Molecular phylogeny and geographic variation of Malagasy iguanas (Oplurus and Chalarodon)

2008 ◽  
Vol 29 (3) ◽  
pp. 319-327 ◽  
Author(s):  
Miguel Vences ◽  
Frank Glaw ◽  
Katharina Wollenberg ◽  
Tobias Münchenberg
Keyword(s):  
Dna Sequences ◽  
Taxonomic Revision ◽  
Rrna Gene ◽  
Separate Species ◽  
North West ◽  
The North ◽  
Sister Clade ◽  
Grande Comore ◽  
Different Populations ◽  
Mitochondrial 16S Rrna Gene

Abstract The iguanid subfamily Oplurinae consists of seven species of small to medium-sized, arboreal, sand-dwelling or rock-dwelling lizards endemic to Madagascar and the Comoros, belonging to the genera Oplurus and Chalarodon. We here present the first complete molecular species-level phylogeny for Oplurinae based on DNA sequences (865 bp) of the mitochondrial 16S rRNA gene and the nuclear c-mos gene. Our study is based on 52 specimens sampled from different populations in Madagascar and includes the geographically isolated population from Grande Comore, hitherto considered as subspecies Oplurus cuvieri comorensis or even as a separate species O. comorensis. Our results confirm that, within the genus Oplurus, the largely arboreal O. cuvieri and O. cyclurus form the sister clade to the remaining, more rock-dwelling species. Within the latter lineage, Oplurus quadrimaculatus is placed most basal, O. fierinensis and O. grandidieri are closely related sister species with high support, and O. saxicola is sister to the fierinensis/grandidieri lineage. Within the arboreal Oplurus, the Comoran sample shows no genetic differentiation relative to O. cuvieri populations from the North West and Sambirano regions of Madagascar, indicating that this population should not be considered as a separate species. In the monotypic genus Chalarodon, we discovered deep genetic divergences among populations of C. madagascariensis indicating the presence of a previously unrecognized cryptic species and the need for taxonomic revision.

A new species of the Spinomantis bertini species complex (Anura: Mantellidae) from Pic d’Ivohibe Special Reserve (Madagascar)

Zootaxa ◽  
2019 ◽  
Vol 4656 (1) ◽  
pp. 133-142 ◽  
Author(s):  
JOANA SABINO-PINTO ◽  
ANDOLALAO RAKOTOARISON ◽  
MOLLY C. BLETZ ◽  
DEVIN EDMONDS ◽  
FRANK GLAW ◽  
...  
Keyword(s):  
New Species ◽  
Dna Sequences ◽  
Species Complex ◽  
Nuclear Dna ◽  
The Other ◽  
Rrna Gene ◽  
Frog Species ◽  
Mitochondrial 16S Rrna Gene ◽  
Morphological Differences ◽  
A New Species

We describe a new frog species of the Spinomantis bertini species complex based on congruent genetic evidence from mitochondrial and nuclear DNA sequences as well as minor morphological differences. A molecular phylogeny derived from the mitochondrial 16S rRNA gene revealed that Spinomantis mirus sp. nov. is sister to a clade containing the other two described species of the species complex, S. bertini and S. beckei, but strongly differentiated from these two species by 8.1–9.8% pairwise distances in this gene. DNA sequences from two nuclear genes revealed that S. mirus sp. nov. shares no alleles with these two species. Phenotypically, S. mirus sp. nov. differs from the other species of the complex by its larger size and some aspects of its coloration, including clear mottling on the flanks, tri-color banding on the legs, and distinct brown dots on the dorsum. The new species is so far only known from Pic d’Ivohibe Special Reserve. Its distribution thus appears to not overlap with those of the other two species, which as far as known are restricted to the Andohahela Massif in the extreme South-East of Madagascar, at a distance of about 250 km from Ivohibe. 

Species boundaries in Zausodes-complex species (Copepoda:Harpacticoida:Harpacticidae) from the north-eastern Gulf of Mexico

2010 ◽  
Vol 24 (3) ◽  
pp. 258 ◽  
Author(s):  
Erin E. Easton ◽  
David Thistle ◽  
Trisha Spears
Keyword(s):  
New Species ◽  
Gulf Of Mexico ◽  
Harpacticoid Copepod ◽  
Taxonomic Revision ◽  
Rrna Gene ◽  
Complex Species ◽  
The North ◽  
Eastern Gulf Of Mexico ◽  
Mitochondrial Cytochrome B ◽  
North Eastern

Before 1999, the harpacticoid copepod species Zausodes arenicolus Wilson, 1932 was the subject of several ecological studies. Based on morphological evaluations of specimens from the north-eastern Gulf of Mexico, Bouck et al.’s (1999) taxonomic revision revealed three new species within what had been Z. arenicolus, making the ecological results suspect. Because harpacticoid copepods show convergent evolution and morphological stasis, Bouck et al.’s morphologically based approach may not have been sufficient. We have therefore re-evaluated their results using a combination of gene-sequencing and morphological methods. Partial mitochondrial cytochrome b (cytb) and 18S rRNA gene regions from individual Zausodes specimens found at five sites in the north-eastern Gulf of Mexico were separately analysed. Individuals of Zausodes septimus Lang, 1965 formed a single cytb gene-sequence clade, whereas Z. arenicolus individuals formed five. The uncorrected genetic divergences among these clades were 10 times those within them, providing evidence that each clade could be assigned to a different species. The 18S rDNA results support those from cytb. Subsequent morphological analysis revealed differences that will allow two clades of Z. arenicolus to be described as new species. Bouck et al. (1999) revealed some but not all of the species present.

Colonisation of the south-west Australian coastline by mud crabs: evidence for a recent range expansion or human-induced translocation?

2003 ◽  
Vol 54 (7) ◽  
pp. 833 ◽  
Author(s):  
David Gopurenko ◽  
Jane M. Hughes ◽  
Lynda Bellchambers
Keyword(s):  
Dna Sequences ◽  
Range Expansion ◽  
Scylla Serrata ◽  
Source Population ◽  
The South ◽  
Effective Population ◽  
North West ◽  
The North ◽  
South West ◽  
Mud Crabs

Mud crabs (Portunidae; Scylla spp.) have become established recently in some south-west Australian estuaries – almost 1000 km south of their recorded distribution. Colonisation may have occurred by a natural range expansion from the north-west or by translocation from source(s) within the Indo-West Pacific. To identify the species and the potential source population(s), genetic analyses was used to compare south-west crabs (N = 32) to other populations. Levels of diversity at two independent genetic markers were also compared to obtain relative estimates of effective population size between colonist and suspected source population(s). Comparisons of mitochondrial DNA sequences (COI) indicated that all south-west crabs were Scylla serrata. Indeed, the sole haplotype found among colonists was identical to one prevalent but endemic to more diverse north-west Australian populations. In contrast, source and colonist populations had equally high levels of genetic diversity at two microsatellite loci. It is argued that the south-west region was colonised by large numbers of S. serrata from north-west Australia through a recruitment event enhanced by the strong 1999/2000 Leeuwin Current. Differences in diversity among nuclear and mitochondrial loci may reflect different responses to the colonisation process; it is predicted that such differences are prevalent among plankton-dispersed species.

A new species of Mantidactylus (subgenus Chonomantis) from Ranomafana National Park, eastern Madagascar (Amphibia, Anura, Mantellidae)

Zootaxa ◽  
2011 ◽  
Vol 2772 (1) ◽  
pp. 52
Author(s):  
PARFAIT BORA ◽  
OLGA RAMILIJAONA ◽  
NOROMALALA RAMINOSOA ◽  
MIGUEL VENCES
Keyword(s):  
New Species ◽  
Dna Sequences ◽  
National Park ◽  
Rrna Gene ◽  
Ranomafana National Park ◽  
Threat Status ◽  
East Region ◽  
Southern Central ◽  
Mitochondrial 16S Rrna Gene ◽  
Data Deficient

We describe a new frog species of Mantidactylus belonging to the subgenus Chonomantis from Ranomafana National Park, in the Southern Central East region of Madagascar, at mid-elevations (about 950 m above sea level). Specimens of Mantidactylus paidroa sp. nov. were observed during the day in cavities under large rocks next to a stream in rainforest. Their advertisement calls are unique in Chonomantis and consist of a long series of note pairs. The new species shows a high divergence to other Chonomantis species in DNA sequences of the mitochondrial 16S rRNA gene (5.6–10.8%). Mantidactylus paidroa is so far only known from several streams in Ranomafana National Park but may have been overlooked at other rainforest sites in eastern Madagascar. We propose an IUCN threat status of Data Deficient for this new species.

Molecular Phylogeny of Dermacentor parumapertus (Acari: Ixodidae) from Two Locations Within Its Geographical Range

2019 ◽  
Vol 56 (4) ◽  
pp. 979-983 ◽  
Author(s):  
J Santos Portugal ◽  
Michelle Allerdice ◽  
Gail M Moraru ◽  
Jonas King ◽  
Christopher D Paddock ◽  
...  
Keyword(s):  
United States ◽  
Mitochondrial Dna ◽  
Dna Sequences ◽  
Western United States ◽  
Separate Species ◽  
Mtdna Coi ◽  
West Texas ◽  
Southern Form ◽  
Different Populations ◽  
Two Populations

Abstract Dermacentor parumapertus Neumann (Acari: Ixodidae) is a rather obscure tick found on jackrabbits in the western United States and parts of Canada and Mexico. Specimens from the northern part of their range are consistently different morphologically from ones found in southern and eastern parts of their range (particularly west Texas), leading some researchers to declare the southern form a variety or subspecies. This study examined field-collected adult D. parumapertus from two main locations—Utah and Texas—within its geographic distribution to ascertain the degree of genetic divergence in the two populations based upon both nuclear and mitochondrial DNA sequences. In total, 30 D. parumapertus were analyzed by PCR using both mtDNA and nDNA genes, and one D. nitens was included for comparison. Trees were constructed for all mtDNA genes individually, as well as after concatenating mtDNA (COI, COII, 12S) and nDNA (2 ITS2 primers), respectively. All constructed trees were exported to FigTree v1.4.3 and TreeGraph v2.14.1–771 beta for visualization. The majority of the Utah and Texas populations of D. parumapertus separated molecularly in both mtDNA and nDNA trees; however, analysis with mtDNA genes showed that 3/13 (23%) of Utah tick specimens were removed molecularly from other specimens collected at the same location. Thus, there was not enough evidence to declare these two disparate and morphologically different populations as distinct and separate species.

scholarly journals Loktanella agnita sp. nov. and Loktanella rosea sp. nov., from the north-west Pacific Ocean

2005 ◽  
Vol 55 (5) ◽  
pp. 2203-2207 ◽  
Author(s):  
Elena P. Ivanova ◽  
Natalia V. Zhukova ◽  
Anatoly M. Lysenko ◽  
Nataliya M. Gorshkova ◽  
Alexander F. Sergeev ◽  
...  
Keyword(s):  
Pacific Ocean ◽  
Sea Water ◽  
Sequence Similarity ◽  
Carbon Sources ◽  
Tween 80 ◽  
Rrna Gene ◽  
North West ◽  
Temperature Range ◽  
West Pacific Ocean ◽  
The North

One whitish and four pinkish strains of Gram-negative, non-motile, aerobic bacteria were isolated from sea-water and sediment samples collected in Chazhma Bay (Sea of Japan, Pacific Ocean). Analysis of 16S rRNA gene sequences revealed that these strains belonged to the ‘Alphaproteobacteria’, having highest sequence similarity of about 94–97 % with species of the genus Loktanella. None of the strains degraded gelatin, casein, chitin, agar, DNA or starch and they had limited ability to utilize carbon sources. The four pinkish strains, Fg36T, Fg1, Fg116 and Fg117, degraded Tween 80. Sea-water strain R10SW5T grew at 3–6 % NaCl and a temperature range of 8–35 °C, whilst strains Fg36T, Fg1, Fg116 and Fg117 grew at NaCl concentrations of 1–12 % and a temperature range of 4–35 °C. Phosphatidylglycerol (58/79 %), diphosphatidylglycerol (11/6 %) and phosphatidylcholine (28/22 %) were the major phospholipids. The predominant fatty acids were 16 : 0 (12·2/8·6 %) and 18 : 1ω7 (76·6/68·4 %). The DNA G+C content of strain R10SW5T was 59·1 mol% and those of the four pinkish strains ranged from 60·5 to 61·8 mol%. Based on the results of phenotypic, genotypic, chemotaxonomic and phylogenetic investigation, two novel species, Loktanella agnita sp. nov. and Loktanella rosea sp. nov., are proposed. The type strains are R10SW5T (=KMM 3788T=CIP 107883T) and Fg36T (=KMM 6003T=CIP 107851T=LMG 22534T), respectively.

Importance of genetic data in resolving cryptic species: A century old problem of understanding the distribution of Minervarya syhadrensis Annandale 1919, (Anura: Dicroglossidae)

Zootaxa ◽  
2020 ◽  
Vol 4869 (4) ◽  
pp. 451-492
Author(s):  
SAMADHAN PHUGE ◽  
AJINKYA BHARATRAJ PATIL ◽  
RADHAKRISHNA PANDIT ◽  
NIRMAL U KULKARNI ◽  
B.H. CHENNAKESHAVAMURTHY ◽  
...  
Keyword(s):  
Cryptic Species ◽  
Dna Sequences ◽  
Taxonomic Revision ◽  
Genetic Data ◽  
Type Specimen ◽  
Dominant Frequency ◽  
Dorsal Side ◽  
Type Locality ◽  
Rrna Gene ◽  
Type Specimens

Frogs of the genus Minervarya are cryptic and widely distributed in South Asia. However, many of them lack information about the precise type locality, genetic data, and distribution range. The present study aimed to examine the genetic affinities of a widely distributed species Minervarya syhadrensis around its type locality in the northern Western Ghats (Pune, Maharashtra). We studied the type specimen of M. syhadrensis and collected similar sized Minervarya frogs from Pune district. In the field, we observed two different calls from morphologically similar (M. syhadrensis like) males suggesting the sympatric occurrence of two cryptic species (that we initially named Minervarya species A and Minervarya species B). We analyzed morphology, call pattern, and mitochondrial 16S rRNA gene sequence of both species. Minervarya species A has a long call with a low pulse repetition rate and higher dominant frequency compared to that of the Minervarya species B. These species cannot be differentiated based on morphometric data. However, they can be sorted out using morphological characters such as the presence of longitudinal skin folds on the dorsal side (Minervarya species A) and differences in foot webbing. DNA sequences of Minervarya species A and Minervarya species B are matching with those of M. caperata and M. agricola respectively. After studying the type specimens of M. syhadrensis and M. caperata, we found morphological similarities (longitudinal skin folds) with the samples of Minervarya species A collected during the present study. Based on the results of our study (morphology and genetic) and available literature, we propose to redefine M. syhadrensis as applying to the lineage initially named Minervarya species A, and to treat the species M. caperata as a junior synonym of M. syhadrensis. Our study will be helpful in further taxonomic revision of the genus, and provides natural history information for M. syhadrensis and M. agricola.  

scholarly journals Exploring the microbial diversity in oil-contaminated mangrove sediments using 16S rRNA metagenomics

2019 ◽  
Author(s):  
Mahdi Ghanbari ◽  
Mansooreh Jami ◽  
Mohsen Shahriari Moghadam ◽  
Konrad J. Domig
Keyword(s):  
16S Rrna ◽  
Habitat Restoration ◽  
Marine Pollution ◽  
Mangrove Ecosystem ◽  
Rrna Gene ◽  
Mangrove Forests ◽  
North West ◽  
The North ◽  
Marine Habitats ◽  
16S Rrna Metagenomics

AbstractWith an area of 390 hectares, the mangrove forests of Nayband Bay are the widest mangrove communities above 27 degrees latitude in the Persian Gulf. They are the last dense, extensive structures of these ecosystems found in the north-west Indian Ocean. Growing industrial activities near the Nayband Bay and the consequent marine pollution has resulted in damage and threatened different marine habitats in recent years. To date, a comprehensive description of the microbial life in the mangrove ecosystem that has been exposed to oil contamination is lacking. This information could significantly contribute to a better overview of the function and resilience of the ecosystem. This work represents a first effort to better understand the Nayband Bay mangrove microbiology by applying 16S rRNA metagenomics. A total of 65,408 readings from the V3–V4 16S rRNA gene regions were obtained from 24 sediment samples, each measuring 440 bp. Most sequences belonged to members of the Proteobacteria phylum (mainly γ-Proteobacteria); however, members of the Bacteroidetes phylum (mainly Flavobacteriia) were also well represented in the samples. We discovered that the community of this ecosystem strongly exhibit typical structures of oil-contaminated marine environments. This is likely due to the growing industrial activity in the area and its consequent marine polluting effects. The use of practicable and applicable bioremediation protocols for habitat restoration in this valuable area is needed.

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