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Srinu, G.; Padmavathi, P., and Chatla, D., 2019. Identification and validation of Anabas spp. (Osteichthyes: Anabantidae) through morphology and DNA barcoding from lake Kolleru, Andhra Pradesh, India. In: Jithendran, K.P.; Saraswathy, R.; Balasubramanian, C.P.; Kumaraguru Vasagam, K.P.; Jayasankar, V.; Raghavan, R.; Alavandi, S.V., and Vijayan, K.K. (eds.), BRAQCON 2019: World Brackishwater Aquaculture Conference. Journal of Coastal Research, Special Issue No. 86, pp. 142–148. Coconut Creek (Florida), ISSN 0749-0208. Anabas Cuvier, 1816 (Pisces: Osteichthyes: Anabantidae) constitutes a major proportion of fisheries with great ecological and commercial importance in lake Kolleru, Andhra Pradesh, India. Morphological analysis based on 54 adult specimens from different parts of the lake revealed two putative species, Anabas testudineus (Bloch, 1795) and A. oligolepis (Bleeker, 1855) which are very closely related to and barely distinguished by few characteristics (e.g. body depth) exclusively in fully matured specimens. In juvenile and sub-adult specimens, considerable overlap in the range of colour patterns has been observed, inturn it may lead to taxonomic confusion. DNA barcoding is a promising technique for accurate species level identification based on partial mitochondrial cytochrome oxidase I (COI) gene. A total of five DNA barcode sequences were generated using universal primers. The average Kimura 2 Parameter (K2P) distances within species and genera were 0.5% and 1.3% respectively. These barcodes discriminated the congeneric species with lower genetic distance when compared to other taxa. This may aid in deciding the threshold value to delineate the species complex of Anabas from lake Kolleru. Neighbour joining (NJ) tree formed two major clades each shared with accessions to the same species. The maximum likelihood (ML) phylogenetic tree was constructed using COI sequences of Anabantidae which were complemented with the sequences of six other families of order Anabantiformes and the phylogenetic position of Anabantidae was discussed. Future studies are needed for deeper insights into genetic diversity and evolutionary relationships of Anabantiformes using multiple molecular markers. [ABSTRACT FROM AUTHOR]

The Philippines is the center of radiation of the land snail subfamily Helicostylinae, with around 253 recognized species. Despite their morphological diversity, research on their biology and taxonomy is lacking. We present here the first mitochondrial COI profiles of 32 species of Philippine helicostyline land snails. With the addition of sequences downloaded from GenBank, we tested the utility of the COI for species identification. Relative distributions of intraspecific and interspecific distances overlapped; hence, no barcoding gap was observed. However, 90% of uncorrected interspecific comparisons can distinguish species at 14% genetic distance or lower. Furthermore, the COI barcodes could not discriminate several co-distributed species that have similar conchological features, which should be flagged for taxonomic re-evaluation. [ABSTRACT FROM AUTHOR]

During a nematode survey in Iran a population of Pratylenchus loosi from tea was collected and herein described using morphometrics and several molecular markers and compared with the previous description of this species. Thus, the 18S rRNA gene, D2-D3 expansion regions of the 28S rRNA gene, ITS region, mitochondrial COI and partial nuclear hsp90 gene were amplified. According to morphometrics, the Iranian population was very close to previously described populations except for the stylet which was slightly longer. The phylogenetic reconstruction based on the sequences of all markers are also provided confirming the species differentiation and displaying the position of P. loosi and its relationship with closely related species. [ABSTRACT FROM AUTHOR]

Biofouling by the coronuloid barnacle Chelonibia patula (synonimized as C. testudinaria) was observed during the collection and maintenance of live broodstock of a few species of commercially important crustaceans at Mandapam Regional Centre of ICAR-CMFRI located along the Coromandel coast of Tamil Nadu, India. We assessed the genetic identity of C. patula found on the various crustacean hosts (Panulirus polyphagus, Portunus pelagicus and Charybdis natator) and turtle, olive ridley (Lepidochelys olivacea) from the Gulf of Mannar Biosphere Reserve. The phylogeographic studies of turtle barnacles from all potential hosts, carried out across world oceans about their species paradox, do not represent collection record from India and hosts like lobsters and olive ridleys. The mitochondrial Cytochrome c oxidase subunit 1 (COI) analysis of this epibiont from various hosts indicated that species from the south-east coast of India belong to the Indian Ocean/Western Pacific clade of C. testudinaria. The very low K2P genetic distance (0.008) between C. patula and C. testudinaria, on comparison with existing GenBank records, supports this finding. The phylogeographic structuring and evolutionary divergence between the clades of C. testudinaria with COI sequence data indicated that the Indian Ocean/Western Pacific and Eastern Pacific clades are the most divergent. [ABSTRACT FROM AUTHOR]

Abstract Strigeids have a cup-shaped fore body, containing a holdfast organ with two lobes and hind body. The species diversity of strigeids remains incomplete, especially in the Indian sub-continent. Here, we described six Tetracotyle type metacercariae (T. muscularis , T. fausti , T. lucknowensis, T. xenentodoni , T. mathuraensis and T. glossogobii) from five fresh water fish, collected at Lucknow (India). Next, we characterized these metacercariae using ribosomal (18S, 28S, ITS2) and mitochondrial DNA (COI) to determine their systematic and phylogenetic position. Molecular identification using inter-specific variation range for all four molecular markers revealed 1.9–4.9% (18S); 3.3–8.8% (28S); 6.8–12.9% (ITS2), and 3.5–9.4% (COI) among six Tetracotyle type metacercariae. In phylogenetic analysis, constructed by neighbour-joining (NJ) and maximum likelihood (ML) methods, T. fausti, T. glossogobii , T. xenentodoni , T. lucknowensis and T. mathuraenis nested as sister groups with the member of strigeids for all four markers used; T. muscularis , however, formed a basal clade. Furthermore, phylogenetic placement states the monophyly of the Tetracotyle type of metacercariae in all the markers (18S, 28S, COI), except ITS2. [ABSTRACT FROM AUTHOR]

In the present study, two pod borer larvae were found to damage pods of the host plant Senna alata. As pods (seeds) are commercially important, it prompted the investigators to find out the adult of pod borer larvae by molecular sequencing and reported in this article for the first time from S. alata. Successful amplification was achieved for chloroplast DNA isolated from leaves of host plant S. alata and tissue DNA from unknown larvae and sequenced. The sequences were submitted to NCBI domain, and the taxonomic position of host plant of pod borer larvae was confirmed as S. alata (L.) Roxb. Of the two sequences belonging to pod borer larvae, specimen 1 (S1) matched with already available three sequences of Thylacoptila sp. AA. But, specimen 2 (S2) showed significant variation in its genetic distance in Neighborhood Joining tree and maximum likelihood tree; these factors imply that specimen 2 (S2) is distinct from Thylacoptila sp. AA. Therefore, it is reported that specimen 2 may be represented as Thylacoptila sp. BB where in BB indicates variant from other available sequences. Nonetheless, reporting species of Thylacoptila as insect pest in pods of S. alata is an important contribution to the annals of insect–pest–plant interaction more importantly in medicinally important plant species S. alata. [ABSTRACT FROM AUTHOR]

Biological invasions represent a major threat to agriculture and forestry across the globe. Thaumastocoris peregrinus is a small sap-sucking heteropteran bug that has recently invaded a number of eucalypt plantations worldwide from its native range in Australia. To date, no studies have examined the range of this insect within Australia, and its population genetics remain poorly understood. We sampled T. peregrinus from 16 populations from South East Queensland, across New South Wales (NSW) and Victoria to south-eastern South Australia, and generated microsatellite and mtDNA data for ~ 200 individuals. Population genetic analyses consistently revealed moderate levels of genetic isolation by distance among populations across the range. Nonetheless, T. peregrinus has undergone dispersal across large distances, as revealed by the presence of identical mitochondrial haplotypes in both South East Queensland and South Australia. Two populations within the Sydney area (NSW) were divergent from other populations based on STRUCTURE and factorial correspondence analysis. They also had relatively low allelic richness and haplotype diversity indices. These results suggest they are the result of a relatively recent invasion event, consistent with their discovery in 2001. Pairwise genetic distance analyses suggest that the source of the invasion may have been central NSW. Our study provides an important framework for understanding the biology of this pest in its native environment, and may have implications for determining how it has invaded multiple areas worldwide. [ABSTRACT FROM AUTHOR]

Aphid species Aphis pomi (de Geer, 1773) is oligophagous on pomoideous host plants, whilst Aphis spiraecola Patch, 1914 is a polyphagous species alternating between Spiraea spp., its primary host, and a wide variety of secondary hosts, also including pomoideous species. Despite the biological distinction, these species are difficult to separate using their morphological characters. Partial sequences of mitochondrial COI and nuclear EF-1α genes were analyzed for samples from Central and Eastern Europe, Germany, Bulgaria, Italy, Turkey, China together with available data from GenBank. Interspecific pairwise sample divergences of the COI fragment ranged from 3.1 to 4.3%. One COI haplotype of A. pomi was predominant (n = 24), with a pan European distribution. The most abundant COI haplotype of A. spiraecola (n = 16) occurred in Lithuania, Latvia, Poland, Italy, Turkey and China. Interspecific pairwise sample divergences of the EF-1α fragment ranged from 0.6 to 1.2%. Analyzed partial sequences of EF-1α were identical in A. pomi. The most abundant EF-1α haplotype of A. spiraecola (n = 14) occurred in Lithuania, Poland, Italy, Turkey and China. The length of ultimate rostral segment appeared to be the most reliable morphological character for discrimination between apple and spirea aphid species. It allowed a 100% correct identification of A. pomi (n = 143) and 91.5% of A. spiraecola (n = 94) specimens in the European samples used for the molecular analysis. The existence of A. spiraecola in the Eastern Baltic region of Europe is documented for the first time.

The bryozoan, Bugula neritina, is one of the most widespread sessile marine invasive species. Since its first discovery in Korea in 1978, the gradual increase in the distribution and abundance of this species resulted in a significant damage to growth of aquaculture. Environmental DNA (eDNA) is a potentially useful tool for species detection including rare, invasive and threatened native species. In this study, species-specific primers and probe were designed to amplify a 185−bp region based on mitochondrial COI of B. neritina for monitoring, and tested on environmental samples from 35 harbors of Korea in 2017. Among 35 sites monitored, B. neritina colonies were detected in 27 sites during field survey. However, B. neritina DNA was detected in all examined eDNA isolated from seawater. These results suggested that eDNA-based methods coupled with simple seawater sampling could be suitable for determining the distribution and abundance of B. neritina as complementary traditional monitoring. [ABSTRACT FROM AUTHOR]

A new species of entomopathogenic nematode, Steinernema borjomiense n. sp., was isolated from the body of the host insect, Oryctes nasicornis (Coleoptera: Scarabaeidae), in Georgia, in the territory of Borjomi-Kharagauli. Morphological characters indicate that the new species is closely related to species of the feltiae-group. The infective juveniles are characterised by the following morphological characters: body length of 879 (777-989) μm, distance between the head and excretory pore = 72 (62-80) μm, pharynx length = 132 (122-142) μm, tail length = 70 (60-80) μm, ratio a = 26.3 (23.0-29.3), H% = 45 (40-51), D% = 54 (47-59), E% = 102 (95-115), and lateral fields consisting of seven ridges (eight incisures) at mid-body. Steinernema borjomiense n. sp. was molecularly characterised by sequencing three ribosomal regions (the ITS, the D2-D3 expansion domains and the 18S rRNA gene) and the mitochondrial COI gene. Phylogenetic analyses revealed that S. borjomiense n. sp. differs from all other known species of Steinernema and is a member of the monticolum-group. [ABSTRACT FROM AUTHOR]

The whitefly Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) is a cryptic species complex and widely distributed throughout tropical and subtropical regions. To understand the B. tabaci cryptic species diversity in China more comprehensively, in the year 2014 and 2016, a large-scale sampling was conducted from the famous biodiversity hotspot of China, Yunnan province. Mitochondrial cytochrome oxidase I gene sequences were used to identify new putative cryptic species. Phylogenetic analyses were performed using Bayesian methods to evaluate the position of new cryptic species in the context of the B. tabaci diversity in Asia. Two new cryptic species, China 5 and Asia V were identified. In total, 19 B. tabaci cryptic species are present in China, two invasive (MED and MEAM1) and 17 indigenous. A new sibling species of B. tabaci was first defined and reported. Based on the mtCOI sequences and haplotype network analyses, the genetic diversity of MED was far higher than MEAM1. We confirmed the exotic MED was originated from the western Mediterranean regions and first invaded into Yunnan, China. The genetic structures of other four indigenous species (Asia I, Asia II 1, Asia II 6, and China 1) with relatively wide distribution ranges in China were also discussed. [ABSTRACT FROM AUTHOR]

The identities of what have been referred to as Epigrapsus notatus (Heller, 1865) and E. villosus Ng, 2003, are evaluated using morphological and molecular methods. Morphological comparisons showed that the main characters used to diagnose E. villosus (viz. the setation of the carapace, the condition of the epigastric cristae, the granulation on the branchial region, and proportions of the ambulatory legs) can be attributed to the small size of the type specimen; and the extreme condition of these structures can be connected to adult forms of E. notatus through transitional phases. One morphological feature (the laterally expanded first epibranchial tooth) is seen only in the holotype of E. villosus, but it can also be regarded as a character state specific to small individuals of E. notatus, and signifying the extreme end of possible variation in that species. The analysis of mitochondrial cytochrome c oxidase subunit I (COI) reveals three haplotypes in the E. notatus/E. villosus complex, but with only as much as 0.61% of nucleotide divergence between them. In conclusion, it is clear that E. notatus undergoes dramatic morphological change during its growth, and that E. villosus should be considered a junior synonym of E. notatus. [ABSTRACT FROM AUTHOR]

Metabarcoding and high-throughput sequencing methods have greatly improved our understanding of protist diversity. Although the V4 region of small subunit ribosomal DNA (SSU-V4 rDNA) is the most widely used marker in DNA metabarcoding of eukaryotic microorganisms, doubts have recently been raised about its suitability. Here, using the widely distributed ciliate genus Pseudokeronopsis as an example, we assessed the potential of SSU-V4 rDNA and four other nuclear and mitochondrial markers for species delimitation and phylogenetic reconstruction. Our studies revealed that SSU-V4 rDNA is too conservative to distinguish species, and a threshold of 97% and 99% sequence similarity detected only one and three OTUs, respectively, from seven species. On the basis of the comparative analysis of the present and previously published data, we proposed the multilocus marker including the nuclear 5.8S rDNA combining the internal transcribed spacer regions (ITS1-5.8S-ITS2) and the hypervariable D2 region of large subunit rDNA (LSU-D2) as an ideal barcode rather than the mitochondrial cytochrome c oxidase subunit 1 gene, and the ITS1-5.8S-ITS2 as a candidate metabarcoding marker for ciliates. Furthermore, the compensating base change and tree-based criteria of ITS2 and LSU-D2 were useful in complementing the DNA barcoding and metabarcoding methods by giving second structure and phylogenetic evidence.

Pink bollworm (PBW),Pectinophora gossypiellais one of the most destructive pest’s globally inflicting huge economic losses in cotton even during later stages of crop growth. In the present investigation, the population genetic structure, distribution, and genetic diversity ofP. gossypiellain cotton growing zones of India using partial mitochondrial DNA cytochrome oxidase-I (COI) gene was addressed. The overall haplotype (Hd),number of nucleotide differences (K), and nucleotide diversity (π) were 0.3028, 0.327, and 0.00047, respectively which suggest that entire population exhibited low level of genetic diversity. Zone-wise clustering of population revealed that central zone recorded low level ofHd(0.2730) as compared to north (0.3619) and south (0.3028) zones. The most common haplotype (H1) reported in all 19 locations could be proposed as ancestral/original haplotype. This haplotype with one mutational step formed star-like phylogeny connected with 11 other haplotypes. The phylogenetic relationship studies revealed that most haplotypes of populations are closely related to each other. Haplotype 5 was exclusively present in Dharwad (South zone) shared with populations of Hanumangarh and Bathinda (North zone). The result indicated that there is no isolation by distance effect among the Indian populations of PBW. The present study reports a low genetic diversity among PBW populations of India and H1, as ancestral haplotype from which other haplotypes have evolved suggests that the migration and dispersal over long distance and invasiveness are major factors. [ABSTRACT FROM PUBLISHER]

The study attempted identification of Gobiid fishes from freshwaters in the east and northeast India on a collection of 20 specimens. The DNA barcode data delineated the collected samples into three species clades in the neighbor-joining tree. The results confirmed the identification of five sample sequences belonging to the subfamily Gobionellinae due to cohesive cladding with Awaous congeners. This is a new subfamily record for the northeastern region. Another 15 sample sequences showed conspecific cladding with Glossogobius giuris in the database. Among the 15 sample sequences, 14 sequences cladded with G. giuris sequences of Indian specimens while one sample sequence cladded with G. giuris sequences of South African specimens. This indicated the presence of either a hidden species or a previously synonymized species in the G. giuris complex. [ABSTRACT FROM AUTHOR]

Sequencing of environmental DNA (eDNA) for community analysis (i.e., eDNA metabarcoding) is already well established and applied in molecular microbial ecology. However, molecular methods for use in soil animal studies require further development before high-throughput sequencing can be considered a reliable technique in community ecology. To aid in this effort, we compare primers that target two frequently used genetic markers, mitochondrial cytochrome oxidase (COI) and ribosomal 18S genes, to determine their utility in broad soil animal eDNA studies. DNA was analyzed from individually identified invertebrates to test the efficiency of the primer sets in successfully targeting animal DNA and identification through sequencing. Primers were also tested for amplification of faunal genes from forest soil and leaf litter eDNA. Targeting the 18S gene resulted in the most successful amplification and correct identification of a wide range of individual invertebrate taxa, and was the most reliable primer set for use in eDNA analysis of invertebrate communities spanning several phyla. In contrast, the selected COI primers were inefficient in identifying a wide range of invertebrates, and amplified mostly bacterial sequences from eDNA. [ABSTRACT FROM AUTHOR]

The shell-boring Polydora websteri is described in detail in the present study for future unambiguous identification using an integrative taxonomic approach that combines morphology and molecular analysis of the mitochondrial cytochrome c oxidase subunit 1 (COI) gene. Adult P. websteri exhibit a high degree of morphological plasticity in the palp pigmentation pattern, the shape of the anterior edge of the prostomium, the shape of the major spines on chaetiger 5, and the shape of the pygidium. The COI gene sequence demonstrated that the intraspecific distance of P. websteri was 0.33%, whereas the interspecific distance of P. websteri ranged from 18.88% (with P. brevipalpa) to 24.79% (with Boccardia proboscidea). The intraspecific genetic distances of polydorids examined in the present study ranged from 0.33% to 1.67%, whereas the interspecific distances ranged from 18.88% to 24.79%. Such large barcoding gaps between intra- and inter-specific distances indicate that the COI is a suitable gene marker for molecular identification of polydorid species. Our results demonstrate that not only did all COI sequences from the larvae show greater than 99% sequence identity to those from adults, but some larvae share the same haplotypes as adults. These findings clearly indicate that the larvae collected from sea waters around an oyster farm belong to P. websteri, the same species as the adult worms collected from the oyster Crassostrea hongkongensis in that locality. Two polydorid-specific primers were successfully designed, for the first time, to amplify target fragments of the COI gene. This study is the first to molecularly validate unidentified larvae from the aquatic environment through the known COI sequences of adults. [ABSTRACT FROM AUTHOR]

Aphid species Brachycaudus divaricatae Shaposhnikov, 1956, originally described from Turkmenistan and earlier known from the Middle East and Eastern Europe only, is a successful invader to Central Europe. Its principal winter host, Prunus cerasifera, was originally distributed in Central Asia, Near East, and South Eastern Europe. Now it is common in Eastern and Central Europe. Brachycaudus divaricatae is closely related to native European aphid species Brachycaudus lychnidis (L., 1758). The aims of this study were: 1) to summarize and present the information on the distribution and host specificity of B. divaricatae from its invasive area in Europe; 2) to analyse and compare partial sequences of mitochondrial COI with those of nuclear EF-1α from samples identified as B. divaricatae and B. lychnidis to find possible hybridization or incomplete lineage sorting between these species. Since the first record from Eastern Baltic region in 2002, B. divaricatae changed its distribution area significantly. Now this aphid species has already reached the northern edge of its winter host distribution area. Five COI and 10 EF-1α haplotypes were detected among the analysed samples of B. divaricatae and B. lychnidis. The most abundant COI haplotype was common for both species. However, EF-1α sequences were species- specific despite their minor difierences. Coalescent simulations were performed using the model assuming no gene flow after the split between species and mimicking the parameters of empirical data. The analysis of genetic distances calculated for simulated data set supported the hypothesis of possible incomplete lineage sorting. [ABSTRACT FROM AUTHOR]

The Asian clam ( Corbicula sp.) is an invasive freshwater bivalve native to Asia, the Middle East, Australia, and Africa. It is now widely distributed around the world producing large ecological and economic impacts. Three well-described invasive lineages form a cryptic species complex with asexual reproduction based on androgenesis. In this study, we collected 175 individuals from different Iberian, European, and North American locations to genetically study Corbicula invasion in the Iberian Peninsula using COI and 28S genes. The use of mitochondrial and nuclear markers allows us to characterize both maternal and paternal inheritance from androgenetic Corbicula locations and to deal with the incongruences caused by egg parasitism. We identified 7 COI and 10 28S haplotypes that grouped individuals within the three invasive Corbicula lineages. Haplotype distribution of mitochondrial and nuclear markers detected genetic divergence between the Ebro Delta location and the rest of Iberian sites, suggesting that at least two invasion episodes occurred in the Iberian Peninsula. Haplotype distribution also suggested secondary contacts between Iberian and other European invaded regions. Additionally, results revealed that nuclear hybridization, a feature more widespread than previously reported, contributes to retain gene diversity in the Corbicula invasion. [ABSTRACT FROM AUTHOR]

The demographic history, population structure, and intraspecific diversity of the Globe Skimmer dragonfly Pantala flavescens Fabricius in Peninsular Malaysia were characterized based on variation of the mitochondria-encoded cytochrome c oxidase subunit I (COI) sequences. A median-joining network of 94 taxa inferred 71 unique haplotypes across four distinct geographic regions (i.e., northern, southern, central, and eastern). The distribution of these haplotypes, however, revealed no apparent geographical pattern, indicating minimal population genetic structure and high gene flow among all populations. A Mantel test showed an absence of isolation by distance (IBD), no significant association between genetic distance and geographic distance was observed. Mismatch distribution and neutrality tests provided evidence of demographic expansion during the Pleistocene dating back to 190,000–260,000 years ago. Additionally, species delimitation analyses revealed two operational taxonomic units (OTUs) within so-called P. flavescens , one restricted to the isolate from Korea; and the other representing isolates from Malaysia, Japan, and India. The present DNA analyses reflect the impact of the Quaternary glaciation in shaping the current genetic diversity and genetic structure of P. flavescens in Peninsular Malaysia. [ABSTRACT FROM AUTHOR]

The distribution range of root-knot nematode Meloidogyne graminicola is rapidly expanding, posing a severe threat to rice production. In this study, the sequences of cytochrome oxidase subunit I ( COI ) genes of rice M. graminicola populations from all reported provinces in China were amplified and sequenced by PCR. The distribution pattern and phylogenetic tree showed that all 54 M. graminicola populations in China have distinct geographical distribution characteristics; specifically, cluster 1 (southern China), cluster 2 (central south and southwest China), and cluster 3 (central and eastern China). The high haplotype diversity (Hd = 0.646) and low nucleotide diversity (π = 0.00682), combined with the negative value of Tajima's D (-1.252) and Fu's Fs (-3.06764), suggested that all nematode populations were expanding. The existence of high genetic differentiation (Fst = 0.5933) and low gene flow (Nm = 0.3333) indicated that there was a block of gene exchange between most populations. Mutation accumulation with population expansion might be directly responsible for the high genetic differentiation; therefore, the tested nematode population showed high within-group genetic variation (96.30%). The haplotype Hap8 was located at the bottom of the network topology, with the widest distribution and the highest frequency (59.26%), indicating that it was the ancestral haplotype. The populations in cluster 3 were newly invasive according to the lowest frequency of occurrence of Hap8, the highest number of endemic haplotypes, and the highest total haplotype frequency (60%). In contrast, cluster 1 having the highest genetic diversity (Hd = 0.772, π = 0.01127) indicated that it was the most primitive. Interestingly, the highest gene flow (Nm > 1), lowest genetic differentiation (Fst ≤ 0.33), and closest genetic distance (0.000) only occurred between the Guangdong/Hainan population and others, which suggested that there might be channels for gene exchange between them and that long-distance dispersal occurred. This suggestion is further confirmed by the weak correlation between genetic distance and geographical distance. Based on these data, a hypothesis can be drawn that M. graminicola populations in China were spreading from south to north, specifically from Guangdong and Hainan Provinces to other regions. Natural selection (including anthropogenic) and genetic drift were the main drivers of their evolution. Coincidentally, this hypothesis was consistent with the gradual warming trend and the chronological order of reporting these populations. The main factors influencing current M. graminicola population expansion and distribution patterns might be geography, climate, long-distance seedling transport, interregional operations of agricultural machinery, and rotation mode. It reminds human beings of the necessity to be vigilant about preventing nematode disease according to local conditions all year round., Competing Interests: The author(s) declare no conflict of interest.

Ancient Egyptians used pigeons not only as food in the form of squab but also as a messenger by virtue of their strong homing ability. Pigeons are bred for many purposes like meat in the form of squabs, exhibition as fancy and ornamental, flying and sports like racing competition, and finally for laboratory experiments of cognitive sciences. In this study, a total of 133 pigeon samples of six Egyptian breeds (n=110) and Japanese racing pigeons (n=23) were surveyed. One sample from each breed was sequenced for mitochondrial COI gene and all samples were genotyped across 11 microsatellites loci. From COI sequence, all the seven studied populations were found to belong to same the species (Columba livia). By the analysis of 11 microsatellite loci a total of 89 alleles were observed with an average of 8.1 alleles per locus. The expected heterozygosities of the six Egyptian breeds and Japanese racing pigeons were 0.580 and 0.630, respectively. FST showed a relatively high mean of 0.203 which indicated that there is a great differentiation among the seven pigeon populations. Zagel breed and Japanese racing pigeons showed the lowest values for both pairwise FST (0.108) and Nei's genetic distance (0.154). The information from this study would be useful for genetic characterization and provide a foundation for developing sustainable genetic improvement and conservation programs of this agriculturally and commercially important species.

The Entiminae are broad-nosed weevils constituting the most diverse subfamily of Curculionidae, with over 50 tribes. We performed Bayesian and Maximum Parsimony combined phylogenetic analyses with the main objective of testing higher-level relationships and the naturalness of the major Neotropical and Southern South American (Patagonia and Andes) tribes, including some members from other regions. We compiled a data matrix of 67 terminal units with 63 Entiminae species, as well as four outgroup taxa from Cyclominae, by 3522 molecular (from nuclear 18S rDNA and 28S rDNA, and mitochondrial 16S rDNA and COI gene sequences) and 70 morphological characters. The resulting trees recover a clade Entiminae with a monophyletic Cylydrorhinini and Premnotrypes branching off early. The tree resulting from parsimony analysis shows a clade of Leptopiini from the Australian region and another clade including taxa mainly distributed in the Palaearctic and Neotropical regions, but in the Bayesian tree the South American and Australian Leptopiini are grouped together. The mainly Palaearctic Entiminae (e.g., Brachyderini, Laparocerini, Otiorhynchini, Peritelini, Polydrusini, Phyllobiini and Sciaphylini) form a subclade separated from Southern Hemisphere taxa. Among the latter, the well-supported Naupactini are the sister group of the South American Tanymecini, excluding Platyaspistes, herein transferred to Leptopiini (new placement). Another well-justified clade is Eustylini–Geonemini, which also includes the enigmatic Galapagonotus, and the genus Artipus, thus corroborating its recent exclusion from Naupactini.

The phylogenetic relationships of the subgenera Polyommatus and Plebicula, within the Palaearctic butterfly genus Polyommatus, were inferred from a combined analysis of the nuclear marker ITS2 and the barcoding section of the mitochondrial gene COI. Eight major clades were recovered within Polyommatus s. l., which correspond closely to subgenera based on traditional systematics and are of late Pliocene to early Pleistocene origin. Extraordinary chromosomal evolution occurred independently in three of these clades. The disputed position of several species formerly placed in the subgenus Plebicula is clarified. A group of Central Asian species (Bryna) was recovered as a monophyletic clade within Polyommatus s. str. The Kurdistanian endemic P. buzulmavi appears as a sister species to P. icarus. P. celina replaces P. icarus in NW Africa and the Canary Islands, and split from the last common ancestor with P. icarus back in the early Pleistocene.

Partial mitochondrial cytochrome c oxidase subunit I (mt COI) sequences were generated from: Toxoplasma gondii (strains CTG, GTI, MAS, ME49, PTG, TgCatBr5, TgCat, Br64, TgCgCal, TgToucan); Neospora caninum (Strain NC1); Hammondia hammondi (Strain H.H-20); H. heydorni; H. cf. triffittae; Cystoisospora felis; C. suis; C. canis; C. rivolta; C. cf. ohioensis; Caryospora bigenetica; Sarcocystis rileyi; and S. neurona. Nuclear 18S rDNA sequences were generated for H. heydorni, H. hammondi, C. suis, C. canis, C. felis, C. rivolta, C. cf. ohioensis, S. neurona, and S. rileyi. Aligned, concatenated 18S rDNA and COI sequences were Bayesian analysed using partitioned nucleotide substitution models [HKY + I +G for 18S; GTR+ I +G codon (code = metmt) for COI]. Phylogenetic hypotheses supported a monophyletic Sarcocystidae and its subfamilie with two major clades within the Toxoplasmatinae: (1) a monophyletic clade of Cystoisospora spp. with Nephroisospora eptesici; and (2) a clade of Toxoplasma, Neospora and Hammondia. Within the latter, Hammondia was shown to be paraphyletic; H. heydorni and H. triffittae were monophyletic with N. caninum [canine definitive hosts (DHs)], whereas H. hammondi was monophyletic with T. gondii (feline DHs). A new genus is erected to resolve the paraphyly of the genus Hammondia confirmed using mt COI and combined 18S/COI sequence datasets. [ABSTRACT FROM AUTHOR]

DNA barcoding is a modern species identification technique that can be used to distinguish morphologically similar species, and is particularly useful when using small amounts of starting material from partial specimens or from immature stages. In order to use DNA barcoding in a surveillance program, a database containing mosquito barcode sequences is required. This study obtained Cytochrome Oxidase I ( COI) sequences for 113 morphologically identified specimens, representing 29 species, six tribes and 12 genera; 17 of these species have not been previously barcoded. Three of the 29 species ─ Culex palpalis, Macleaya macmillani, and an unknown species originally identified as Tripteroides atripes ─ were initially misidentified as they are difficult to separate morphologically, highlighting the utility of DNA barcoding. While most species grouped separately (reciprocally monophyletic), the Cx. pipiens subgroup could not be genetically separated using COI. The average conspecific and congeneric p-distance was 0.8% and 7.6%, respectively. In our study, we also demonstrate the utility of DNA barcoding in distinguishing exotics from endemic mosquitoes by identifying a single intercepted Stegomyia aegypti egg at an international airport. The use of DNA barcoding dramatically reduced the identification time required compared with rearing specimens through to adults, thereby demonstrating the value of this technique in biosecurity surveillance. The DNA barcodes produced by this study have been uploaded to the 'Mosquitoes of Australia-Victoria' project on the Barcode of Life Database (BOLD), which will serve as a resource for the Victorian Arbovirus Disease Control Program and other national and international mosquito surveillance programs. [ABSTRACT FROM AUTHOR]

The whitefly Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae), with its global distribution and extensive genetic diversity, is now known to be a complex of over 35 cryptic species. However, a satisfactory resolution of the systematics of this species complex is yet to be achieved. Here, we designed experiments to examine reproductive compatibility among species with different levels of mitochondrial cytochrome oxidase I (mtCOI) divergence. The data show that putative species with mtCOI divergence of >8% between them consistently exhibited complete reproductive isolation. However, two of the putative species, Asia II 9 and Asia II 3, with mtCOI divergence of 4.47% between them, exhibited near complete reproductive compatibility in one direction of their cross, and partial reproductive compatibility in the other direction. Together with some recent reports on this topic from the literature, our data indicates that, while divergence in the mtCOI sequences provides a valid molecular marker for species delimitation in most clades, more genetic markers and more sophisticated molecular phylogeny will be required to achieve adequate delimitation of all species in this whitefly complex. While many attempts have been made to examine the reproductive compatibility among genetic groups of the B. tabaci complex, our study represents the first effort to conduct crossing experiments with putative species that were chosen with considerations of their genetic divergence. In light of the new data, we discuss the best strategy and protocols to conduct further molecular phylogenetic analysis and crossing trials, in order to reveal the overall pattern of reproductive incompatibility among species of this whitefly complex. [ABSTRACT FROM AUTHOR]

Despite the importance of gelatinous zooplankton as components of marine ecosystems, both ecologically and socio-economically, relatively little information is known about population persistence or connectivity in jellyfish. In the present study, we employed a combination of nuclear microsatellite markers and sequence data from the mitochondrial cytochrome oxidase I (COI) gene to determine levels and patterns of population genetic structuring in the holoplanktonic jellyfish Pelagia noctiluca across the northeast Atlantic Ocean and Mediterranean Sea. Our results indicate a high degree of connectivity in P. noctiluca, with little evidence of geographical structuring of genetic variation. A small but significant differentiation of Atlantic Ocean and Mediterranean stocks was detected based on the microsatellite data, but no evidence of differentiation was observed with the mtDNA, probably due to the higher power of the microsatellites to detect low levels of genetic structuring. Two clearly distinct groups of genotypes were observed within the mtDNA COI, which probably diverged in the early Pleistocene, but with no evidence of geographical structuring. Palaeodistribution modelling of P. noctiluca at the Last Glacial Maximum (LGM; c. 21 Kya) indicated large areas of suitable habitat south of the species' current-day distribution, with little reduction in area. The congruent evidence for minimal genetic differentiation from the nuclear microsatellites and the mtDNA, coupled with the results of the palaeodistribution modelling, supports the idea of long-term population stability and connectivity, thus providing key insights into the population dynamics and demography of this important species. [ABSTRACT FROM AUTHOR]

A molecular taxonomic study of the bladed Bangiales of the South Eastern Pacific (coast of Chile) was undertaken based on sequence data of the mitochondrial COI and chloroplast rbc L for 193 specimens collected from Arica (18°S) in the north to South Patagonia (53°S) in the south. The results revealed for the first time that four genera, Porphyra , Pyropia , Fuscifolium and Wildemania were present in the region. Species delimitation was determined based on a combination of a General Mixed Yule Coalescence model (GMYC) and Automatic Barcode Gap Discovery (ABGD) coupled with detection of monophyly in tree reconstruction. The overall incongruence between the species delimitation methods within each gene was 29%. The GMYC method led to over-splitting groups, whereas the ABGD method had a tendency to lump groups. Taking a conservative approach to the number of putative species, at least 18 were recognized and, with the exception of the recently described Pyropia orbicularis , all were new to the Chilean flora. Porphyra and Pyropia were the most diverse genera with eight ‘species’ each, whereas only a ‘single’ species each was found for Fuscifolium and Wildemania . There was also evidence of recently diverging groups: Wildemania sp. was distinct but very closely related to W. amplissima from the Northern Hemisphere and raises questions in relation to such disjunct distributions. Pyropia orbicularis was very closely related to two other species, making species delimitation very difficult but provides evidence of an incipient speciation. The difference between the ‘species’ discovered and those previously reported for the region is discussed in relation to the difficulty of distinguishing species based on morphological identification. [ABSTRACT FROM AUTHOR]

Understanding the spatial integrity and connectivity of jellyfish blooms is important for ecologists and coastal stakeholders alike. Previous studies have shown that the distribution of jellyfish blooms can display a marked consistency in space and time, suggesting that such patterns cannot be attributed to passive processes alone. In the present study, we used a combination of microsatellite markers and mitochondrial cytochrome oxidase I sequences to investigate genetic structuring of the scyphozoan jellyfish Rhizostoma octopus in the Irish and Celtic Seas. The mitochondrial data indicated far higher levels of population differentiation than the microsatellites: ΦST[MT] = 0.300 vs. ΦST[NUC] = 0.013. Simulation studies indicated that the low levels of nuclear differentiation were not the result of limited power because of low levels of polymorphism. These findings, supported by palaeodistribution modelling and mismatch distribution analysis, are consistent with expansion of R. octopus from a single, limited refugium after the Last Glacial Maximum, followed by subsequent isolation, and that the discrepancy between the mitochondrial and nuclear markers is a result of the nuclear loci taking longer to reach mutation-drift equilibrium following the expansion as a result of their four-fold larger effective population size. The populations studied are probably not well connected via gene flow, and thus genetically as well as geographically distinct, although our findings also highlight the need to use a combination of organellar and nuclear markers to enable a more complete understanding of population demography and structure, particularly for species with large effective population sizes. [ABSTRACT FROM AUTHOR]

To assist with plant quarantine inspections, we developed a specific primer set for use in a diagnostic polymerase chain reaction method of distinguishing the codling moth Cydia pomonella (L.). from other tortricid pests in cherries imported from western North America: Archips argyrospila (Walker), A. rosana (L.), Argyrotaenia franciscana (Walsingham), Cacoecimorpha pronubana (Hübner), Choristoneura rosaceana (Harris), Epiphyas postvittana (Walker), Grapholita molesta (Busck), G. packardi Zeller, G. prunivora (Walsh), Pandemis pyrusana (Kearfott), and Spilonota ocellana (Denis and Schiffermüller). A 472-bp fragment of mitochondrial cytochrome oxidase subunit I (COI) gene was sequenced in 3-18 specimens of each species except for A. rosana and P. pyrusana. C. pomonella demonstrated consistent and diagnostic differences from other species in two regions of the COI gene from which forward and reverse primers were designed to amplify a 326-bp segment. The primer sets were used to selectively amplify DNA from specimens obtained from various geographic origins to check for C. pomonella. This method enabled immediate and accurate identification of C. pomonella, and thus provides an effective tool for nations concerned about possible invasions of this pest. [ABSTRACT FROM AUTHOR]

Thrips tabaci Lindeman is one of the most serious insect pests of onion and other Allium spp. in many parts of the world. Moreover, T. tabaci is also a vector of two important plant infecting tospovirus: Tomato spotted wilt virus (TSWV) and Iris yellow spot virus (IYSV). The latest has been recorded from Northen Italy since 2008 and recently it has been reported in Calabria Region (South Italy) on onion crops. In the last two years, surveys of T. tabaci have been carried out on in the southern Region, in order to investigate the genetic variation in the field populations. [ABSTRACT FROM AUTHOR]

Aphid species Aphis pomi (de Geer, 1773) is oligophagous on pomoideous host plants, whilst Aphis spiraecola Patch, 1914 is a polyphagous species alternating between Spiraea spp., its primary host, and a wide variety of secondary hosts, also including pomoideous species. Despite the biological distinction, these species are difficult to separate using their morphological characters. Partial sequences of mitochondrial COI and nuclear EF-1α genes were analyzed for samples from Central and Eastern Europe, Germany, Bulgaria, Italy, Turkey, China together with available data from GenBank. Interspecific pairwise sample divergences of the COI fragment ranged from 3.1 to 4.3%. One COI haplotype of A. pomi was predominant (n = 24), with a pan European distribution. The most abundant COI haplotype of A. spiraecola (n = 16) occurred in Lithuania, Latvia, Poland, Italy, Turkey and China. Interspecific pairwise sample divergences of the EF-1α fragment ranged from 0.6 to 1.2%. Analyzed partial sequences of EF-1α were identical in A. pomi. The most abundant EF-1α haplotype of A. spiraecola (n = 14) occurred in Lithuania, Poland, Italy, Turkey and China. The length of ultimate rostral segment appeared to be the most reliable morphological character for discrimination between apple and spirea aphid species. It allowed a 100% correct identification of A. pomi (n = 143) and 91.5% of A. spiraecola (n = 94) specimens in the European samples used for the molecular analysis. The existence of A. spiraecola in the Eastern Baltic region of Europe is documented for the first time. [ABSTRACT FROM AUTHOR]

The whitefly, Bemisia tabaci (Hemiptera: Aleyrodidiae), is a cryptic species complex comprising a minimum of 24 cryptic species. Some members of this complex are important agricultural pests, causing considerable damage to vegetable as well as ornamental and horticultural crops. Asia I, one of the cryptic species of B. tabaci, is widely distributed in Asia. One hundred and sixty mitochondrial cytochrome oxidase I (COI) sequences from eight countries have been analyzed to investigate the geographic origin and current genetic structure of this cryptic species. Sixty different haplotypes were identified, with levels of genetic distances ranging from 0.001 to 0.021. A sign of possible genetic differentiation emerges from the differential distribution of dominant haplotypes in Indonesia and India compared to China. A possible ancient separation between Asia I in India and Indonesia and secondary contact in China has been hypothesized. [ABSTRACT FROM AUTHOR]

Molecular markers facilitate the quantification of parasitization of pest species and the distinction of related parasitoid species. We designed new markers that allow the distinction of often misidentified Diadegma semiclausum and D. fenestrale parasitization in field-collected diamondback moth ( Plutella xylostella) larvae. The markers were applied to study if cornflower ( Centaurea cyanus) companion plants increase parasitization of the diamondback moth by Diadegma parasitoids in cabbage fields, as they do in the Mamestra brassicae- Microplitis mediator pest-parasitoid pair. Among 1708 P. xylostella larvae analyzed, we found a high parasitization rate (72.2 % total, 41.7 % by D. semiclausum, 24.9 % by D. fenestrale, 5.6 % by both), but no significant effects of cornflower presence. Our results highlight the need for species-specific markers and the specific action of companion plants. To increase natural control in crop fields, habitat management needs to be tailored to-and acts on-specific target species. [ABSTRACT FROM AUTHOR]