scholarly journals DNA-based diversity assessment reveals a new coral barnacle, Cantellius alveoporae sp. nov. (Balanomorpha: Pyrgomatidae) exclusively associated with the high latitude coral Alveopora japonica in the waters of southern Korea

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11284
Author(s):  
Hyun Kyong Kim ◽  
Benny K.K. Chan ◽  
Sung Joon Song ◽  
Jong Seong Khim
Keyword(s):  
Cryptic Species ◽  
Dna Sequences ◽  
Distinct Species ◽  
Andaman Sea ◽  
Morphological Examination ◽  
Species Identity ◽  
Diversity Assessment ◽  
Molecular Studies ◽  
Southern Korea ◽  
Specialist Species

In the present study, the Indo-Pacific coral associated barnacle Cantellius euspinulosum (Broch, 1931) was found to have cryptic species in Korea, Taiwan and other regions based on molecular studies. However, the original specimens of C. euspinulosum from Broch have not been previously described or illustrated, making it difficult to assign which cryptic species to the original C. euspinulosum. The original specimen of C. euspinulosum was examined and illustrated here, and the species identity of C. cf. euspinulosum collected from Jejudo Island in the present study and other cryptic species (based on literature illustrations) in the Indo-Pacific were evaluated.C. euspinulosum from Singapore, Java, Mergui Archipelago in Andaman Sea and Nha Trang represented the C. euspinulosum identified by Broch (1931). It is a generalist on Acropora, Favia, Favites, Leptoria, Montipora, Pachyseris and Pocillipora corals and distributed in the Indo-Pacific region. Morphological examination and DNA sequencing (COI, 12S DNA sequences) in the present study showed that C. cf. euspinulosum from Jejudo Island, Korea represents a distinct species, herein named C. alveoporae sp. nov. Cantellius alveroporae sp. nov. is a specialist species that only grows on Alveopora and also present in Palau, and Ogasawara Island in Japan. Cantellius cf. euspinuloum in Taiwan, the Moscos Island, and Australia belong to several other distinct species awaiting further morphological and molecular studies. At least five cryptic species of C. euspinulosum were identified in the present study, including both specialist and generalists.

scholarly journals Genetic diversity and species identity of the critically endangered Rote Island snake-necked turtle, Chelodina mccordi Rhodin, 1994

2021 ◽  
Vol 948 (1) ◽  
pp. 012001
Author(s):  
N A Devi ◽  
R Eprilurahman ◽  
D S Yudha ◽  
S Raharjo ◽  
M As-Singkily ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Dna Sequences ◽  
Captive Breeding ◽  
Haplotype Diversity ◽  
Genetic Distances ◽  
Ex Situ ◽  
Species Identity ◽  
Natural Habitats ◽  
Diversity Assessment

Abstract The endemic Chelodina mccordi is considered extinct in the wild; however, ex-situ populations are thriving and sampled for our genetic diversity assessment. We used three sequences resulting from blood and tissue samples of five individual turtles amplified for 650-bp cytochrome oxidase I (COI) fragment of the mitochondrial DNA. We analysed a total of 30 barcoding DNA sequences for phylogenetic relationships and genetic distances among Chelodina spp. Nucleotide diversity of eight C. mccordi samples is 0.007 ± 0.001 with a haplotype diversity of 0.893 ± 0.086. All these samples form a monophyletic clade that is sister to a clade of Australian and New Guinean long-necked turtles. Genetic distances calculated using Kimura 2-paramater model among C. mccordi sequences range between 0.2% and 1.5%, while a few others are without distance. The shortest genetic distance is between individuals from Rote Island, whereas the longest distance was found between individuals, each of which was derived from parental stocks originating in Rote and Timor islands. A genetic distance of 1.1% - 1.5% is likely to denote distinction at subspecies level. Results of this study could help in reintroducing captive individuals into their natural habitats. Thus, captive breeding programme of this species may help its conservation.

Detection of hybrid Pyganodon grandis and P. lacustris (Bivalvia: Unionidae) using F- and M-type mitochondrial DNA sequences and geometric morphometrics

2020 ◽  
Vol 86 (3) ◽  
pp. 233-239 ◽  
Author(s):  
Kate C Beauchamp ◽  
Tyler W Beyett ◽  
Mariah W Scott ◽  
David T Zanatta
Keyword(s):  
Dna Sequences ◽  
Lake Michigan ◽  
Morphological Variability ◽  
Distinct Species ◽  
Shell Shape ◽  
Species Identity ◽  
Mt Dna ◽  
Pyganodon Grandis ◽  
Coi Sequences ◽  
Putative Hybrids

ABSTRACT Pyganodon grandis and P. lacustris, widespread and common species in North America, are known to co-occur across parts of their distributions. These mussels are genetically distinguishable with a sequence divergence between 9% and 13% for the mitochondrial (mt) DNA barcoding region, cytochrome c oxidase subunit I (COI), which is well beyond thresholds for distinct species. The objectives of this study were to (1) confirm the presence of two genetically distinct species (P. grandis and P. lacustris) in Font Lake and Lake Geneserath on Beaver Island in northern Lake Michigan, (2) identify hybrids using mitogenotype mismatch and (3) compare species and populations morphometrically. Of the 212 specimens sequenced, 146 (68.9%) were found to be heteroplasmic, with successful amplifications of both maternally (F-type, from mantle tissue) and paternally (M-type, from gonad tissue) inherited mt DNA sequences. Mismatches in species identity of the F- and M-type COI sequences were found in 22 specimens (15.1% of heteroplasmic specimens), with these being considered putative hybrids. Geometric morphometric analyses of shell shape reliably differentiated specimens by species (identified using COI sequences) and between lakes, correctly assigning 97.4% of homoplasmic and heteroplasmic specimens with matching mitogenomes to both species and lake of origin. The shape of putative hybrids generally resembled those of the F-type mt DNA sequence that was recovered. This study confirms that hybridization does occur between sympatric Pyganodon species. Additionally, our results reemphasize the value of modern morphometric techniques for distinguishing among species and populations with overlapping morphological variability.

scholarly journals Rapid, large-scale species discovery in hyperdiverse taxa using 1D MinION sequencing

BMC Biology ◽  
2019 ◽  
Vol 17 (1) ◽  
Author(s):  
Amrita Srivathsan ◽  
Emily Hartop ◽  
Jayanthi Puniamoorthy ◽  
Wan Ting Lee ◽  
Sujatha Narayanan Kutty ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Large Scale ◽  
Low Cost ◽  
Small Body ◽  
Small Subset ◽  
Similar Species ◽  
Large Species ◽  
Morphological Examination ◽  
Species Discovery ◽  
Short Period

Abstract Background More than 80% of all animal species remain unknown to science. Most of these species live in the tropics and belong to animal taxa that combine small body size with high specimen abundance and large species richness. For such clades, using morphology for species discovery is slow because large numbers of specimens must be sorted based on detailed microscopic investigations. Fortunately, species discovery could be greatly accelerated if DNA sequences could be used for sorting specimens to species. Morphological verification of such “molecular operational taxonomic units” (mOTUs) could then be based on dissection of a small subset of specimens. However, this approach requires cost-effective and low-tech DNA barcoding techniques because well-equipped, well-funded molecular laboratories are not readily available in many biodiverse countries. Results We here document how MinION sequencing can be used for large-scale species discovery in a specimen- and species-rich taxon like the hyperdiverse fly family Phoridae (Diptera). We sequenced 7059 specimens collected in a single Malaise trap in Kibale National Park, Uganda, over the short period of 8 weeks. We discovered > 650 species which exceeds the number of phorid species currently described for the entire Afrotropical region. The barcodes were obtained using an improved low-cost MinION pipeline that increased the barcoding capacity sevenfold from 500 to 3500 barcodes per flowcell. This was achieved by adopting 1D sequencing, resequencing weak amplicons on a used flowcell, and improving demultiplexing. Comparison with Illumina data revealed that the MinION barcodes were very accurate (99.99% accuracy, 0.46% Ns) and thus yielded very similar species units (match ratio 0.991). Morphological examination of 100 mOTUs also confirmed good congruence with morphology (93% of mOTUs; > 99% of specimens) and revealed that 90% of the putative species belong to the neglected, megadiverse genus Megaselia. We demonstrate for one Megaselia species how the molecular data can guide the description of a new species (Megaselia sepsioides sp. nov.). Conclusions We document that one field site in Africa can be home to an estimated 1000 species of phorids and speculate that the Afrotropical diversity could exceed 200,000 species. We furthermore conclude that low-cost MinION sequencers are very suitable for reliable, rapid, and large-scale species discovery in hyperdiverse taxa. MinION sequencing could quickly reveal the extent of the unknown diversity and is especially suitable for biodiverse countries with limited access to capital-intensive sequencing facilities.

scholarly journals Mitochondrial phylogeography of baboons (Papiospp.) – Indication for introgressive hybridization?

2009 ◽  
Vol 9 (1) ◽  
Author(s):  
Dietmar Zinner ◽  
Linn F Groeneveld ◽  
Christina Keller ◽  
Christian Roos
Keyword(s):  
Phylogenetic Relationships ◽  
Evolutionary History ◽  
Introgressive Hybridization ◽  
Distinct Species ◽  
Eastern Africa ◽  
East African ◽  
Hamadryas Baboons ◽  
Olive Baboons ◽  
Initial Separation ◽  
Molecular Studies

Abstract Background Baboons of the genus Papio are distributed over wide ranges of Africa and even colonized parts of the Arabian Peninsula. Traditionally, five phenotypically distinct species are recognized, but recent molecular studies were not able to resolve their phylogenetic relationships. Moreover, these studies revealed para- and polyphyletic (hereafter paraphyletic) mitochondrial clades for baboons from eastern Africa, and it was hypothesized that introgressive hybridization might have contributed substantially to their evolutionary history. To further elucidate the phylogenetic relationships among baboons, we extended earlier studies by analysing the complete mitochondrial cytochrome b gene and the 'Brown region' from 67 specimens collected at 53 sites, which represent all species and which cover most of the baboons' range. Results Based on phylogenetic tree reconstructions seven well supported major haplogroups were detected, which reflect geographic populations and discordance between mitochondrial phylogeny and baboon morphology. Our divergence age estimates indicate an initial separation into southern and northern baboon clades 2.09 (1.54–2.71) million years ago (mya). We found deep divergences between haplogroups within several species (~2 mya, northern and southern yellow baboons, western and eastern olive baboons and northern and southern chacma baboons), but also recent divergence ages among species (< 0.7 mya, yellow, olive and hamadryas baboons in eastern Africa). Conclusion Our study confirms earlier findings for eastern Africa, but shows that baboon species from other parts of the continent are also mitochondrially paraphyletic. The phylogenetic patterns suggest a complex evolutionary history with multiple phases of isolation and reconnection of populations. Most likely all these biogeographic events were triggered by multiple cycles of expansion and retreat of savannah biomes during Pleistocene glacial and inter-glacial periods. During contact phases of populations reticulate events (i.e. introgressive hybridization) were highly likely, similar to ongoing hybridization, which is observed between East African baboon populations. Defining the extent of the introgressive hybridization will require further molecular studies that incorporate additional sampling sites and nuclear loci.

scholarly journals Benchmarking DNA barcodes: an assessment using available primate sequences

Genome ◽  
2006 ◽  
Vol 49 (7) ◽  
pp. 851-854 ◽  
Author(s):  
Mehrdad Hajibabaei ◽  
Gregory AC Singer ◽  
Donal A Hickey
Keyword(s):  
New Species ◽  
Cryptic Species ◽  
Dna Barcoding ◽  
Species Identification ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Primate Species ◽  
Dna Barcodes ◽  
Global Biodiversity ◽  
Efficient Sequence

DNA barcoding has been recently promoted as a method for both assigning specimens to known species and for discovering new and cryptic species. Here we test both the potential and the limitations of DNA barcodes by analysing a group of well-studied organisms—the primates. Our results show that DNA barcodes provide enough information to efficiently identify and delineate primate species, but that they cannot reliably uncover many of the deeper phylogenetic relationships. Our conclusion is that these short DNA sequences do not contain enough information to build reliable molecular phylogenies or define new species, but that they can provide efficient sequence tags for assigning unknown specimens to known species. As such, DNA barcoding provides enormous potential for use in global biodiversity studies.Key words: DNA barcoding, species identification, primate, biodiversity.

An updated look at the uneven distribution of cryptic diversity among parasitic helminths

2017 ◽  
Vol 92 (2) ◽  
pp. 197-202 ◽  
Author(s):  
G. Pérez-Ponce de León ◽  
R. Poulin
Keyword(s):  
Cryptic Species ◽  
Dna Sequences ◽  
Meta Analysis ◽  
Parasitic Nematodes ◽  
Trematode Species ◽  
Sampling Effort ◽  
Separate Analysis ◽  
Cryptic Diversity ◽  
Parasite Diversity ◽  
Parasitic Helminths

AbstractCryptic parasite diversity is a major issue for taxonomy and systematics, and for attempts to control diseases of humans, domestic animals and wildlife. Here, we re-examine an earlier report that, after correcting for sampling effort, more cryptic species of trematodes are found per published study than for other helminth taxa. We performed a meta-analysis of 110 studies that used DNA sequences to search for cryptic species in parasitic helminth taxa. After correcting for study effort and accounting for the biogeographical region of origins, we found that more cryptic species tend to be uncovered among trematodes, and fewer among cestodes and animal-parasitic nematodes, than in other helminth groups. However, this pattern was only apparent when we included only studies using nuclear markers in the analysis; it was not seen in a separate analysis based only on mitochondrial markers. We propose that the greater occurrence of cryptic diversity among trematodes may be due to some of their unique features, such as their mode of reproduction or frequent lack of hard morphological structures, or to the way in which trematode species are described. Whatever the reason, the high frequency of cryptic species among trematodes has huge implications for estimates of parasite diversity and for future taxonomic research.

scholarly journals Altitudinal distribution and advertisement call of Colostethus latinasus (Amphibia: Dendrobatidae), endemic species from eastern Panama and type species of Colostethus , with a molecular assessment of similar sympatric species

Zootaxa ◽  
2017 ◽  
Vol 4254 (1) ◽  
pp. 91 ◽  
Author(s):  
ROBERTO D. IBÁÑEZ ◽  
EDGARDO J. GRIFFITH ◽  
KAREN R. LIPS ◽  
ANDREW J. CRAWFORD
Keyword(s):  
Dna Sequences ◽  
Endemic Species ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
Sympatric Species ◽  
Advertisement Call ◽  
Mountain Range ◽  
Altitudinal Distribution ◽  
Species Identity ◽  
Molecular Assessment

We conducted a molecular assessment of Colostethus-like frogs along an elevational gradient in the Serranía de Pirre, above Santa Cruz de Cana, eastern Panama, aiming to establish their species identity and to determine the altitudinal distribution of C. latinasus. Our findings confirm the view of C. latinasus as an endemic species restricted to the highlands of this mountain range, i.e., 1350–1475 m.a.s.l., considered to be type locality of this species. We described the advertisement call of C. latinasus that consists of a series of 4–18 single, short and relatively loud “peep”-like notes given in rapid succession, and its spectral and temporal features were compared with calls of congeneric species. For the first time, DNA sequences from C. latinasus were obtained, since previously reported sequences were based on misidentified specimens. This is particularly important because C. latinasus is the type species of Colostethus, a genus considered paraphyletic according to recent phylogenetic analyses based on molecular data. 

scholarly journals Dimorphic Sessile Apterae of the Aphid Neothoracaphis glaucae (Hemiptera) on the Evergreen Oak Quercus glauca

2019 ◽  
Vol 2019 ◽  
pp. 1-15
Author(s):  
Shigeyuki Aoki ◽  
Utako Kurosu ◽  
Keigo Uematsu ◽  
Takema Fukatsu ◽  
Mayako Kutsukake
Keyword(s):  
Mitochondrial Dna ◽  
Dna Sequences ◽  
Distinct Species ◽  
Japanese Species ◽  
Quercus Glauca ◽  
Evergreen Oak

Species of the aphid genus Neothoracaphis (Hormaphidinae, Nipponaphidini) produce tiny, sessile, sclerotized apterous adults on leaves of oaks. Among Japanese species, “N. glaucae” has been known to have the largest, ovate apterae, while “N. saramaoensis” has smaller, elongated oval apterae on Quercus glauca. Through examining mitochondrial DNA sequences of Japanese Neothoracaphis species, we found that the two are the same species with a clear dimorphism. Neothoracaphis glaucae (Takahashi) was adopted as the valid name for the species. In Tokyo, Japan, apterae of the smaller type are abundantly seen throughout the year, and those of the larger type are generally few in number from summer to autumn. Alates, which are supposed to be sexuparae, appear from November to January. Nymphs developing into the alates are covered with long, semitransparent, bristle-like wax filaments. We conclude that N. querciphaga, N. elongata, and N. yanonis are distinct species and that both the genus Neothoracaphis and the three Neothoracaphis species other than N. yanonis form monophyletic groups among Japanese Nipponaphidini species we have examined.

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 ◽  
2011 ◽  
Vol 2876 (1) ◽  
pp. 1 ◽  
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.

An analysis of Hydrophis ornatus (Gray), H. lamberti Smith, and H. inornatus (Gray) (Hydrophiidae, Serpentes) based on samples from various localities, with remarks on feeding and breeding biology of H. ornatus

1989 ◽  
Vol 10 (4) ◽  
pp. 397-417 ◽  
Author(s):  
Arne Redsted Rasmussen
Keyword(s):  
Type Specimen ◽  
Distinct Species ◽  
Breeding Biology ◽  
New Method ◽  
Andaman Sea ◽  
Type Locality ◽  
Internal Organs ◽  
Sea Snakes

AbstractHydrophis ornatus (Gray) is described from Phuket Island, Andaman Sea, Siam Gulf, and the Philippine Islands, with remarks on feeding and breeding biology. Hydrophis lamberti Smith, is recognised as a distinct species and described from type locality (Bight of Bangkok), Siam Gulf, and the Philippine Islands. The type specimen of Hydrophis inornatus was reexamined. The results showed certain similarities between H. ornatus and the type specimen of H. inornatus, however, in the present paper the type specimen is maintained as a distinct species. Position of internal organs, in relation to number of vertebrae and ventral scales, is used as a new method for identifying sea snakes. Furthermore the number of vertebrae appeared to be a useful character to distinguish between H. ornatus and H. lamberti.

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