Molecular phylogenetics of stream treefrogs of the Hyloscirtus larinopygion  group (Anura: Hylidae), and description of two new species from Ecuador

We review the systematics of frogs of the Hyloscirtus larinopygion group. A new phylogenetic tree inferred frommitochondrial DNA (partial sequences of 12S rRNA, valine-tRNA, and 16S rRNA genes; ~2.3 kb) of eleven species ofthe H. larinopygion group is provided, based on maximum parsimony, maximum likelihood, and Bayesian analyses. Ourphylogeny confirms the close relationship of members of the H. larinopygion group with Andean relatives of the H.armatus group, which also occurs in the Andes. Hyloscirtus tapichalaca is placed as sister species to the rest of the H.larinopygion group, in which two clades (A+B) are evident. Although ingroup relationships are well supported, themonophyly of the H. larinopygion group and placement of H. tapichalaca require additional testing. Genetic divergencesamong species of the H. larinopygion group are shallow compared to those observed in many other anurans, with geneticdistance among sister species (H. princecharlesi and H. ptychodactylus) as low as 1.31%. However, this pattern isconcordant with radiations in other highland Andean lineages of anurans that show marked morphological or behavioraldifferentiation, but low divergence in mitochondrial markers. Divergence-time analyses (using BEAST) indicate that theHyloscirtus clade is a relatively ancient lineage that appeared in the Eocene, at a minimum age of 51.2 million years ago(MYA), while the H. larinopygion group originated in the Middle-Late Eocene at a minimum age of 40.9 MYA. Ourresults might suggest a rapid radiation of Hyloscirtus starting in the Miocene into the Pliocene, from at least 14.2 MYA tothe most recent divergence between sister taxa at ~2.6 MYA. We also describe two sympatric new species of Hyloscirtusfrom northwestern Ecuador: H. criptico sp. nov. and H. princecharlesi sp. nov. We diagnose them by their phylogeneticposition (they are not sister to each other), genetic divergence, and a unique combination of color patterns, and othermorphological features. Additionally, we describe the suctorial tadpoles and the extreme ontogenic color changes in H.larinopygion, H. lindae, H. pantostictus, H. princecharlesi, H. psarolaimus, and H. tigrinus. Furthermore, we describe theosteology of H. criptico, H. lindae, H. pacha, H. pantostictus, H. princecharlesi, H. psarolaimus, H. ptychodactylus, andH. staufferorum. We describe vocalizations of H. lindae, H. pacha, H. pantostictus, H. pasarolaimus, H. staufferorum, andH. tapichalaca. Hyloscirtus tigrinus is recorded for the first time in Ecuador and its range is extended 62.4 km (airlinedistance), from its southernmost locality record in Departamento de Nariño, Colombia. Most species of the H.larinopygion group are currently severely threatened by extinction, after surviving the catastrophic extinctions in the1980s and 1990s that led to the disappearance of many other sympatric anurans that bred in swiftly flowing water and hadlotic water tadpoles in the Andean highlands. Research and conservation actions are urgently needed for these species. Inorder to better call attention to these conservation issues, we name one of the new species in honor of Prince Charles ofWales, who is contributing significantly to the growth of awareness in the battle against tropical deforestation, climate change, and the catastrophic extinction of rainforest amphibians.

Download Full-text

A new species of the genus Xenophrys (Amphibia: Anura: Megophryidae) from an offshore island in Guangdong Province, southeastern China

Zootaxa ◽

10.11646/zootaxa.4324.3.8 ◽

2017 ◽

Vol 4324 (3) ◽

pp. 541 ◽

Cited By ~ 10

Author(s):

JIAN WANG ◽

ZU-YAO LIU ◽

ZHI-TONG LYU ◽

ZHAO-CHI ZENG ◽

YING-YONG WANG

Keyword(s):

New Species ◽

Gravid Female ◽

Guangdong Province ◽

16S Rrna Genes ◽

Rrna Genes ◽

12S Rrna ◽

Head Width ◽

Adult Males ◽

Offshore Island ◽

A New Species

A new species, Xenophrys insularis sp. nov., is described based on a series of specimens collected from Nan’ao Island, Shantou City, Guangdong Province, China. The new species is a separately evolving lineage that was robustly supported by the phylogenetic analysis based on the mitochondrial CO1 + 12S rRNA + 16S rRNA genes; morphologically, it can be distinguished from other known congeners by the following combination of characteristics: body size moderate, SVL 38.6–41.2 mm in adult males, 47.1 mm in a single adult female; snout obtusely rounded in dorsal view; head width slightly larger than head length; strong vomerine ridge bearing vomerine teeth; margin of tongue weakly notched behind; supratympanic fold forming a large swollen supraaxillary gland above insertion of arm; hindlimbs relatively short, heels not meeting when thighs are held at right angles to body, tibio-tarsal articulation reaches forward the posterior edge of tympanum; fingers and toes without lateral fringes, with rudiment of web at bases of toes, distinct subarticular tubercle only at the base of each finger and toe; single vocal sac in males; gravid female bears pure white oocytes. Xenophrys insularis sp. nov. is endemic to the Nan’ao Island and represents the first Xenophrys species found on and possibly endemic to a small offshore island.

Download Full-text

The genus Neoromicia (Family Vespertilionidae) in Madagascar, with the description of a new species

Zootaxa ◽

10.11646/zootaxa.3250.1.1 ◽

2012 ◽

Vol 3250 (1) ◽

pp. 1 ◽

Cited By ~ 14

Author(s):

STEVEN M. GOODMAN ◽

PETER J. TAYLOR ◽

FANJA RATRIMOMANARIVO ◽

STEVEN R. HOOFER

Keyword(s):

New Species ◽

16S Rrna ◽

16S Rrna Genes ◽

Rrna Genes ◽

12S Rrna ◽

Sexual Organ ◽

Unknown Species ◽

Dental Measurements ◽

Conservation Concern ◽

A New Species

Using molecular genetics, male sexual organ morphology (baculum), and cranio-dental characters, we describe a new spe-cies of the genus Neoromicia from Madagascar, N. robertsi sp. nov. It is presumed to be endemic to the island and isknown from three specimens taken in montane areas of the eastern central region. The new species shows 1.0 % and 2.8%divergence in the 12S rRNA and 16S rRNA genes, respectively, from its nearest congener and is notably larger in cranio-dental measurements than other members of the genus occurring on Madagascar. This new species was previously iden-tified as N. melckorum, which is considered a junior synonym of southern African N. capensis. Neoromicia malagasyen-sis, an endemic to central western Madagascar, is the sister species to N. robertsi and the two are best considered vicariantspecies. Specimens provisionally assigned to N. malagasyensis, but notably smaller in baculum and skull size, and withdifferent baculum morphology, probably represent another unknown species from the island. Given the apparent rarity ofN. robertsi compared with other Malagasy members of this genus living in the eastern portion of Madagascar, it is considered a taxon of conservation concern.

Download Full-text

A molecular phylogeny of the eastern group of ocellated lizard genus Timon (Sauria: Lacertidae) based on mitochondrial and nuclear DNA sequences

Amphibia-Reptilia ◽

10.1163/156853811x619718 ◽

2012 ◽

Vol 33 (1) ◽

pp. 1-10 ◽

Cited By ~ 20

Author(s):

Faraham Ahmadzadeh ◽

Miguel Angel Carretero ◽

D. James Harris ◽

Ana Perera ◽

Wolfgang Böhme

Keyword(s):

Dna Sequences ◽

Nuclear Dna ◽

Divergence Time ◽

Taxonomic Status ◽

16S Rrna Genes ◽

Rrna Genes ◽

12S Rrna ◽

Zagros Mountains ◽

Divergence Time Estimates ◽

Eastern Group

Timon, a small genus of lacertid lizards, includes four species distributed in two separate ranges in the western and eastern part of the Mediterranean Basin. Phylogenetic relationships between the two groups have not been resolved, and the taxonomic situation of the two subspecies of the eastern representative of the genus, Timon princeps, is not clear. To address these questions, partial DNA sequences of two nuclear (β-fibrinogen intron 7 and C-mos) and three mitochondrial (cytochrome b, 12S rRNA and 16S rRNA) genes were analyzed. Based on the high genetic distance between the two subspecies of T. princeps we promote their taxonomic status to full species, Timon princeps and Timon kurdistanicus. Divergence time estimates based on other lacertid species suggest that the separation of the green (Lacerta) and ocellated (Timon) lizards took place around 12 My ago, and that the Eastern group underwent speciation around 4-5 my ago, perhaps associated with the uplifting of the Zagros mountains. As expected given this ancient divergence and complex paleogeography, considerable levels of genetic diversity are recovered within both taxa, with geographically close individuals showing very divergent haplotypes.

Download Full-text

A new species of the Dendropsophus parviceps group from the western Amazon Basin (Amphibia: Anura: Hylidae)

Zootaxa ◽

10.11646/zootaxa.3249.1.2 ◽

2012 ◽

Vol 3249 (1) ◽

pp. 18 ◽

Cited By ~ 10

Author(s):

ANA P. MOTTA ◽

SANTIAGO CASTROVIEJO-FISHER ◽

PABLO J. VENEGAS ◽

VICTOR G.D. ORRICO ◽

JOSÉ M. PADIAL

Keyword(s):

New Species ◽

Maximum Likelihood ◽

16S Rrna ◽

Amazon Basin ◽

16S Rrna Genes ◽

Rrna Genes ◽

Terra Firme ◽

Base Pairs ◽

White Spots ◽

A New Species

We describe Dendropsophus frosti sp. nov. from lowland terra firme rainforests of the headwaters of the Amazon RiverBasin in Colombia and Peru. The new species is known from only two localities, the type locality near Leticia (Departa-mento Amazonas, Colombia, 04° 06' 24.2" S, 69° 56' 57.4" W; 103 m.a.s.l.), and the paratopotypic locality, Piedras in thePutumayo basin (Departamento Loreto, Peru, 02.79278° S, 72.91750° W; 90–170 m.a.s.l.). Maximum likelihood and par-simony analyses of 2436 aligned base pairs of the 12S and 16S rRNA genes recovered the new species as a member of D.parviceps group and sister to D. brevifrons. The new species is most closely related to D. parviceps, D. brevifrons, and D.koechlini, and it can be readily distinguished from these and all other members of the D. parviceps group by, among othercharacters, its plain dorsal light brown coloration, copper iris, plain immaculate pale yellow to white venter coloration, lack of flash marks on groin and axillae, and absence of white spots on lips.

Download Full-text

Complete Mitogenomes of Three Carangidae (Perciformes) Fishes: Genome Description and Phylogenetic Considerations

International Journal of Molecular Sciences ◽

10.3390/ijms21134685 ◽

2020 ◽

Vol 21 (13) ◽

pp. 4685

Author(s):

Zhenhai Li ◽

Min Li ◽

Shannan Xu ◽

Li Liu ◽

Zuozhi Chen ◽

...

Keyword(s):

Divergence Time ◽

Rrna Genes ◽

12S Rrna ◽

Trna Genes ◽

Coding Region ◽

Protein Coding ◽

Protein Coding Genes ◽

Gc Skew ◽

The Family ◽

Conserved Genes

Carangidae are ecologically and economically important marine fish. The complete mitogenomes of three Carangidae species (Alectis indicus, Decapterus tabl, and Alepes djedaba) were sequenced, characterized, and compared with 29 other species of the family Carangidae in this study. The length of the three mitogenomes ranged from 16,530 to 16,610 bp, and the structures included 2 rRNA genes (12S rRNA and 16S rRNA), 1 control region (a non-coding region), 13 protein-coding genes, and 22 tRNA genes. Among the 22 tRNA genes, only tRNA-Ser (GCT) was not folded into a typical cloverleaf secondary structure and had no recognizable DHU stem. The full-length sequences and protein-coding genes (PCGs) of the mitogenomes of the three species all had obvious AT biases. The majority of the AT-skew and GC-skew values of the PCGs among the three species were negative, demonstrating bases T and C were more plentiful than A and G. Analyses of Ka/Ks and overall p-genetic distance demonstrated that ATP8 showed the highest evolutionary rate and COXI/COXII were the most conserved genes in the three species. The phylogenetic tree based on PCGs sequences of mitogenomes using maximum likelihood and Bayesian inference analyses showed that three clades were divided corresponding to the subfamilies Caranginae, Naucratinae, and Trachinotinae. The monophyly of each superfamily was generally well supported. The divergence time analyses showed that Carangidae evolved during three geological periods, the Cretaceous, Paleogene, and Neogene. A. indicus began to differentiate from other species about 27.20 million years ago (Mya) in the early Miocene, while D. tabl (21.25 Mya) and A. djedaba (14.67 Mya) differentiated in the middle Oligocene.

Download Full-text

Two new species of the “kuhlii” complex of the genus Limnonectes from Thailand (Anura: Dicroglossidae)

Zootaxa ◽

10.11646/zootaxa.2615.1.1 ◽

2010 ◽

Vol 2615 (1) ◽

pp. 1 ◽

Cited By ~ 11

Author(s):

MASAFUMI MATSUI ◽

SOMSAK PANHA ◽

WICHASE KHONSUE ◽

NORIHIRO KURAISHI

Keyword(s):

Genetic Distances ◽

16S Rrna Genes ◽

Rrna Genes ◽

Morphological Evidence ◽

12S Rrna ◽

Morphological Investigation ◽

Japanese Species ◽

Morphometric Characters ◽

Mitochondrial 12S Rrna ◽

Rag 1

Phylogenetic relationships inferred from sequences of the mitochondrial 12S rRNA, tRNA val , and 16S rRNA genes and nuclear POMC and RAG-1 genes revealed that fanged frogs from Thailand usually associated with Limnonectes kuhlii are monophyletic and are collectively sister to the clade containing three Chinese and Japanese species. Within the Thai clade, the northern lineage, the southern lineage, and a population originally assigned to L. megastomias show unresolved relationships with each other, but are separated by genetic distances that correspond to values found among species of the Chinese-Japanese clade. Hybridization and past gene introgression are not detected among these three lineages of fanged frogs from Thailand. Adult specimens of the northern and southern lineages are phenotypically similar to each other, but can be separated by the combination of several morphometric characters. From the genetic and morphological evidence, they are considered to represent taxonomically different species. We therefore describe the northern lineage as L. taylori sp. nov. and the southern lineage as L. jarujini sp. nov. Taxonomic identity of the Loei population of L. megastomias requires future morphological investigation. The distribution pattern of fanged frogs within Thailand is discussed and the significance of the Three Pagodas Fault Zone is noted.

Download Full-text

PHYLOGENETIC RELATIONSHIPS OF LEPTOBRACHIUM HASSELTII TSCHUDI, 1838 (AMPHIBIA, ANURA, MEGOPHRYIDAE) - DETECTION OF A POSSIBLE CRYPTIC SPECIES

TREUBIA ◽

10.14203/treubia.v44i0.3286 ◽

2018 ◽

Vol 44 ◽

pp. 15 ◽

Cited By ~ 1

Author(s):

Amir Hamidy ◽

Masafumi Matsui

Keyword(s):

Sequence Data ◽

Taxonomic Status ◽

Species Level ◽

16S Rrna Genes ◽

Rrna Genes ◽

12S Rrna ◽

The West ◽

Major Clade ◽

Dna Phylogeny ◽

Acoustic Data

By examining mitochondrial DNA phylogeny using 2424bp of sequence data 12S rRNA, tRNAval, and 16S rRNA genes, we evaluated the taxonomic relationships among Javan litter frogs Leptobrachium hasseltii from southern Sumatra, Java, and Bali. Leptobrachium hasseltii formed a well-supported monophyletic group, which comprised two major clades. One major clade represented the southern Sumatran and Javan populations and the other consisted of the population from Bali. The Javan and southern Sumatran clade included two subclades: the West Javan-southern Sumatran group and the Central Javan group. The genetic divergence between the two major clades (Bali vs. Java-Sumatra) suggested their separation happen at species level. Further studies using morphological and acoustic data are needed to determine the taxonomic status of Bali population.

Download Full-text

Mitogenomics and the Phylogeny of Mantis Shrimps (Crustacea: Stomatopoda)

Diversity ◽

10.3390/d13120647 ◽

2021 ◽

Vol 13 (12) ◽

pp. 647

Author(s):

Cassandra Koga ◽

Greg W. Rouse

Keyword(s):

Sister Group ◽

18S Rrna Gene ◽

16S Rrna Genes ◽

Rrna Genes ◽

Mitochondrial Genomes ◽

12S Rrna ◽

Rrna Gene ◽

Slight Variation ◽

Ancestral State ◽

Protein Coding

Stomatopoda, commonly known as mantis shrimps, are notable for their enlarged second maxillipeds encompassing the raptorial claw. The form of the claw can be used to divide them into two basic groups: smashers and spearers. Previous phylogenetic studies of Stomatopoda have focused on morphology or a few genes, though there have been whole mitochondrial genomes published for 15 members of Stomatopoda. However, the sampling has been somewhat limited with key taxa not included. Here, nine additional stomatopod mitochondrial genomes were generated and combined with the other available mitogenomes for a phylogenetic analysis. We used the 13 protein coding genes, as well as 12S rRNA, 16S rRNA genes, and included nuclear 18S rRNA gene sequences. Different rooting options were used for the analyses: (1) single and multiple outgroups from various eumalocostracan relatives and (2) a stomatopod-only dataset, with Hemisquilla californiensis used to root the topologies, based on the current hypothesis that Hemisquilla is the sister group to the rest of Stomatopoda. The eumalocostracan-rooted analyses all showed H. californiensis nested within Stomatopoda, raising doubts as to previous hypotheses as to its placement. Allowing for the rooting difference, the H. californiensis outgroup datasets had the same tree topology as the eumalocostracan outgroup datasets with slight variation at poorly supported nodes. Of the major taxonomic groupings sampled to date, Squilloidea was generally found to be monophyletic while Gonodactyloidea was not. The position of H. californiensis was found inside its superfamily, Gonodactyloidea, and grouped in a weakly supported clade containing Odontodactylus havanensis and Lysiosquillina maculata for the eumalocostracan-rooted datasets. An ancestral state reconstruction was performed on the raptorial claw form and provides support that spearing is the ancestral state for extant Stomatopoda, with smashing evolving subsequently one or more times.

Download Full-text

Review of the systematics, morphology and distribution of Asian Clawed Salamanders, genus Onychodactylus (Amphibia, Caudata: Hynobiidae), with the description of four new species

Zootaxa ◽

10.11646/zootaxa.3465.1.1 ◽

2012 ◽

Vol 3465 (1) ◽

pp. 1 ◽

Cited By ~ 16

Author(s):

NIKOLAY A. POYARKOV, JR. ◽

JING CHE ◽

MI-SOOK MIN ◽

MASAKI KURO-O ◽

FANG YAN ◽

...

Keyword(s):

New Species ◽

Phylogenetic Analyses ◽

Russian Far East ◽

Far East ◽

Molecular Data ◽

16S Rrna Genes ◽

Rrna Genes ◽

Mitochondrial Coi ◽

Threat Status ◽

Molecular Phylogenetic

We describe four new species of Asian Clawed salamanders of the genus Onychodactylus (Caudata: Hynobiidae), basedon fresh material collected during fieldwork in Japan, Korea, the Russian Far East and northeastern China between 2003and 2010, as well as older voucher specimens deposited in several museums. Our analyses comprise all species currentlyrecognized within this genus across its entire distribution range. We follow an integrative taxonomic approach bycombining detailed morphological comparative analyses with molecular phylogenetic analyses. We find significantdifferences among species in this genus, based on morphological and molecular data, which resulted in the recognitionand description of four new species within this genus. The new species have uncorrected molecular divergences of over4.5–7.4% and 1.9–4.1% to their closest relatives in the mitochondrial COI and 16S rRNA genes respectively. In themolecular analyses, we found two very divergent lineages in Korea and Japan that need further investigation, as detailedmorphological data are not available for them. We also discuss our approach to delimit species on salamanders. For thenew species described in this group we evaluate their threat status according to IUCN criteria: O. koreanus sp. nov. Min,Poyarkov & Vieites and O. nipponoborealis sp. nov. Kuro-o, Poyarkov & Vieites are classified as Least Concern, whileO. zhaoermii sp. nov. Che, Poyarkov & Yan and O. zhangyapingi sp. nov. Che, Poyarkov, Li & Yan are classified as Vulnerable (Vu2a).

Download Full-text

A new species of Okanagana from the Walker Lane region of Nevada and California (Hemiptera: Auchenorrhyncha: Cicadidae)

Zootaxa ◽

10.11646/zootaxa.4868.4.3 ◽

2020 ◽

Vol 4868 (4) ◽

pp. 515-530

Author(s):

WILL CHATFIELD-TAYLOR ◽

JEFFREY A. COLE

Keyword(s):

New Species ◽

North America ◽

Great Basin ◽

Molecular Phylogenetics ◽

Sister Species ◽

Western Margin ◽

Walker Lane ◽

A New Species ◽

Molecular Characters

Okanagana boweni sp. n. is described from the western margin of the Great Basin of North America. The new species is diagnosed from allopatric O. simulata Davis and sympatric O. utahensis Davis using morphological, bioacoustical, and molecular characters. The distribution of this new species coincides with the Walker Lane region that lies along the border of California and Nevada, USA. Based on geography, bioacoustics, morphology, and molecular phylogenetics, we hypothesize that O. boweni sp. n. is the allopatric sister species of O. simulata.

Download Full-text