308 research outputs found
FIGURE 2. Garra longchuanensis, ihb 201306027 in Garra longchuanensis, a new cyprinid (Teleostei: Cypriniformes) from southern China
No full textFIGURE 2. Garra longchuanensis, ihb 201306027, holotype, 145.2 mm SL, China, Yunnan Province, Yiluowadi Jiang basin, Longchuan Jiang River in Tengchong; dorsal and ventral views of head.Published as part of Yu, Qian, Wang, Xuzheng, Xiong, Huan & He, Shunping, 2016, Garra longchuanensis, a new cyprinid (Teleostei: Cypriniformes) from southern China, pp. 295-300 in Zootaxa 4126 (2) on page 298, DOI: 10.11646/zootaxa.4126.2.10, http://zenodo.org/record/27173
FIGURE 2 in Systematics and molecular phylogenetics of Asian snail-eating snakes (Pareatidae)
No full textFIGURE 2. Variation in the frontal scale (top row) and the anterior pair of the chin shields (lower row) in Pareas. Both characters are shaded black. A & H: P. hamptoni (A–C, H–J all modified from Pope 1935); B & I: P. stanleyi; C & J: P. boulengeri; D & K: P. iwasakii (modified from Ota et al. 1997); E & L: P. nigriceps (modified from Guo and Deng 2009); F & M: P. carinatus (modified from Rao and Yang 1992); G & N: P. nuchalis (modified from Boulenger 1900).Published as part of Guo, Yuhong, Wu, Yunke, He, Shunping, Shi, Haitao & Zhao, Ermi, 2011, Systematics and molecular phylogenetics of Asian snail-eating snakes (Pareatidae), pp. 57-64 in Zootaxa 3001 (1) on page 62, DOI: 10.11646/zootaxa.3001.1.4, http://zenodo.org/record/528086
Phylogenetic relationships of the Chinese sisorid catfishes: a nuclear intron versus mitochondrial gene approach
No full textSeveral recent molecular phylogenetic studies of the sisorid catfishes (Sisoridae) have challenged some aspects of their traditional taxonomy and cladistic hypotheses of their phylogeny. However, disagreement with respect to relationships within this family in these studies highlights the need for additional data and analyses. Here we subjected 15 taxa representing 12 sisorids genera to comprehensive phylogenetic analyses using the second intron of low-copy nuclear S7 ribosomal protein (rpS7) gene and the mitochondrial 16S rRNA gene segments both individually and in combination. The competing sisorid topologies were then tested by using the approximately unbiased (AU) test and the Shimodaira-Hasegawa (SH) test. Our results support previously suggested polyphyly of Pareuchiloglanis. The genus Pseudecheneis is likely to be nested in the glyptosternoids and Glaridoglanis might be basal to the tribe Glyptosternini. However, justified by AU and SH test, the sister-group relationship between Pseudecheneis and the monophyletic glyptosternoids cannot be rejected based on the second intron of rpS7 gene and combined data analyses. It follows that both gene segments are not suitable for resolving the phylogenetic relationships within the sisorid catfishes. Overall, the second intron of rpS7 gene yielded poor phylogenetic performance when compared to 16S rRNA gene, the evolutionary hypothesis of which virtually agreed with the combined data analyses tree. This phenomenon can be explained by the insufficient length and fast saturation of substitutions in the second intron of rpS7 gene, due to substitution patterns such as frequent indels (insertion/deletion events) of bases in the sequences during the evolution.Several recent molecular phylogenetic studies of the sisorid catfishes (Sisoridae) have challenged some aspects of their traditional taxonomy and cladistic hypotheses of their phylogeny. However, disagreement with respect to relationships within this family in these studies highlights the need for additional data and analyses. Here we subjected 15 taxa representing 12 sisorids genera to comprehensive phylogenetic analyses using the second intron of low-copy nuclear S7 ribosomal protein (rpS7) gene and the mitochondrial 16S rRNA gene segments both individually and in combination. The competing sisorid topologies were then tested by using the approximately unbiased (AU) test and the Shimodaira-Hasegawa (SH) test. Our results support previously suggested polyphyly of Pareuchiloglanis. The genus Pseudecheneis is likely to be nested in the glyptosternoids and Glaridoglanis might be basal to the tribe Glyptosternini. However, justified by AU and SH test, the sister-group relationship between Pseudecheneis and the monophyletic glyptosternoids cannot be rejected based on the second intron of rpS7 gene and combined data analyses. It follows that both gene segments are not suitable for resolving the phylogenetic relationships within the sisorid catfishes. Overall, the second intron of rpS7 gene yielded poor phylogenetic performance when compared to 16S rRNA gene, the evolutionary hypothesis of which virtually agreed with the combined data analyses tree. This phenomenon can be explained by the insufficient length and fast saturation of substitutions in the second intron of rpS7 gene, due to substitution patterns such as frequent indels (insertion/deletion events) of bases in the sequences during the evolution
Garra longchuanensis Yu, Wang, Xiong & He, 2016, new species
No full textGarra longchuanensis, new species Holotype. ihb 201306027, 145.2 mm SL; Longchuan Jiang River, a tributary flowing to the Yiluowadi Jiang (Irrawaddy River) basin in Tengchong, Yunnan, China (24 ° 53 ′ 27 ″N, 98 ° 40 ′ 31 ″E, 1207m), 5 March 2014, Weitao Chen. Paratypes. ihb201305991, 201305993, 201305996, 201305997, 201306018, 201306022–201306024, 201306026, 9 ex., 130.5–161.2 mm SL, locality and date same as for holotype. Diagnosis. A medium-sized species of Garra possessing a slightly pointed snout in dorsal view with a welldeveloped and deep transverse groove. Rostral lobe well-developed, with acanthoid tubercles distributed irregularly. Well-developed forehead proboscis represented by quadrate area in front of nostril with row of pointed and acanthoid tubercles. Predorsal region, chest and abdomen scaled; two pairs of barbels. Lateral-line scale rows 33–35; circumpeduncular scale rows 12. Branched pectoral-fin rays 15-16; branched pelvic-fin rays 9. Series of distinct black spots at bases of branched dorsal-fin rays; black mark at tip of upper caudal-fin rays. Description. Measurements and counts of specimens are given in Table 1. A comparison of G. longchuanensis with its closest congeners is in Table 2. The general appearance of the body is shown in Figure 1, and the morphology of the snout and mental disc are pictured in Figure 2. Body elongate, anteriorly cylindrical and posteriorly slightly compressed laterally. Head moderately large; height less than length; width greater than height. Caudal peduncle slender, length 1.4–1.9 times in width. Snout slightly pointed with deep groove across tip to forming transverse lobe and conspicuous, tuberculated and quadrate forehead proboscis before nostril, deflected downward against snout. Proboscis in small specimens not as conspicuous as in large specimens. Eye small, dorsolaterally located in posterior of head; interorbital width broad and flat. Two pairs of barbels; rostral barbels anterolaterally located, shorter than eye diameter; maxillary barbels at corner of mouth, far shorter than rostral ones. Rostral cap moderately crenulated, and with numerous papillae, separated from upper jaw by a deep groove and posteriorly continuous with lower lip. Upper and lower jaw with a thin horny sheath edge. Upper lip absent, lower lip modified into mental adhesive disc. Disc elliptical, shorter than wide; lateral and posterior margins with profuse papillae; anterior margin modified to form transverse, fleshy, bulged skin fold covered heavily by tiny papillae. Anteromedial fold separated from lower jaw by deep groove and posteriorly bordered in notch with central callous pad; lateral and posterior margins surrounding central callous pad papillate and free; posteriormost margin not reaching vertical from posterior margin of eye. Morphometrics G. longchuanensis Holotype 10 specimens including holotype Min Max Mean SD SL (mm) 145.2 130.5 161.2 146.3 % SL Body depth 20.7 19.2 24.7 22.3 2.0 Head length 23.6 22.4 25.6 24.2 0.9 Head height 14.5 14.5 16.5 15.4 0.6 Head width 17.4 17.0 18.3 17.8 0.4 Dorsal-fin length 22.7 21.4 26.2 23.4 11.7 Pectoral-fin length 18.9 18.8 21.8 20.4 0.9 Pelvic-fin length 18.7 18.7 21.8 19.8 0.9 Anal-fin length 16.9 16.9 19.6 18.3 0.9 Caudal-peduncle length 20.6 17.8 20.6 19.5 0.9 Caudal-peduncle height 11.1 10.9 12.6 11.6 0.6 Predorsal length 46.5 43.5 48.7 45.8 1.4 Prepectoral length 21.5 20.5 23.2 22.1 0.8 Prepelvic length 52.5 49.1 54.2 51.8 1.6 Preanal length 75.7 73.1 76.6 75.2 1.2 % HL Snout length 50.2 50.2 55.9 53.7 2.0 Eye diameter 14.5 13.0 16.3 14.8 2.1 Interorbital space 54.6 50.0 57.1 54.1 2.1 Disc length 48.0 44.5 53.0 48.1 2.3 Disc width 61.1 57.3 69.2 62.4 3.6 % Pelvic-anal distance Anus–anal distance 30.1 27.2 39.1 32.6 4.2 a Data from Zhang (2005) Lateral line complete, with 33 (5), 34 (7) and 35 (3) scale rows; 4 transverse scale rows above lateral line and 3 below. Circumpeduncular scale rows 12. Predosal scale rows 9 (5), 10 (10); relatively smaller than flank scales. Chest and belly scaled. Long axillary scale present at base of pelvic fin. Dorsal fin with 4 simple and 7 (4) or 8 (11) branched rays, last one spilt to base; origin closer to snout tip than to caudal-fin base; distal margin concave; first branched ray longest, last branched ray not extending to vertical from anal-fin origin. Pectoral and pelvic fins nearly horizontal. Pectoral fin with 1 simple and 15 (2), 16 (13) branched rays; not reaching pelvic-fin origin; fin length less than head length. Pelvic fin with 1 simple and 9 branched rays; tip surpassing anus; fin length less than head length and close to pectoral-fin length; origin of fin closer to caudal-fin base than to snout tip. Anal fin with 3 simple and 5 branched rays, last ray spilt to base; fin not reaching ventral origin of caudal-fin base; origin of anal fin closer to caudal-fin base than to pelvic-fin origin. Vent located closer to anal-fin origin than to pelvic-fin origin; distance of 4 scale rows to anal-fin origin. Caudal fin forked; longest rays about 1.5 –2.0 times as long as shortest rays; upper lobe slightly shorter than lower lobe; a black mark at tip of upper caudal-fin rays. Coloration. Preserved specimens: dorsum and sides of head dark gray; disc and belly faint yellow; lower half of body grayish-white. Six longitudinal blackish stripes extending along lateral portion of body, more conspicuous on caudal peduncle. Pectoral fin with dark dorsal surface on outside rays; caudal fin with black median rays; other fins dusky. Series of distinct black spots at bases of the branched dorsal-fin rays; black mark at tip of upper caudalfin rays. Distribution. Known from the Longchuan Jiang River, a tributary flowing to the Yiluowadi Jiang (Irrawaddy River) basin in Tengchong, Yunnan, southern China (Fig. 3). Etymology. The species is named after the Longchuan Jiang River, its type locality.Published as part of Yu, Qian, Wang, Xuzheng, Xiong, Huan & He, Shunping, 2016, Garra longchuanensis, a new cyprinid (Teleostei: Cypriniformes) from southern China, pp. 295-300 in Zootaxa 4126 (2) on pages 296-299, DOI: 10.11646/zootaxa.4126.2.10, http://zenodo.org/record/27173
Systematics and molecular phylogenetics of Asian snail-eating snakes (Pareatidae)
No full textThe taxonomy of the Asian snail-eating snakes (Pareatidae) is an ongoing controversy, partly because morphological characters do not yield consistent results across studies. We infer phylogenetic relationships within Pareatidae using similar to 2 kilo-bases of DNA sequences including two mitochondrial (cyt b and ND4) and one nuclear gene (c-mos). Results reveal four major lineages: Aplopeltura, Asthenodipsas, a clade formed by Pareas carinatus and P. nuchalis, and a clade comprising all other species of Pareas sampled in this study. Our data do not have enough signal to either support or reject a monophyletic Pareas. However, large molecular divergence (16.5%) is observed between the two major clades of Pareas, a level that is comparable to that between Pareas and Aplopeltura. Scale characters also suggest that P. carinatus and P. nuchalis are distinct from congeners, and future morphological and/or molecular studies might assess whether a distinct genus should be recognized. The molecular phylogeny further suggests a distant relationship between P. chinensis and P. formosensis and supports the validity of the former species
Identification of novel SINEs from Cyprinidae and their evolutionary significance
No full textShort interspersed nuclear elements (SINEs) are widespread among eukaryotic genomes. They are repetitive DNA sequences that have been amplified by retrotransposition. In this study, a class of SINEs were isolated from the Opsariichthys bidens genome, and named Opsar. Sequence analysis confirmed that Opsar is a new class of typical SINEs derived from tRNA molecules. With the tRNA-derived region of Opsar and through BLASTN search, we further identified Zb-SINEs from the zebrafish genome, which includes two groups: Zb-SINE-A and Zb-SINE-B. The Zb-SINE-A group comprises subfamilies of -Al--A5, and the Zb-SINE-B group is a dimer of the tRNA(Ala)-derived region and shares a similar dimeric composition to Alu. Zb-SINEs are composed of three distinct regions: a 5 end tRNA-derived region, a tRNA-unrelated region and a 3 end AT-rich region. The flanking regions are AT rich. The average length of Zb-SINEs elements is about 340 6p. Zb-SINEs account for as much as 0.1% of the whole zebrafish genome. About 70% of the Zb-SINEs are on chromosomes 11, 18, and 19. These Zb-SINEs were characterized by PCR and dot hybridization. The distribution pattern of Zb-SINEs in genome strongly supports the master genes model. The tRNA-derived regions of Opsar and Zb-SINEs were compared with the tRNA(Ala) gene, and they showed 76% similarity, indicating that Opsar and Zb-SINEs originated from an inactive tRNA(Ala) sequence or a tRNA(Ala)-like sequence. In view of the evolutionary status of zebrafish in the Cyprinidae, we deduced that Zb-SINEs were a very old class of interspersed sequences.Short interspersed nuclear elements (SINEs) are widespread among eukaryotic genomes. They are repetitive DNA sequences that have been amplified by retrotransposition. In this study, a class of SINEs were isolated from the Opsariichthys bidens genome, and named Opsar. Sequence analysis confirmed that Opsar is a new class of typical SINEs derived from tRNA molecules. With the tRNA-derived region of Opsar and through BLASTN search, we further identified Zb-SINEs from the zebrafish genome, which includes two groups: Zb-SINE-A and Zb-SINE-B. The Zb-SINE-A group comprises subfamilies of -Al--A5, and the Zb-SINE-B group is a dimer of the tRNA(Ala)-derived region and shares a similar dimeric composition to Alu. Zb-SINEs are composed of three distinct regions: a 5 end tRNA-derived region, a tRNA-unrelated region and a 3 end AT-rich region. The flanking regions are AT rich. The average length of Zb-SINEs elements is about 340 6p. Zb-SINEs account for as much as 0.1% of the whole zebrafish genome. About 70% of the Zb-SINEs are on chromosomes 11, 18, and 19. These Zb-SINEs were characterized by PCR and dot hybridization. The distribution pattern of Zb-SINEs in genome strongly supports the master genes model. The tRNA-derived regions of Opsar and Zb-SINEs were compared with the tRNA(Ala) gene, and they showed 76% similarity, indicating that Opsar and Zb-SINEs originated from an inactive tRNA(Ala) sequence or a tRNA(Ala)-like sequence. In view of the evolutionary status of zebrafish in the Cyprinidae, we deduced that Zb-SINEs were a very old class of interspersed sequences
FIGURE 5. Bayesian tree, 50 in Gill arch and hyoid arch diversity and cypriniform phylogeny: Distributed integration of morphology and web-based tools
No full textFIGURE 5. Bayesian tree, 50% majority rule consensus using Saitoh et al. (2006) outgroups (Appendix III) recovered from 15,002 trees. Nodal values indicate posterior probabilities.Published as part of Mabee, Paula M., Grey, Ericka A., Arratia, Gloria, Bogutskaya, Nina, Boron, Alicja, Coburn, Miles M., Conway, Kevin W., He, Shunping, Naseka, Alexander, Rios, Nelson, Simons, Andrew, Szlachciak, Jolanta & Wang, Xuzhen, 2011, Gill arch and hyoid arch diversity and cypriniform phylogeny: Distributed integration of morphology and web-based tools, pp. 1-40 in Zootaxa 2877 (1) on page 10, DOI: 10.11646/zootaxa.2877.1.1, http://zenodo.org/record/528594
Mitochondrial cytochrome b sequence variations and phylogeny of the East Asian bagrid catfishes
No full textThe mitochondrial DNA cytochrome b gene was sequenced from 8 bagrid catfishes in China. Aligned with cytochrome b sequences from 9 bagrid catfishes in Japan, Korea and Russia retrieved from GenBank, and selected Silurus meridionalis, Liobagrus anguillicauda, Liobagrus reini and Phenacogrammus interruptus as outgroups, we constructed a matrix of 21 DNA sequences. The Kimura's two-parameter distances were calculated and molecule phylogenetic trees were constructed by using the maximum parsimony (MP) and neighbor-joining (NJ) methods. The results show that (i) there exist 3-bp deletions of mitochondrial cytochrome b gene compared with cypriniforms and characiforms; (ii) the molecular phylogenetic tree suggests that bagrid catfishes form a monophyletic group, and the genus Mystus is the earliest divergent in the East Asian bagrid catfishes, as well as the genus Pseudobagrus is a monophyletic group but the genus Pelteobagrus and Leiocassis are complicated; and 60 the evolution rate of the East Asian bagrids mitochondrial cytochrome b gene is about 0.18%-0.30% sequence divergence per million years
Sequences of cytochrome b gene for primitive cyprinid fishes in East Asia and their phylogenetic concerning
No full text1140 bp of cytochrome b gene were amplified and sequenced from 14 species of primitive cyprinid fishes in East Asia. Aligned with other ten cytochrome b gene sequences of cyprinid fish from Europe and North America retrieved from Gene bank, we obtained a matrix of 24 DNA sequences. A cladogram was generated by the method of Maximum likelihood for the primitive cyprinid fishes. The result indicated that subfamily Leuciscinae and Danioninae do not form a monophyletic group. In the subfamily Danioninae, Opsariichthys biden and Zacco platypus are very primitive and form a natural group and located at the root. But the genera in subfamily Danioninae are included in different groups and have not direct relationship. Among them, Aphyocypris chinensis and Yaoshanicus arcus form a monophyletic group. Tanichthys albonubes and Gobiocypris rarus have a close relation to Gobioninae. The genus Danio is far from other genera in Danioninae, In our cladogram, the genera in Leuciscinae were divided into two groups that have no direct relationship. The genera in Leuciscinae distributed in Europe, Sibera and North America, including Leuciscus, Rutilus, Phoxinus, N. crysole, Opsopoeodus emilae, form a monophyletic group. And the Leuciscinae in southern China including Ctenopharyngodon idellus, Mylopharyngodon piceus, Squalibarbus and Ochetobius elongatus have a common origination
Mitochondrial 16S rRNA sequence variations and phylogeny of the Chinese sisorid catfishes
No full textPartial sequences of mitochondrial 16S rRNA gene were obtained by PCR amplification for comparisons among nine species of glyptosternoid fishes and six species of non-glyptosternoids representing 10 sisorid genera. There are compositional biases in the A-rich impaired regions and G-rich paired regions. A-G transitions are primarily responsible for the Ts/Tv bias in impaired regions. The overall substitution rate in impaired regions is almost two times higher than that in the paired regions. Saturation plots at comparable levels of sequence divergence demonstrate no saturation effects. Phylogenetic analyses using both maximum likelihood and Bayesian methods support the monophyly of Sisoridae. Chinese sisorid catfishes are composed of two major lineages, one represented by (Gagata (Bagarius, Glyptothorax)) and the other by "glyptosternoids + Pseudecheneis". The glyptosternoids may not be a monophyletic group. A previous hypothesis referring to Pseudecheneis as the sister group of monophyletic glyptosternoids, based on morphological evidence, is not supported by the molecular data. Pseudecheneis is shown to be a sister taxon of Glaridoglanis. Pareuchiloglanis might be paraphyletic with Pseudexostoma and Euchiloglanis. Our results also support the hypothesis that Pareuchiloglanis anteanalis might be considered as the synonyms of Pareuchiloglanis sinensis, and genus Euchiloglanis might have only one valid species, Euchiloglanis davidi
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