New genetic lineages within Moroccan day geckos Quedenfeldtia (Sphaerodactylidae) revealed by mitochondrial and nuclear DNA sequence data

The genus Quedenfeldtia is composed of two species, Q. moerens and Q. trachyblepharus, both endemic to the Atlas Mountains region of Morocco. Previous studies recovered two main genetic lineages within each Quedenfeldtia species, although sampling did not cover a substantial portion of their known distribution. In this study we collected individuals from previously unsampled localities of Quedenfeldtia and carried out genetic analyses in order to assess the range of previously identified lineages and the occurrence of additional lineages. Phylogenetic reconstruction based on both mitochondrial (12S and ND4 + tRNA) and nuclear (MC1R) markers revealed that while the new individuals of Q. moerens belong to previously described lineages, two new lineages of Q. trachyblepharus were uncovered from the northern and southern parts of the range. Genetic divergence of these new lineages (8-9% ND4 + tRNA p-distance) was higher than values observed between other lizard sister species. In the future a thorough morphological assessment is needed to complement this study and allow a taxonomic revision of these taxa. The results of this study highlight the importance of biodiversity assessments in mountainous regions characterized by high endemicity but which are difficult to access.

Download Full-text

Phylogeny, taxonomy, and zoogeography of the genus Gekko Laurenti, 1768 with the revalidation of G. reevesii Gray, 1831 (Sauria: Gekkonidae)

Zootaxa ◽

10.11646/zootaxa.2989.1.1 ◽

2011 ◽

Vol 2989 (1) ◽

pp. 1 ◽

Cited By ~ 26

Author(s):

HERBERT RÖSLER ◽

AARON M. BAUER ◽

MATTHEW P. HEINICKE ◽

ELI GREENBAUM ◽

TODD JACKMAN ◽

...

Keyword(s):

Dna Sequence ◽

Molecular Phylogenetics ◽

Nuclear Dna ◽

Sequence Data ◽

Identification Key ◽

Dna Sequence Data ◽

Preliminary Identification ◽

Specific Rank ◽

Species Groups

A review of the taxonomy, phylogeny, and zoogeography of all currently recognized Gekko species is provided based on morphology (including size, scalation, color, and pattern) and mitochondrial and nuclear DNA sequence data. We distinguish six morphological (phenotypic) species groups within the gekkonid genus Gekko: the G. gecko, G. japonicus, G. monarchus, G. petricolus, G. porosus, and G. vittatus groups, all of which receive support from molecular phylogenetics. The taxon G. reevesii, formerly evaluated as a synonym of G. gekko, is revalidated herein at specific rank. Furthermore, a preliminary identification key of all currently recognized Gekko taxa is provided.

Download Full-text

Validation of three sympatric Thoracophelia species (Annelida: Opheliidae) from Dillon Beach, California using mitochondrial and nuclear DNA sequence data

Zootaxa ◽

10.11646/zootaxa.3608.1.4 ◽

2013 ◽

Vol 3608 (1) ◽

pp. 67-74 ◽

Cited By ~ 1

Author(s):

Chris J. LAW ◽

KELLY M. DORGAN ◽

GREG W. ROUSE

Keyword(s):

Dna Sequence ◽

Nuclear Dna ◽

Sequence Data ◽

Hemoglobin Concentration ◽

Sympatric Species ◽

Sandy Beaches ◽

Additional Species ◽

Dna Sequence Data ◽

C Subunit ◽

Coi Sequences

Thoracophelia (Annelida, Opheliidae) are burrowing deposit feeders generally found in the mid- to upper intertidal areas of sandy beaches. Thoracophelia mucronata (Treadwell, 1914) is found along the west coast of North America, including at Dillon Beach, CA. Two additional species, Thoracophelia dillonensis (Hartman, 1938) and T. williamsi (Hartman, 1938) were also described from this beach. These three sympatric species have been primarily distinguished by branchial morphology, and efforts to determine the validity of the species have been based on morphological, reproductive and ecological studies. Here we demonstrate using mitochondrial and nuclear DNA sequence data that these three species are valid. Mitochondrial Cytochrome c subunit 1 (COI) sequences show uncorrected interspecific distances of ~9–13%. We found no inter—specific differences in body color or in hemoglobin concentration, but found that reproductive males were pinkish-red in color and had lower hemoglobin concentrations than purplish—red reproductive females.

Download Full-text

When forms meet genes: revision of the scleractinian genera Micromussa and Homophyllia (Lobophylliidae) with a description of two new species and one new genus

Contributions to Zoology ◽

10.1163/18759866-08504002 ◽

2016 ◽

Vol 85 (4) ◽

pp. 387-422 ◽

Cited By ~ 16

Author(s):

Roberto Arrigoni ◽

Francesca Benzoni ◽

Danwei Huang ◽

Hironobu Fukami ◽

Chaolun Allen Chen ◽

...

Keyword(s):

New Genus ◽

Nuclear Dna ◽

New Caledonia ◽

Sequence Data ◽

Intergenic Spacer ◽

Taxonomic Revision ◽

Its Region ◽

Distinct Species ◽

Morphological Data ◽

Eastern Australia

The scleractinian family Lobophylliidae is undergoing a major taxonomic revision thanks to the combination of molecular and morphological data. In this study, we investigate the evolutionary relationships and the macro- and micromorphology of six nominal coral species belonging to two of the nine molecular clades of the Lobophylliidae, clades A and B, and of Symphyllia wilsoni, a lobophylliid species analyzed from a molecular point of view for the first time. Sequence data from mitochondrial DNA (COI and the intergenic spacer between COI and l-rRNA), and nuclear DNA (histone H3 and ITS region) are used to generate robust molecular phylogenies and a median-joining haplotype network. Molecular results are strongly in agreement with detailed observations of gross- and fine-scale morphology of skeletons, leading to the formal revision of the genera Micromussa and Homophyllia and the description of two newly discovered zooxanthellate shallow-water species, Micromussa pacifica sp. nov. Benzoni & Arrigoni and Micromussa indiana sp. nov. Benzoni & Arrigoni, and a new genus, Australophyllia gen. nov. Benzoni & Arrigoni. In particular, Acanthastrea lordhowensis and Montastraea multipunctata are moved into Micromussa, A. hillae is synonymized with A. bowerbanki and is transferred to Homophyllia, and a revised diagnosis for both genera is provided. Micromussa pacifica sp. nov. is described from the Gambier Islands with its distribution spanning New Caledonia and eastern Australia. Despite a superficial resemblance with Homophyllia australis, it has distinctive macroand micromorphological septal features. Micromussa indiana sp. nov., previously identified as M. amakusensis, is here described from the Gulf of Aden and the southern Red Sea as a distinct species that is genetically separated from M. amakusensis and is morphologically distinct from the latter due to its smaller corallite size and lower number of septa. Finally, molecular trees show that S. wilsoni is closely related, but molecularly separated from clades A and B, and, also based on a unique combination of corallite and sub-corallite characters, the species is moved into Australophyllia gen. nov. These findings confirm the need for using both genetic and morphological datasets for the ongoing taxonomic revision of scleractinian corals.

Download Full-text

Towards rectifying limitations on species delineation in dusky salamanders (Desmognathus: Plethodontidae): An ecoregion-drainage sampling grid reveals additional cryptic clades

Zootaxa ◽

10.11646/zootaxa.4734.1.1 ◽

2020 ◽

Vol 4734 (1) ◽

pp. 1-61 ◽

Cited By ~ 1

Author(s):

DAVID A. BEAMER ◽

TRIP LAMB

Keyword(s):

Sequence Data ◽

Phylogenetic Reconstruction ◽

Large Species ◽

Eastern United States ◽

Species Delineation ◽

Molecular Systematic ◽

Dna Sequence Data ◽

Species Complexes ◽

Sampling Regime ◽

Comprehensive Recovery

Dusky salamanders (Desmognathus) constitute a large, species-rich group within the family Plethodontidae, and though their systematic relationships have been addressed extensively, most studies have centered on particular species complexes and therefore offer only piecemeal phylogenetic perspective on the genus. Recent work has revealed Desmognathus to be far more clade rich—35 reciprocally monophyletic clades versus 22 recognized species—than previously imagined, results that, in turn, provide impetus for additional survey effort within clades and across geographic areas thus far sparsely sampled. We conceived and implemented a sampling regime combining level IV ecoregions and independent river drainages to yield a geographic grid for comprehensive recovery of all genealogically exclusive clades. We sampled over 550 populations throughout the distribution of Desmognathus in the eastern United States of America and generated mitochondrial DNA sequence data (mtDNA; 1,991 bp) for 536 specimens. A Bayesian phylogenetic reconstruction of the resulting haplotypes revealed forty-five reciprocally monophyletic clades, eleven of which have never been included in a comprehensive phylogenetic reconstruction, and an additional three not represented in any molecular systematic survey. Although general limitations associated with mtDNA data preclude new species delineation, we profile each of the 45 clades and assign names to 10 new clades (following a protocol for previous clade nomenclature). We also redefine several species complexes and erect new informal species complexes. Our dataset, which contains topotypic samples for nearly every currently recognized species and most synonymies, will offer a robust framework for future efforts to delimit species within Desmognathus.

Download Full-text

Genetic analyses of the parasitic nematode, Parelaphostrongylus tenuis, in Missouri and Kentucky reveal unexpected levels of diversity and population differentiation

Parasitology ◽

10.1017/s0031182020001912 ◽

2020 ◽

pp. 1-11

Author(s):

L. S. Eggert ◽

L. K. Berkman ◽

K. Budd ◽

B. J. Keller ◽

A. M. Hildreth ◽

...

Keyword(s):

Nuclear Dna ◽

Disease Risk ◽

Sequence Data ◽

Release Site ◽

Primary Host ◽

Dna Sequence Data ◽

Increased Risk ◽

Parelaphostrongylus Tenuis ◽

Risk Of Disease ◽

High Level

Abstract Wildlife translocations, which involve the introduction of naive hosts into new environments with novel pathogens, invariably pose an increased risk of disease. The meningeal worm Parelaphostrongylus tenuis is a nematode parasite of the white-tailed deer (Odocoileus virginianus), which serves as its primary host and rarely suffers adverse effects from infection. Attempts to restore elk (Cervus canadensis) to the eastern US have been hampered by disease caused by this parasite. Using DNA sequence data from mitochondrial and nuclear genes, we examined the hypothesis that elk translocated within the eastern US could be exposed to novel genetic variants of P. tenuis by detailing the genetic structure among P. tenuis taken from white-tailed deer and elk at a source (Kentucky) and a release site (Missouri). We found high levels of diversity at both mitochondrial and nuclear DNA in Missouri and Kentucky and a high level of differentiation between states. Our results highlight the importance of considering the potential for increased disease risk from exposure to novel strains of parasites in the decision-making process of a reintroduction or restoration.

Download Full-text

A new species of cat-eyed snake (Serpentes: Dipsadinae: Leptodeirini) from the Andes of southern Ecuador

Zootaxa ◽

10.11646/zootaxa.4895.3.3 ◽

2020 ◽

Vol 4895 (3) ◽

pp. 357-380

Author(s):

OMAR TORRES-CARVAJAL ◽

JUAN C. SÁNCHEZ-NIVICELA ◽

VALENTINA POSSE ◽

ELVIS CELI ◽

CLAUDIA KOCH

Keyword(s):

New Species ◽

Nuclear Dna ◽

Sequence Data ◽

Molecular Data ◽

Genetic Distances ◽

Dna Sequence Data ◽

The Andes ◽

Southern Ecuador ◽

Morphological And Molecular Data ◽

A New Species

Leptodeira is one of the most widespread and taxonomically problematic snake taxa in the Americas. Here we describe a new species of Leptodeira from the Andes of southern Ecuador based on morphological and molecular data. The new species is geographically close and morphologically similar to L. ornata and L. larcorum, from which it can be distinguished by having smaller dorsal body blotches, a longer tail, and shorter spines on the hemipenial body. The shortest genetic distances between the new species and its congeners are 0.02 (16S), 0.05 (cytb), and 0.18 (ND4). The new species is restricted to the Jubones River Basin in southern Ecuador, an area of endemism for other reptile species. Our phylogenetic analysis based on mitochondrial and nuclear DNA sequence data also supports recognition of the names L. larcorum (restricted to Peru) for “L. septentrionalis larcorum”, and L. ornata for populations of “L. s. ornata” from central and eastern Panama, western Colombia, and western Ecuador. However, some samples of “L. s. ornata” from Panama and Costa Rica, as well as the new species described herein, are not included within or more closely related to L. ornata, which is sister to the clade (L. bakeri, L. ashmeadii).

Download Full-text

Is Ronnbergia (Bromeliaceae, Bromelioideae) a geographically disjunct genus? Evidence from morphology and chloroplast DNA sequence data

Phytotaxa ◽

10.11646/phytotaxa.219.3.6 ◽

2015 ◽

Vol 219 (3) ◽

pp. 261 ◽

Cited By ~ 7

Author(s):

Julian Aguirre-Santoro ◽

Julio Betancur ◽

Gregory K. Brown ◽

Timothy M. Evans ◽

Fabiano Salgueiro ◽

...

Keyword(s):

Chloroplast Dna ◽

Dna Sequence ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Phylogenetic Reconstruction ◽

Morphological Data ◽

Phylogenetic Study ◽

Geographic Ranges ◽

Dna Sequence Data ◽

Disjunct Genus

A phylogenetic study testing the monophyly of the geographically disjunct genus Ronnbergia (Bromeliaceae, Bromelioideae) is presented. The phylogenetic analyses were based on taxon sampling that included all but one species of Ronnbergia, and representative lineages across the subfamily Bromelioideae. Three chloroplast DNA sequence markers (matK, psbA-trnH, and trnL-trnF) and morphological data were used for the phylogenetic reconstruction. Both the molecular and morphological datasets supported the polyphyly of Ronnbergia, either independently or in combination. These findings suggest that the geographic disjunction of this genus is most likely a product of taxonomic misinterpretation. The results also indicate that the species currently circumscribed in Ronnbergia are closely related to species in the genus Aechmea with similar geographic ranges. The datasets do not have enough resolution power to reconstruct a deep phylogenetic history that involves all the species of Ronnbergia. Nevertheless, this study provides clues for future approaches that should focus on a larger species sampling and the use of multi-locus DNA sequence data.

Download Full-text

Status of the New Zealand cave weta (Rhaphidophoridae) genera Pachyrhamma, Gymnoplectron and Turbottoplectron

Invertebrate Systematics ◽

10.1071/is09047 ◽

2010 ◽

Vol 24 (2) ◽

pp. 131 ◽

Cited By ~ 6

Author(s):

Lorraine D. Cook ◽

Steven A. Trewick ◽

Mary Morgan-Richards ◽

Peter M. Johns

Keyword(s):

Mitochondrial Dna ◽

New Zealand ◽

Sequence Data ◽

Taxonomic Revision ◽

Spatial Diversity ◽

Species Level ◽

Dna Sequence Data ◽

Poorly Differentiated ◽

Single Genus ◽

Endemic Genera

The New Zealand Rhaphidophoridae Walker, 1869 comprise 18 endemic genera (including 8 that are monotypic). Although there are many new species to be described, rationalisation at the genus level is also required due to inconsistencies in their current systematics. Even the largest and best known taxa, including those that occupy cave systems and are the most frequently encountered by people, require taxonomic revision. These cave weta include species assigned to three poorly differentiated genera, Pachyrhamma Brunner v. Wattenwyl, 1888, Gymnoplectron Hutton, 1897 and Turbottoplectron Salmon, 1948, that are best known from North Island New Zealand. We used mitochondrial DNA sequence data to examine their relationships using representatives of each genus. The results indicate that a single genus Pachyrhamma would be appropriate for all, as Gymnoplectron and Turbottoplectron nest phylogenetically within it. There are insufficient morphological, spatial or ecological reasons to justify retention of all three. However, we also note that species level diversity does not correlate with genetic or spatial diversity; some species are genetically well partitioned and widespread while others have narrow ranges in single cave systems and are closely related to one another.

Download Full-text