DNA-Barcoding of Some Medicinal Plant Species in Saudi Arabia Using <i>rbcL</i> and <i>matK</i> Genes

In the Kingdom of Saudi Arabia (KSA), thousands of plants are considered to have therapeutic value. The ambiguous use of identification mainly morphological characteristics of many plants has resulted in the adulteration and displacement of plant products which undermine their therapeutic value and weak documentation of plant resources. The aims of this study were therefore to evaluate genetic variability and explore the phylogeographic architecture for Saudi medicinal plant samples using rbcL and matK genes as barcodes for genomic identification. The matK and rbcL sequences collected for these samples were used as key markers for examining the relationship between Saudi medicinal plant species based on genetic diversity. During our study we were successful in identifying and documenting 4 different species (Foeniculum vulgare, Nitraria retusa, Dodonaea viscosa, and Rumex nervosus) located in Saudi Arabia using DNA barcoding technique. A total number of 8 sequences were obtained with a total sequence length of 6176 bp, where it ranged from 617 bp to 878 bp with an average length of 772 bp. The total number of rbcL sequences length is 2801 bp, where it ranges from 617 bp to 807 bp with an average length of 700.2 bp. Out of the 4 plant samples used, only three samples were identified correctly on the species level with an identity percentage higher than 95% using rbcL gene. Additionally, 4 matK sequences have been retrieved belong to 4 species. The total number of matK sequences length is 3375 bp, where it ranges from 819 bp to 878 bp with an average length of 843.8 bp. Out of the 4 plant samples used, only two samples were identified correctly on the species level with an identity percentage higher than 98% using matK gene. Both rbcL and matK have been able to identify most of our collected plant samples by genus, and some by species. Using only one DNA-barcoding technique was not reliable for plant identification, where matK and rbcL must be used as a dual DNA-barcoding procedure.     

A new species of deepwater cardinalfish, <Emphasis Type="Italic">Epigonus mayeri</Emphasis>, from the eastern Central Atlantic,and redescription of <Emphasis Type="Italic">Epigonus heracleus</Emphasis> Parin and Abramov 1986 (Perciformes: Epigonidae)

A new epigonid fish, Epigonus mayeri, is described on the basis of two specimens (109.7–113.8 mm in standard length: SL) from off Angola, and Epigonus heracleus Parin and Abramov 1986 is redescribed on the basis of 12 additional specimens with type specimens from off eastern New Zealand. These species belong to a subgroup of Epigonus, known as the “Epigonus robustus group,” which have a pungent opercular spine and VII-I, 9 dorsal-fin rays. The new species differs from other species of the group by having a sharp-pointed mustache-like process, presence of a rib on the last abdominal vertebra, vertebrae 10 + 15, tongue toothless, pyloric caeca 5, pectoral fin reaching to vertical line from anus (length 22.2–23.6% SL), orbital diameter 16.4–17.0% SL, head length 37.8–38.0% SL, and lower jaw length 16.7–17.0% SL.     

<Emphasis Type="Italic">Amblyceps improcerum</Emphasis>, a new sisoroid catfish from Kachin State,Myanmar (Teleostei: Siluriformes: Amblycipitidae)

A new species of amblycipitid catfish is here described from the Indawgyi Lake basin of the Irrawaddy River drainage in Kachin State, Myanmar as Amblyceps improcerum, new species. It can be distinguished from congeners in having a unique combination of the following characters: lower jaw longer than upper; head length 17.4–22.3% SL; head width 13.7–15.2% SL; head depth 9.0–11.7% SL; interorbital distance 31–39% HL; eye diameter 7–10% HL; 37–38 vertebrae; lateral line incomplete; predorsal length 25.5–30.7% SL; smooth posterior margin of pectoral spine; pectoral-fin length 13.5–16.8% SL; pelvic-fin length 9.6–13.4% SL; dorsal-to-adipose distance 25.2–28.7% SL; length of adipose-fin base 19.4–23.3% SL; adipose fin separate from dorsal procurrent caudal-fin rays; preanal length 62.1–66.9% SL; body depth at anus 9.8–12.8% SL; depth of caudal peduncle 10.1–12.6% SL; length of caudal peduncle 21.4–24.0% SL, post-adipose distance 15.8–17.8% SL; weakly-forked caudal fin with short broadly, rounded lobes (length of longest ray 1.3–1.5 times length of median rays); centrally projecting hooks on proximal lepidotrichia of median caudal-fin rays absent.     

Morphological and molecular comparison of <Emphasis Type="Italic">Myxobolus procerus</Emphasis> (Kudo, 1934) and <Emphasis Type="Italic">M. intramusculi</Emphasis> n. sp. (Myxozoa) parasitising muscles of the trout-perch <Emphasis Type="Italic">Percopsis omiscomaycus</Emphasis>

Inter- and intracellular cysts from a presumed single species, Myxobolus procerus (Kudo, 1934), parasitising the trout-perch Percopsis omiscomaycus were compared with respect to their spore morphology and small subunit 18S ribosomal DNA. The two cyst types have similar pyriform spores and comparable ranges in spore length and width, size of the polar capsules and number of filament coils. However, fixed spores of the intracellular cysts are significantly shorter (p < 0.05) in mean length than those from intercellular cysts, giving them a broader appearance. Comparing 991 base pairs of 18S rDNA revealed a 20 bp difference between the two cyst types (97.9% similarity), 10 due to base substitutions and 10 due to the presence or absence of a base. The described morphological differences and consistent 2.1% difference in the 18S rDNA reveal that the intracellular form is a separate species, which is described herein as Myxobolus intramusculi n. sp. M. intramusculi n. sp. and M. procerus may be sister species and it is suggested that the two species arose through sympatric speciation involving a switch in site specificity within a single host species.     

<Emphasis Type="Italic">Microrasbora</Emphasis> Annandale,a new genus record in China,with description of a new species (Teleostei: Cyprinidae)

A new species of genus Microrasbora Annandale (1918), M. microphthalma, is described from the Nanwan River, a tributary of the Ruili River, Irrawaddy drainage, in southwest Yunnan province, China. This new species is the first record of the genus Microrasbora in China. Microrasbora microphthalma can be distinguished from the other species of Microrasbora by the following combination of characters: 15–16 predorsal scales, eye diameter/head length 27–38%, eye diameter/interorbital width 70–93%, predorsal length/ standard length 60–68%, the preanal length/ standard length 65–71% and the origin of dorsal fin is posterior of that of the ventral fin. Xiao-Yong Chen and Jun-Xing Yang contributed equally to this paper.     

A new species of sisorid catfish genus <Emphasis Type="Italic">Glyptothorax</Emphasis> (Teleostei: Sisoridae) from Salween drainage of Yunnan,China

A new species of the genus Glyptothorax, Glyptothorax obliquimaculatus sp. nov. is described from the Xiaohei River, a tributary of the Nanting River, Salween drainage, in southwestern Yunnan province, China. This new species can be distinguished from its congeners by the following combination of characteristics: unculiferous ridges of the thoracic adhesive apparatus extending anteriorly onto the gular region; body with irregular dark blotches scattered along lateral surface (blotches mostly oblique); skin smooth on head and body; dorsal spine smooth without serrations on its posterior margin; lips smooth; posterior margin of pectoral spine with 7–8 serrations; dorsal-fin base 11.0–13.2% SL; pectoral-fin length 15.6–19.6% SL; depth of caudal peduncle 8.6–9.8% SL; head width 19.1–24.0% SL; nasal barbel length 23.3–33.3% HL.     

A new armored searobin <Emphasis Type="Italic">Paraheminodus longirostralis</Emphasis> (Teleostei: Peristediidae) from New Caledonia

A new species of armored searobin, Paraheminodus longirostralis, is described from five specimens collected from New Caledonia at depths of 412–467 m. It is distinguishable from its three known congeners in having 34 bony plates in the upper lateral row, a forward-directed spine on each plate between the 23rd–26th and 31st–32nd plates in the upper lateral row, 6–7 + 1 + 20–21 = 27–28 gill rakers, an elongate body posterior to the anus (49.9–52.1% standard length), an elongate rostral projection (53.0–59.3% head length), short upper jaw (42.1–43.4% head length), an elongate pectoral fin (70.6–79.4% head length), and long preopercular spine (39.2–57.7% head length).     

Spore morphology of Isoëtes (Isoëtaceae) from China

Micromorphological characters of mega- and microspores of five Isoëtes species from China were observed under scanning electron microscope (SEM). Megaspores of I. hypsophila have a levigate ornamentation, and are 358 µm in diameter (mean, n=30), microspores of this species have a gyrus ornamentation, and are 22 µm in length (mean, n=30); megaspores of I. yunguiensis have a cristate-reticulate ornamentation, with a size of 390 µm in diameter (mean, n=30), while microspores nearly smooth with some fine granulates, and with a size of 22 µm in length (mean, n=30); megaspores of I. taiwanensis are tuberculate and 312 µm in diameter (mean, n=30), echinate microspores are 24 µm in length (mean, n=30); cristate megaspores of I. sinensis are 409 µm in diameter (mean, n=30), and echinate microspores are 28 µm in length (mean, n=30); megaspores of I. orientalis have a cristate-reticulate ornamentation, with diameter of 420 µm (mean, n=30), microspores of this species have an echinate-tuberculate ornamentation with a size of 34 µm in length (mean, n=30). Based on the morphological characters of spores and chromosome numbers among taxa, it was found that mean spore size in each species of Isoëtes generally reflected the ploidy level. I. hypsophila, I. yunguiensis and I. taiwanensis, with smaller mean spore size, are diploidy with 2n=22; I. sinensis (2n=44) and I. orientalis (2n=66), with larger mean spore size, are polyploidy. The spore morphology of Isoëtes still plays an important role in identification and classification of Isoëtes from China.     

Length–weight relationships of fish species caught by bottom trawl in Jiaozhou Bay,China

Length–weight relationships (LWRs) were estimated for 31 fish species caught by bottom trawl surveys in Jiaozhou Bay on the west coast of the south Yellow Sea. Specimens were collected from September 2008 to August 2009 at monthly intervals. This study presents the first reference on LWRs for 15 of these species and new records of maximum total length for two species. Most of the b values fell within the expected range of 2.5–3.5. The mean value of b was 3.094 ± 0.064 (95% CL), which was significantly larger than 3.0, indicating a slight but significant tendency towards positive allometric growth in most of the fishes. Effects of the sex, season and growth phase were taken into account in this study. Results showed significantly different relationships between males and females in three of the species. Four species were found to have highly significant seasonal differences in the regression slope of b. Two different growth stanzas were detected using the double‐logarithmic plot of body weight vs total length for three species. The finding that the absolute residuals of b from 3.0 would become smaller with the increase in length‐range used was confirmed in this study.     

<Emphasis Type="Italic">Epigonus cavaticus</Emphasis> (Teleostei: Perciformes), a new epigonid fish from Palau,western Central Pacific

A new epigonid fish, Epigonus cavaticus, is described on the basis of eight specimens (59.2–69.5 in standard length: SL) collected from a cave at depth 20 m, southern fringing reef of Ngemelis Island, Palau. The species differs from other congeners by having minute teeth on both jaws, no opercular spine, pyloric caeca 7–8, gill rakers 25–27, total pored lateral line scales 48–50, dorsal fin rays VII-I, 10–11 (mode VII-I, 10), pectoral fin rays 16, vertebrae 10 + 15, body depth 21.4–25.0% SL, pectoral fin length 22.7–24.6% SL, eye diameter 44.4–47.5% head length: HL, upper jaw length 40.2–42.5% HL. Four paratypes (63.7–66.8 mm SL) of the new species are female with mature gonads, it is the smallest in size at sexual maturity among the congeners.     

<Emphasis Type="Italic">Trichiurus nickolensis</Emphasis>, a new hairtail from Australia belonging to the <Emphasis Type="Italic">Trichiurus russelli</Emphasis> complex (Perciformes: Trichiuridae)

A new hairtail, Trichiurus nickolensis, is described on the basis of ten specimens collected off northwestern Australia, off the Northern Territory, and in the Gulf of Carpentaria, Queensland. The new species strongly resembles T. brevis Wang and You in Wang et al., 1992, off Hainan Island, South China Sea, and T. russelli Dutt and Thankam, 1966, off the Waltair Coast, Andhra Pradesh, India, in having the highest point of the supraoccipital crest situated directly above the posterior margin of the eye and a relatively short caudal peduncle. Trichiurus nickolensis differs from those two species in being strongly pigmented on the anterior section of the dorsal fin membrane (vs. slightly pigmented), and having a dorsal head margin that appears concave in lateral view, rises gently from snout tip to above middle of orbit, and then extends more steeply to dorsal fin origin (vs. rising gently from tip of snout to dorsal fin origin). The new species also has a greater number of dorsal fin rays (III, 138–143 vs. III, 127–132 and III, 127–131 in T. brevis and T. russelli, respectively) and total vertebrae (160–166 vs. 147–155 and 149–153), and shorter preanal length (mean 30% TL vs. 33% TL and 35% TL), head length (11% TL vs. 12% TL and 13% TL) and upper jaw length (4% TL vs. 5% TL and 5% TL).     

Artificial neural networks for fly identification: A case study from the genera <Emphasis Type="Italic">Tachina</Emphasis> and <Emphasis Type="Italic">Ectophasia</Emphasis> (Diptera,Tachinidae)

The classification methodology based on morphometric data and supervised artificial neural networks (ANN) was tested on five fly species of the parasitoid genera Tachina and Ectophasia (Diptera, Tachinidae). Objects were initially photographed, then digitalized; consequently the picture was scaled and measured by means of an image analyser. The 16 variables used for classification included length of different wing veins or their parts and width of antennal segments. The sex was found to have some influence on the data and was included in the study as another input variable. Better and reliable classification was obtained when data from both the right and left wings were entered, the data from one wing were however found to be sufficient. The prediction success (correct identification of unknown test samples) varied from 88 to 100% throughout the study depending especially on the number of specimens in the training set. Classification of the studied Diptera species using ANN is possible assuming a sufficiently high number (tens) of specimens of each species is available for the ANN training. The methodology proposed is quite general and can be applied for all biological objects where it is possible to define adequate diagnostic characters and create the appropriate database.     

<Emphasis Type="Italic">Polylepis</Emphasis> woodland remnants as biodiversity islands in the Bolivian high Andes

Mountain forests deserve special attention from ecologists and conservation biologists given the ecosystem services they provide to society, and their threat under global change. In the subalpine region of the Andes, Polylepis woodlands occur as arboreal islands in a matrix of grassland and scrub. Due to overgrazing and burning, however, these woodland patches are believed to cover only 11% of their potential area in Bolivia, core area for Polylepis. We reviewed the knowledge on the species diversity for the Bolivian Polylepis woodland remnants, assessed the conservation status of the occurring species, determined their trophic niche, and related species richness with climatic variables and elevation. Based in 31 publications, we found 780 identified species occurring in Polylepis woodlands: 425 plants, 266 birds, 46 mammals, 35 butterflies and 8 reptiles. Ten of the 13 Bolivian Polylepis species, as well as 7 other plant species, 14 bird species and 4 mammal species were categorized as threatened or near threatened according to IUCN criteria. In general, plant species richness increased with increased precipitation and length of the growth season, while it decreased with increasing elevation. There was a positive relationship between bird species richness, precipitation and length of the growth season. The highest bird endemism in Polylepis woodland remnants occurred at intermediate elevations, temperatures and precipitation. Mammal species richness decreased with increasing maximum temperature. Finally, we discuss the most important knowledge gaps regarding biodiversity in Bolivian Polylepis woodland remnants.     

Heads up: evolution of exaggerated head length in the minute litter bug genus <Emphasis Type="Italic">Nannocoris</Emphasis> Reuter (Hemiptera: Schizopteridae)

Evolutionary biologists have long been intrigued by exaggerated morphologies tied to sexual or natural selection. In insects, relatively few studies have investigated the evolution of such traits at the genus level and above and have used comparative phylogenetic methods to do so. We here investigate the interspecific evolution of head length in the minute litter bug genus Nannocoris Reuter based on the first phylogenetic hypothesis of the group (25 ingroup species, five gene regions, 3409 bp) and ancestral state reconstruction. Head lengths in this speciose genus range from approximately one sixth of the total body length to more than a quarter of the body length, while the head and mouthpart (rostrum) lengths are correlated. Different species therefore possess a markedly different reach of the rostrum when extended. The analyses show that head length evolution in Nannocoris is plastic, with head length elongations and reductions occurring in several clades, derived from ancestors with moderately elongated heads. Evidence is provided that exaggerated head lengths evolved through elongation of either the genal (pricei group) or the tip (arimensis group) region of the head. The biology of species in the genus Nannocoris is unknown, but given the lack of sexual dimorphism of head lengths, we speculate that head evolution in this genus may be driven by natural selection, potentially in the context of prey capture.     

Review of the <Emphasis Type="Italic">Chromis xanthura</Emphasis> species group (Perciformes: Pomacentridae), with description of a new species

A taxonomic review of the Chromis xanthura species group, defined here as having 13 dorsal-fin spines, three upper and three lower procurrent caudal-fin rays, two black bands at the preopercular and opercular margins, and a yellow caudal fin when juvenile, resulted in the recognition of three species, Chromis xanthura (Bleeker 1854), Chromis opercularis (Günther 1867), and Chromis anadema sp. nov. Chromis xanthura and C. opercularis, the Pacific and Indian Ocean paired sister species, respectively, are redescribed, with confirmation of two color types of C. xanthura (having a white or black caudal peduncle and fin) as a single species on the basis of morphological and molecular analyses. Chromis anadema sp. nov., described from the oceanic islands of the Pacific Ocean on the basis of 21 specimens, is characterized by having 28–33 gill rakers; longest dorsal-fin soft ray length 20.0–24.7% of standard length (SL); first anal-fin spine length 5.0–6.1% of SL; caudal-fin length 33.4–43.8% of SL; posterior tips of caudal-fin lobes not filamentous in adults; broad black bands along preopercular and opercular margins, sum width of two bands 28.9–38.7% of head length; distal half of soft-rayed portion of dorsal fin transparent in adults; triangular black blotches at upper and lower caudal-fin base in adults; caudal peduncle and fin bluish black in adults; and body grayish, and all fins (except for pectoral fin) bright yellow in juveniles.     

A new species of the genus <Emphasis Type="Italic">Triplophysa</Emphasis> (Nemacheilinae: Balitoridae), <Emphasis Type="Italic">Triplophysa jianchuanensis</Emphasis> sp. nov,from Yunnan,China

A new loach species, named Triplophysa jianchuanensis, has been recognized in collections from Jianchuan in Dali Prefecture, Yunnan, China. Triplophysa jianchuanensis can be distinguished from the other Triplophysa species by the following combination of characteristics: smooth skin, scaleless; lateral line complete; head long (26.7–29.8% of SL); eyes large (25.9–31.0% of dorsal head length); snout shorter than postorbital length (26.9–30.1% of HL); middle of lower lip interrupted and forming a pair of furrows; lower jaw spoon-like with obtuse edge; posterior chamber of air bladder completely degenerated; intestines short, bending in zigzag-shape behind stomach; pelvic-fin tip not reaching anus; caudal fin emarginate; branched rays of dorsal fin 7; branched rays of caudal fin 16. A key to the known species of Triplophysa from the Lancangjiang River is provided.     

Female reproductive biology of two sympatric incirrate octopod species, <Emphasis Type="Italic">Adelieledone polymorpha</Emphasis> (Robson 1930) and <Emphasis Type="Italic">Pareledone turqueti</Emphasis> (Joubin 1905) (Cephalopoda: Octopodidae), from South Georgia

The reproductive biology of two species of endemic Southern Ocean octopods was investigated around the sub-Antarctic islands of South Georgia and Shag Rocks. The females of both the species produce few, large eggs. This appears to be governed by phylogenetic constraint. No evidence was found for ontogenetic migration or seasonality associated with gonad maturation. Based on oocyte length frequency distributions and observations of oocyte development within the ovary, it is possible that both species could have either a single or multiple-batch spawning strategy. Pareledone turqueti ovaries contained fewer larger oocytes than those of Adelieledone polymorpha, which may help to reduce competition for resources immediately after hatching.     

Length–weight and length–length relationships of eight endemic Aphanius species from Turkey

Length–weight and length–length relationships were assessed for eight endemic Aphanius species from Turkey. This study provides a new reference on length–weight and length–length relationships and new maximum sizes for all species examined.     

Evaluation of cleaved amplified polymorphic sequence markers for <Emphasis Type="Italic">Chamaecyparis obtusa</Emphasis> based on expressed sequence tag information from <Emphasis Type="Italic">Cryptomeria japonica</Emphasis>

We have developed and evaluated sequence-tagged site (STS) primers based on expressed sequence-tag information derived from sugi (Cryptomeria japonica) for use in hinoki (Chamaecyparis obtusa), a species that belongs to a different family (although it appears to be fairly closely related to sugi). Of the 417 C. japonica STS primer pairs we screened, 120 (~30%) were transferable and provided specific PCR amplification products from 16 C. obtusa plus trees. We used haploid megagametophytes to investigate the homology of 80 STS fragments between C. obtusa and C. japonica and to identify orthologous loci. Nearly 90% of the fragments showed high (>70%) degrees of similarity between the species, and 35 STSs indicated homology to entries with the same putative function in a public DNA database. Of the 120 STS fragments amplified, 72 showed restriction fragment length polymorphisms; in addition, the CC2430 primers detected amplicon length polymorphism. We assessed the inheritance pattern of 27 cleaved amplified polymorphic sequence markers, using 20 individuals from the segregation population. All the markers analyzed were consistent with the marker inheritance patterns obtained from the screening panel, and no markers (except CC2716) showed significant (P<0.01) deviation from the expected segregation ratio. In total, 136 polymorphic markers were developed using C. japonica-based STS primers without any sequence modification. In addition, the applicability of STS-based markers developed in one species to other species was found to closely reflect the evolutionary distance between the species, which is roughly concordant with the difference between their rbcL sequences. We plan to use these markers for genetic studies in C. obtusa. Most of the markers should also provide reliable anchor loci for comparative mapping studies of the C. obtusa and C. japonica genomes.     

Complete chloroplast genome sequence of <Emphasis Type="Italic">Capsicum</Emphasis><Emphasis Type="Italic">baccatum</Emphasis> var. <Emphasis Type="Italic">baccatum</Emphasis>

Molecular markers derived from the complete chloroplast genome can provide effective tools for species identification and phylogenetic resolution. Complete chloroplast (cp) genome sequences of Capsicum species have been reported. We herein report the complete chloroplast genome sequence of Capsicum baccatum var. baccatum, a wild Capsicum species. The total length of the chloroplast genome is 157,145 bp with 37.7 % overall GC content. One pair of inverted repeats, 25,910 bp in length, was separated by a small single-copy region (17,974 bp) and large single-copy region (87,351 bp). This region contains 86 protein-coding genes, 30 tRNA genes, 4 rRNA genes, and 11 genes contain one or two introns. Pair-wise alignments of chloroplast genome were performed for genome-wide comparison. Analysis revealed a total of 134 simple sequence repeat (SSR) motifs and 282 insertions or deletions variants in the C. baccatum var. baccatum cp genome. The types and abundances of repeat units in Capsicum species were relatively conserved, and these loci could be used in future studies to investigate and conserve the genetic diversity of the Capsicum species.