Haplotype Network Analysis Research Articles

Italian odonates in the Pandora's box: A comprehensive DNA barcoding inventory shows taxonomic warnings at the Holarctic scale.

The Odonata are considered among the most endangered freshwater faunal taxa. Their DNA-based monitoring relies on validated reference data sets that are often lacking or do not cover important biogeographical centres of diversification. This study presents the results of a DNA barcoding campaign on Odonata, based on the standard 658-bp 5' end region of the mitochondrial COI gene, involving the collection of 812 specimens (409 of which barcoded) from peninsular Italy and its main islands (328 localities), belonging to all the 88 species (31 Zygoptera and 57 Anisoptera) known from the country. Additional BOLD and GenBank data from Holarctic samples expanded the data set to 1,294 DNA barcodes. A multi-approach species delimitation analysis involving two distance (OT and ABGD) and four tree-based (PTP, MPTP, GMYC and bGMYC) methods was used to explore these data. Of the 88 investigated morphospecies, 75 (85%) unequivocally corresponded to distinct molecular operational units, whereas the remaining ones were classified as 'warnings' (i.e. showing a mismatch between morphospecies assignment and DNA-based species delimitation). These results are in contrast with other DNA barcoding studies on Odonata showing up to 95% of identification success. The species causing warnings were grouped into three categories depending on if they showed low, high or mixed genetic divergence patterns. The analysis of haplotype networks revealed unexpected intraspecific complexity at the Italian, Palearctic and Holarctic scale, possibly indicating the occurrence of cryptic species. Overall, this study provides new insights into the taxonomy of odonates and a valuable basis for future DNA and eDNA-based monitoring studies.

From Persian Gulf to Indonesia: interrelated phylogeographic distance and chemistry within the genus Peronia (Onchidiidae, Gastropoda, Mollusca)

The knowledge of relationships between taxa is essential to understand and explain the chemical diversity of the respective groups. Here, twelve individuals of the panpulmonate slug Peronia persiae from two localities in Persian Gulf, and one animal of P. verruculata from Bangka Island, Indonesia, were analyzed in a phylogenetic and chemotaxonomic framework. Based on the ABGD test and haplotype networking using COI gene sequences of Peronia specimens, nine well-supported clades were found. Haplotype network analysis highlighted a considerable distance between the specimens of P. persiae and other clades. Metabolomic analysis of both species using tandem mass spectrometry-based GNPS molecular networking revealed a large chemical diversity within Peronia of different clades and localities. While P. persiae from different localities showed a highly similar metabolome, only few identical chemical features were found across the clades. The main common metabolites in both Peronia species were assigned as polypropionate esters of onchitriols and ilikonapyrones, and osmoprotectant amino acid-betaine compounds. On the other hand, the isoflavonoids genistein and daidzein were exclusively detected in P. persiae, while cholesterol and conjugated chenodeoxycholic acids were only found in P. verruculata. Flavonoids, bile acids, and amino acid-betaine compounds were not reported before from Onchidiidae, some are even new for panpulmonates. Our chemical analyses indicate a close chemotaxonomic relation between phylogeographically distant Peronia species.

Integrative taxonomy reveals a cryptic species of the nudibranch genus Polycera (Polyceridae) in European waters

AbstractThis work aimed to test whether the colour variability featured by the European nudibranch Polycera quadrilineata is consistent with the concept of a single polychromatic species or may hide multiple lineages. Samples from across the geographic range of P. quadrilineata together with representatives from worldwide species with a focus on Atlantic diversity, were gathered and studied using an integrative taxonomic approach. Morpho-anatomical characters were investigated by light and scanning electron microscopy. Bayesian molecular phylogenetics using MrBayes, the Automatic Barcode Gap Discovery species delimitation method, and haplotype network analysis using the PopArt software were employed to help delimit species using the mitochondrial gene cytochrome c oxidase subunit I (COI). The results supported the existence of a second species, here described and named Polycera norvegica sp. nov., only known from Norway where it is sympatric with P. quadrilineata. The COI uncorrected p-genetic distance between the two species was estimated at 9.6–12.4%. Polycera norvegica sp. nov. differs by exhibiting a black dotted or patchy dotted pattern occasionally with more or less defined orange/brown patches, but never black continuous or dashed stripes as in P. quadrilineata. The two species share a common colouration with a whitish base and yellow/orange tubercles. Anatomically, P. norvegica sp. nov. has a weaker labial cuticle, a smaller radula with fewer rows, and only four marginal teeth, a reproductive system with a single lobed bursa copulatrix, shorter reproductive ducts, and a penis armed with two kinds of spines: needle-like and hook-shaped penile spines.

Identical 18S rRNA haplotypes of Hepatozoon canis in dogs and foxes in Brandenburg, Germany

Hepatozoon canis is a blood parasite of the suborder Adeleorina infecting wild and domestic canids. Transmission occurs by oral uptake of Rhipicephalus sanguineus sensu lato vector ticks infected with H. canis, but vertical transmission is also assumed to be possible. In German foxes, a high prevalence of H. canis has previously been reported despite the fact that R. sanguineus s.l. is not endemic. In the absence of knowledge about local transmission pathways, foxes should be considered to be possible reservoirs of H. canis and contribute to infection of domestic dogs. The present study aimed to determine how often foxes and dogs are infected in Brandenburg (Germany) and if identical or different H. canis 18S rRNA haplotypes are found in these host species. Hepatozoon spp. were detected by PCR in 46/1050 (4.4 %) of dog blood and 176/201 (77.6 %) of fox spleen samples from Brandenburg. Sequencing of 19 dog and 56 fox samples identified all as H. canis. For nine positive dogs, owners stated that they had never left Germany suggesting that autochthonous transmission occurs not only in foxes but also in dogs. Sequences for seven of these possible autochthonous cases were obtained and six were identical to the predominant haplotype found in the foxes. Haplotype network analysis confirmed that many dogs, including some without travel history, carried the same or very similar 18S rRNA haplotypes as the foxes suggesting that both hosts participate in the same epidemiological cycle.

Tracing temporal and geographic distribution of resistance to pyrethroids in the arboviral vector Aedes albopictus.

BackgroundThe arboviral vector Aedes albopictus became established on all continents except Antarctica in the past 50 years. A consequence of its rapid global invasion is the transmission of diseases previously confined to the tropics and subtropics occurring in temperate regions of the world, including the re-emergence of chikungunya and dengue in Europe. Application of pyrethroids is among the most widely-used interventions for vector control, especially in the presence of an arboviral outbreak. Studies are emerging that reveal phenotypic resistance and monitor mutations at the target site, the para sodium channel gene, primarily on a local scale.MethodsA total of 512 Ae. albopictus mosquitoes from twelve geographic sites, including those from the native home range and invaded areas, were sampled between 2011 and 2018, and were analyzed at five codons of the para sodium channel gene with mutations predictive of resistance phenotype. Additionally, to test for the origin of unique kdr mutations in Mexico, we analyzed the genetic connectivity of southern Mexico mosquitoes with mosquitoes from home range, the Reunion Island, America and Europe.ResultsWe detected mutations at all tested positions of the para sodium channel gene, with heterozygotes predominating and rare instance of double mutants. We observed an increase in the distribution and frequency of F1534C/L/S mutations in the ancestral China population and populations in the Mediterranean Greece, the appearance of the V1016G/I mutations as early as 2011 in Italy and mutations at position 410 and 989 in Mexico. The analyses of the distribution pattern of kdr alleles and haplotype network analyses showed evidence for multiple origins of all kdr mutations.ConclusionsHere we provide the most-up-to-date survey on the geographic and temporal distribution of pyrethroid-predictive mutations in Ae. albopictus by combining kdr genotyping on current and historical samples with published data. While we confirm low levels of pyrethroid resistance in most analyzed samples, we find increasing frequencies of F1534C/S and V1016G in China and Greece or Italy, respectively. The observed patterns of kdr allele distribution support the hypothesis that on site emergence of resistance has contributed more than spread of resistance through mosquito migration/invasions to the current widespread of kdr alleles, emphasizing the importance of local surveillance programs and resistance management.

A molecular phylogeny of the genus Laubuka (Teleostei: Cyprinidae) in Sri Lanka reveals multiple origins and a cryptic species

The freshwater-fish genus Laubuka contains ∼13 species distributed through the lowlands of tropical South and South-east Asia. Four of these species (Laubuka lankensis, L. varuna, L. ruhuna, and L. insularis) are reported as endemic to Sri Lanka, a remarkable datum given the island’s small size. We sampled populations of Laubuka at 56 locations in 14 of the island’s principal river basins and analysed their morphological, meristic, phylogenetic, and phylogeographic relationships using the mitochondrial genes cytochrome b and cytochrome c oxidase subunit 1 and the nuclear recombination activating protein 1. We investigated the geographic structure, and delineated species using molecular species delimitation methods and morphological analysis within the general lineage concept of species. Molecular and morphological analyses failed to identify L. ruhuna and L. insularis as distinct species; we show them to be synonyms of L. varuna and L. lankensis, respectively. Taxonomic inflation in previous literature is attributed as a result of limited sampling and negligence of size allometry. Additionally, a third, cryptic species discovered in this study is described as L. hema sp. nov. which is evidently confined to the headwaters of the Gal basin in eastern Sri Lanka. Phylogenetic and haplotype network analyses suggest phylogeographic structure within both the southwest-endemic L. varuna and the dry-zone endemic L. lankensis, but the former shows strong phylogeographic structure between adjacent basins. The Sri Lankan species of Laubuka do not form a monophyletic group: they stem from two dispersal or vicariance events, one involving the lineage that led to L. varuna in south-western Sri Lanka, and the other, of [L. lankensis + L. hema] in the dry zone. http://zoobank.org/urn:lsid:zoobank.org:pub:D2A29329-E0E7-447E-B316-81049212CCCBhttp://zoobank.org/urn:lsid:zoobank.org:act:920E5DC0-CEDC-4243-98C7-12CCF829CBCD

Mitochondrial COI Sequence Variations within and among Geographic Samples of the Hemp Pest Psylliodes attenuata from China.

The hemp flea beetle Psylliodes attenuata (Coleoptera: Chrysomelidae: Psylliodes) is a common pest of Cannabis sativa, including cultivars of both industrial hemp and medicinal marijuana. Both the larval and adult stages of this beetle can cause significant damages to C. sativa, resulting in substantial crop losses. At present, little is known about the populations of this pest, including its genetic diversity. In this study, we obtained 281 P. attenuata samples from nine field sites representing broad industrial hemp productions in China and analyzed their DNA sequences at the mitochondrial COI gene, the insect DNA barcode. Our analyses revealed a total of 48 haplotypes, with 28 being found only in one specimen each while the remaining 20 were shared by two or more specimens each. Of the 20 shared haplotypes, eight were shared among local populations often from far away locations, consistent with recent long-distance dispersals. However, the observed putative long-distance dispersals have not obscured the significant genetic differentiations among the regional populations from northeastern, eastern, central and southwestern China. Interestingly, haplotype network analyses suggest evidence for potential mitochondrial recombination in natural populations of this species. We briefly discuss the implications of our results on its evolution, center of diversity, route of spread, and pest management strategies in hemp fields.

Identification and genetic analysis of qCL1.2, a novel allele of the \u201cgreen revolution\u201d gene SD1 from wild rice (Oryza rufipogon) that enhances plant height

BackgroundThe exploitation of novel alleles from wild rice that were lost during rice cultivation could be very important for rice breeding and evolutionary studies. Plant height (PH) was a target of artificial selection during rice domestication and is still a target of modern breeding. The “green revolution” gene semi-dwarf 1 (SD1) were well documented and used in the past decades, allele from wild rice could provide new insights into the functions and evolution of this gene.ResultsWe identified a PH-related quantitative trait locus, qCL1.2,from wild riceusing a set of chromosome segment substitution lines. qCL1.2encodesa novel allele of SD1 gene. The wild allele of SD1 is a dominant locus that can significantly promote rice internode length by regulating the expression levels of genes involved in gibberellin biosynthesis and signal transduction. Nucleotide diversity and haplotype network analyses of the SD1 gene were performed using 2822 rice landraces. Two previously reported functional nucleotide polymorphisms clearly differentiated japonica and indica rice; however, they were not associated with PH selection. Other new functional nucleotide polymorphisms in the coding, but not promoter, regions were involved in PH selection during rice domestication. Our study increasesunderstanding of the rice SD1 gene and provides additional evidence of this gene’s selection during rice domestication.ConclusionsOur findings provide evidence thatSD1 gene from wild rice enhances plant height and new functional nucleotide polymorphisms of this gene were artificially selected during cultivated rice differentiation.

SARS-CoV-2 Genome Analysis of Japanese Travelers in Nile River Cruise.

Japan has reported 26 cases of coronavirus disease 2019 (COVID-19) linked to cruise tours on the River Nile in Egypt between March 5 and 15, 2020. Here, we characterized the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome of isolates from 10 travelers who returned from Egypt and from patients possibly associated with these travelers. We performed haplotype network analysis of SARS-CoV-2 isolates using genome-wide single-nucleotide variations. Our analysis identified two potential Egypt-related clusters from these imported cases, and these clusters were related to globally detected viruses in different countries.

Occurrence and ecological implication of a tropical anguillid eel, Anguilla marmorata, in Brunei Darussalam, Borneo Island

Tropical anguillid eels account for two-thirds of the 19 species in Anguilla Schrank, 1798. However, information on the species diversity, geographical distribution, and life histories of the tropical eels is very limited. Recent studies suggested that morphological species identification of the tropical anguillid eels should be validated by molecular analysis for accurate identification. After surveying for three years, two anguillid eels were found in Brunei Darussalam, Borneo Island. They were firstly identified as Anguilla marmorata Quoy & Gaimard, 1824 using morphological analysis and further gene analysis of cytochrome c oxidase subunit I (COI) confirmed the species identification. This study is the first comprehensive description of A. marmorata in Brunei Darussalam, Borneo Island. Furthermore, it is also the first study to validate two anguillid eels collected from the tropical Bonin Islands of Japan as A. marmorata by means of morphological and COI analyses. The molecular phylogenetic tree and haplotype network analyses suggest that A. marmorata found in Brunei Darussalam would belong to the North Pacific population of the westernmost distribution.

Molecular identity of the Antarctic heteronemertean Parborlasia corrugata (Nemertea: Pilidiophora) from Lützow-Holm Bay

The Antarctic heteronemertean Parborlasia corrugata (McIntosh, 1876) (originally Lineus corrugatus) shows a circumpolar distribution in the Southern Ocean, putatively with high dispersal capacity of the planktonic larva. From the eastern coast of Lützow-Holm Bay near Syowa Station (69°00′S, 39°35′E), several records of heteronemerteans have been made under the name of Lineus corrugatus. However, they have never been explicitly identified by molecular data. In the present study, we determined a partial sequence of the mitochondrial cytochrome c oxidase subunit I (COI) gene for 11 specimens of P. corrugata collected from depths of 17–27 m under sea ice near Syowa Station. A haplotype-network analysis along with other COI sequences from 66 individuals collected at different places in the Antarctic and sub-Antarctic islands, available at public databases, resulted in that all the 11 specimens from Lützow-Holm Bay possessed either of two major haplotypes detected in previous studies. It reflects the effective dispersal of the species between the localities including Lützow-Holm Bay.

Hidden diversity within theDiopatra cupreacomplex (Annelida: Onuphidae): morphological and genetics analyses reveal four new species in the south-west Atlantic

AbstractDiopatra is the most species-rich genus of Onuphidae with about 60 species. Although 14 species have been reported for Brazil, the cosmopolitan D. cuprea is the most commonly reported from the area, including populations with a large morphological diversity. To better elucidate this species complex, we use morphological and molecular data, and reveal a hidden diversity. Thus, we describe four new species (D. hannelorae sp. nov., D. marinae sp. nov., D. pectiniconicum sp. nov. and D. victoriae sp. nov.) and discuss their geographical and bathymetrical distributions. None of the analysed specimens could be identified as D. cuprea based on available sequences. New taxonomic characters were highlighted, including jaw morphology, which was the determinant factor to differentiate D. marinae from D. victoriae. Phylogenetic analysis indicates three (COI and ND4) or four (concatenated) lineages, because D. marinae was not always reciprocally monophyletic. Sequence-based species delimitation also indicates three to five species, depending on the method used. Inter- and intragroup genetic divergence and haplotype network analysis supported four species. The divergence time among species indicates that Pleistocene sea-level fluctuations and the Vitória–Trindade chain limited the gene flow between northern and southern populations and contributed to the emergence of species, mainly in the case of D. marinae and D. victoriae.

Genetic Diversity and Evolutionary Relationships of Chinese Pepper Based on nrDNA Markers

Chinese pepper, referring to Zanthoxylum bungeanum Maxim. and Zanthoxylum armatum DC. species, is an important spice crop that has long attracted people’s interest due to its extensive application in Asian cuisine to improve taste. Numerous cultivars have been developed during the long history of domestication and cultivation. However, little to no information is available on the genetic diversity and evolutionary relationships of Chinese pepper cultivars and their historical diversification has not been clarified. Herein, we sequenced two nrDNA non-coding region markers, the external transcribed spacer (ETS) and the internal transcribed spacer 2 (ITS2), to assess genetic diversity and phylogenetic relationships among 39 cultivated and wild populations of Chinese pepper from eight provinces and to address the question of ancient demographic trends which were probably influenced by changing climate during evolutionary history. In total, 31 haplotypes were identified based on 101 polymorphism sites. Our results revealed relatively high level of genetic variation despite long-term cultivation of this crop. AMOVA revealed that genetic variation existed predominantly within provinces rather than among provinces. The genetic structure result based on haplotype network analysis largely reflected historical records, which suggested a Gansu origin for Chinese pepper and an ancient west-to-east spread of Chinese pepper circulating in China. We also provided evidence that changing Pleistocene climates had shaped the demographic trends of Chinese pepper. Taken together, our findings not only suggest that Chinese pepper is a dynamic genetic system that responds to evolutionary forces, but it also provides a fundamental genetic profile for the conservation and responsible exploitation of the extant germplasm of Chinese pepper and for improving the genetic basis for breeding the cultivars.

Genetic Characterization of Porcine Circovirus 3 Strains Circulating in Sardinian Pigs and Wild Boars.

Porcine circovirus 3 (PCV3) is a recently discovered member of the Circoviridae family. So far, its presence has been reported in North America, Asia, South America, and Europe. In this study, blood and tissue samples from 189 Sardinian suids (34 domestic pigs, 115 feral free ranging pigs, and 39 wild boars) were used to genetically characterize the PCV3 strains from Sardinia. PCV3 infection in the animals was confirmed by real time PCR. The detection rate in the three groups analyzed was l7.64% in domestic pigs, 77.39% in free ranging pigs, and 61.54% in wild boars. Moreover, our results showed that co-infection of PCV3 with other viruses is quite a common occurrence. Molecular characterization of Sardinian PCV3 strains was performed by sequencing 6 complete genomes and 12 complete cap genes. Our results revealed that there is a high similarity between our strains and those identified in different countries, confirming the genetic stability of PCV3 regardless of geographical origin. Haplotype network analysis revealed the presence of 6 whole genomes or 12 unique ORF2 haplotypes and a nonsynonymous mutation in ORF2 that leads to an R14K amino acid substitution. Phylogenetic analysis of whole genome and ORF2 was also conducted. The Sardinian strains were allocated in three different clusters of phylogenetic trees of both complete genome and ORF2. With this study, we have provided a snapshot of PCV3 circulation in Sardinia. Our findings might help to achieve a deeper understanding of this emerging porcine virus.

Multimammate mice of the genus Mastomys (Rodentia: Muridae) in Ethiopia – diversity and distribution assessed by genetic approaches and environmental niche modelling

Multimammate mice of the genus Mastomys are widespread in sub-Saharan Africa and occur in a wide range of open habitats. Representatives of this genus are the most common African rodents, the main vertebrate agricultural pests and vectors of human pathogens. In Ethiopia, the biogeographically most complex eastern African country, several species have been reported, but their distribution has never been described because of their cryptic morphology. Here we present genetically identified species from 377 Ethiopian Mastomys specimens and analyse their distributional patterns. The genus, represented by four species, inhabits most of the country, with the exception of the highest mountains and dry areas, such as the Afar triangle and the Somali region. For the first time we document M. kollmannspergeri from a single locality in the northernmost part of Ethiopia. Three previously recorded species are more widespread – M. erythroleucus was found at 32 localities, M. natalensis at 13 localities and the Ethiopian endemic species M. awashensis at 18 localities. Phylogenetic analysis of mitochondrial cytochrome b gene sequences indicates that only one of the six phylogroups of M. natalensis and one of the four phylogroups of M. erythroleucus are represented in Ethiopia. Haplotype network analysis indicates two subclades of Ethiopian M. erythroleucus separated by the Ethiopian Rift Valley. Using presence records, we constructed distribution models for the species and analysed the level of overlap. The predicted distribution shows most overlap between M. awashensis and M. natalensis, which is in agreement with empirical data as both species were found in sympatry at four localities. A medium level of overlap was predicted between M. natalensis and M. erythroleucus and both species were found co-existing at two localities. This study not only presents the first detailed distribution of cryptic Mastomys species, but also clearly identifies multimammate mice as model taxa for future evolutionary studies (e.g. the evolution of coexistence or host-parasite interactions) and indicates the regions suitable for such studies.

Genetic diversity and geographic distribution of Bemisia tabaci species complex in Nepal

Abstract Bemisia tabaci species complex comprises at least 44 cryptic species worldwide. Here, we analyze the nucleotide sequences of mitochondrial cytochrome oxidase subunit 1 (COI) gene obtained from 76 samples of B. tabaci collected from 23 districts in Nepal. This is the first genetic and geographic study of B. tabaci species complex in Nepal. Our phylogenetic study identified the presence of three cryptic species—Asia I, Asia II 1, and Asia II 5—with high interspecific but low intraspecific variations. Among the three cryptic species, Asia II 5 was the most prevalent in Nepal, constituting 64.47% of all the sequenced samples. Based on haplotype network analysis of COI sequences, Asia II 1 was more genetically diversified than the other two cryptic species. Our results provided useful information on the genetic diversity and geographic distribution of B. tabaci in Nepal, which help monitor population changes of B. tabaci at cryptic species level and develop sustainable management strategies for its control.

A 62K genic-SNP chip array for genetic studies and breeding applications in pigeonpea (Cajanus cajan L. Millsp.)

Pigeonpea is the second most important pulse legume crop for food and nutritional security of South Asia that requires accelerated breeding using high throughput genomic tools. Single nucleotide polymorphisms (SNPs) are highly suitable markers for this purpose because of their bi-allelic nature, reproducibility and high abundance in the genome. Here we report on development and use of a pigeonpea 62 K SNP chip array ‘CcSNPnks’ for Affymetrix GeneTitan® platform. The array was designed after filtering 645,662 genic-SNPs identified by re-sequencing of 45 diverse genotypes and has 62,053 SNPs from 9629 genes belonging to five different categories, including 4314 single-copy genes unique to pigeonpea, 4328 single-copy genes conserved between soybean and pigeonpea, 156 homologs of agronomically important cloned genes, 746 disease resistance and defense response genes and 85 multi-copy genes of pigeonpea. This fully genic chip has 28.94% exonic, 33.04% intronic, 27.56% 5′UTR and 10.46% 3′UTR SNPs and incorporates multiple SNPs per gene allowing gene haplotype network analysis. It was used successfully for the analysis of genetic diversity and population structure of 95 pigeonpea varieties and high resolution mapping of 11 yield related QTLs for number of branches, pod bearing length and number of seeds per pod in a biparental RIL population. As an accurate high-density genotyping tool, ‘CcSNPnks’ chip array will be useful for high resolution fingerprinting, QTL mapping and genome wide as well as gene-based association studies in pigeonpea.

Free to Circulate: An Update on the Epidemiological Dynamics of Porcine Circovirus 2 (PCV-2) in Italy Reveals the Role of Local Spreading, Wild Populations, and Foreign Countries.

Porcine circovirus 2 (PCV-2) is one of the most impactful and widespread pathogens of the modern swine industry. Unlike other DNA viruses, PCV-2 is featured by a remarkable genetic variability, which has led to the emergence and recognition of different genotypes, some of which (PCV-2a, 2b, and 2d) have alternated over time. Currently, PCV-2d is considered the most prevalent genotype, and some evidence of differential virulence and vaccine efficacy have been reported. Despite the potential practical relevance, the data on PCV-2 epidemiology in Italy are quite outdated and do not quantify the actual circulation of this genotype in Italy. In the present study, 82 complete ORF2 sequences were obtained from domestic pigs and wild boars sampled in Northern Italy in the period 2013–2018 and merged with those previously obtained from Italy and other countries. A combination of phylogenetic, haplotype network, and phylodynamic analyses were used to genotype the collected strains and evaluate the temporal trend and the spatial and host spread dynamics. A rising number of PCV-2d detections was observed in domestic pigs, particularly since 2013, reaching a detection frequency comparable to PCV-2b. A similar picture was observed in wild boars, although a lower sequence number was available. Overall, the present study demonstrates the extreme complexity of PCV-2 molecular epidemiology in Italy, the significant spread across different regions, the recurrent introduction from foreign countries, and the frequent occurrence of recombination events. Although a higher viral flux occurred from domestic to wild populations than vice versa, wild boars seem to maintain PCV-2 infection and spread it over relatively long distances.

Phylogeographic and population genetic analyses of Cucurbita moschata reveal divergence of two mitochondrial lineages linked to an elevational gradient.

Domestication usually involves local adaptation to environmental conditions. Cucurbita species are a promising model for studying these processes. Cucurbita moschata is the third major crop in the genus because of its economic value and because it displays high landrace diversity, but research about its genetic diversity, population structure, and phylogeography is limited. We aimed at understanding how geography and elevation shape the distribution of genetic diversity in C. moschata landraces in Mexico. We sampled fruits from 24 localities throughout Mexico. We assessed 11 nuclear microsatellite loci, one mtDNA region, and three cpDNA regions but found no variation in cpDNA. We explored genetic structure with cluster analysis, and phylogeographic relationships with haplotype network analysis. Mitochondrial genetic diversity was high, and nuclear genetic differentiation among localities was intermediate compared to other domesticated Cucurbita. We found high levels of inbreeding. We recovered two mitochondrial lineages: highland (associated with the Trans-Mexican Volcanic Belt) and lowland. Nuclear microsatellites show that localities from the Yucatan Peninsula constitute a well-differentiated group. Mexico is an area of high diversity for C. moschata, and these landraces represent important plant genetic resources. In Mexico this species is characterized by divergence processes linked to an elevational gradient, which could be related to adaptation and may be of value for applications in agriculture. The Isthmus of Tehuantepec may be a partial barrier to gene flow. Morphological variation, agricultural management, and cultural differences may be related to this pattern of genetic structure, but further studies are needed.

Native bighead carp Hypophthalmichthys nobilis and silver carp Hypophthalmichthys molitrix populations in the Pearl River are threatened by Yangtze River introductions as revealed by mitochondrial DNA.

Bighead carp Hypophthalmichthys nobilis and silver carp Hypophthalmichthys molitrix have been two economically important aquaculture species in China for centuries. In the past decades, bighead and silver carp have been introduced from the Yangtze River to many river systems in China, including the Pearl River, in annual, large-scale, stocking activities to enhance wild fisheries. Nonetheless, few studies have assessed the ecological or genetic impacts of such introductions on native conspecific fish populations. An mtDNA D-loop segment of 978 bp from 213 bighead carp samples from 9 populations and a 975 bp segment from 204 silver carp samples from 10 populations were obtained to evaluate genetic diversity and population integrity. Results from a haplotype network analysis revealed that most haplotypes of the Pearl River clustered with those of Yangtze River origin and only a small proportion were distinct, suggesting that both the native Pearl River bighead and silver carp populations are currently dominated by genetic material from the Yangtze River. The genetic diversity of Pearl River populations is high in both species because of this inter-population gene flow, but the diversity of native Pearl River populations is low. To preserve the native genetic diversity, stocking of non-native fingerlings should cease immediately and native Pearl River bighead and silver carp fish farms should be established. This research demonstrates the danger to native biodiversity across China because of the substantial, ongoing stock-enhancement activities without prior genetic assessment.