The identification of the species of the ‘Spilogona contractifrons species-group’ and the ‘Spilogona nitidicauda species-group’ (Diptera, Muscidae) based on morphological and molecular analysis

Muscid species of the ‘Spilogona contractifrons species-group’ (Spilogona alticola (Malloch, 1920), S. arctica (Zetterstedt, 1838), S. contractifrons (Zetterstedt, 1838), S. orthosurstyla Xue & Tian, 1988) and of the ‘Spilogona nitidicauda species-group’ (S. nitidicauda (Schnabl, 1911), S. hissarensis Hennig, 1959, S. imitatrix (Malloch, 1921), S. platyfrons Sorokina, 2018) are notoriously difficult to distinguish. In this paper, their morphological features are analysed, images of the male head, frons and abdomen of all the species are given, and the male terminalia are figured. The study of extensive material has shown that all the morphologically recognised species in each of these groups are valid species. An identification key is provided for both groups of species. To confirm the morphological differences, genetic differences in the cytochrome oxidase I gene of flies of the ‘Spilogona contractifrons species-group’ and of the ‘Spilogona nitidicauda species-group’ were analysed. It is shown that members of both groups of species have not only distinguishing morphological characters but also fixed substitutions in the DNA sequences. Since a low interspecific polymorphism is known in the Muscidae Latreille, 1802, the revealed genetic distances confirm the existence of separate species or subspecies in each of the groups studied.

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A phylogenetic approach to the Philippines endemic centipedes of the genus Scolopendra Linnaeus, 1758 (Scolopendromorpha, Scolopendridae), with the description of a new species

Zootaxa ◽

10.11646/zootaxa.4483.3.1 ◽

2018 ◽

Vol 4483 (3) ◽

pp. 401

Author(s):

CARLES DOMÉNECH ◽

VICTOR M. BARBERA ◽

EDUARDO LARRIBA

Keyword(s):

Dna Sequences ◽

Endemic Species ◽

Phylogenetic Trees ◽

Morphological Characters ◽

Genetic Distances ◽

The Philippines ◽

Neighbor Joining ◽

Separate Species ◽

Additional Species ◽

A New Species

The genus Scolopendra Linnaeus, 1758 is represented in the Philippines’ fauna by five species, two of which are endemic. Mitochondrial DNA sequences of gene cytochrome c oxidase subunit I (COI) were obtained from six Scolopendra specimens belonging to two endemic species and a new one, described here as Scolopendra paradoxa Doménech sp. nov. These sequences were analyzed together with another forty-one sequences from GenBank, including additional species of Scolopendra and a few representatives of other Scolopendridae genera. Phylogenetic trees inferred from the COI analysis using maximum likelihood and neighbor joining showed the three Philippines Scolopendra endemic species as a polyphyletic group coherent with their respective morphologies, although the position of S. spinosissima Kraepelin, 1903 varied within the obtained trees. Species delimitation based on standard external morphological characters was also concordant with the observed genetic distances, monophyly and node support, confirming S. subcrustalis Kronmüller, 2009 and S. paradoxa sp. nov. as separate species also at the molecular level, while only the position of S. spinosissima could not be properly established with any of the statistical methods used. In addition, the male genitalia of the three studied species were found to lack gonopods and a penis. Remarks on the ultimate legs prefemoral spinous formula of S. spinosissima plus a key to the species of the genus Scolopendra in the Philippines are provided.

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Revision of moles in the genus Scapanus

Therya ◽

10.12933/therya-21-1174 ◽

2021 ◽

Vol 12 (2) ◽

pp. 275-281

Author(s):

Sergio Ticul Alvarez Castañeda ◽

Patricia Cortés-Calva

Keyword(s):

Cytochrome C ◽

Cytochrome C Oxidase ◽

Genetic Distances ◽

Valid Species ◽

Bootstrap Support ◽

Oxidase Subunit ◽

Morphological Studies ◽

Subspecies Level ◽

Taxonomic Changes ◽

Morphological Differences

Scapanus latimanus is a species with many morphological differences among its populations. This variation is associated with multiple taxonomic changes at the species or subspecies level. This study incorporates genetic analyses and comparisons with previous morphological studies to propose a better understanding of the latimanus complex. Mitochondrial markers (cytochrome b; cytochrome c oxidase subunit I; and cytochrome c oxidase subunit III) were sequenced to construct a phylogeny for the subfamily Scalopinae in North America. Genetic distances ranged from 2.49 to 10.50 % among geographic areas. Results identified three monophyletic clades with high bootstrap support values. Based on our phylogenetic analysis and previous morphological analyses, we confirm S. anthonyi from San Pedro Mártir as a valid species and propose that S. occultus from southern California and northern Baja California peninsula be considered as a species

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Molecular phylogenetic position of Haplometroides intercaecalis (Digenea, Plagiorchiidae)

Acta Parasitologica ◽

10.1515/ap-2018-0062 ◽

2018 ◽

Vol 63 (3) ◽

pp. 522-526 ◽

Cited By ~ 1

Author(s):

Maria Isabel Müller ◽

Drausio Honorio Morais ◽

Reinaldo José da Silva

Keyword(s):

Dna Sequences ◽

Additional Data ◽

Ribosomal Gene ◽

Valid Species ◽

Phylogenetic Position ◽

Systematic Analysis ◽

Future Studies ◽

New Family ◽

Molecular Phylogenetic ◽

Morphological Differences

Abstract Three valid species of Haplometroides Odhner, 1910 parasitise snakes and amphisbaenians from South America. This study provides additional data on morphometric and molecular phylogenetic position inferred from the nuclear ribosomal gene 28S (partial). DNA sequences were isolated from Haplometroides intercaecalis Silva, Ferreira and Strüssmann, 2007 found in one specimen of Phalotris matogrossensis Lema, D’Agostini and Cappellari, 2005. Five digenean specimens were recovered from the esophagus of this snake, and four specimens were used for morphometrical studies and one specimen for molecular analysis. Phylogenetic analysis using maximum likelihood and Bayesian methods was conducted with sequences available for the order Plagiorchiida and its phylogenetic position places H. intercaecalis among the brachycoeliids Brachycoelium (Dujardin, 1845) Stiles and Hassall, 1898 and Parabrachycoelium Pérez-Ponce de León, Mendoza-Garfias, Razo-Mendivil and Parra-Olea, 2011, and the mesocoeliid Mesocoelium Odhner, 1910, not closely related to plagiorchids as expected. Due to morphological differences among these families, it may be necessary to create a new family to accommodate Haplometroides spp. However, more genera/taxa as well as other molecular markers should be added in future studies to confirm our results and resolve this matter. This is the first phylogenetic positioning of digeneans of the genus Haplometroides, contributing to the systematic analysis of the helminthological biodiversity of Neotropical snakes.

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Fishes collected during the 2017 MarineGEO assessment of Kāne‘ohe Bay, O‘ahu, Hawai‘i

Journal of the Marine Biological Association of the United Kingdom ◽

10.1017/s0025315420000417 ◽

2020 ◽

Vol 100 (4) ◽

pp. 607-637

Author(s):

Lynne R. Parenti ◽

Diane E. Pitassy ◽

Zeehan Jaafar ◽

Kirill Vinnikov ◽

Niamh E. Redmond ◽

...

Keyword(s):

Smithsonian Institution ◽

Genetic Distances ◽

Taxonomic Identification ◽

Tissue Samples ◽

Long Term Storage ◽

Cytochrome Oxidase I Gene ◽

Mitochondrial Cytochrome Oxidase ◽

Term Storage ◽

I Gene

AbstractWe report the results of a survey of the fishes of Kāne‘ohe Bay, O‘ahu, conducted in 2017 as part of the Smithsonian Institution MarineGEO Hawaii bioassessment. We recorded 109 species in 43 families. The most speciose families were Acanthuridae (11 species), Gobiidae (11 species), Pomacentridae (10) and Chaetodontidae (9 species). Nine of the species that we collected are known or suspected to be introduced to the Hawaiian Islands. Specimens were identified, measured and photographed. All specimen vouchers were fixed in formalin and ultimately transferred to 75% ethanol for long-term storage. For nearly all species, we took multiple tissue samples from specimen vouchers prior to formalin-fixation; we preserved tissues in 95% ethanol and then stored them at −80°C. The 5′-end of the mitochondrial cytochrome oxidase I gene (mtCOI) was sequenced for 94 species to confirm their taxonomic identification. Using these barcode sequences, we also measured genetic distances between collected individuals and their conspecifics from other localities outside Hawaii to verify the hypothesis that Hawaiian populations of species broadly distributed throughout the Indo-Pacific may be genetically distinct. We present select case studies to demonstrate the potential for undiscovered endemism in the Hawaiian fish biota.

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Mitochondrial DNA sequence evidence supporting the recognition of a new North Atlantic Pseudostichopus species (Echinodermata: Holothuroidea)

Journal of the Marine Biological Association of the United Kingdom ◽

10.1017/s002531540401046xh ◽

2004 ◽

Vol 84 (5) ◽

pp. 1077-1084 ◽

Cited By ~ 4

Author(s):

Francisco A. Solís-Marín ◽

David S.M. Billett ◽

Joanne Preston ◽

Alex D. Rogers

Keyword(s):

Dna Sequences ◽

Mitochondrial Gene ◽

Distinct Species ◽

Molecular Study ◽

Morphological Characters ◽

Coi Gene ◽

Species Status ◽

Separate Species ◽

The Family ◽

A New Species

A new species of the synallactid sea cucumber genus Pseudostichopus is described, P. aemulatus sp. nov., based on genetic (DNA sequences of the mitochondrial gene Cytochrome Oxidase I [COI] gene) and morphological characters. A comparative molecular study with two other species of the same genus (P. villosus and P. mollis) and from a different family (Isostichopus fuscus) was carried out in order to clarify its taxonomic identity. The nucleotide distance between P. aemulatus sp. nov. and P. villosus and P. mollis is sufficient to support distinct species status. The estimated difference in the number of amino acids, coded for by a partially sequenced COI gene, within the species of the family Synallactidae ranged from 4 to 18. The phylogenetic analysis clearly supports separate species status of these sympatric morphotypes, as indicated by the morphological analysis.

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Systematics of the Boana semilineata species group (Anura: Hylidae), with a description of two new species from Amazonian Ecuador

Zoological Journal of the Linnean Society ◽

10.1093/zoolinnean/zlaa002 ◽

2020 ◽

Vol 190 (1) ◽

pp. 149-180

Author(s):

Marcel A Caminer ◽

Santiago R Ron

Keyword(s):

Dna Sequences ◽

Phylogenetic Relationships ◽

Species Group ◽

Valid Species ◽

Undescribed Species ◽

Phenotypic Characters ◽

Species Complexes ◽

Candidate Species ◽

Amazonian Ecuador ◽

First Time

Abstract The combination of genetic and phenotypic characters for species delimitation has allowed the discovery of many undescribed species of Neotropical amphibians. In this study, we used DNA sequences (genes 12S, 16S, ND1 and COI) and morphologic, bioacoustic and environmental characters of the Boana semilineata group to evaluate their phylogenetic relationships and assess their species limits. In addition, we included DNA sequences of several species of Boana to explore cryptic diversity in other groups. We found three Confirmed Candidate Species (CCS) within the B. semilineata group. Holotype examination of Hyla appendiculata shows that it is a valid species that corresponds to one of the CCS, which is here transferred to Boana. We describe the two remaining CCS. Our phylogeny highlights a number of secondary but meaningful observations that deserve further investigation: (1) populations of B. pellucens from northern Ecuador are more closely related to B. rufitela from Panama than to other Ecuadorian populations of B. pellucens; (2) we report, for the first time, the phylogenetic relationships of B. rubracyla showing that it is closely related to B. rufitela and B. pellucens; and (3) B. cinerascens and B. punctata form two species complexes consisting of several unnamed highly divergent lineages. Each of these lineages likely represents an undescribed species.

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Systematic relationships of the Guianan brush-tailed rat (Isothrix sinnamariensis ) and its first occurrence in Guyana / Systématique du rat à queue en brosse de Guyane ( Isothrix sinnamariensis ) et première découverte en Guyane

Mammalia ◽

10.1515/mamm.2006.007 ◽

2006 ◽

Vol 70 (1-2) ◽

Cited By ~ 1

Author(s):

Burton K. Lim ◽

Mark D. Engstrom ◽

John C. Patton ◽

John W. Bickham

Keyword(s):

Dna Sequences ◽

French Guiana ◽

Tropical Rainforest ◽

Sequence Difference ◽

Separate Species ◽

Adult Females ◽

First Occurrence ◽

Systematic Relationships ◽

Average Sequence ◽

Morphological Differences

AbstractIsothrix sinnamariensis was originally described and known only from French Guiana. We document the first occurence of this species from Guyana. A single sub-adult male was collected in lowland tropical rainforest near the headwaters of the Essequibo River. Although smaller in external and cranial size than the two adult females of the type description, our third known specimen represents the basal lineage to the type-series clade, with an average sequence difference of 1.72% based on cytochrome b mitochondrial DNA sequences. However, the degree of morphological and genetic divergence (2.67%) between I. sinnamariensis and its sister taxon I. pagurus is substantially less than the chromosomal differences originally used to distinguish them as two separate species. In contrast, distinctive karyotypes, morphological differences, and higher levels of mtDNA divergence (13.48%) between the other two species recognized, I. negrensis that was recently separated from I. bistriata , suggest an earlier and deeper diversification for these taxa.

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Using more than the oldest fossils: Dating Osmundaceae by three Bayesian clock approaches

10.1101/010496 ◽

2014 ◽

Author(s):

Guido Grimm ◽

Pashalia Kapli ◽

Benjamin Bomfleur ◽

Stephen McLoughlin ◽

Susanne S Renner

Keyword(s):

Dna Sequences ◽

Fossil Record ◽

Morphological Characters ◽

Genetic Distances ◽

Total Evidence ◽

Extinction Rates ◽

Sister Clade ◽

Extant Species ◽

Dating Methods ◽

Divergence Dates

A major concern in molecular clock dating is how to use information from the fossil record to calibrate genetic distances from DNA sequences. Here we apply three Bayesian dating methods that differ in how calibration is achieved--"node dating" (ND) in BEAST, "total evidence" (TE) dating in MrBayes, and the "fossilized birth-death" (FBD) in FDPPDiv--to infer divergence times in the Osmundaceae or royal ferns. Osmundaceae have 13 species in four genera, two mainly in the Northern Hemisphere and two in South Africa and Australasia; they are the sister clade to the remaining leptosporangiate ferns. Their fossil record consists of at least 150 species in ~17 genera and three extinct families. For ND, we used the five oldest fossils, while for TE and FBD dating, which do not require forcing fossils to nodes and thus can use more fossils, we included up to 36 rhizome and frond compression/impression fossils, which for TE dating were scored for 33 morphological characters. We also subsampled 10%, 25%, and 50% of the 36 fossils to assess model sensitivity. FBD-derived divergence dates were generally greater than ages inferred from ND dating; two of seven TE-derived ages agreed with FBD-obtained ages, the others were much younger or much older than ND or FBD ages. We favour the FBD-derived ages because they best match the Osmundales fossil record (including Triassic fossils not used in our study). Under the preferred model, the clade encompassing extant Osmundaceae (and many fossils) dates to the latest Palaeozoic to Early Triassic; divergences of the extant species occurred during the Neogene. Under the assumption of constant speciation and extinction rates, FBD yielded 0.0299 (0.0099--0.0549) and 0.0240 (0.0039--0.0495) for these rates, whereas neontological data yielded 0.0314 and 0.0339. However, FBD estimates of speciation and extinction are sensitive to violations in the assumption of continuous fossil sampling, therefore these estimates should be treated with caution.

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Konservasi Genetik Ikan Kakap Putih (Lates calcarifer, Bloch, 1790) Melalui Pendekatan DNA Barcoding dan Analisis Filogenetik di Sungai Kumbe Merauke Papua

Jurnal Kelautan Tropis ◽

10.14710/jkt.v24i2.10760 ◽

2021 ◽

Vol 24 (2) ◽

pp. 141-150

Author(s):

Dandi Saleky ◽

Muhammad Dailami

Keyword(s):

Fisheries Management ◽

Dna Sequences ◽

Economic Value ◽

Genetic Data ◽

Swim Bladder ◽

Molecular Approach ◽

Lates Calcarifer ◽

Cytochrome Oxidase I Gene ◽

Management And Conservation ◽

I Gene

Genetic data is very important as the basis for fisheries management and conservation related to connectivity between regions and population structure. White snapper Fish is one of the fish that has high economic value which is utilized either by its meat or by its swim bladder. This research was aimed to identify the species of white snapper fish were collected from the Kumbe River, Merauke Regency, Papua using the Cytochrome Oxidase I gene. The results shows that this sample is a species of Lates calcarifer, Bloch, 1790 with 100% similarity. The haplotype of white snapper fish from Merauke has similarities with the haplotype from Australia, Malaysia and China, this indicating that there is gene flow and connectivity among those locations. The phylogenetic tree explains the grouping of species based on genetic distance and the level of DNA Sequences similarities. Molecular approach can be used in the management and conservation of fish with high economic value.

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Genetic analysis reveals Finnish Formica fennica populations do not form a separate genetic entity from F. exsecta

PeerJ ◽

10.7717/peerj.6013 ◽

2018 ◽

Vol 6 ◽

pp. e6013 ◽

Cited By ~ 4

Author(s):

Sanja Maria Hakala ◽

Perttu Seppä ◽

Maria Heikkilä ◽

Pekka Punttila ◽

Jouni Sorvari ◽

...

Keyword(s):

Genetic Variation ◽

Morphological Characters ◽

Coi Gene ◽

Species Status ◽

Separate Species ◽

Mitochondrial Coi ◽

Recent Addition ◽

Morphological Differences ◽

Dna Microsatellite ◽

Dna Microsatellite Markers

Coptoformica Müller, 1923 is a subgenus of Formica Linnaeus, 1758 that consists of c. a dozen species of ants that typically inhabit open grassy habitats and build small nest mounds. The most recent addition to the group is Formica fennica Seifert, 2000. The description was based on morphological characters, but the species status has not been confirmed by molecular methods. In this study, we use thirteen DNA microsatellite markers and a partial mitochondrial COI gene sequence to assess the species status of F. fennica, by comparing the genetic variation among samples identified as F. fennica and six other boreal Formica (Coptoformica) species. Most of the species studied form separate, discontinuous clusters in phylogenetic and spatial analyses with only little intraspecific genetic variation. However, both nuclear and mitochondrial markers fail to separate the species pair F. exsecta Nylander, 1846 and F. fennica despite established morphological differences. The genetic variation within the F. exsecta/fennica group is extensive, but reflects spatial rather than morphological differences. Finnish F. fennica populations studied so far should not be considered a separate species, but merely a morph of F. exsecta.

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