Nuclear DNA Regions Research Articles

Pseudosperma albobrunneum sp. nov. from coniferous forests of Pakistan

A new species, Pseudosperma albobrunneum, is described and illustrated. The specimens are from different areas of Khyber Pakhtunkhwa province, Pakistan. The identification is based on morphological characters, in combination with molecular phylogenetic analysis of sequences of the ITS region of nuclear ribosomal DNA. The species is found distinct morphologically from all closely related taxa, and molecular data confirm its novelty.

Phylogenetic analyses and modelling distributions guide conservation of a critically endangered liana species, Eleutharrhena macrocarpa (Menispermaceae)

AbstractPhylogenetic analyses can provide an accurate identification for endangered species, which is a prerequisite for their conservation. Understanding how threats shape the current realized niche of declining species can effectively improve conservation policies. In this study, we used molecular data to identify the real Eleutharrhena macrocarpa, a critically endangered species in Yunnan, China. A niche reduction approach was used to model its range change by predicting the historic and current distributions. Our subfamily‐wide phylogenetic analyses based on five plastid DNA regions indicate that the E. macrocarpa with pinnate‐nerved leaves is real and is a member of Tiliacoreae, whereas the so‐called E. macrocarpa with triplinerved leaves is actually Haematocarpus subpeltatus, which is for the first time reported to be distributed in China. Our subsequent analyses of Tiliacoreae using seven plastid and two nuclear DNA regions further support Eleutharrhena as a distinctly monotypic genus and as sister to Pycnarrhena. Among the four prevalent barcodes in plants, three plastid DNA fragments (rbcL, matK, trnH‐psbA) failed to discriminate E. macrocarpa from Pycnarrhena; however, nuclear ribosomal internal transcribed spacer (ITS) regions could well recognize this endangered species. The distributional range of E. macrocarpa has undergone a dramatic contraction over the last 100 years and may further shrink southwestwards in the future. This dramatic range contraction might be associated with habitat loss due to increasing drought and expansion of rubber plantation. We point out the need for in situ conservation of E. macrocarpa populations, and suggest to establish a large nature reserve in southern and western Yunnan to effectively protect E. macrocarpa and other declining species that exhibit similar distribution and habitat requirements. This study highlights the significance of taxonomy and molecular phylogenetics in biological conservation.

Signatures of mitonuclear coevolution in a warbler species complex

Divergent mitonuclear coadaptation could facilitate speciation. We investigate this possibility in two hybridizing species of warblers, Setophaga occidentalis and S. townsendi, in western North America. Inland S. townsendi harbor distinct mitochondrial DNA haplotypes from those of S. occidentalis. These populations also differ in several nuclear DNA regions. Coastal S. townsendi demonstrate mixed mitonuclear ancestry from S. occidentalis and inland S. townsendi. Of the few highly-differentiated chromosomal regions between inland S. townsendi and S. occidentalis, a 1.2 Mb gene block on chromosome 5 is also differentiated between coastal and inland S. townsendi. Genes in this block are associated with fatty acid oxidation and energy-related signaling transduction, thus linked to mitochondrial functions. Genetic variation within this candidate gene block covaries with mitochondrial DNA and shows signatures of divergent selection. Spatial variation in mitonuclear ancestries is correlated with climatic conditions. Together, these observations suggest divergent mitonuclear coadaptation underpins cryptic differentiation in this species complex.

Phylogenetics and comparative plastome genomics of two of the largest genera of angiosperms, Piper and Peperomia (Piperaceae)

Biological radiations provide unique opportunities to understand the evolution of biodiversity. One such radiation is the pepper plant family Piperaceae, an early-diverging and mega-diverse lineage that could serve as a model to study the diversification of angiosperms. However, traditional genetic markers lack sufficient variation for such studies, and testing hypotheses on poorly resolved phylogenetic frameworks becomes challenging. Limited genomic data is available for Piperaceae, which contains two of the largest genera of angiosperms, Piper (>2100 species) and Peperomia (>1300 species). To address this gap, we used genome skimming to assemble and annotate whole plastomes (152–161kbp) and >5kbp nuclear ribosomal DNA region from representatives of Piper and Peperomia. We conducted phylogenetic and comparative genomic analyses to study plastome evolution and investigate the role of hybridization in this group. Plastome phylogenetic trees were well resolved and highly supported, with a hard incongruence observed between plastome and nuclear phylogenetic trees suggesting hybridization in Piper. While all plastomes of Piper and Peperomia had the same gene content and order, there were informative structural differences between them. First, ycf1 was more variable and longer in Piper than Peperomia, extending well into the small single copy region by thousands of base pairs. We also discovered previously unknown structural variation in 14 out of 25 Piper taxa, tandem duplication of the trnH-GUG gene resulting in an expanded large single copy region. Other early-diverging angiosperms have a duplicated trnH-GUG, but the specific rearrangement we found is unique to Piper and serves to refine knowledge of relationships among early-diverging angiosperms. Our study demonstrates that genome skimming is an efficient approach to produce plastome assemblies for comparative genomics and robust phylogenies of species-rich plant genera.

The Evaluations and Comparisons of Nuclear and Chloroplast DNA Regions Based on Species Identification and Phylogenetic Relationships of Crocus L. Taxa

The genus Crocus L. (Iridaceae) consists of about 200 species distributed from western Europe and north west Africa to western China. The genus is taxonomically very problematic and day after day it becomes more difficult to understand the relationships between Crocus species because of the identification of new species. Recently, the studies based on DNA sequences are frequently used for the solution of taxonomic problems, the determination of species diversity and especially the evaluation of phylogenetic relationships among the studied taxa. The use of the regions belonging to nuclear DNA and especially chloroplast genome and the combinations of these regions are frequently recommended in many studies. However, there is no information about suitable barcoding regions that can be used for all plant groups. This study focuses on determination of the most succesful barcoding regions, understanding the species discrimination abilities and finally evaluation of phylogenetic relationships among the Crocus taxa using one region from nuclear DNA (ITS1-5.8S rRNA gene-ITS2) and four regions from chloroplast DNA (1. trnK-matK IGS, 2. partial psbA gene-psbA/trnH IGS-partial trnH gene, 3. rpoC1 gene, 4. partial trnL gene-trnL/trnF IGS-partial trnF gene). Sequence informations for related DNA regions were obtained from NCBI. As a result, it can be stated that the region which is only covering ITS1-5.8S rRNA gene-ITS2 separated the all taxa in species level and it is more beneficial for the phylogenetically evaluation of Crocus taxa. Furthermore, dendrogram show taxonomic problems belonging to some species in the genus such as C. biflorus taxa.

Effects of Mountain Uplift and Climatic Oscillations on Phylogeography and Species Divergence of Chamaesium (Apiaceae).

Exploring the effects of orographic events and climatic shifts on the geographic distribution of organisms in the Himalayas-Hengduan Mountains (HHM) region and Qinghai-Tibetan Plateau (QTP) is crucial to understand the impact of environmental changes on organism evolution. To gain further insight into these processes, we reconstructed the evolutionary history of nine Chamaesium species distributed across the HHM and QTP regions. In total, 525 individuals from 56 populations of the nine species were analyzed based on three maternally inherited chloroplast fragments (rpl16, trnT-trnL, and trnQ-rps16) and one nuclear DNA region (internal transcribed spacer, ITS). Fifty-two chloroplast DNA (cpDNA) and 47 ITS haplotypes were identified in nine species. All of the cpDNA and ITS haplotypes were species-specific. Phylogenetic analysis suggested that all nine species form a monophyletic clade with high support. Dating analysis and ancestral area reconstruction revealed that the ancestral group of Chamaesium originated in the southern Himalayan region at the beginning of the Paleogene (60.85 Ma). The nine species of Chamaesium then separated well during the last 25 million years started in Miocene. Our maxent modeling indicated the broad-scale distributions of all nine species remained fairly stable from LIG to the present and predicted that it will remain stable into the future. The initial split of Chamaesium was triggered by climate changes following the collision of the Indian plate with the Eurasia plate during the Eocene. Subsequently, divergences within Chamaesium may have been induced by the intense uplift of the QTP, the onset of the monsoon system, and Central Asian aridification. Long evolutionary history, sexual reproduction, and habitat fragmentation could contribute to the high level of genetic diversity of Chamaesium. The higher genetic differentiation among Chamaesium populations may be related to the drastic changes of the external environment in this region and limited seed/pollen dispersal capacity.

An integrative monograph of Carex section Schoenoxiphium (Cyperaceae)

Carex section Schoenoxiphium (Cariceae, Cyperaceae) is endemic to the Afrotropical biogeographic region and is mainly distributed in southern and eastern Africa, with its center of diversity in eastern South Africa. The taxon was formerly recognized as a distinct genus and has a long history of taxonomic controversy. It has also an important morphological and molecular background in particular dealing with the complexity of its inflorescence and the phylogenetic relationships of its species. We here present a fully updated and integrative monograph of Carex section Schoenoxiphium based on morphological, molecular and cytogenetic data. A total of 1,017 herbarium specimens were examined and the majority of the species were studied in the field. Previous molecular phylogenies based on Sanger-sequencing of four nuclear and plastid DNA regions and RAD-seq were expanded. For the first time, chromosome numbers were obtained, with cytogenetic counts on 44 populations from 15 species and one hybrid. Our taxonomic treatment recognizes 21 species, one of them herein newly described (C. gordon-grayae). Our results agree with previous molecular works that have found five main lineages in Schoenoxiphium. We provide detailed morphological descriptions, distribution maps and analytical drawings of all accepted species in section Schoenoxiphium, an identification key, and a thorough nomenclatural survey including 19 new typifications and one nomen novum.

Morphological ontogeny and molecular analyses of geographic strains of two closely related Neoseiulus species (Acari: Phytoseiidae)

The predatory mites, Neoseiulus longispinosus (Evans) and N. womersleyi (Schicha) (Phytoseiidae) are two morphologically close species. Although they can be mainly separated by the length of the dorsal seta S5, misidentifications may occur. The present study investigated various strains of the two closely related species collected from Japan, Taiwan and/or Thailand using a combination of morphological and molecular data. We described and illustrated the adults and immature stages. We also sequenced the 28S region of nuclear ribosomal DNA to determine whether these strains represent different species. The two species could be clearly separated based on the length of seta S5 and the ratio of setae Z5/S5. In a 28S tree, the examined strains also formed separate clades with 100% bootstrap values. We conclude that a combination of different methods is often necessary to precisely distinguish these closely related taxa.

Geographic origin of Explanatum explanatum (Creplin, 1847) Fukui, 1929 detected from domestic water buffaloes in Sri Lanka.

The adult stage of Explanatum explanatum has economic importance in the production of ruminants, especially water buffaloes. This species has been widely reported in the Indian sub-continent. Recently, molecular analyses to reveal the dispersal route of this species were performed in Bangladesh, Nepal, and India. In the present study, we focused on E. explanatum distributed in Sri Lanka. A total of 52 flukes were collected from water buffaloes in Sri Lanka and identified as E. explanatum based on the internal transcribed spacer 2 (ITS2) region of nuclear ribosomal DNA. Analysis of the mitochondrial NADH dehydrogenase subunit 1 (nad1) gene from DNA samples detected 18 haplotypes, and five of them were identical to those from the Indian E. explanatum. The pairwise fixation index value indicated that the Sri Lankan population had a comparatively closer relationship with the Indian population than with the Bangladeshi or Nepalese populations. The Sri Lankan population showed significantly lower genetic variability than the Indian population, suggesting that the Indian population was the ancestor of the Sri Lankan population. The movement of host ruminants, including water buffaloes, was probably involved in the introduction of the fluke into Sri Lanka. The results of our study provide useful information for elucidating the geographic origin of E. explanatum distributed in the Indian subcontinent.

Polyploidy Expands the Range of Centaurium (Gentianaceae).

The Mediterranean region is one of the most important worldwide hotspots in terms of number of species and endemism, and multiple hypotheses have been proposed to explain how diversification occurred in this area. The contribution of different traits to the diversification process has been evaluated in different groups of plants. In the case of Centaurium (Gentianaceae), a genus with a center of diversity placed in the Mediterranean region, polyploidy seems to have been an important driver of diversification as more than half of species are polyploids. Moreover, ploidy levels are strongly geographically structured across the range of the genus, with tetraploids distributed towards more temperate areas in the north and hexaploids in more arid areas towards the south. We hypothesize that the diversification processes and biodiversity patterns in Centaurium are explained by the coupled formation of polyploid lineages and the colonization of different areas. A MCC tree from BEAST2 based on three nuclear DNA regions of a total of 26 taxa (full sampling, of 18 species and 8 subspecies) was used to perform ancestral area reconstruction analysis in “BioGeoBEARS.” Chromosome evolution was analyzed in chromEvol and diversification in BAMM to estimate diversification rates. Our results suggest that two major clades diverged early from the common ancestor, one most likely in the western Mediterranean and the other in a widespread area including west and central Asia (but with high uncertainty in the exact composition of this widespread area). Most ancestral lineages in the western clade remained in or around the western Mediterranean, and dispersal to other areas (mainly northward and eastward), occurred at the tips. Contrarily, most ancestral lineages in the widespread clade had larger ancestral areas. Polyploidization events in the western clade occurred at the tips of the phylogeny (with one exception of a polyploidization event in a very shallow node) and were mainly tetraploid, while polyploidization events occurred in the widespread clade were at the tips and in an ancestral node of the phylogeny, and were mainly hexaploid. We show how ancestral diploid lineages remained in the area of origin, whereas recent and ancestral polyploidization could have facilitated colonization and establishment in other areas.

Phylogenetic placement of Cailliella praerupticola (Melastomataceae), a rare, monospecific lineage from Guinea, West Africa

The genus Cailliella includes a single species, C. praerupticola, restricted to a sandstone plateau region in Coyah, Dubreka, Forécariah and Kindia Préfectures, Guinea, West Africa. Until its rediscovery in 2016, this species was known only by the type gathering made in 1937. We provide an emended description, photographs of living material, locality and habitat data, and a discussion of its conservation status. We further designate a lectotype for C. praerupticola. On the basis of morphology, Cailliella had been considered an isolated member of the tribe Melastomateae, possibly sister to Melastomastrum. We tested the classification of Cailliella by means of a phylogenetic analysis of C. praerupticola and 40 other samples of African Melastomateae, based on molecular sequence data from the external and internal transcribed spacer regions of nuclear ribosomal DNA (nrETS and nrITS) as well as the ndhF, psbK-psbL and accD-psaI regions of chloroplast DNA. Our results corroborate the placement of Cailliella in the Melastomateae, where it was resolved as sister to a clade consisting of both Melastomastrum and Tristemma. The hypothesis of C. praerupticola being an evolutionary relict or “palaeoendemic” is supported by our findings.Citation: Veranso-Libalah M. C., Stone R. D., Haba P. M., Magassouba S., Kadereit G. & Burgt X. M. van der 2021: Phylogenetic placement of Cailliella praerupticola (Melastomataceae), a rare, monospecific lineage from Guinea, West Africa. – Willdenowia 51: 47–56.Version of record first published online on 9 March 2021 ahead of inclusion in April 2021 issue.

Geographically extensive larval surveys reveal an unexpected scarcity of primary vector mosquitoes in a region of persistent malaria transmission in western Zambia

BackgroundThe Barotse floodplains of the upper Zambezi River and its tributaries are a highly dynamic environment, with seasonal flooding and transhumance presenting a shifting mosaic of potential larval habitat and human and livestock blood meals for malaria vector mosquitoes. However, limited entomological surveillance has been undertaken to characterize the vector community in these floodplains and their environs. Such information is necessary as, despite substantial deployment of insecticide-treated nets (ITNs) and indoor residual spraying (IRS) against Anopheles vectors, malaria transmission persists across Barotseland in Zambia’s Western Province.MethodsGeographically extensive larval surveys were undertaken in two health districts along 102 km of transects, at fine spatial resolution, during a dry season and following the peak of the successive wet season. Larvae were sampled within typical Anopheles flight range of human settlements and identified through genetic sequencing of cytochrome c oxidase I and internal transcribed spacer two regions of mitochondrial and nuclear DNA. This facilitated detailed comparison of taxon-specific abundance patterns between ecological zones differentiated by hydrological controls.ResultsAn unexpected paucity of primary vectors was revealed, with An. gambiae s.l. and An. funestus representing < 2% of 995 sequenced anophelines. Potential secondary vectors predominated in the vector community, primarily An. coustani group species and An. squamosus. While the distribution of An. gambiae s.l. in the study area was highly clustered, secondary vector species were ubiquitous across the landscape in both dry and wet seasons, with some taxon-specific relationships between abundance and ecological zones by season.ConclusionsThe diversity of candidate vector species and their high relative abundance observed across diverse hydro-ecosystems indicate a highly adaptable transmission system, resilient to environmental variation and, potentially, interventions that target only part of the vector community. Larval survey results imply that residual transmission of malaria in Barotseland is being mediated predominantly by secondary vector species, whose known tendencies for crepuscular and outdoor biting renders them largely insensitive to prevalent vector control methods.Graphical

Fungi Present in Antarctic Deep-Sea Sediments Assessed Using DNA Metabarcoding.

We assessed fungal diversity in deep-sea sediments obtained from different depths in the Southern Ocean using the internal transcribed spacer 2 (ITS2) region of nuclear ribosomal DNA bymetabarcoding through high-throughput sequencing (HTS). We detected 655,991 DNA reads representing 263 fungal amplicon sequence variants (ASVs), dominated by Ascomycota, Basidiomycota, Mortierellomycota, Mucoromycota, Chytridiomycota and Rozellomycota, confirming that deep-sea sediments can represent a hotspot of fungal diversity in Antarctica. The community diversity detected included 17 dominant fungal ASVs, 62 intermediate and 213 rare. The dominant fungi included taxa of Mortierella, Penicillium, Cladosporium, Pseudogymnoascus, Phaeosphaeria and Torula. Despite the extreme conditions of the Southern Ocean benthos, the total fungal community detected in these marine sediments displayed high indices of diversity and richness, and moderate dominance, which varied between the different depths sampled. The highest diversity indices were obtained in sediments from 550m and 250m depths. Only 49 ASVs (18.63%) were detected at all the depths sampled, while 16 ASVs were detected only in the deepest sediment sampled at 1463m. Based on sequence identities, the fungal community included some globally distributed taxa, primarily recorded otherwise from terrestrial environments, suggesting transport from these to deep marine sediments. The assigned taxa included symbionts, decomposers and plant-, animal- and human-pathogenic fungi, suggesting that deep-sea sediments host a complex fungal diversity, although metabarcoding does not itself confirm that living or viable organisms are present.

Population genetic analysis of two Polylepis microphylla (Wedd.) Bitter (Rosaceae) forests in Ecuador

ABSTRACT Habitat fragmentation is a severe problem that negatively affects forests around the world. This phenomenon has consequences at a genetic level in populations such as genetic diversity and gene flow reduction. As a result, population fitness decreases, and the possibility of extinction increases. Polylepis (Rosaceae) forests are endemic to the Andes and their distribution reflects hundreds of years of human activities. Polylepis microphylla is the most endangered species of the genus in Ecuador and is represented by only two known forests in Chimborazo province, separated from each other by 1,6 km. The present study focused on i) exploring the genetic structure and connectivity, ii) analyzing the genetic diversity patterns in these two forests of P. microphylla. Parameters such as Fixation index, molecular variance (AMOVA) and genetic diversity estimators were calculated from the haplotypic sequences of one chloroplastic DNA region (trnG intron), one nuclear DNA region (ITS), and the concatenation of both. We found that DNA regions used were highly polymorphic with a total of nine, four and thirteen segregation sites, respectively, and nine, six and fifteen haplotypes, respectively. Also, we detected that both forest work as a single population unit due to low fixation index values (Fst = 0,03822, −0,03883 and −0,00469, respectively), which indicate high gene flow between these two forests. In addition, we detected high genetic diversity reflected by haplotype diversity in both forest (hd = 0,54204, 0,63664 and 0,81682, respectively). Likewise, haplotype relationships were visualized in networks, which demonstrated limited spatial structuring between haplotypes, corroborating the low genetic differentiation among these forests. In conclusion, our results suggest there is a single population unit of P. microphylla in Ecuador. Habitat fragmentation does not seem to have negative effects on the genetic diversity of this species. Nevertheless, the species may be vulnerable to rapid environmental fluctuations despite having relatively high genetic diversity. Its long generational time causes increased susceptibility of P. microphylla to environmental changes and may eventually lead to the extinction of the species in Ecuador.

Enterocytozoon bieneusi of animals-With an 'Australian twist'.

Enterocytozoon bieneusi is a microsporidian microorganism that causes intestinal disease in animals including humans. E. bieneusi is an obligate intracellular pathogen, typically causing severe or chronic diarrhoea, malabsorption and/or wasting. Currently, E. bieneusi is recognised as a fungus, although its exact classification remains contentious. The transmission of E. bieneusi can occur from person to person and/or animals to people. Transmission is usually via the faecal-oral route through E. bieneusi spore-contaminated water, environment or food, or direct contact with infected individuals. Enterocytozoon bieneusi genotypes are usually identified and classified by PCR-based sequencing of the internal transcribed spacer region (ITS) of nuclear ribosomal DNA. To date, ~600 distinct genotypes of E. bieneusi have been recorded in ~170 species of animals, including various orders of mammals and reptiles as well as insects in >40 countries. Moreover, E. bieneusi has also been found in recreational water, irrigation water, and treated raw- and waste-waters. Although many studies have been conducted on the epidemiology of E. bieneusi, prevalence surveys of animals and humans are scant in some countries, such as Australia, and transmission routes of individual genotypes and related risk factors are poorly understood. This article/chapter reviews aspects of the taxonomy, biology and epidemiology of E. bieneusi; the diagnosis, treatment and prevention of microsporidiosis; critically appraises the naming system for E. bieneusi genotypes as well as the phylogenetic relationships of these genotypes; provides new insights into the prevalence and genetic composition of E. bieneusi populations in animals in parts of Australia using molecular epidemiological tools; and proposes some areas for future research in the E. bieneusi/microsporidiosis field.

Analyses of molecular markers and leaf morphology of two rare birches, Betula obscura and B. pendula var. carelica

Trees and shrubs belonging to the Betula L. genus seem to represent one of the most confused interspecific relationships, and hybridization is considered to be one of the main factors responsible for the substantial genetic and morphological variation of birches. In the present investigation, the internal transcribed spacer ITS1 and ITS2 regions of nuclear ribosomal DNA, nuclear alcohol dehydrogenase (ADH) gene sequences and amplified fragment length polymorphisms (AFLPs) as well as the Atkinson discriminant function (ADF) of leaf morphology were used to verify hypotheses concerning the origin of the dark barked Betula obscura and B. pendula var. carelica with the patterned wood. Both plants were considered by different authors to be distinct species, intraspecific forms of common B. pendula or B. pubescens, or hybrid taxa between B. pendula and B. pubescens. In the phylogenetic trees, the ITS and ADH gene sequences of both B. obscura and B. pendula var. carelica clustered with those of B. pendula, whereas B. pubescens trees were somewhat distinct. In turn, the AFLPs revealed genetic similarity of B. pendula var. carelica to both frequent species, whereas B. obscura was clearly distinct from other birches. Values of the ADF indices of the rare birches were typical for B. pendula. In the light of the results obtained, we imply that B. obscura and B. pendula var. carelica represent an intraspecific variation of B. pendula, they are neither intraspecific taxa of B. pubescens nor hybrid species between the common birches. Different grouping of B. obscura in the AFLPs and DNA sequences analyses is likely a result of an unreliable phylogenetic signal of the former molecular markers.

Non-Destructive Genotyping of Honeybee Queens to Support Selection and Breeding

Simple SummaryGenotyping of an individual usually requires tissue samples obtained by methods that may cause an injury. In the case of honeybee queens, most of such injuries cause supersedure of the queen. We have investigated the possibility of using two non-destructive sources to obtain genetic information from an individual queen: feces and exuviae. Both sources turned out to be acceptable in terms of quality of DNA and usefulness in genotyping. In practical use, any of the two could be used to shorten generation interval in queen breeding and decrease costs of the selection process. In traditional bee breeding, the honeybee queen is chosen for breeding based on the performance of the colony produced by its mother. However, we cannot be entirely certain that a specific queen will produce offspring with desirable traits until we observe the young queen’s new colony. Collecting the queen’s genetic material enables quick and reliable determination of the relevant information. We sampled exuviae, feces, and wingtips for DNA extraction to avoid fatally injuring the queen when using tissue samples. Quantity and purity of extracted DNA were measured. Two mitochondrial markers were used to determine the lineage affiliation and exclude possible contamination of DNA extracts with non-honeybee DNA. dCAPS (derived Cleaved Amplified Polymorphic Sequences) markers allowed detection of single nucleotide polymorphisms (SNPs) in nuclear DNA regions presumably associated with Varroa sensitive hygiene and set the example of successful development of genotyping protocol from non-destructive DNA sources. One of the logical future steps in honeybee breeding is introducing genomic selection and non-destructive sampling methods of genetic material may be the prerequisite for successful genotyping. Our results demonstrate that the extraction of DNA from feces and exuviae can be introduced into practice. The advantage of these two sources over wingtips is reducing the time window for processing the samples, thus enabling genotyping directly after the queen’s emergence.

Explaining the worldwide distributions of two highly mobile species: Cakile edentula and Cakile maritima

AbstractAimIf we are able to determine the geographic origin of an invasion, as well as its known area of introduction, we can better appreciate the innate environmental tolerance of a species and the strength of selection for adaptation that colonizing populations have undergone. It also enables us to maximize the success of searches for effective biological control agents. We determined the number of successful colonization events that have occurred throughout the world for two Cakile species and compared the climates from which they originated, in which they established and then spread.LocationWorldwide.TaxonSea‐Rockets (Cakile spp.), Brassicaceae.MethodsWe used a high‐throughput sequencing and a genome skimming approach combined with Bayesian Inference phylogenetics to examine variation in entire chloroplast genomes and regions of nuclear ribosomal DNA within native and introduced areas. Databases were used to compare climates between native ranges and introduced regions for multiple clades within each species.ResultsAt least seven clades have invaded different regions of the world. In most cases we were able to identify their source regions and climates. The environmental bottlenecks differed in intensity: while some clades colonized into climates that were similar to climates in their native range, other clades had a very broad innate environmental tolerance such that new invasions succeeded beyond the climate range of native populations. We found clear evidence of hybridization—specifically, chloroplast capture—between two species in Australia.ConclusionsResults here show that these species are sometimes capable of colonizing in climates that are beyond the climate range of native populations. Whether successful colonization beyond native climate niches requires de novo adaptation, or whether it represents an innate broad fundamental niche requires further investigation. Cakile species provide an excellent opportunity to study replicated climate adaptation trajectories.

Genetic data of the ITS1-5.8S rDNA sequences of small liver flukes (Opisthorchiidae) from cats in Northern Vietnam

Domestic cats and humans are favorite final hosts for some hepatic trematodes of Opisthorchiidae. The present study examined the sequence variation in the nuclear ribosomal DNA (rDNA) region, including the internal transcribed spacer (ITS1) and the 5.8S gene, of two human opisthorchiid species Clonorchis sinensis (Cobbold, 1875) Looss, 1907 and Opisthorchis viverrini (Poirier, 1886) Stiles &amp; Hassal, 1896, in cats sampled in Northern Vietnam. The length of 30 partial ITS1‒5.8S rDNA sequences of C. sinensis from different hosts and localities varied from 761 to 766 bp. The results showed completely identity for all investigated 5.8S rDNA sequences of C. sinensis. In contrast, the variations were revealed in the complete ITS1 sequences of C. sinensis. Three polymorphic sites, indel and new sites with intragenomic polymorphism were detected. The length of the complete ITS1 rDNA region ranged from 656 to 661 bp. There are no substitutions downstream of the 5 bp insertion, and the different ratio of nucleotide in polymorphic sites with presence/absence of insertion leads to the existence of 6 genotypes in the investigated samples. The major genotype was obtained in 70% of sequences, other genotypes were presented by 1, 2 or 3 sequences. Nucleotide diversity in whole sample of C. sinensis was 0.00122 ± 0.00073. Partial sequences of ITS1‒5.8S rDNA of O. viverrini were 745 bp in length, and no difference was observed. Phylogenetic analyses by neighbor joining phylogram inferred from ITS1‒5.8S rDNA of 3 sequences of O. viverrini and 30 sequences of C. sinensis were formed two separately monophyletic clades.

Morphological and Genetic Diversity of Two Forms of Muksun Coregonus muksun (Salmonidae) of the Khatanga River Basin as a Key for Understanding the Phylogenetic Relationships between Muksun and Whitefish C. lavaretus

Morphological analysis of muksun Coregonus muksun of the Khatanga River basin revealed that along with its typical high-density-rakered form, individuals of the low-density-rakered form also live in this region. Analysis of the genetic polymorphism of three marker regions of mitochondrial (ND1 and COI fragments) and nuclear (ITS1) DNA indicates the polyphyletic origin of these forms. The revealed low level of genetic differentiation of muksun and whitefish C. lavaretus, along with the available data on the absence of clear diagnostic species characteristics, suggest that they belong to the same biological species C. lavaretus.