Nuclear Gene Markers Research Articles

Population genetics and evolutionary history of the intertidal brittle star Ophiothrix (Ophiothrix) exigua in the northern China Sea.

Ophiothrix (Ophiothrix) exigua is a common brittle star in the northwestern Pacific. As a dominant species, O. exigua inhabiting the intertidal rocky ecosystem are affected by multiple environmental stressors, but molecular insights into their genetic population structure remain poorly studied. In this study, we investigated the population genetics and evolutionary history of six O. exigua populations from the northern China Sea using mitochondrial (COI, NAD4) and nuclear (ITS2, 18S) gene markers. High haplotype diversity, low nucleotide diversity, and low rates of gene differentiation among the populations of O. exigua were detected. Pairwise genetic differentiation (ΦST) statistics between different localities were negative or low and insignificant, suggesting strong gene flow of this species over the study areas. The phylogenetic analyses showed that the populations exhibited high homogeneity between localities in our study area. Demographic analyses indicated that the populations experienced sustained expansion around 0.2 million years ago. This expansion was likely related to transgressions events in the Yellow Sea during the Pleistocene period. Additional samples of O. exigua from disparate geographical locations, especially the Japan Sea and the Korean Peninsula, will be needed to unravel the population genetic patterns and evolutionary history of this species.

Molecular phylogeny and species diversity of the genus Dichaetophora Duda and related taxa (Diptera: Drosophilidae)

Our intensive surveys of wild drosophilids in East and Southeast Asia discovered a great species diversity (more than 100 putatively new species) of the genus Dichaetophora, which is currently comprised of 67 formally described species assigned into five species groups, i.e., agbo, tenuicauda, acutissima, sinensis and trilobita. In the present study, we delimited species from a huge amount of samples of Dichaetophora and allied taxa (the genus Mulgravea and the subgenus Dudaica of Drosophila) collected from a wide range of the Oriental and east Palearctic regions. We first sorted all specimens into morpho-species, and representative specimen(s) selected from each morpho-species were subjected to barcoding of COI (the cytochrome c oxidase subunit I gene) sequences. The applied ASAP (Assemble Species by Automatic Partitioning) analysis estimated a total of 166 to 168 MOTUs (molecular operational taxonomic units). Integrating this result with morphological evidence from re-examined, detailed structures of male terminalia, we recognized a total of 144 (109 new and 35 known) species in our sample. Out of them, 83 species representing the supraspecific taxa of Dichaetophora, Mulgravea and Dudaica were selected, along with 33 species from major genera and subgenera of Drosophila in the tribe Drosophilini, as in-group and four species from the tribe Colocasiomyini as out-group for phylogenetic reconstruction based on 12 nuclear gene markers. In the trees constructed by the maximum likelihood and Bayesian inference methods, the three focal taxa (i.e., Dichaetophora, Mulgravea and Dudaica) formed a clade provisionally called the “pan-Dichaetophora”. Within this large clade, the agbo, tenuicauda, sinensis and trilobita groups of Dichaetophora, Mulgravea and Dudaica were recovered as monophyletic groups, but Dichaetophora and its acutissima group were regarded as paraphyletic. In addition, two clusters were recognized among ungrouped species of Dichaetophora. Thus, the present study has uncovered some issues concerning the taxonomy of the pan-Dichaetophora. Such issues will be addressed elsewhere in the phylogenetic reclassification of the pan-Dichaetophora, along with descriptions/redescriptions of a large number of new/known species delimited in the present study.

Multi-gene-based investigation on the molecular phylogeny of the hypotrichous family Strongylidiidae (Protista, Ciliophora), with notes on the ontogeny of a new genus and new species

Ciliates in the subclass Hypotrichia have long been difficult to classify as they are one of the most polymorphic and highly differentiated groups, leading to their systematics remaining unresolved. Phylogenetic relationships within the hypotrich family Strongylidiidae have been ambiguous due to discordance between the morphological and genetic data. In this study, a new strongylidiid genus Heterouroleptus is established, mainly based on the novel mode of origin of the ventral cirral rows: left ventral cirral row (LVR) originates from frontal–ventral–transverse cirral anlagen (FVTA) III (anterior portion), IV (middle portion), and V (rear portion); right ventral cirral row comes from the entire FVTA VI. A new species, Heterouroleptus weishanensis gen. nov., sp. nov., is investigated along with the morphometric and molecular data from a population of Strongylidium wuhanense. Eight new sequences and nuclear gene markers (single-gene and multi-gene) are provided to analyze the phylogenetic relationships of strongylidiids, with the COI gene utilized to uncover further genetic information at species level and below. The results reveal that: (1) Strongylidiidae is monophyletic and has a close relationship with Dorsomarginalia; (2) Heterouroleptus gen. nov. forms a clade that is sister to all the other strongylidiids; (3) Hemiamphisiella Foissner, 1988 and Pseudouroleptus Hemberger, 1985 should not be synonyms, and both genera should be subdivided due to their variable morphological characteristics; (4) LVR originating from three anlagen is a plesiomorphy of Strongylidiidae. The discovery of the origin of the LVR not only contributes to the establishment of the genus Heterouroleptus, but also helps to improve the diagnosis of the family Strongylidiidae.

Fish parvalbumin gene: Detection and quantification by universal primers for forensic application

The substitution of illegal fish species poses economic, health and environmental risks. Identifying fish species, particularly closely related ones lacking external features, is a challenge. This study introduces an alternative approach using nuclear gene markers for positive detection, identification, and quantification of mitochondrial gene markers common in existing assays. We developed a universal primer targeting the parvalbumin (pvalb) β gene, a common fish allergen with an amplicon size of 117 bp long. The developed fish-specific primer assay was tested on a diverse panel of 54 fish species, including commonly consumed species such as salmon, carp, and cod, along with non-fish species such as Buffalo, chicken and pork, and vegetables such as wheat, celery, and mint. The assay consistently identified the fish pvalb gene, demonstrating our assay's high specificity and effectiveness in detecting this gene in a variety of fish species. The assay exhibited a low limit of detection (LOD) of 5 pg, detecting trace DNA quantities. The assay also effectively quantified parvalbumin with good efficiency and linearity. These findings highlight pvalb as a reliable forensic tool for the identification of fish species. Implementing nuclear gene markers mitigates fish mislabelling and fraud, reducing economic and environmental impacts.

Biogeography and evolutionary history of Puntius sensu lato (Teleostei: Cyprinidae) in Sri Lanka

Sri Lanka’s biota is derived largely from Southeast Asian lineages which immigrated via India following its early-Eocene contact with Laurasia. The island is now separated from southeastern India by the 30 km wide Palk Strait which, during sea-level low-stands, was bridged by the 140 km-wide Palk Isthmus. Consequently, biotic ingress and egress were mediated largely by the climate of the isthmus. Because of their dependence on perennial aquatic habitats, freshwater fish are useful models for biogeographic studies. Here we investigate the timing and dynamics of the colonization of—and diversification on—Sri Lanka by a group of four closely-related genera of cyprinid fishes (Puntius sensu lato). We construct a molecular phylogeny based on two mitochondrial and two nuclear gene markers, conduct divergence timing analyses and ancestral-range estimations to infer historical biogeography, and use haplotype networks to discern phylogeographic patterns. The origin of Puntius s.l. is dated to ~ 20 Ma. The source of diversification of Puntius s.l. is Sri Lanka-Peninsular India. Species confined to perhumid rainforests show strong phylogeographic structure, while habitat generalists show little or no such structure. Ancestral range estimations for Plesiopuntius bimaculatus and Puntius dorsalis support an ‘Out of Sri Lanka’ scenario. Sri Lankan Puntius s.l. derive from multiple migrations across the Palk Isthmus between the early Miocene and the late Pleistocene. Species dependent on an aseasonal climate survived aridification in rainforest refugia in the island’s perhumid southwest and went on to recolonize the island and even southern India when pluvial conditions resumed. Our results support an historical extinction of Sri Lanka’s montane aquatic fauna, followed by a recent partial recolonization of the highlands, showing also that headwater stream capture facilitated dispersal across basin boundaries.

Characterization of complete mitochondrial genome of three Horse flies of the genus Tabanus (Diptera: Tabanidae): comparative analysis.

Tabanidae (Horse-Flies or Deer-Flies) are one of the most economically important as well as medically significant haematophagous insect family within the order Diptera. Members of this group are also responsible for the mortality of substantial number of live-stock every year. Due to their pathogen transmission potential and vector competencies makes them an important insect group to study. Till now, mitochondrial genome of 18 species of tabanids were available. The complete mitogenome of three species T. diversifrons (15,809bp), T. rubidus (15,878bp) and T. tenens (15,872bp) were generated by Next generation sequencing method. They consist 37 genes, with a positive AT skew and a negative GC skew. The gene order of these three species is similar to the typical gene arrangement of infra-order Tabanomorpha. Most of the tRNAs showed typical clover-leaf secondary structure except trnS1, which lacks the DHU arm. The sliding window analysis showed that thenad4L is the most conserved while atp8, and nad6 are the most variable genes. Moreover, the ratios of non-synonymous to synonymous substitution rates indicated that all PCGs under the purifying selection. Phylogeny revealed Chrysops and Haematopota are monophyletic while species of Hybomitra are nested within the polyphyletic clade of Tabanus. T. diversifrons exhibits sister relationship with Atylotus miser. Two morphologically divergent species T. rubidus and T. tenens are found to be genetically similar and indistinguishable by mitochondrial genome. The hypervariable genes like atp8 and nad6 can be used as molecular markers for the identification of recently diverged lineages of family Tabanidae. Further, to address uncertainties arising from the two morphological divergent species, it is imperative to obtain data from nuclear gene markers.

Invasion genetics of the yellow-legged hornet Vespa velutina in the Westernmost Mediterranean archipelago

AbstractThe yellow-legged hornet (Vespa velutina) is a social Hymenoptera native from Asia and an invasive species in Europe, where it was first detected in France in 2004. Since then, the species has spread across the continent invading mainland Spain and Mallorca island (Balearic archipelago, Western Mediterranean) in 2010 and 2015, respectively. Yellow-legged hornets cause severe damage to ecosystem by predating over a wide variety of pollinators including honeybees. Such a threat situation requires the development of effective management and prevention plans, which can greatly benefit from knowing both the origin and the genetic structure of the invading populations. Here we conduct a genetic study to shed light on both the origin and the phylogenetic relationships of V. velutina populations from Mallorca and mainland Spain using nuclear (STRs) and mitochondrial (cytochrome oxidase c subunit 1) gene markers. Our results show that Mallorca populations originated from invasive European specimens. Moreover, FST values, DAPC and genetic structure analysis suggest two independent incursions in the island with bottleneck and founder effect signatures. Finally, we contribute additional genetic evidence of the polyandrous behavior of this invasive species based on the inference of a mean number of mattings per nest of 3.94 (range 2–6.5). This study supports the human-mediated pathways of this species and highlights the importance of implementing effective biosecurity measures to prevent the spread of invasive alien species in island habitats.

At the edge of the sea: the supralittoral nemertean, Acteonemertes orientalis sp. nov. (Nemertea: Eumonostilifera: Plectonemertidae) from Japan

Ribbon worms (phylum Nemertea) are found in oceans worldwide; however, only a few inhabit terrestrial, semiterrestrial and freshwater environments. In our study, we describe Acteonemertes orientalis sp. nov., a new species of Plectonemertidae Gibson, 1990 and the first plectonemertid discovered in Japan. The species was found in the supralittoral zone, from which nemerteans have rarely been reported and inhabits areas under rocks, wave-dissipating concrete blocks, and fallen leaves and stocks, along the coast of the Sea of Japan. Multi-locus phylogenetic analyses based on two mitochondrial (16S rRNA and cytochrome c oxidase subunit I) and two nuclear gene markers (18S rRNA and 28S rRNA) revealed that A. orientalis sp. nov. formed a clade with Leptonemertes cf. chalicophora collected from Florida. Although the external and internal morphology of A. orientalis sp. nov. is largely consistent with the generic diagnosis, this species differs in having a large proboscis. Based on the molecular and morphological data, we propose to amend the diagnosis of Acteonemertes by excluding proboscis size. ZooBank: urn:lsid:zoobank.org:pub:BBBE9549-5DCE-424F-9A39-930F8243C28B

Fluorescent Anemones in Japan—Comprehensive Revision of Japanese Actinernoidea (Cnidaria: Anthozoa: Actiniaria: Anenthemonae) with Rearrangements of the Classification

Actinernoidea is a superfamily of the suborder Anenthemonae of the order Actiniaria, subclass Hexacorallia. This superfamily has been diagnosed by a peculiar endocoeletic mesenterial arrangement and included two families, Actinernidae and Halcuriidae. Although the monophyly of this superfamily is anticipated based on preceding molecular phylogenetic works, the relationship between these two families was not certain because of the rarity of actinernoidean anemones. We conducted comprehensive sampling in Japan, where the highest diversity of actinernoideans is known, and conducted phylogenetic analyses using nuclear and mitochondrial gene markers. According to the comprehensive analyses, both Actinernidae and Halcuriidae were not indicated as monophyletic but rather as poly- or paraphyletic. Based on our phylogeny reconstruction, we propose a new classification for Actinernoidea composed of three families, including Isactinernidae fam. nov., and seven genera, including Isohalcurias gen. nov. We also describe four new species, Halcurias hiroomii sp. nov., H. fragum sp. nov., Isohalcurias citreum sp. nov., and I. malum sp. nov.; and propose a new combination, Isohalcurias carlgreni comb. nov. This work is the first study of Actinernoidea that comprehensively analyzes its phylogeny and rearranges its classification, showing that there is highly divergent fauna in the seas around Japan.

Low Genetic Diversity of Vector-Borne Haemoparasites in Dogs and Their Ticks Revealed Local and Long-Range Transmission in Peninsular Malaysia

Molecular methods coupled with phylogenetic analysis are sensitive tools for detecting and classifying parasites. This study used nuclear and mitochondrial gene markers to investigate the host-vector interaction of the vector-borne haemoparasites. The population genetic structures of important vector-borne haemoparasites in dogs, namely, Anaplasma platys, Ehrlichia canis, Babesia vogeli, and Babesia gibsoni, were determined from the nuclear gene of 16S or 18S rRNA gene, gltA and groESL and mitochondrial gene of COX1 across dogs and vector ticks. A total of 220 blood samples and 140 ticks were collected from shelter dogs in Peninsular Malaysia. Out of the positive samples for the vector-borne haemoparasites, 28 positive blood isolates and six tick isolates were selected and characterised. There was a low diversity in tick sequences, while varying degree of variability was observed in dogs’ sequences. Overlapped haplotypes were observed in sequences of dogs and ticks, revealing the possibility of the same infection origin. No regional separation was detected, but similar haplotypes from different regions were observed. These findings contribute to the epidemiology of vector-borne haemoparasites in dogs in Malaysia.

Low Genetic Diversity of Vector-Borne Haemoparasites in Dogs and Their Ticks Revealed Local and Long-Range Transmission in Peninsular Malaysia

Molecular methods coupled with phylogenetic analysis are sensitive tools for detecting and classifying parasites. This study used nuclear and mitochondrial gene markers to investigate the host-vector interaction of the vector-borne haemoparasites. The population genetic structures of important vector-borne haemoparasites in dogs, namely, Anaplasma platys, Ehrlichia canis, Babesia vogeli, and Babesia gibsoni, were determined from the nuclear gene of 16S or 18S rRNA gene, gltA and groESL and mitochondrial gene of COX1 across dogs and vector ticks. A total of 220 blood samples and 140 ticks were collected from shelter dogs in Peninsular Malaysia. Out of the positive samples for the vector-borne haemoparasites, 28 positive blood isolates and six tick isolates were selected and characterised. There was a low diversity in tick sequences, while varying degree of variability was observed in dogs’ sequences. Overlapped haplotypes were observed in sequences of dogs and ticks, revealing the possibility of the same infection origin. No regional separation was detected, but similar haplotypes from different regions were observed. These findings contribute to the epidemiology of vector-borne haemoparasites in dogs in Malaysia.

Trypanosoma cruzi in Mexican Neotropical vectors and mammals: wildlife, livestock, pets, and human population

Objective. To provide primary evidence of Trypanosoma cruzi landscape genetics in the Mexican Neotropics. Materials and methods. Trypanosoma cruzi and discrete typing units (DTU) prevalence were analyzed in landscape communities of vectors, wildlife, livestock, pets, and sympatric human populations using endpoint PCR and sequencing of all relevant amplicons from mitochondrial (kDNA) and nuclear (ME, 18S, 24Sα) gene markers. Results. Although 98% of the infected sample-set (N=2 963) contained single or mixed infections of DTUI (TcI, 96.2%) and TcVI (22.6%), TcIV and TcII were also identified. Sensitivity of individual markers varied and was dependent on host taxon; kDNA, ME and 18S combined identified 95% of infections. ME genotyped 90% of vector infections, but 60% of mammals (36% wildlife), while neither 18S nor 24Sα typed more than 20% of mammal infections. Conclusion. Available gene fragments to identify or genotype T. cruzi are not universally sensitive for all landscape parasite populations, highlighting important T. cruzi heteroge- neity among mammal reservoir taxa and triatomine species.

Molecular assessment of the taxonomic status of pine vole species Microtus subterraneus and Microtus majori in southeastern Europe and Turkey

Intra– and inter–specific phylogenetic relationships and the taxonomic status of pine vole populations have been controversial for years, and cryptic species are thought to exist, especially concering the species' distribution area. To clarify the taxonomic status of Turkish populations we analysed mitochondrial (cytochrome–b and cytochrome oxidase–I) and nuclear (interphotoreceptor retinoid binding protein) gene markers, adding GenBank data from Europe and Caucasia. Considering the data obtained based on mean genetic distance, genetic diversity and fixation index values, Bayesian trees and Median–joining networks, we found that M. subterraneus and M. majori are valid species which have diverged since 1.28 Mya. Findings also suggested that although Anatolian, Thracian (Turkish Thrace and Greece) and European populations of M. subterraneus and Anatolian and Caucasian populations of M. majori have been in the process of divergency since 0.528–0.337 Mya correspond to the Pleistocene glacial periods, these intrapopulations do not appear to be different species.Besides, considering the high intraspecific variation in M. subterraneus, it remains likely that new species could be identified in future studies.

Paraphyly of the Pipistrelles (Pipistrellus; Vespertilionidae) is Confirmed by the Analysis of the Nuclear Gene Markers.

There are evidences that the genus Pipistrellus (true pipistrelles) in its current understanding may be paraphyletic. We have studied for the first time the phylogenetic relationships between the majority of supraspecific taxa of the subtribe Pipistrellina based on the analysis of the sequences of three nuclear genes (RAG2, APOB, and DMP1). Our data support the monophyly of the subtribe itself, but definitely show that the genus Pipistrellus in the modern sense is paraphyletic with respect to noctules, Nyctalus, and thick thumb pipistrelles, Glischropus (which both are morphologically distinct taxa). Moreover, noctules are extremely close to the "western" clade of Pipistrellus. The latter genus should probably be divided into two or more separate genera, or Nyctalus and Glischropus should be treated as its subgenera.

Molecular Phylogeny of the Genus Nipponnemertes (Nemertea: Monostilifera: Cratenemertidae) and Descriptions of 10 New Species, With Notes on Small Body Size in a Newly Discovered Clade

Nemerteans, or ribbon worms, have been reported from intertidal to hadal depths, often showing bathymetrically wide distribution in genus levels. Although current nemertean systematics practices require to provide DNA sequences and infer phylogenetic relationships with suitable molecular markers, previous molecular systematics on nemerteans are mostly biased toward shallow-water species. Members in the genus Nipponnemertes occur worldwide, from tropical to polar waters and intertidal to bathyal waters. Molecular phylogenetic studies are scarce for the genus; only six shallow-water species of 18 species in the genus were subject to molecular phylogeny. Thus, Nipponnemertes is one candidate that needs to be assessed by genetic approaches. In this study, we performed molecular phylogenetic analyses using 59 specimens in 23 species based on partial sequences of two mitochondrial (16S rRNA and cytochrome c oxidase subunit I) and three nuclear gene markers (18S rRNA, 28S rRNA, and histone H3). Our extensive sampling from intertidal to bathyal waters in the Northwest Pacific significantly updated the fauna of Nipponnemertes in this region from four to 17 species. We herein establish 10 new species and provide an updated species list concisely summarizing all the congeners known from the world. Our phylogenetic tree indicated three major lineages within the genus (herein referred to as “Clade A, B, and C”), each presumably characterized by the combination of morphological characters in the head region. Members in Clade A are: Nipponnemertes pulchra (Johnston, 1837), Nipponnemertes ogumai (Yamaoka, 1947), and several unidentified congeners, characterized by having demarcated head without cephalic patches; members in Clade B are: Nipponnemertes crypta sp. nov., Nipponnemertes jambio sp. nov., Nipponnemertes neonilae sp. nov., and Nipponnemertes ojimaorum sp. nov., species having demarcated head with cephalic patches; members in Clade C are: Nipponnemertes ganahai sp. nov., Nipponnemertes kozaensis sp. nov., Nipponnemertes lactea sp. nov., Nipponnemertes notoensis sp. nov., Nipponnemertes ornata sp. nov., Nipponnemertes sugashimaensis sp. nov., and two unidentified forms collected off Jogashima (Japan) and Guam (USA), species with non-demarcated head lacking cephalic patches. Furthermore, we discuss the evolution of remarkably small body size retained among Clade C.

Evolution of the Colocasiomyia gigantea Species Group (Diptera: Drosophilidae): Phylogeny, Biogeography and Shift of Host Use.

Simple SummaryAll the species in the Colocasiomyia gigantea group breed on monsteroid host plants (aroids in the subfamily Monsteroideae). So far, we have not resolved the phylogenetic relationship among these fly species, making it difficult to trace the origin and history of the species diversification, biogeography and host plant selection. In this study, we reconstructed the evolutionary relationships between these species using multilocus DNA sequence data, and we inferred their ancestral areas and host plants. According to the results, this group diverged from its sister taxon through a split between the northeastern Oriental region and Sundaland + Wallacea, with the subsequent diversification occurring largely in the first region. We inferred the most likely ancestral host genus of this group to be Rhaphidophora Hassk, with possible subsequent shifts to Scindapsus Schott and/or Epipremnum Schott. We discuss the potential of the group as a model system for studies in evolutionary ecology and developmental genetics.The gigantea species group of the genus Colocasiomyia de Meijere (Diptera: Drosophilidae) is among the four aroid-breeding species groups in this genus; however, it differs from the remaining three groups in the host use: all the flies in this group use plants from the subfamily Monsteroideae instead of from the subfamily Aroideae. So far, we have not resolved the phylogenetic relationship within this group, making it difficult to trace its geographical origin, pattern of species diversification and history of host plant use. In this study, we reconstructed the phylogenetic relationships within the C. gigantea group using DNA sequences of eight (two mitochondrial and six nuclear) gene markers, and we inferred the ancestral areas and host plants of the group based on the resulting phylogeny. According to the results, the C. gigantea group may have diverged from its sister group (i.e., the C. cristata group) through vicariance between the northeastern Oriental region and Sundaland + Wallacea, and the subsequent diversification of the C. gigantea group occurred mostly in the northeastern Oriental region, although an Oriental-to-Sundaland dispersal was followed by vicariance between these two areas, which finally gave rise to the C. gigantea-C. scindapsae lineage in the latter area. We inferred the most likely ancestral host plant of the C. gigantea group to be of the genus Rhaphidophora Hassk, with possible subsequent shifts to Scindapsus Schott and/or Epipremnum Schott plants. We discuss the potential for the egg filaments in the C. gigantea group to be used as a model system for comparative studies in pollination mutualism and developmental genetics concerning tubulogenesis.

First record of metacercariae trematodes Opisthioglyphe ranae (Digenea: Telorchiidae) and Echinostoma bolschewense (Digenea: Echinostomatidae) in Dreissena polymorpha (Bivalvia: Dreissenidae) from the Don and Volga river basins, Russia

It is well known that an invasive bivalve mollusk species Dreissena polymorpha plays a significant role as a host to parasites. Currently, the interaction between digenean trematodes and their bivalve hosts remains relatively poorly understood. In this study we investigate infection of D. polymorpha by trematodes using molecular genetics, histological, and light microscopy methods. We obtained sequences of one mitochondrial (molecular cytochrome c oxidase subunit 1 (COI)) and two nuclear (ITS2, rDNA 28S) gene markers. To the best of our knowledge, this is the first time that infection of metacercariae of Opisthioglyphe ranae and Echinostoma bolschewense in D. polymorpha has been detected. Our sequence was 100% identical to the 28S rDNA of the species O. ranae recorded in Penza Oblast (Russia) in pond frog. At the same time, some sequences of the 28S rDNA of O. ranae detected in Penza Oblast (Russia) and Ivano-Frankovsk Region (Ukraine) were different from our sequence by 0.2%. Our sequence was 100% identical to the 28S rDNA of the species E. bolschewense sequenced in Slovakia. In addition, we received sequences of COI for both trematode species and ITS2 of E. bolschewense for the first time.

Genetic diversity and population dynamic of Ziziphus jujuba var. spinosa (Bunge) Hu ex H. F. Chow in Central China.

Phylogeographic research concerning Central China has been rarely conducted. Population genetic and phylogeography of Ziziphus jujuba var. spinosa (also called sour jujube) were investigated to improve our understanding of plant phylogeographic patterns in Central China. Single‐copy nuclear gene markers and complete chloroplast genome data were applied to 328 individuals collected from 21 natural populations of sour jujube in China. Nucleotide variation of sour jujube was relatively high (π = 0.00720, θ w = 0.00925), which resulted from the mating system and complex population dynamics. Analysis of molecular variation analysis revealed that most of the total variation was attributed to variation within populations, and a high level of genetic differentiation among populations was detected (F st = 0.197). Relatively low long‐distance dispersal capability and vitality of pollen contributed to high genetic differentiation among populations. Differences in the environmental conditions and long distance among populations further restricted gene flow. Structure clustering analysis uncovered intraspecific divergence between central and marginal populations. Migrate analysis found a high level of gene flow between these two intraspecific groups. Bayesian skyline plot detected population expansion of these two intraspecific groups. Network and phylogeny analysis of chloroplast haplotypes also found intraspecific divergence, and the divergence time was estimated to occur at about 55.86 Ma. Haplotype native to the Loess Plateau was more ancient, and multiple glacial refugia of sour jujube were found to locate at the Loess Plateau, areas adjacent to the Qinling Mountains and Tianmu Mountains. Species distribution model analysis found a typical contraction‐expansion model corresponding to the Quaternary climatic oscillations. In the future, the distribution of sour jujube may shift to high‐latitude areas. This study provides new insights for phylogeographic research of temperate plant species distributed in Central China and sets a solid foundation for the application of the scientific management strategy of Z. jujuba var. spinosa.

A Multistep DNA-Based Methodology for Accurate Authentication of Sturgeon Species.

The sturgeons (order Acipenseriformes) are caviar producers and some of the most valuable fish species worldwide. Due to different reasons, wild populations are now at the brink of extinction. The high demand for caviar has led to the development of aquaculture for restocking and caviar production. Since the caviar from different species has different prices depending on the quality and attempts of commercial fraud based on species substitution have been found, correct species identification is more than necessary. We report a new multistep methodology for an accurate species identification based on both nuclear and mitochondrial markers. Our test integrates data from the analysis of microsatellites (Afu19, Afu34, Afu39, Afu54, Aox27, AoxD234, AnacC11 and AnacE4), nuclear gene markers (RPS7, vimentin and rhodopsin) and mtDNA barcoding to give a reliable molecular diagnostic for five sturgeon species (Huso huso, Acipenser stellatus, Acipenser ruthenus, Acipenser gueldenstaedtii and Acipenser baerii). In addition to species identification, our methodology allows the identification of bester, sterbe and best beluga hybrids, but also the identification of hybrids of unknown origin. This methodology has a good potential to contribute to the conservation of highly threatened sturgeon populations and also to the traceability of their products.

Impact of Gene Flow and Introgression on the Range Wide Genetic Structure of Quercus robur (L.) in Europe

As for most other temperate broadleaved tree species, large-scale genetic inventories of pedunculate oak (Quercus robur L.) have focused on the plastidial genome, which showed the impact of post-glacial recolonization and manmade seed transfer. However, how have pollen mediated gene flow and introgression impacted the large-scale genetic structure? To answer these questions, we did a genetic inventory on 1970 pedunculate oak trees from 197 locations in 13 European countries. All samples were screened with a targeted sequencing approach on a set of 381 polymorphic loci (356 nuclear SNPs, 3 nuclear InDels, 17 chloroplast SNPs, and 5 mitochondrial SNPs). In a former analysis with additional 1763 putative Quercus petraea trees screened for the same gene markers we obtained estimates on the species admixture of all pedunculate oak trees. We identified 13 plastidial haplotypes, which showed a strong spatial pattern with a highly significant autocorrelation up to a range of 1250 km. Significant spatial genetic structure up to 1250 km was also observed at the nuclear loci. However, the differentiation at the nuclear gene markers was much lower compared to the organelle gene markers. The matrix of genetic distances among locations was partially correlated between nuclear and organelle genomes. Bayesian clustering analysis revealed the best fit to the data for a sub-division into two gene pools. One gene pool is dominating the west and the other is the most abundant in the east. The western gene pool was significantly influenced by introgression from Quercus petraea in the past. In Germany, we identified a contact zone of pedunculate oaks with different introgression intensity, likely resulting from different historical levels of introgression in glacial refugia or during postglacial recolonization. The main directions of postglacial recolonization were south to north and south to northwest in West and Central Europe, and for the eastern haplotypes also east to west in Central Europe. By contrast, the pollen mediated gene flow and introgression from Q. petraea modified the large-scale structure at the nuclear gene markers with significant west–east direction.