and 12S rRNA haplotypes. CO1 nucleotide difference betweenT. ovis ovisandT. asiaticawas 13.6% that is lesser than the corresponding difference betweenT. ovis ovisandT. ovis krabbei, warranting the designation of two separate species asT. ovisandT. krabbei. Interclass correlation coefficients showed that there was no significant association between rostellar hook length variation and the variability of the mitochondrial genes.

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