New acoustic and molecular data shed light on the poorly known Amazonian frog Adenomera simonstuarti (Leptodactylidae): implications for distribution and conservation

Adenomera simonstuarti is a poorly known species complex inhabiting western Amazonia. Here we reevaluate the species diversity within this complex based on previously documented and newly acquired molecular and phenotypic data. We also redescribe the calling pattern of the nominal species based on the original recording (Peru) and a new recording (Brazil). Our results indicate eight geographically structured genetic lineages and the nominal species with a multi-note call pattern. This is the first association of calls and DNA sequence from a voucher specimen, thereby enabling the assignment of A. simonstuarti to one specific lineage within the complex. The multi-note call was not previously reported and represents an important additional diagnostic character within Adenomera. The geographic distribution of A. simonstuarti is substantially narrowed down to the southwestern portion of the entire geographic range recognized for the complex. The lack of taxonomic resolution in the complex is a major conservation concern by preventing us from evaluating the potential threats and extinction risks of each of the lineages. Future research should follow the protocol of combining calls and DNA sequences associated with voucher specimens as a means to address the taxonomic status of genetic lineages within the A. simonstuarti complex.

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Unraveling the species diversity and relationships in the Leptodactylus mystaceus complex (Anura: Leptodactylidae), with the description of three new Brazilian species

Zootaxa ◽

10.11646/zootaxa.4779.2.1 ◽

2020 ◽

Vol 4779 (2) ◽

pp. 151-189 ◽

Cited By ~ 5

Author(s):

LEANDRO A. DA SILVA ◽

FELIPE M. MAGALHÃES ◽

HANS THOMASSEN ◽

FELIPE S. F. LEITE ◽

ADRIAN A. GARDA ◽

...

Keyword(s):

Species Diversity ◽

Dna Sequences ◽

Taxonomic Status ◽

Molecular Data ◽

Species Discrimination ◽

Nominal Species ◽

South American ◽

Geographic Ranges ◽

The Andes ◽

Three New Species

Members of the Leptodactylus mystaceus species complex are widely distributed in forests and open formations of South America east of the Andes. Species of the complex are morphologically similar or indistinguishable among each other, but acoustic data have been the cornerstone for species discrimination across their geographic ranges. In this paper, we re-examine the monophyly, species diversity, and relationships in the L. mystaceus complex on the basis of morphology, coloration, acoustics, and DNA sequences. Morphological and color patterns originally used to the allocation of species to the L. mystaceus complex are also reassessed. Our results revealed three new species from the Brazilian Atlantic Forest and Cerrado, which are named and described herein, based mainly on acoustic and molecular data. Populations assigned to the lineage widely distributed across the South American Dry Diagonal (DD), reported in this study as L. cf. mystaceus, is likely paraphyletic with respect to the nominal species (Amazonian lineage), but additional data are still needed to address the taxonomic status of the DD lineage.

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A molecular phylogeny of the “Madascincus polleni species complex”, with description of a new species of scincid lizard from the coastal dune area of northern Madagascar

Zootaxa ◽

10.11646/zootaxa.2876.1.1 ◽

2011 ◽

Vol 2876 (1) ◽

pp. 1 ◽

Cited By ~ 8

Author(s):

AURÉLIEN MIRALLES ◽

JÖRN KÖHLER ◽

FRANK GLAW ◽

MIGUEL VENCES

Keyword(s):

Dna Sequences ◽

Species Complex ◽

Nuclear Dna ◽

Taxonomic Status ◽

Nominal Species ◽

Morphological Examination ◽

Closely Related Species ◽

A New Species ◽

Evolutionary Lineages ◽

Dune Area

The present paper constitutes a study on a taxonomically confusing group of closely related species belonging to the Malagasy skink genus Madascincus, currently encompassing the nominal species M. polleni, M. intermedius and M. stumpffi. Based on combined analyses of mitochondrial and nuclear DNA sequences (ND1 and RAG2 genes, respectively), and morphological examination, we provide evidence for the existence of at least four distinct evolutionary lineages within this complex: Madascincus stumpffi; Madascincus arenicola sp. nov. from northern Madagascar; and two cryptic species morphologically similar to the name-bearing types of M. polleni and M. intermedius. The two latter species, although genetically distinct, appear to be morphologically indistinguishable and their taxonomic status cannot be resolved until a better sampling will be available.

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New insight into the taxonomic resolution of the genus Bythotrephes Leydig (Crustacea: Cladocera) based on molecular data from Central Europe

Scientific Reports ◽

10.1038/s41598-021-02648-7 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Maciej Karpowicz ◽

Magdalena Świsłocka ◽

Joanna Moroz ◽

Łukasz Sługocki

Keyword(s):

Genetic Analysis ◽

Central Europe ◽

Taxonomic Status ◽

Molecular Data ◽

Coi Gene ◽

Taxonomic Resolution ◽

Monotypic Genus ◽

Mtdna Coi ◽

Xix Century ◽

Insight Into

AbstractThe taxonomic status of the genus Bythotrephes Leydig (Crustacea: Cladocera) has been debated since the second half of the XIX century. The most widespread view of recent decades has been that Bythotrephes is a monotypic genus, which was support by preliminary molecular data. However, the recent detailed morphological revision of this genus clearly distinguishes at least seven species. Therefore, we performed a multi-lake survey in Central Europe to give new insight into the taxonomic status of Bythotrephes by combining genetic analysis with traditional morphology-based taxonomy. Based on the morphology we identified two species in Central Europe, B. brevimanus and B. lilljeborgi, as well as hybrid forms. For the genetic analysis, we used newly obtained 113 sequences of mtDNA COI gene of the 535-bp length Bythotrephes from Central Europe and sequences downloaded from GenBank. There were no significant differences between all analyzed sequences, which supports the hypothesis that Bythotrephes is a monotypic genus, with only one highly polymorphic species. On the other hand, the results of our work could point out that the COI gene is insufficient to evaluate the taxonomic status of Bythotrephes. Nonetheless, we have identified 29 new haplotypes of mtDNA COI, and one which was the same as the haplotype found in North America and Finland. Furthermore, this haplotype was the source variant from which most other haplotypes were derived.

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Split distribution, biogeography and morphological and genetic diversity of the Iberobathynellini Tribe in the family Parabathynellidae (Crustacea, Malacostraca, Bathynellacea)

Contributions to Zoology ◽

10.1163/18759866-bja10024 ◽

2022 ◽

pp. 1-61

Author(s):

Ana Isabel Camacho ◽

Paloma Mas-Peinado ◽

E. Karen López-Estrada ◽

Beatriz A. Dorda ◽

Isabel Rey

Keyword(s):

North America ◽

Cryptic Species ◽

Plate Tectonics ◽

Taxonomic Status ◽

Molecular Data ◽

Molecular Dating ◽

Nominal Species ◽

The Family ◽

Well Differentiated ◽

Morphological And Molecular Data

Abstract The “Iberobathynella group”, or Iberobathynellini tribe, is a complex of six genera consisting of 33 nominal species and several cryptic species with an amphiatlantic distribution (in Europe, North Africa and North America). A modern systematic revision of this group of subterranean crustaceans is presented here. A phylogenetic and biogeographic study using morphological and molecular data (mitocondrial coi and nuclear 18S) was carried out and allowed to a) re-evaluate the taxonomic status and validity of previously erected subtribes, genera and subgenera that show congruence in the data; b) assess whether the identified mitochondrial lineages represent cryptic species; c) provide a plausible phylogenetic hypothesis for the relationships within Iberobathynellini and with the other two genera of the family Parabathynellidae that inhabit North America and Europe (Montanabathynella and Parabathynella, respectively); d) propose a plausible temporal and historical framework (paleobiogeographic scenario) for the diversification and evolution of the Iberobathynellini tribe based on the current distribution of morphotypes and their estimated times of divergence. Our results show that in parabathynellids, molecular and morphological divergences are not always congruent. Subtribe and subgenus are invalid categories so they must be eliminated. Paraiberobathynella genus needs to be revisited. The molecular dating results support the early divergence of the Iberobathynellini Tribe (Upper Cretaceous, around 78 Mya) and the vicariance by plate tectonics as main factor to explain the amphi-Atlantic distribution shown by this ancient subterranean crustacean group. Since there are species morphologically very similar to I. magna and I. imuniensis, but genetically different, we can ensure the existence of at least three cryptic species. Texanobathynella is undoubtedly a valid genus distinct from Iberobathynella. Montanabathynella and Parabathynella are two well-differentiated genera closely related to the Iberobathynellini tribe.

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Craniodental morphology and phylogeny of marsupials

10.31233/osf.io/rph78 ◽

2021 ◽

Author(s):

Robin M. D. Beck ◽

Robert Voss ◽

Sharon Jansa

Keyword(s):

Phylogenetic Analysis ◽

Dna Sequences ◽

Morphological Characters ◽

Molecular Data ◽

Morphological Data ◽

Future Research ◽

Data Types ◽

Wide Range ◽

Morphological And Molecular Data ◽

Dense Sampling

The current literature on marsupial phylogenetics includes numerous studies based on analyses of morphological data with relatively limited sampling of Recent and fossil taxa, and many studies based on analyses of molecular data that include a dense sampling of Recent taxa, but relatively few that combine both data types. Another dichotomy in the marsupial phylogenetic literature is between studies that focus on New World taxa, others that focus on Sahulian taxa. To date, there has been no attempt to assess the phylogenetic relationships of the global marsupial fauna, based on combined analyses of morphology and molecular sequences, for a dense sampling of Recent and fossil taxa. For this report, we compiled morphological and molecular data from an unprecedented number of Recent and fossil marsupials. Our morphological data consist of 180 craniodental characters that we scored for 97 species representing every currently recognized Recent genus, 42 additional ingroup (crown-clade marsupial) taxa represented by well-preserved fossils, and 5 outgroups (non-marsupial metatherians). Our molecular data comprise 24.5 kb of DNA sequences from whole-mitochondrial genomes and six nuclear loci (APOB, BRCA1, GHR, RAG1, RBP3 and VWF) for 97 marsupial terminals (the same Recent taxa scored for craniodental morphology) and several placental and monotreme outgroups. The results of separate and combined analyses of these data using a wide range of phylogenetic methods support many currently accepted hypotheses of ingroup (marsupial) relationships, but they also underscore the difficulty of placing fossils with key missing data (e.g., †Evolestes), and the unique difficulty of placing others that exhibit mosaics of plesiomorphic and autapomorphic traits (e.g., †Yalkaparidon). Unique contributions of our study are (1) critical discussions and illustrations of marsupial craniodental morphology, including descriptions and illustrations of some features never previously coded for phylogenetic analysis; (2) critical assessments of relative support for many suprageneric clades; (3) estimates of divergence times derived from tip-and-node dating based on uniquely taxon-dense analyses; and (4) a revised, higher-order classification of marsupials accompanied by lists of supporting craniodental synapomorphies. Far from the last word on these topics, this report lays the foundation for future research that may be enabled by the discovery of new fossil taxa, better-preserved material of previously described taxa, novel morphological characters, and improved methods of phylogenetic analysis.

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The taxonomic status of Cryptobatrachus frogs (Anura: Hemiphractidae) from the Serranía del Perijá

Zootaxa ◽

10.11646/zootaxa.5068.2.5 ◽

2021 ◽

Vol 5068 (2) ◽

pp. 247-262

Author(s):

FABIO LEONARDO MEZA-JOYA ◽

ELIANA RAMOS ◽

FERNANDO J. M. ROJAS-RUNJAIC ◽

ANDRÉS OVALLE-PACHECO

Keyword(s):

Dna Sequences ◽

Genetic Divergence ◽

Morphological Traits ◽

Phylogenetic Analyses ◽

Taxonomic Status ◽

Molecular Data ◽

The Other ◽

Taxon Sampling ◽

Morphological Similarity ◽

Morphological And Molecular Data

The Neotropical frog genus Cryptobatrachus includes six currently recognized species distributed throughout the northern Andes in Colombia and Venezuela. Cryptobatrachus conditus, C. pedroruizi, and C. remotus were described from the Colombian and Venezuelan slopes of the Serranía del Perijá. Due to the great morphological similarity among these species, we re-assess their taxonomic status based on morphological and molecular data from types, topotypes, and specimens from localities referred to in the original descriptions of these species. Morphometric comparisons showed that all these species are virtually indistinguishable, although some subtle qualitative differences in morphological traits distinguish C. conditus from the other species. Phylogenetic analyses of DNA sequences found that C. remotus and C. pedroruizi are not reciprocally monophyletic and exhibit low genetic divergence (< 1 %). Therefore, C. remotus should be considered a junior synonym of C. pedroruizi. This work stresses the importance of comprehensive taxon sampling in poorly explored areas, especially between neighbouring countries.

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A new species of sinistral flatfish of the genus Chascanopsetta (Teleostei: Bothidae) from off Papua New Guinea, western Pacific Ocean

Zootaxa ◽

10.11646/zootaxa.4476.1.16 ◽

2018 ◽

Vol 4476 (1) ◽

pp. 168

Author(s):

PAKORN TONGBOONKUA ◽

MAO-YING LEE ◽

WEI-JEN CHEN

Keyword(s):

New Species ◽

Papua New Guinea ◽

Dna Sequences ◽

Taxonomic Status ◽

New Guinea ◽

Coi Gene ◽

Phylogenetic Position ◽

Nominal Species ◽

The West ◽

West Pacific

Left-eyed flounders of the genus Chascanopsetta Alcock 1894 (Bothidae) occur in the Indian, Pacific, and Atlantic oceans at depths ranging from 120 to 1500 meters. They possess some unique features in bothid fishes including a strongly compressed and elongated body and a tremendously large mouth. Currently, nine species of Chascanopsetta are recognized, and three of them (C. micrognatha Amaoka & Yamamoto 1984, C. lugubris Alcock 1894 and C. prognatha Norman 1939) are distributed in the West Pacific. We collected 25 specimens of Chascanopsetta during 11 biodiversity expeditions carried out mainly in the West Pacific. Among them, eight specimens taken off Papua New Guinea present morphological features that differ from those of the three nominal species known in the West Pacific. In this study, we examined these eight specimens of unknown affinity and compared their morphology to that of specimens of other congeneric species. Results of these comparisons showed that these specimens represent an undescribed species of Chascanopsetta, named herein, C. novaeguineae sp. nov.. The new species resembles C. elski Foroshchuk 1991, which is known only from the Saya de Malha Bank in the western Indian Ocean, in having a high number of gill rakers (> 13). However, the combination of the following characters further distinguishes C. novaeguineae sp. nov. from C. elski: longer jaws, narrower interorbital width, and number of pseudobranches (21–25 vs. 26–27). The DNA sequences from the mitochondrial cytochrome oxidase subunit I (COI) gene from C. novaeguineae sp. nov. and other species were obtained and compared to confirm its taxonomic status and to infer its tentative phylogenetic position within the Chascanopsetta.

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Taxonomic resolution of Stylonychia notophora (Alveolata, Ciliophora, Hypotricha) sensu Sapra and Dass 1970 using an integrative approach

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijsem.0.004207 ◽

2020 ◽

Vol 70 (6) ◽

pp. 3939-3952

Author(s):

Harpreet Kaur ◽

Shashi ◽

Alan Warren ◽

Ram Krishan Negi ◽

Komal Kamra

Keyword(s):

18S Rdna ◽

Species Delimitation ◽

Indian Population ◽

Taxonomic Status ◽

Molecular Data ◽

Taxonomic Resolution ◽

Integrative Approach ◽

Rdna Sequences ◽

18S Rdna Sequences ◽

River Yamuna

The spirotrichean ciliate Stylonychia notophora has previously been recorded in India although the descriptions are lacking in detail. It has been suggested several times that the Indian population, S. notophora sensu Sapra and Dass, 1970 collected along the Delhi stretch of the River Yamuna, is identical to Tetmemena pustulata, but this has never been confirmed due to insufficient data for the former. The present study includes detailed descriptions (classical and molecular) of populations of Tetmemena isolated from six locations along the River Yamuna, India. These include four from the Delhi stretch including that from which Sapra and Dass, 1970 isolated their population of S. notophora. Due to the lack of a sufficiently detailed description, the taxonomic status of S. notophora sensu Sapra and Dass, 1970 was not clear. Comparisons among the populations isolated in the present study with previous descriptions of T. pustulata and S. notophora sensu Sapra and Dass, 1970 show only minor differences in morphometry, morphogenesis and in 18S rDNA sequences. The 18S rDNA sequences of all six populations had 99% similarity to both T. pustulata and S. notophora. These findings support the contention that S. notophora sensu Sapra and Dass, 1970 was misidentified and is a population of T. pustulata. This study supports the need for adopting an integrative approach based on morphological, morphogenetic and molecular data in order to understand species delimitation in ciliated protists.

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Biology of tiny animals: three new species of minute salamanders (Plethodontidae:Thorius) from Oaxaca, Mexico

PeerJ ◽

10.7717/peerj.2694 ◽

2016 ◽

Vol 4 ◽

pp. e2694 ◽

Cited By ~ 7

Author(s):

Gabriela Parra-Olea ◽

Sean M. Rovito ◽

Mario García-París ◽

Jessica A. Maisano ◽

David B. Wake ◽

...

Keyword(s):

New Species ◽

Dna Sequences ◽

Taxonomic Status ◽

Single Species ◽

Molecular Data ◽

Future Studies ◽

Sierra Madre ◽

Disjunct Populations ◽

Sierra Madre Del Sur ◽

Three New Species

We describe three new species of minute salamanders, genusThorius, from the Sierra Madre del Sur of Oaxaca, Mexico. Until now only a single species,T. minutissimus, has been reported from this region, although molecular data have long shown extensive genetic differentiation among geographically disjunct populations. AdultThorius pinicolasp. nov.,T. longicaudussp. nov., andT. tlaxiacussp. nov. are larger thanT. minutissimusand possess elliptical rather than oval nostrils;T. pinicolaandT. longicaudusalso have longer tails. All three new species occur west of the range ofT. minutissimus, which has the easternmost distribution of any member of the genus. The new species are distinguished from each other and from other namedThoriusin Oaxaca by a combination of adult body size, external morphology and osteology, and by protein characters (allozymes) and differences in DNA sequences. In addition, we redescribeT. minutissimusand a related species,T. narisovalis, to further clarify the taxonomic status of Oaxacan populations and to facilitate future studies of the remaining genetically differentiatedThoriusthat cannot be satisfactorily assigned to any named species. Populations of all five species considered here appear to have declined dramatically over the last one or two decades and live specimens are difficult to find in nature.Thoriusmay be the most endangered genus of amphibians in the world. All species may go extinct before the end of this century.

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‘Barcode fishing’ for archival DNA from historical type material overcomes taxonomic hurdles, enabling the description of a new frog species

Scientific Reports ◽

10.1038/s41598-020-75431-9 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Mark D. Scherz ◽

Safidy M. Rasolonjatovo ◽

Jörn Köhler ◽

Loïs Rancilhac ◽

Andolalao Rakotoarison ◽

...

Keyword(s):

Dna Sequences ◽

Sequence Data ◽

High Elevation ◽

Degraded Dna ◽

Taxonomic Resolution ◽

Type Specimens ◽

Extrinsic Factors ◽

Diagnostic Characters ◽

Genetic Lineages ◽

Intrinsic Factors

Abstract Taxonomic progress is often hindered by intrinsic factors, such as morphologically cryptic species that require a broad suite of methods to distinguish, and extrinsic factors, such as uncertainties in the allocation of scientific names to species. These uncertainties can be due to a wide variety of factors, including old and poorly preserved type specimens (which contain only heavily degraded DNA or have lost important diagnostic characters), inappropriately chosen type specimens (e.g. juveniles without diagnostic characters) or poorly documented type specimens (with unprecise, incorrect, or missing locality data). Thanks to modern sequencing technologies it is now possible to overcome many such extrinsic factors by sequencing DNA from name-bearing type specimens of uncertain assignment and assigning these to known genetic lineages. Here, we apply this approach to frogs of the Mantidactylus ambreensis complex, which was recently shown to consist of two genetic lineages supported by concordant differentiation in mitochondrial and nuclear genes. These lineages co-occur on the Montagne dʼAmbre Massif in northern Madagascar but appear to have diverged in allopatry. We use a recently published bait set based on three mitochondrial markers from all known Malagasy frog lineages to capture DNA sequences from the 127-year-old holotype of Mantidactylus ambreensis Mocquard, 1895. With the obtained sequences we are able to assign the name M. ambreensis to the lowland lineage, which is rather widespread in the rainforests of northern Madagascar, leaving the microendemic high-elevation lineage on Montagne d’Ambre in north Madagascar in need of description. We describe this species as Mantidactylus ambony sp. nov., differing from M. ambreensis in call parameters and a smaller body size. Thus, using target enrichment to obtain DNA sequence data from this old specimen, we were able to resolve the extrinsic (nomenclatural) hindrances to taxonomic resolution of this complex. We discuss the broad-scale versatility of this ‘barcode fishing’ approach, which can draw on the enormous success of global DNA barcoding initiatives to quickly and efficiently assign type specimens to lineages.

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