McAN: a novel computational algorithm and platform for constructing and visualizing haplotype networks.

Haplotype networks are graphs used to represent evolutionary relationships between a set of taxa and are characterized by intuitiveness in analyzing genealogical relationships of closely related genomes. We here propose a novel algorithm termed McAN that considers mutation spectrum history (mutations in ancestry haplotype should be contained in descendant haplotype), node size (corresponding to sample count for a given node) and sampling time when constructing haplotype network. We show that McAN is two orders of magnitude faster than state-of-the-art algorithms without losing accuracy, making it suitable for analysis of a large number of sequences. Based on our algorithm, we developed an online web server and offline tool for haplotype network construction, community lineage determination, and interactive network visualization. We demonstrate that McAN is highly suitable for analyzing and visualizing massive genomic data and is helpful to enhance the understanding of genome evolution. Availability: Source code is written in C/C++ and available at https://github.com/Theory-Lun/McAN and https://ngdc.cncb.ac.cn/biocode/tools/BT007301 under the MIT license. Web server is available at https://ngdc.cncb.ac.cn/bit/hapnet/. SARS-CoV-2 dataset are available at https://ngdc.cncb.ac.cn/ncov/. Contact: songshh@big.ac.cn (Song S), zhaowm@big.ac.cn (Zhao W), baoym@big.ac.cn (Bao Y), zhangzhang@big.ac.cn (Zhang Z), ybxue@big.ac.cn (Xue Y).

Genetic differentiation of Plasmodium vivax duffy binding protein in Ethiopia and comparison with other geographical isolates.

BACKGROUND: Plasmodium vivax Duffy binding protein (PvDBP) is a merozoite surface protein located in the micronemes of P. vivax. The invasion of human reticulocytes by P. vivax merozoites depends on the parasite DBP binding domain engaging Duffy Antigen Receptor for Chemokine (DARC) on these red blood cells (RBCs). PvDBPII shows high genetic diversity which is a major challenge to its use in the development of a vaccine against vivax malaria. METHODS: A cross-sectional study was conducted from February 2021 to September 2022 in five study sites across Ethiopia. A total of 58 blood samples confirmed positive for P. vivax by polymerase chain reaction (PCR) were included in the study to determine PvDBPII genetic diversity. PvDBPII were amplified using primers designed from reference sequence of P. vivax Sal I strain. Assembling of sequences was done using Geneious Prime version 2023.2.1. Alignment and phylogenetic tree constructions using MEGA version 10.1.1. Nucleotide diversity and haplotype diversity were analysed using DnaSP version 6.12.03, and haplotype network was generated with PopART version 1.7. RESULTS: The mean age of the participants was 25 years, 5 (8.6%) participants were Duffy negatives. From the 58 PvDBPII sequences, seven haplotypes based on nucleotide differences at 8 positions were identified. Nucleotide diversity and haplotype diversity were 0.00267 ± 0.00023 and 0.731 ± 0.036, respectively. Among the five study sites, the highest numbers of haplotypes were identified in Arbaminch with six different haplotypes while only two haplotypes were identified in Gambella. The phylogenetic tree based on PvDBPII revealed that parasites of different study sites shared similar genetic clusters with few exceptions. Globally, a total of 39 haplotypes were identified from 223 PvDBPII sequences representing different geographical isolates obtained from NCBI archive. The nucleotide and haplotype diversity were 0.00373 and 0.845 ± 0.015, respectively. The haplotype prevalence ranged from 0.45% to 27.3%. Two haplotypes were shared among isolates from all geographical areas of the globe. CONCLUSIONS: PvDBPII of the Ethiopian P. vivax isolates showed low nucleotide but high haplotype diversity, this pattern of genetic variability suggests that the population may have undergone a recent expansion. Among the Ethiopian P. vivax isolates, almost half of the sequences were identical to the Sal-I reference sequence. However, there were unique haplotypes observed in the Ethiopian isolates, which does not share with isolates from other geographical areas. There were two haplotypes that were common among populations across the globe. Categorizing population haplotype frequency can help to determine common haplotypes for designing an effective blood-stage vaccine which will have a significant role for the control and elimination of P. vivax.

Phylo-geo haplotype network-based characterization of SARS-CoV-2 strains circulating in India (2020-2022).

Background & objectives Genetic analysis of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) strains circulating in India during 2020-2022 was carried out to understand the evolution of potentially expanding and divergent clades. Methods SARS-CoV-2 sequences (n=612) randomly selected from among the sequences of samples collected through a nationwide network of Virus Research Diagnostic Laboratories during 2020 (n=1532) and Indian sequences available in Global Initiative on Sharing All Influenza Data during March 2020-March 2022 (n=53077), were analyzed using the phylo-geo haplotype network approach with reference to the Wuhan prototype sequence. Results On haplotype analysis, 420 haplotypes were revealed from 643 segregating sites among the sequences. Haplotype sharing was noted among the strains from different geographical regions. Nevertheless, the genetic distance among the viral haplotypes from different clades could differentiate the strains into distinct haplo groups regarding variant emergence. Interpretation & conclusions The haplotype analysis revealed that the G and GR clades were co-evolved and an epicentrefor the evolution of the GH, GK and GRA clades. GH was more frequently identified in northern parts of India than in other parts, whereas GK was detected less in north India than in other parts. Thus, the network analysis facilitated a detailed illustration of the pathways of evolution and circulation of SARS-CoV-2 variants.

Population structure and haplotype network analyses of Hyalomma anatolicum based on the large subunit ribosomal RNA (16S rRNA) gene.

Hyalomma anatolicum, an Anatolian hard tick is a well-recognized vector involved in the transmission of various pathogens to animals and humans. The present study elucidated the population structure and haplotype network of H. anatolicum based on the mitochondrial large subunit ribosomal RNA (16S rRNA) gene sequence. The population structure and haplotype network analysis of 75 sequences archived in the GenBank, including the 15 sequences generated herein, yielded 24 haplotypes. Haplotype 1 (Hap_1) was the predominant haplotype consisting of 45 sequences from India, China, Pakistan, Turkey, Egypt, Iraq, and Tajikistan. The complete haplotype network exhibited a stellate conformation, highlighting a recent population expansion. The overall dataset, together with the sequences corresponding to India, China, and Pakistan, showed a high haplotype (0.638 ± 0.065, 0.671 ± 0.103, 0.753 ± 0.099, and 0.854 ± 0.061, respectively) and low nucleotide (0.00407 ± 0.00090, 0.00525 ± 0.00196, 0.00680 ± 0.00233, and 0.00453 ± 0.00056, respectively) diversity, further emphasized a recent population expansion. The neutrality indices including Tajima's D, Fu and Li's D, and Fu and Li's F for the complete dataset (- 2.661, - 6.008, and - 5.649, respectively) as well as for the sequences from India (- 2.223, - 3.414, and - 3.567, respectively) were negative, suggesting deviation from neutrality and a recent population expansion. The present study provided novel insights into the population structure and haplotype networks of H. anatolicum based on the mitochondrial 16S rRNA gene, and the different tests inferred a low genetic differentiation and suggested a recent population expansion of this economically important tick species.

Phylogenetic analysis and haplotype networking of Hepatozoon felis infecting wild animals in Gir National Park, Gujarat, India.

The present study was aimed to determine the phylogenetic relationship, haplotype network, and demographic dynamics of H. felis infecting the endangered Asiatic lions in Gir National Park, Gujarat, India, on the basis of partial 18S rRNA gene. The phylogenetic analysis based on the partial 18S rRNA gene sequences of H. felis exhibited the presence of two distinct genotypes of H. felis (HfG1 and HfG2) infecting the Indian wild felids, viz., the Asiatic lion, Royal Bengal tiger, and Indian leopard. The HfG1 and HfG2 genotypes exhibited 97.6-100% and 99.7-100%, and 96.9-98.7% nucleotide identity within and between themselves, respectively. The HfG1 genotype exhibited a higher genetic diversity as compared to HfG2. A total of 22 molecular signatures were identified in the 18S rRNA gene between these genotypes. Further, analysis of a total 67 sequences of H. felis (13 different host species from 13 countries of Africa, South America, Asia, and Europe) that were downloaded from GenBankTM, generated 30 haplotypes. Among all the haplotypes, Hap_17 (h=12) was the most frequent followed by Hap_12 (h=09) and Hap_4 (h=05). Out of 13 location-wise populations, India (h=12) shared the highest number of haplotypes followed by Japan (h=08), and the least number of haplotypes were found in Hungary (h=02). Population dynamics study involving neutrality tests and mismatch distribution, and genetic differentiation indices, revealed the presence of phylogeographic population structure and a constant population size indicating a uniform gene flow among the populations worldwide. In conclusion, a high genetic diversity along with the presence of two distinct genotypes of H. felis were observed on the basis of 18S rRNA gene sequence analysis.

Global genomic signature reveals the evolution of fall armyworm in the Eastern hemisphere.

The major plant pest fall armyworm (FAW), Spodoptera frugiperda, is native to the Americas and has colonized Africa and Asia within the Eastern hemisphere since 2016, causing severe damage to multiple agricultural crop species. However, the genetic origin of these invasive populations requires more in-depth exploration. We analysed genetic variation across the genomes of 280 FAW individuals from both the Eastern hemisphere and the Americas. The global range-wide genetic structure of FAW shows that the FAW in America has experienced deep differentiation, largely consistent with the Z-chromosomal Tpi haplotypes commonly used to differentiate 'corn-strain' and 'rice-strain' populations. The invasive populations from Africa and Asia are different from the American ones and have a relatively homogeneous population structure, consistent with the common origin and recent spreading from Africa to Asia. Our analyses suggest that north- and central American 'corn-strain' FAW are the most likely sources of the invasion into the Eastern hemisphere. Furthermore, evidence based on genomic, transcriptomic and mitochondrial haplotype network analyses indicates an earlier, independent introduction of FAW into Africa, with subsequent migration into the recent invasive population.

Molecular and Morphological Assessment of Juvenile and Adult Forms in the Giant Worm Eunice Cf. Aphroditois (Annelida: Eunicidae) and Its Phylogenetic Position in the Family.

Eunice aphroditois (Pallas, 1788) is a large polychaete worm (up to 3 m in length) and the type species of the genus. In Japan, a similar but potentially different species, Eunice cf. aphroditois, is distributed mainly in the rocky shores of the temperate and warm Pacific coasts. Juveniles and adults were suggested to be distinguished by their body color. The juvenile form was previously regarded as distinct species, Eunice flavopicta Izuka, 1912 and Eunice ovalifera Fauvel, 1936, although they are now considered synonymous with E. aphroditois. In this study, we revisited the validity of the present taxonomy based on morphological observations including SEM and microCT, and three molecular markers (cytochrome c oxidase subunit I [COI], 16S rRNA, and histone H3 genes) and investigated the phylogenetic position of E. cf. aphroditois in the family Eunicidae using the combined dataset of three genes (COI + 16S rRNA + 18S rRNA). The adult and juvenile forms were different in body size, color, the distribution of the branchiae and subacicular hooks, and maxillae shape, but not in other characteristics. One individual showed an intermediate body color between the two forms. The adult and juvenile forms shared major haplotypes and the maximum K2P genetic distance of COI was 1.7%, which can be considered within intraspecific variation. In the phylogenetic tree based on the combined gene dataset, E. cf. aphroditois was closely related to Eunice roussaei Quatrefages, 1866 and Eunice cf. violaceomaculata Ehlers, 1887, which are large species from the Mediterranean Sea and the Caribbean Sea, respectively.

Molecular investigation of bovine tropical theileriosis outbreak in an organized dairy cattle farm in Madhya Pradesh, India.

The present study aimed to investigate an outbreak of Theileria annulata (T. annulata) infection in an organized dairy cattle farm in Madhya Pradesh, India, using clinical and molecular techniques. Following the deaths of two crossbred cattle in March 2021, 43 blood samples were collected from infected and apparently healthy animals and examined by blood smear and polymerase chain reaction (PCR) techniques. The blood smear examination showed that 23.25% of samples were positive for Theileria organisms, while conventional PCR targeting the 18S ribosomal RNA (18S rRNA) and T. annulata merozoite surface antigen-1 (TAMS-1) genes revealed that 32.55% of samples were positive for T. annulata. PCR targeting cytochrome b (Cytb) gene showed 46.51% of samples were positive for T. annulata. Haematological analysis confirmed clinical signs of infection in affected animals, which were treated with buparvaquone @ 2.5 mg/kg body weight intramuscularly along with supportive medicine. Two 18S rRNA gene amplicons were sequenced and analysed in a phylogenetic tree and haplotype network with 54 Indian and 38 foreign sequences. The phylogenetic tree revealed two groups with a high posterior probability and bootstrap value, while the haplotype network revealed 35 haplotypes, with haplotype 1 (H1) being the most abundant and several single haplotypes clustering around it, indicating fast and widespread expansion. Genetic diversity indices and neutrality tests confirmed that the population was expanding. These studies highlight the significance of prompt and precise diagnosis and management of T. annulata outbreaks and provide insights into its evolutionary history and population dynamics of T. annulata in India, which could aid improving disease preventive and control strategies.

Molecular and morphological characterization of Andracantha gravida (Alegret, 1941) (Acanthocephala: Polymorphidae) in piscivorous birds from the Gulf of Mexico.

Adult specimens of Andracantha gravida (Alegret, 1941) were recorded from the intestines of the double-crested cormorant Nannopterum auritus (Lesson) (type host) and brown pelican Pelecanus occidentalis L. in two localities from Mexico: Celestún, Yucatan (south-eastern) and Punta Piedra, Tamaulipas (north-eastern). The specimens of A. gravida are morphologically characterized by having a pipe-shaped body without swellings, the absence of small trunk spines between the two fields of spines on the foretrunk and a cylindrical proboscis with 14-16 rows of 10-12 hooks per row. Newly generated partial sequences of the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene were generated from adult isolates of A. gravida from Mexico and compared with one sequence of A. gravida and with sequences of other polymorphid acanthocephalans available in GenBank. Phylogenetic analyses based on maximum likelihood and Bayesian inference methods of the cox1 dataset placed all the species of Andracantha in a single clade, with weak support. The analyses of the cox1 dataset placed Andracantha sigma Presswell, García-Varela & Smales, , as sister to the clade formed by A. gravida, Andracantha phalacrocoracis (Yamaguti, 1939), Andracantha leucocarboi Presswell, García-Varela & Smales, and an unidentified species of Andracantha from Japan. The newly generated cox1 sequences of A. gravida from piscivorous birds of Mexico formed a strongly supported clade with the published sequence of A. gravida from the double-crested cormorant from the south-eastern coast of Mexico. The intraspecific genetic divergence among isolates identified as A. gravida ranged from 0.0% to 2.2%. A cox1 haplotype network inferred with 14 sequences revealed the presence of nine haplotypes, two of which were shared between the populations of piscivorous birds from the north-eastern and south-eastern coasts of Mexico and seven of which were unique. The fixation index between the populations from north-eastern and south-eastern Mexico was low (0.06949), which suggests genetic flow. This can be explained by the migration patterns of the brown pelican and the double-crested cormorant along the coasts of the Gulf of Mexico.

A new isolate of Mesorhabditis monhystera (Bütschli, 1873) Dougherty, 1955 (Rhabditida: Rhabditidae): re-evaluated with molecular data and scanning electron microscopic observations.

A new isolate of Mesorhabditis monhystera (Bütschli, ) Dougherty, is described and illustrated with morphological and molecular data. The phylogenetic analysis based on the D2/D3 segment of 28S rDNA using the Bayesian inference method, revealed monophyly of the genus Mesorhabditis as the subordinate taxa clustered in one clade. The clade further divided into two subclades representing the Monhystera-group and Spiculigera-group with 100% posterior probability values. However, GenBank sequences of several species constituting the Monhystera-group, showed high similarity and very little genetic divergence (98-99%) of up to 4-5 bases. In order to ascertain the status of those isolates, detailed morphological comparison is provided along with a pictorial key. A sequence-based phylogeography of haplogroups of Mesorhabditis using the median-joining network method, was also inferred. The results suggested the need for morphological validation of a species before its sequences are deposited in GenBank.

The evolutionary history of the Caribbean magnolias (Magnoliaceae): Testing species delimitations and biogeographical hypotheses using molecular data.

The Caribbean islands provide an ideal setting for studying biodiversity, given their complex geological and environmental history, and their historical and current geographical proximity to the American mainland. Magnolia, a flagship tree genus that has 15 endemic and threatened taxa (12 species and 3 subspecies) on the Caribbean islands, offers an excellent case study to empirically test Caribbean biogeographical hypotheses. We constructed phylogenetic hypotheses to: (1) reveal their evolutionary history, (2) test the current largely morphology-based classification and assess species limits, and (3) investigate major biogeographic hypotheses proposed for the region. Nuclear and chloroplast DNA sequence data of all 15 Caribbean Magnolia taxa are included, supplemented by a selection of American mainland species, and species representing most major clades of the Magnoliaceae family. We constructed phylogenetic hypotheses in a time-calibrated Bayesian framework, supplemented with haplotype network analyses and ancestral range estimations. Genetic synapomorphies in the studied markers confirm the species limits of 14 out of 15 morphologically recognizable Caribbean Magnolia taxa. There is evidence for four colonization events of Magnolia into the Caribbean from the American mainland, which most likely occurred by overwater dispersal, given age estimates of maximum 16 mya for their presence on the Caribbean islands.

Comprehensive analysis of mitogenome of native Henan pig breeds with 58 worldwide pig breeds.

Mitochondria follow non-Mendelian maternal inheritance, and thus can be used to compare genetic diversity and infer the expansion and migration between animal populations. Based on the mitochondrial DNA sequences of 58 pig breeds from Asia, Europe, Oceania, and America, we observed a distinct division of Eurasian pig species into two main Haplogroups (A and B), with the exception of the Berkshire and Yorkshire breeds. Oceanian pigs were much more similar to European and American pigs in Haplogroup A. Additionally, native Chinese pigs exhibited the most abundant genetic polymorphisms and occupied the centre of Haplogroup B. Miyazaki (Japan) and Siberia (Russia) are two distant and disconnected regions; however, most pigs from these regions were clustered into a subcluster, while native pigs from Korea clustered into a second subcluster. This study is the first to report that pigs from Thailand and Vietnam had haplotypes similar to those of Henan, where the earliest evidence of domestic pigs was found from the Yellow River Basin of North China. Local Henan pig breeds are related to many Asian breeds while still having their own mutation identity, such as g.314 delins T>AC/AT/C of the 12S rRNA gene in Yuxi. Some pigs from Palawan, Itbayat, and Batan Islands of the Philippines and Lanyu Island of China were distinct from other Asian pigs and clustered together into Haplogroup C. These findings show that the complexity of domestication of worldwide pig breeds and mitochondria could reflect genetic communication between pig breeds due to geographical proximity and human activities.

Novel real-time PCR assay detects widespread distribution of knock down resistance (kdr) mutations associated with pyrethroid resistance in the mosquito, Culex quinquefasciatus, in Thailand.

Susceptibility to pyrethroids in the mosquito Culex quinquefasciatus, the major vector of lymphatic filariasis, is being seriously threatened worldwide. Knockdown resistance (kdr), caused by mutations in the voltage gated sodium channel (VGSC) gene, particularly the L1014F mutation, is an important resistance mechanism. Our aim was to develop a real-time PCR with melt curve analysis to evaluate the distribution of the L1014F mutation in Cx. quinquefasciatus throughout Thailand and to determine the polymorphism pattern of a VGSC gene fragment spanning the L1014F mutation. A total of 3760 females from 18 localities across five regions of Thailand were bio-assayed by exposure to 0.05% deltamethrin WHO papers, showing mortality rates ranging from 2.4% to 83.0%. Genotyping of 753 dead and surviving mosquitoes using our novel real-time PCR assay with melt curve analysis and tetra-primer allele-specific PCR revealed the mutant F1014 allele is closely associated with the deltamethrin resistance phenotype. The L1014F mutation was found at high frequency throughout Thailand, particularly in the North. However, some survivors were homozygous for wild type L1014 allele, which were further sequenced for the IIP-IIS6 region of VGSC gene. The haplotype network of phenotypically characterized individuals indicated the presence of other possible kdr alleles/resistance mechanisms at play including two novel mutations, V978E and D992E. The finding of new putative kdr alleles and widespread distribution of the F1014 allele emphasizes the significant role of kdr mutations in pyrethroid resistance in Thai Cx. quinquefasciatus populations. Monitoring kdr variations and phenotypic resistance is critical for managing resistance in Cx. quinquefasciatus.

Identification and Pathogenicity of Fungi Associated with Leaf Spot of Muskmelon in Eastern Shandong Province, China.

Leaf spot is a serious disease in the growth and development of muskmelon, which can affect its quality and yield. Over the past years, Malianzhuang Muskmelon Base, the main muskmelon producing area in Shandong Province, China, has been seriously affected by leaf spot. Since 2018, symptomatic leaves were collected from 11 production areas of this base to determine the pathogens of muskmelon foliar diseases. Two-hundred fungal strains were isolated and 10 genera and 17 species were identified based on morphological characteristics and multilocus phylogenetic analysis (ITS, GADPH, RPB2, HIS3, EF-1α, and LSU). The most frequently isolated species from each sampling area was Alternaria tenuissima with 77 strains, followed by A. alternata. Pathogenicity experiments showed that A. alternata, A. tenuissima, Fusarium neocosmosporiellum (formerly Neocosmospora vasinfecta), F. acuminatum, Exserohilum rostratum, Bipolaris sorokiniana, and Stagonosporopsis cucurbitacearum (formerly Didymella bryoniae) could cause symptoms highly similar to those of infected leaves observed under natural conditions in the field. Therefore, these fungal isolates are considered to be the primary pathogens causing muskmelon leaf spot, and A. tenuissima and A. alternata were the most common and virulent pathogens in this study. In addition, this is the first study of F. neocosmosporiellum, F. acuminatum, E. rostratum, and B. sorokiniana as pathogens associated to muskmelon leaf spot in China as well as the world.

The importance of DNA barcode choice in biogeographic analyses - a case study on marine midges of the genus Clunio.

DNA barcodes are widely used for species identification and biogeographic studies. Here, we compare the use of full mitochondrial genomes versus DNA barcodes and other mitochondrial DNA fragments for biogeographic and ecological analyses. Our dataset comprised 120 mitochondrial genomes from the genus Clunio (Diptera: Chironomidae), comprising five populations from two closely related species (Clunio marinus and Clunio balticus) and three ecotypes. We extracted cytochrome oxidase c subunit I (COI) barcodes and partitioned the mitochondrial genomes into non-overlapping windows of 750 or 1500 bp. Haplotype networks and diversity indices were compared for these windows and full mitochondrial genomes (15.4 kb). Full mitochondrial genomes indicate complete geographic isolation between populations, but do not allow for conclusions on the separation of ecotypes or species. COI barcodes have comparatively few polymorphisms, ideal for species identification, but do not resolve geographic isolation. Many of the similarly sized 750 bp windows have higher nucleotide and haplotype diversity than COI barcodes, but still do not resolve biogeography. Only when increasing the window size to 1500 bp, two windows resolve biogeography reasonably well. Our results suggest that the design and use of DNA barcodes in biogeographic studies must be carefully evaluated for each investigated species.

Global Distribution and Variation of the Invasive Cheilostome Bryozoan Cribrilina mutabilis.

Viable populations of the cheilostome bryozoan Cribrilina mutabilis Ito, Onishi & Dick exist in the NW Pacific (Russian Far East and northern Japan), NE Atlantic (Scandinavia and Scotland), and NW Atlantic (Maine, USA). The first NE and NW Atlantic records are from Norway (2008) and Casco Bay, Maine, USA (2018), respectively, indicating a relatively recent introduction to the region. Mitochondrial COI gene sequences from North Atlantic populations (Sweden, Norway, and Maine) showed two haplotypes differing by one substitution, but differed from two haplotypes from Akkeshi, northern Japan, by 6-8 substitutions. North Atlantic populations differed morphologically from the Akkeshi population in that some zooids formed a suboral projection, and frontal zooids were more common. While C. mutabilis in northern Japan has been found only on natural or artificial eelgrass (Zostera marina), across its range it has been found on several species of algae, plastic panels and strips, several species of Zostera, and mollusc shells. Similar frequencies of heteromorphic zooids with differing degree of frontal wall calcification, i.e., R (rib)-, I (intermediate)-, and S (shield)-type zooids, in colonies on eelgrass at comparable times of the season and across populations suggest an innate response to seasonal environmental fluctuations, although zooid frequencies were different on non-eelgrass substrates. The increase in trans-Arctic shipping along the Northern Sea Route in recent decades, and previous documentation of C. mutabilis on ship hulls in the Sea of Japan, indicate a clear mechanism for anthropogenic introduction from the Far East to Europe in recent decades.

Origin of the critically endangered endemic species Scrophularia takesimensis (Scrophulariaceae) on Ulleung Island, Korea: implications for conservation.

Scrophularia takesimensis is a critically endangered endemic species of Ulleung Island, Korea. A previous molecular phylogenetic study based on nuclear ribosomal DNA (nrDNA) internal transcribed spacer (ITS) sequences with very limited sampling suggested that it is most closely related to the clade comprising S. alata and S. grayanoides. To determine the origin of S. takesimensis, we sampled a total of 171 accessions including S. takesimensis (9 populations and 63 individuals) and two closely related species, S. alata (11 populations and 68 individuals) and S. grayanoides (5 populations and 40 individuals) from eastern Asia and sequenced ITS and two chloroplast DNA (cpDNA) non-coding regions. Previously sequenced representative species of Scrophularia (109 taxa for ITS and 80 taxa for cpDNA) were combined with our data set and analyzed. While the global scale ITS phylogenetic tree suggests monophyly for each of the three eastern Asian species, S. takesimensis appears to be more closely related (albeit weakly) to a clade containing eastern North American/Caribbean species than to either S. alata or S. grayanoides. By contrast, the global scale cpDNA phylogenetic tree demonstrates that the eastern North America/Caribbean clade is sister to a clade comprising the three eastern Asian species. In addition, the monophyletic S. takesimensis is deeply embedded within paraphyletic S. alata, sharing its most recent common ancestor with populations from Japan/Sakhalin. Two divergent, geographically structured cp haplotype groups within S. takesimensis suggest at least two independent introductions from different source areas. A new and accurate chromosome number of S. takesimensis (2n = 94) is reported and some conservation strategies are discussed.

Inferring boundaries among fish species of the new world silversides (Atherinopsidae; genus Odontesthes): new evidences of incipient speciation between marine and brackish populations of Odontesthes argentinensis.

Species of new world silversides (Actinopterygii; Atherinopsidae; genus Odontesthes) possess economic relevance, biological interest and ecological importance. In the present paper we: (A) investigate the molecular diversity in marine species of Odontesthes from the South West Atlantic Ocean (SWAO), and analyse their interspecific relationships and divergence by means of DNA Barcoding, including its freshwater congeners, as well. (B) Explore the suitability of DNA Barcoding to analyse the diversity and distribution of haplotypes in Odontesthes argentinensis, the only well documented marine species from the SWAO that exhibit putative estuarine and marine populations. Molecular analysis revealed 100% of agreement between morphological identification and molecular identity. Odontesthes argentinensis, Odontesthes platensis, Odontesthes smitti, Odontesthes nigricans and Odontesthes incisa were assigned to five different barcode index numbers (BINs). Maximum-likelihood analysis showed that all marine species of Odontesthes clustered separately in a unique monophyletic phylogroup, comprising five well defined haplogroups, with genetic divergence between groups ranging from 2.75 to 7.11%. The genetic analysis including freshwater congeners showed that O. incisa clustered alone occupying a basal position. The Fst pairwise comparisons within O. argentinensis support the existence of three population groups: one conformed by Mar Chiquita Lagoon (MCh) specimens, and the others by Mar del Plata/Mar Chiquita coast and San Blas Bay coastal specimens, respectively. The AMOVA showed significant overall differentiation (Fst = 0.238; p = 0.00001) for the entire data set. The previous/present evidence is discussed, and strongly suggests that incipient speciation is occurring in O. argentinensis argentinean populations, and specimens from MCh would be considered at present as the leading candidate of a marine to freshwater incipient speciation event.

Anadromy and heterogenous population of a tropical shad Tenualosa ilisha in Malaysia, as revealed by otolith microchemistry and molecular evidence.

Tenualosa ilisha was found recently in the Perak River in western Peninsular Malaysia. Molecular phylogenetic and haplotype network analyses suggest that T. ilisha has two genetically distinct populations/groups: (i) Peninsular Malaysia (Malaysia population), and (ii) Peninsular Malaysia, Thailand, India and Bangladesh (Indian Ocean population). The results also suggest that the T ilisha population in Peninsular Malaysia is genetically heterogeneous with a typical anadromous migration pattern.

Short communication: New data support phylogeographic patterns in a marine parasite Tristriata anatis (Digenea: Notocotylidae).

Intraspecific diversity in parasites with heteroxenous life cycles is guided by reproduction mode, host vagility and dispersal, transmission features and many other factors. Studies of these factors in Digenea have highlighted several important patterns. However, little is known about intraspecific variation for digeneans in the marine Arctic ecosystems. Here we analyse an extended dataset of partial cox1 and nadh1 sequences for Tristriata anatis (Notocotylidae) and confirm the preliminary findings on its distribution across Eurasia. Haplotypes are not shared between Europe and the North Pacific, suggesting a lack of current connection between these populations. Periwinkle distribution and anatid migration routes are consistent with such a structure of haplotype network. The North Pacific population appears ancestral, with later expansion of T. anatis to the North Atlantic. Here the parasite circulates widely, but the direction of haplotype transfer from the north-east to the south-west is more likely than the opposite. In the eastern Barents Sea, the local transmission hotspot is favoured.