High temperatures and low humidity promote the occurrence of microsporidians (Microsporidia) in mosquitoes (Culicidae)

BACKGROUND

In the context of climate change, a growing concern is that vector-pathogen or host-parasite interactions may be correlated with climatic factors, especially increasing temperatures. In the present study, we used a mosquito-microsporidian model to determine the impact of environmental factors such as temperature, humidity, wind and rainfall on the occurrence rates of opportunistic obligate microparasites (Microsporidia) in hosts from a family that includes important disease vectors (Culicidae).

METHODS

In our study, 3000 adult mosquitoes collected from the field over 3 years were analysed. Mosquitoes and microsporidia were identified using PCR and sequencing of the hypervariable V5 region of the small subunit ribosomal RNA gene and a shortened fragment of the cytochrome c oxidase subunit I gene, respectively.

RESULTS

DNA metabarcoding was used to identify nine mosquito species, all of which were hosts of 12 microsporidian species. The prevalence of microsporidian DNA across all mosquito samples was 34.6%. Microsporidian prevalence in mosquitoes was more frequent during warm months (> 19 °C; humidity < 65%), as was the co-occurrence of two or three microsporidian species in a single host individual. During warm months, microsporidian occurrence was noted 1.6-fold more often than during the cold periods. Among the microsporidians found in the mosquitoes, five (representing the genera Enterocytospora, Vairimorpha and Microsporidium) were positively correlated with an increase in temperature, whereas one (Hazardia sp.) was significantly correlated with a decrease in temperature. Threefold more microsporidian co-occurrences were recorded in the warm months than in the cold months.

CONCLUSIONS

These results suggest that the susceptibility of mosquitoes to parasite occurrence is primarily determined by environmental conditions, such as, for example, temperatures > 19 °C and humidity not exceeding 62%. Collectively, our data provide a better understanding of the effects of the environment on microsporidian-mosquito interactions.

Co-Occurrence of Borrelia burgdorferi Sensu Lato and Babesia spp. DNA in Ixodes ricinus Ticks Collected from Vegetation and Pets in the City of Poznań, Poland

Here, we described the prevalence of Borrelia burgdorferi s.l. and Babesia species found in mono- and double infections among Ixodes ricinus ticks occurring in urban areas of the city of Poznań, Poland. We tested 1029 host-seeking ticks and 1268 engorged ticks removed from pet animals. Borrelia afzelii and B. garinii prevailed both in ticks from vegetation (3.7% and 3.7%, respectively) and from pets (3.7% and 0.6%, respectively). Babesia canis and Ba. microti were the most prevalent in host-seeking (2.6% and 1.4%, respectively) and feeding ticks (2.8% and 2.2%, respectively). Babesia microti sequences proved to be identical to the human pathogenic Ba. microti genotype "Jena/Germany". Sequences of the rarest piroplasm Ba. venatorum (0.7%) were identical with those isolated from European patients. About 1.0% of tested ticks yielded dual infections; in host-seeking ticks, Ba. canis prevailed in co-infections with B. afzelii and B. garinii, whereas Ba. microti and B. afzelii dominated in double-infected feeding ticks. Dual infections, even with a low prevalence, pose a challenge for differential diagnosis in patients with acute febrile disease after a tick bite. The finding of Ba. canis in both tick groups suggests that I. ricinus could be involved in the circulation of this piroplasm.

Evaluation of Genetic Diversity in Quill Mites of the Genus Syringophiloidus Kethley, 1970 (Prostigmata: Syringophilidae) with Six New-to-Science Species

Quill mites (Acariformes: Syringophilidae) are poorly explored bird parasites. Syringophiloidus Kethley, 1970, is the most specious and widespread genus in this family. It is believed to contain mono-, steno- and poly-xenous parasites and thus seems to be an exemplary for studies on biodiversity and host associations. In this work, we applied the DNA barcode marker (mitochondrial cytochrome c oxidase subunit I gene fragment, COI) to analyze the species composition and host specificity of representatives of fifteen Syringophiloidus populations parasitizing fifteen bird species. The neighbor joining analyses distinguished thirteen monophyletic lineages, almost completely corresponding to seven previously known species recognized based on morphological features, and six new-to-science species. The only exception is S. amazilia Skoracki, 2017, which is most likely conspecific with Syringophiloidus stawarczyki Skoracki, 2004. The intraspecific distances of all species were not higher than 0.9%, whilst the interspecific diversity ranged from 5.9% to 19.2% and 6.3-22.4%, inferred as the distances p and K2P, respectively. Although all putative species (except S. amazilia) are highly supported, the relationships between them have not been fully resolved and only faintly indicate that both host phylogeny and distributions influence the phylogenetic structure of quill mite taxa.

Differences in the proliferation trend of 'Microsporidium' sp. PL03 in Culex pipiens and C. torrentium larvae

Our study aimed to examine whether there are differences in the proliferation trend of microsporidia in mosquito larvae of the same genus (Culex spp.). DNA-barcoding and quantitative analyses were used to determine microsporidian rDNA copies in 'early' (L1 + L2) and 'late' (L3 + L4) Culex larvae in a natural population. In the study area, C. pipiens and C. torrentium larvae were infected by 'Microsporidium' sp. PL03 at similar levels. Infection by this microsporidian species probably elicits a notable immune response in C. pipiens, whereas in C. torrentium, it may evade or suppress the host immune response.

Patrilocality and hunter-gatherer-related ancestry of populations in East-Central Europe during the Middle Bronze Age

The demographic history of East-Central Europe after the Neolithic period remains poorly explored, despite this region being on the confluence of various ecological zones and cultural entities. Here, the descendants of societies associated with steppe pastoralists form Early Bronze Age were followed by Middle Bronze Age populations displaying unique characteristics. Particularly, the predominance of collective burials, the scale of which, was previously seen only in the Neolithic. The extent to which this re-emergence of older traditions is a result of genetic shift or social changes in the MBA is a subject of debate. Here by analysing 91 newly generated genomes from Bronze Age individuals from present Poland and Ukraine, we discovered that Middle Bronze Age populations were formed by an additional admixture event involving a population with relatively high proportions of genetic component associated with European hunter-gatherers and that their social structure was based on, primarily patrilocal, multigenerational kin-groups.

Microsporidian Infection in Mosquitoes (Culicidae) Is Associated with Gut Microbiome Composition and Predicted Gut Microbiome Functional Content

The animal gut microbiota consist of many different microorganisms, mainly bacteria, but archaea, fungi, protozoans, and viruses may also be present. This complex and dynamic community of microorganisms may change during parasitic infection. In the present study, we investigated the effect of the presence of microsporidians on the composition of the mosquito gut microbiota and linked some microbiome taxa and functionalities to infections caused by these parasites. We characterised bacterial communities of 188 mosquito females, of which 108 were positive for microsporidian DNA. To assess how bacterial communities change during microsporidian infection, microbiome structures were identified using 16S rRNA microbial profiling. In total, we identified 46 families and four higher taxa, of which Comamonadaceae, Enterobacteriaceae, Flavobacteriaceae and Pseudomonadaceae were the most abundant mosquito-associated bacterial families. Our data suggest that the mosquito gut microbial composition varies among host species. In addition, we found a correlation between the microbiome composition and the presence of microsporidians. The prediction of metagenome functional content from the 16S rRNA gene sequencing suggests that microsporidian infection is characterised by some bacterial species capable of specific metabolic functions, especially the biosynthesis of ansamycins and vancomycin antibiotics and the pentose phosphate pathway. Moreover, we detected a positive correlation between the presence of microsporidian DNA and bacteria belonging to Spiroplasmataceae and Leuconostocaceae, each represented by a single species, Spiroplasma sp. PL03 and Weissella cf. viridescens, respectively. Additionally, W. cf. viridescens was observed only in microsporidian-infected mosquitoes. More extensive research, including intensive and varied host sampling, as well as determination of metabolic activities based on quantitative methods, should be carried out to confirm our results.

Trophic and symbiotic links between obligate-glacier water bears (Tardigrada) and cryoconite microorganisms

Insights into biodiversity and trophic webs are important for understanding ecosystem functions. Although the surfaces of glaciers are one of the most productive and biologically diverse parts of the cryosphere, the links between top consumers, their diet and microbial communities are poorly understood. In this study, for the first time we investigated the relationships between bacteria, fungi and other microeukaryotes as they relate to tardigrades, microscopic metazoans that are top consumers in cryoconite, a biologically rich and productive biogenic sediment found on glacier surfaces. Using metabarcoding (16S rDNA for bacteria, ITS1 for fungi, and 18S rDNA for other microeukaryotes), we analyzed the microbial community structures of cryoconite and compared them with the community found in both fully fed and starved tardigrades. The community structure of each microbial group (bacteria, fungi, microeukaryotes) were similar within each host group (cryoconite, fully fed tardigrades and starved tardigrades), and differed significantly between groups, as indicated by redundancy analyses. The relative number of operational taxonomic units (ZOTUs, OTUs) and the Shannon index differed significantly between cryoconite and tardigrades. Species indicator analysis highlighted a group of microbial taxa typical of both fully fed and starved tardigrades (potential commensals), like the bacteria of the genera Staphylococcus and Stenotrophomonas, as well as a group of taxa typical of both cryoconite and fully fed tardigrades (likely part of the tardigrade diet; bacteria Flavobacterium sp., fungi Preussia sp., algae Trebouxiophyceae sp.). Tardigrades are consumers of bacteria, fungi and other microeukaryotes in cryoconite and, being hosts for diverse microbes, their presence can enrich the microbiome of glaciers.

Metabarcoding reveals low prevalence of microsporidian infections in castor bean tick (Ixodes ricinus)

BACKGROUND

Microsporidia is a large group of eukaryotic obligate intracellular spore-forming parasites, of which 17 species can cause microsporidiosis in humans. Most human-infecting microsporidians belong to the genera Enterocytozoon and Encephalitozoon. To date, only five microsporidian species, including Encephalitozoon-like, have been found in hard ticks (Ixodidae) using microscopic methods, but no sequence data are available for them. Furthermore, no widespread screening for microsporidian-infected ticks based on DNA analysis has been carried out to date. Thus, in this study, we applied a recently developed DNA metabarcoding method for efficient microsporidian DNA identification to assess the role of ticks as potential vectors of microsporidian species causing diseases in humans.

METHODS

In total, 1070 (493 juvenile and 577 adult) unfed host-seeking Ixodes ricinus ticks collected at urban parks in the city of Poznan, Poland, and 94 engorged tick females fed on dogs and cats were screened for microsporidian DNA. Microsporidians were detected by PCR amplification and sequencing of the hypervariable V5 region of 18S rRNA gene (18S profiling) using the microsporidian-specific primer set. Tick species were identified morphologically and confirmed by amplification and sequencing of the shortened fragment of cytochrome c oxidase subunit I gene (mini-COI).

RESULTS

All collected ticks were unambiguously assigned to I. ricinus. Potentially zoonotic Encephalitozoon intestinalis was identified in three fed ticks (3.2%) collected from three different dogs. In eight unfed host-seeking ticks (0.8%), including three males (1.1%), two females (0.7%) and three nymphs (0.7%), the new microsporidian sequence representing a species belonging to the genus Endoreticulatus was identified.

CONCLUSIONS

The lack of zoonotic microsporidians in host-seeking ticks suggests that I. ricinus is not involved in transmission of human-infecting microsporidians. Moreover, a very low occurrence of the other microsporidian species in both fed and host-seeking ticks implies that mechanisms exist to defend ticks against infection with these parasites.

Sweet or salty? The origin of freshwater gastrotrichs (Gastrotricha, Chaetonotida) revealed by molecular phylogenetic analysis

Chaetonotidae is the most diverse and widely distributed family of the order Chaetonotida (Gastrotricha) and includes both marine and freshwater species. Although the family is regarded as a sister taxon to the exclusively marine Xenotrichulidae, the type of environment, marine or freshwater, where Chaetonotidae originated is still not known. Here, we reconstructed the phylogeny of the family based on molecular sequence data and mapped both morphological and ecological characters to determine the ancestral environment of the first members of the family. Our results revealed that the freshwater genus Bifidochaetus is the earliest branching lineage in the paraphyletic Chaetonotidae (encompassing Dasydytidae and Neogosseidae). Moreover, we reconstructed Lepidochaetus-Cephalionotus clade as a monophyletic sister group to the remaining chaetonotids, which supports Kisielewski's morphological based hypothesis concerning undifferentiated type of body scales as a most primary character in Chaetonotidae. We also found that reversals to marine habitats occurred independently in different Chaetonotidae lineages, thus marine species in the genera Heterolepidoderma, Halichaetonotus, Aspidiophorus and subgenera Chaetonotus (Schizochaetonotus) or Chaetonotus (Marinochaetus) should be assumed as having secondarily invaded the marine environment. Character mapping revealed a series of synapomorphies that define the clade that includes Chaetonotidae (with Dasydytidae and Neogosseidae), the most important of which may be those linked to reproduction.

The explosive radiation, intense host-shifts and long-term failure to speciate in the evolutionary history of the feather mite genus Analges (Acariformes: Analgidae) from European passerines

Mites of the genus Analges (Acariformes: Analgidae) inhabit the down feathers of passeriform birds. The evolutionary history of Analges and the co-phylogentic relationships between these mites and their hosts are unknown. Our phylogenetic analysis supported the monophyly of the genus, but it did not support previous taxonomic hypotheses subdividing the genus into the subgenera Analges and Analgopsis or arranging some species into the A. chelopus and A. passerinus species groups. Molecular data reveal seven new species inhabiting Eurasian passerines and support the existence of several multi-host species. According to molecular dating, the origin of the Analges (c. 41 Mya) coincided with the Eocene diversification of Passerida into Sylvioidea and Muscicapoidea–Passeroidea. The initial diversification of Analges took place on the Muscicapoidea clade, while remaining passerine superfamilies appear to have been colonized because of host-switching. Co-speciation appears to be relatively common among Analges species and their hosts, but the most striking pattern in the co-phylogenetic scenario involves numerous complete host-switches, spreads and several failures to speciate. The mechanism of long-term gene-flow among different populations of multi-host Analges species is enigmatic and difficult to resolve. Probably, in some cases mites could be transferred between birds via feathers used as nest material.

Maternal genetic origin of the late and final Neolithic human populations from present-day Poland

OBJECTIVE

We aim to identify maternal genetic affinities between the Middle to Final Neolithic (3850-2300 BC) populations from present-day Poland and possible genetic influences from the Pontic steppe.

MATERIALS AND METHODS

We conducted ancient DNA studies from populations associated with Złota, Globular Amphora, Funnel Beaker, and Corded Ware cultures (CWC). We sequenced genomic libraries on Illumina platform to generate 86 complete ancient mitochondrial genomes. Some of the samples were enriched for mitochondrial DNA using hybridization capture.

RESULTS

The maternal genetic composition found in Złota-associated individuals resembled that found in people associated with the Globular Amphora culture which indicates that both groups likely originated from the same maternal genetic background. Further, these two groups were closely related to the Funnel Beaker culture-associated population. None of these groups shared a close affinity to CWC-associated people. Haplogroup U4 was present only in the CWC group and absent in Złota group, Globular Amphora, and Funnel Beaker cultures.

DISCUSSION

The prevalence of mitochondrial haplogroups of Neolithic farmer origin identified in Early, Middle and Late Neolithic populations suggests a genetic continuity of these maternal lineages in the studied area. Although overlapping in time - and to some extent - in cultural expressions, none of the studied groups (Złota, Globular Amphora, Funnel Beaker), shared a close genetic affinity to CWC-associated people, indicating a larger extent of cultural influence from the Pontic steppe than genetic exchange. The higher frequency of haplogroup U5b found in populations associated with Funnel Beaker, Globular Amphora, and Złota cultures suggest a gradual maternal genetic influx from Mesolithic hunter-gatherers. Moreover, presence of haplogroup U4 in Corded Ware groups is most likely associated with the migrations from the Pontic steppe at the end of the Neolithic and supports the observed genetic distances.

Zoonotic Giardia duodenalis sub-assemblage BIV in wild raccoons (Procyon lotor) from Germany and Luxembourg

Giardia duodenalis is a cosmopolitan flagellate that causes giardiasis, one of the most significant gastrointestinal diseases in humans. This parasite can be a serious threat to public health because it can cause waterborne outbreaks as well as sporadic infections in humans. Invasive raccoons (Procyon lotor) may play a role in disseminating Giardia into the environment and transmitting it to humans and domestic animals because they live in high densities and deposit their faces in latrines near areas used by humans. While Giardia infections have been reported from raccoons in North America, it is unknown whether they carry G. duodenalis with zoonotic assemblage A and B, which have the potential to cause illness in humans. We collected faecal samples from 66 legally harvested raccoons in Germany and Luxembourg and examined for Giardia using molecular techniques. Using a quantitative PCR based on primers specific to Giardia genetic assemblages A and B, we detected the presence of zoonotic assemblage B in 27% (95% CI, 17.0-39.6) of all examined faecal samples from raccoons, including animals sampled in buildings. We did not detect genetic assemblage A in any of the samples. Sequences obtained from the glutamate dehydrogenase and beta-giardin gene fragments from a selection of three of the positive samples showed that raccoons carried a zoonotic G. duodenalis genotype belonging to sub-assemblage BIV, which is commonly found in humans and animals worldwide. Our results suggest that free-ranging raccoons have the potential to play an increasingly important role in the epidemiology of Giardia and pose a threat to public health in Europe and other regions where this species is common and lives in close association with humans.

A new method of metabarcoding Microsporidia and their hosts reveals high levels of microsporidian infections in mosquitoes (Culicidae)

DNA metabarcoding offers new perspectives, especially with regard to the high‐throughput identification and diagnostics of pathogens. Microsporidia are an example of widely distributed, opportunistic and pathogenic microorganisms in which molecular identification is important for both environmental research and clinical diagnostics. We have developed a method for parallel detection of both microsporidian infection and the host species. We designed new primer sets: one specific for the classical Microsporidia (targeting the hypervariable V5 region of small subunit [ssu] rDNA), and a second one targeting a shortened fragment of the COI gene (standard metazoan DNA‐barcode); both markers are well suited for next generation sequencing. Analysis of the ssu rDNA data set representing 607 microsporidian species (120 genera) indicated that the V5 region enables identification of >98% species in the data set (596/607). To test the method, we used microsporidians that infect mosquitoes in natural populations. Using mini‐COI data, all field‐collected mosquitoes were unambiguously assigned to seven species; among them almost 60% of specimens were positive for at least 11 different microsporidian species, including a new microsporidian ssu rDNA sequence (Microsporidium sp. PL01). Phylogenetic analysis showed that this species belongs to one of the two main clades in the Terresporidia. We found a high rate of microsporidian co‐infections (9.4%). The numbers of sequence reads for the operational taxonomic units suggest that the occurrence of Nosema spp. in co‐infections could benefit them; however, this observation should be retested using a more intensive host sampling. Our results show that DNA barcoding is a rapid and cost‐effective method for deciphering sample diversity in greater resolution, including the hidden biodiversity that may be overlooked using classical methodology.

Mitochondrial genomes from Bronze Age Poland reveal genetic continuity from the Late Neolithic and additional genetic affinities with the steppe populations

OBJECTIVE

In this work we aim to investigate the origins and genetic affinities of Bronze Age populations (2,400-1,100 BC) from the region of southern Poland and to trace maternal kinship patterns present in the burials of those populations by the use of complete mitochondrial genomes.

MATERIALS AND METHODS

We performed ancient DNA analyses for Bronze Age individuals from present-day Poland associated with the Strzyżow culture, the Mierzanowice culture, and the Trzciniec Cultural circle. To obtain complete mitochondrial genomes, we sequenced genomic libraries using Illumina platform. Additionally, hybridization capture was used to enrich some of the samples for mitochondrial DNA. AMS ¹⁴ C-dating was conducted for 51 individuals to verify chronological and cultural attribution of the analyzed samples.

RESULTS

Complete ancient mitochondrial genomes were generated for 80 of the Bronze Age individuals from present-day Poland. The results of the population genetic analyses indicate close maternal genetic affinity between Mierzanowice, Trzciniec, and Corded Ware culture-associated populations. This is in contrast to the genetically more distant Strzyżów people that displayed closer maternal genetic relation to steppe populations associated with the preceding Yamnaya culture and Catacomb culture, and with later Scythians. Potential maternal kinship relations were identified in burials of Mierzanowice and Trzciniec populations analyzed in this study.

DISCUSSION

Results revealed genetic continuity from the Late Neolithic Corded Ware groups to Bronze Age Mierzanowice and Trzciniec-associated populations, and possible additional genetic contribution from the steppe to the formation of the Strzyżów-associated group at the end of 3rd millennium BC. Mitochondrial patterns indicated several pairs of potentially maternally related individuals mostly in Trzciniec-associated group.

Microbial composition of enigmatic bird parasites: Wolbachia and Spiroplasma are the most important bacterial associates of quill mites (Acariformes: Syringophilidae)

Background

The microbiome is an integral component of many animal species, potentially affecting behavior, physiology, and other biological properties. Despite this importance, bacterial communities remain vastly understudied in many groups of invertebrates, including mites. Quill mites (Acariformes: Syringophilidae) are a poorly known group of permanent bird ectoparasites that occupy quills of feathers and feed on bird subcutaneous tissue and fluids. Most of the known species have strongly female‐biased sex ratio, and it was hypothesized that this is caused by endosymbiotic bacteria. Previously, Anaplasma phagocytophilum (Foggie) and a high diversity of Wolbachia strains were detected in quill mites via targeted PCR screens. Here, we use an unbiased 16S rRNA gene amplicon sequencing approach to determine other bacteria that potentially impact quill mite biology.

Results

We performed 16S rRNA gene amplicon sequencing of 126 quill mite individuals from eleven species parasitizing twelve species (four families) of passeriform birds. In addition to Wolbachia, we found Spiroplasma as potential symbiont of quill mites. Consistently, high Spiroplasma titers were only found in individuals of two mite species associated with finches of the genus Carduelis, suggesting a history of horizontal transfers of Spiroplasma via the bird host. Furthermore, there was evidence for Spiroplasma negatively affecting Wolbachia titers. We found no evidence for the previously reported Anaplasma in quill mites, but detected sequences of high similarity to the potential pathogens Brucella and Bartonella at low abundances. Other amplicon sequence variants (ASVs) could be assigned to a diverse number of bacterial taxa, including several that were previously isolated from bird skin. Further, many frequently found ASVs were assigned to taxa that show a very broad distribution with no strong prior evidence for symbiotic association with animals. We interpret these findings as evidence for a scarcity of resident microbial associates (other than inherited symbionts) in quill mites.

Insight into the species diversity of the quill mite genus Betasyringophiloidus Skoracki, 2011 (Prostigmata: Syringophilidae) on the basis of the DNA barcodes

Betasyringophiloidus Skoracki, 2011 is a genus of quill mites (Prostigmata: Syringophilidae) that is believed to contain mono-, steno- and polyxenous parasites associated with a wide range of passerine birds (Passeriformes) across the world. In this work we applied the DNA-barcode marker (mitochondrial cytochrome c oxidase subunit I gene fragment, COI) to verify whether Betasyringophiloidus schoeniclus (Skoracki, 2002) and Betasyringophiloidus seiuri (Clark, 1964) are actual steno- and polyxenous species associated with the currently recognised host ranges, or their populations are highly host-specific, cryptic species. Our results revealed that a population living on the Tristram's bunting Emberiza tristrami Swinhoe (Emberizidae) in Russia, so far classified as B. schoeniclus, is a new cryptic species Betasyringophiloidus emberizae sp. nov. Both topologies of the neighbor-joining and maximum likelihood phylogenetic trees as well as genetic distance (11.9% Kimura 2-parameter distance) (K2P) support species status of the mite population from E. tristrami. The same data support previously established conspecific status of B. seiuri found on the ovenbird Seiurus aurocapilla (Linnaeus) (Parulidae) (type host) and the northern waterthrush Parkesia noveboracensis (Gmelin) (Parulidae) and expand its range with a population found on a new host species Icterus pustulatus (Wagler) (Icteridae) with intraspecific K2P distance up to 1.9% and interpopulation distances ranging from 1.3 to 3.1%.

A new quill mite Torotrogla emberizae sp. nov. (Acariformes: Syringophilidae) from the Chestnut-eared Bunting (Passeriformes: Emberizidae) in Japan (morphology and DNA barcode data)

A new quill mite Torotrogla emberizae sp. nov. (Acariformes: Syringophilidae) parasitizing the Chestnut-eared Bunting Emberiza fucata Pallas, 1776 (Passeriformes: Emberizidae) in Japan is described based on the external morphology and DNA barcode data (mitochondrial cytochrome c oxidase subunit I sequences, COI). Females of T. emberizae sp. nov. differ from T. volgini Skoracki and Mironov, 2013 by having the short, wide and blunt-ended hypostomal protuberances (vs long, thin and sharp-ended), setae h1 ca. twice shorter than f1 (vs h1 longer than f1), the fan-like setae p' and p" of legs III-IV provided with ca. 10 tines (vs 7-8 tines) and lengths of setae vi 70-105 (vs 55-65), ve 105-135 (vs 85-90) and h1 55-60 (vs 95-120).

The occurrence of Microstoma protracta (Fr.) Kanouse in Poland and assessment of its threat status

<em>Microstoma protracta</em> (Fr.) Kanouse is a strictly protected species in Poland, which is also present on the red list with the category R (rare). In Poland, there are five known localities for the species, including four historical sites discovered at the beginning of the twentieth century and one contemporary site discovered at the end of the twentieth century. In this paper, we present two new localities for <em>M. protracta</em>, discovered in April 2006 in Czeszewo (Wielkopolska Lowland, Jarocin Forest District) and in April 2017 in Krakow-Tyniec (Krakow-Częstochowa Upland, Myślenice Forest District). Sequences of the nuclear ribosomal DNA internal transcribed spacer regions of sporocarps from contemporary localities have been deposited in the GenBank database. This is the first record of the DNA barcode for this species. According to Criterion D of the IUCN recommendations, it has been suggested that <em>M. protracta</em> should be considered as a critically endangered species (CR: D) in Poland.

Combined description (morphology with DNA barcode data) of a new quill mite Torotrogla paenae n. sp. (Acariformes: Syringophilidae) parasitising the Kalahari scrub-robin Cercotrichas paena (Smith) (Passeriformes: Muscicapidae) in Namibia

A new quill mite species Torotrogla paenae n. sp. (Acariformes: Syringophilidae) parasitising the Kalahari scrub-robin Cercotrichas paena (Smith) (Passeriformes: Muscicapidae) in Namibia is described based on the external morphology and DNA barcode data (the mitochondrial cytochrome c oxidase subunit 1 sequences, cox1). Females of T. paenae n. sp. morphologically differ from the most similar species T. lusciniae Skoracki, 2004 by the total body length (780-830 vs 645-715 µm in T. lusciniae) and the presence of hysteronotal shields (vs absence), apunctate propodonotal and pygidial shields (vs punctate), apunctate coxal fields (vs punctate), the fan-like setae p' and p" of legs III-IV provided with c.10 tines (vs 14-15) and the length of setae si (140-180 vs 190-210 µm) and se (160-185 vs 210-225 µm). The male of T. paenae n. sp. morphologically differs from T. lusciniae by the lateral branch of peritremes composed of 4 chambers (vs 7-8 chambers) and lengths of setae ve (45 vs 70-75 µm) and se (120 vs 165 µm).

Mitochondrial genomes reveal an east to west cline of steppe ancestry in Corded Ware populations

From around 4,000 to 2,000 BC the forest-steppe north-western Pontic region was occupied by people who shared a nomadic lifestyle, pastoral economy and barrow burial rituals. It has been shown that these groups, especially those associated with the Yamnaya culture, played an important role in shaping the gene pool of Bronze Age Europeans, which extends into present-day patterns of genetic variation in Europe. Although the genetic impact of these migrations from the forest-steppe Pontic region into central Europe have previously been addressed in several studies, the contribution of mitochondrial lineages to the people associated with the Corded Ware culture in the eastern part of the North European Plain remains contentious. In this study, we present mitochondrial genomes from 23 Late Eneolithic and Bronze Age individuals, including representatives of the north-western Pontic region and the Corded Ware culture from the eastern part of the North European Plain. We identified, for the first time in ancient populations, the rare mitochondrial haplogroup X4 in two Bronze Age Catacomb culture-associated individuals. Genetic similarity analyses show close maternal genetic affinities between populations associated with both eastern and Baltic Corded Ware culture, and the Yamnaya horizon, in contrast to larger genetic differentiation between populations associated with western Corded Ware culture and the Yamnaya horizon. This indicates that females with steppe ancestry contributed to the formation of populations associated with the eastern Corded Ware culture while more local people, likely of Neolithic farmer ancestry, contributed to the formation of populations associated with western Corded Ware culture.

Analysis of LCT-13910 genotypes and bone mineral density in ancient skeletal materials

The relation of LCT-13910 genotypes and bone mineral density (BMD) has been the subject of modern-day human population studies, giving inconsistent results. In the present study we analyze for the first time a relation of LCT-13910 genotypes and BMD in historical skeletal individuals. Ancient population might be a model for testing this association due to elimination of non-natural factors affecting bone density. Among 22 medieval individuals from Sanok churchyard (South-Eastern Poland; dated from XIV to XVII c. AD) we identified 4 individuals with osteoporosis (mean BMD = 0.468 g/cm2, SD = 0.090), 10 individuals with osteopenia (mean BMD = 0.531 g/cm2, SD = 0.066) and 8 individuals with normal BMD values (mean BMD = 0,642 g/cm2, SD = 0.060). Analyses of BMD and LCT-13910 genotypes revealed that mean BMD was the highest (0.583 g/cm2, SD = 0.065) in the individuals with lactose tolerance genotypes (TT and CT). We also found possible association of lower BMD at the radius and CC genotypes due to higher but not statistically significant frequency of osteoporosis in the lactose intolerant group (p = 0.60). Statistically significant correlation was found between BMD and females aged 20-35 years, with tendency to reduce BMD with age (p = 0.02).

Late Danubian mitochondrial genomes shed light into the Neolithisation of Central Europe in the 5th millennium BC

Background

Recent aDNA studies are progressively focusing on various Neolithic and Hunter - Gatherer (HG) populations, providing arguments in favor of major migrations accompanying European Neolithisation. The major focus was so far on the Linear Pottery Culture (LBK), which introduced the Neolithic way of life in Central Europe in the second half of 6th millennium BC. It is widely agreed that people of this culture were genetically different from local HGs and no genetic exchange is seen between the two groups. From the other hand some degree of resurgence of HGs genetic component is seen in late Neolithic groups belonging to the complex of the Funnel Beaker Cultures (TRB). Less attention is brought to various middle Neolithic cultures belonging to Late Danubian sequence which chronologically fall in between those two abovementioned groups. We suspected that genetic influx from HG to farming communities might have happened in Late Danubian cultures since archaeologists see extensive contacts between those two communities.

Results

Here we address this issue by presenting 5 complete mitochondrial genomes of various late Danubian individuals from modern-day Poland and combining it with available published data. Our data show that Late Danubian cultures are maternally closely related to Funnel Beaker groups instead of culturally similar LBK.

Conclusions

We assume that it is an effect of the presence of individuals belonging to U5 haplogroup both in Late Danubians and the TRB. The U5 haplogroup is thought to be a typical for HGs of Europe and therefore we argue that it is an additional evidence of genetic exchange between farming and HG groups taking place at least as far back as in middle Neolithic, in the Late Danubian communities.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-017-0924-0) contains supplementary material, which is available to authorized users.

Diverse origin of mitochondrial lineages in Iron Age Black Sea Scythians

Scythians were nomadic and semi-nomadic people that ruled the Eurasian steppe during much of the first millennium BCE. While having been extensively studied by archaeology, very little is known about their genetic identity. To fill this gap, we analyzed ancient mitochondrial DNA (mtDNA) from Scythians of the North Pontic Region (NPR) and successfully retrieved 19 whole mtDNA genomes. We have identified three potential mtDNA lineage ancestries of the NPR Scythians tracing back to hunter-gatherer and nomadic populations of east and west Eurasia as well as the Neolithic farming expansion into Europe. One third of all mt lineages in our dataset belonged to subdivisions of mt haplogroup U5. A comparison of NPR Scythian mtDNA linages with other contemporaneous Scythian groups, the Saka and the Pazyryks, reveals a common mtDNA package comprised of haplogroups H/H5, U5a, A, D/D4, and F1/F2. Of these, west Eurasian lineages show a downward cline in the west-east direction while east Eurasian haplogroups display the opposite trajectory. An overall similarity in mtDNA lineages of the NPR Scythians was found with the late Bronze Age Srubnaya population of the Northern Black Sea region which supports the archaeological hypothesis suggesting Srubnaya people as ancestors of the NPR Scythians.

Investigating kinship of Neolithic post-LBK human remains from Krusza Zamkowa, Poland using ancient DNA

We applied an interdisciplinary approach to investigate kinship patterns and funerary practices during the middle Neolithic. Genetic studies, radiocarbon dating, and taphonomic analyses were used to examine two grave clusters from Krusza Zamkowa, Poland. To reconstruct kinship and determine biological sex, we extracted DNA from bones and teeth, analyzed mitochondrial genomes and nuclear SNPs using the HID-Ion AmpliSeq™ Identity panel generated on Illumina and Ion Torrent platforms, respectively. We further dated the material (AMS ¹⁴C) and to exclude aquatic radiocarbon reservoir effects, measures of carbon and nitrogen stable isotopes for diet reconstruction were used. We found distinct mitochondrial genomes belonging to haplogroups U5b2a1a, K1c and H3d in the first grave cluster, and excluded maternal kin patterns among the three analyzed individuals. In the second grave cluster one individual belonged to K1a4. However, we could not affiliate the second individual to a certain haplogroup due to the fragmented state of the mitochondrial genome. Although the individuals from the second grave cluster differ at position 6643, we believe that more data is needed to fully resolve this issue. We retrieved between 26 and 77 autosomal SNPs from three of the individuals. Based on kinship estimations, taking into account the allelic dropout distribution, we could not exclude first degree kin relation between the two individuals from the second grave cluster. We could, however, exclude a first degree kinship between these two individuals and an individual from the first grave cluster. Presumably, not only biological kinship, but also social relations played an important role in the funerary practice during this time period. We further conclude that the HID-Ion AmpliSeq™ Identity Panel may prove useful for first degree kin relation studies for samples with good DNA preservation, and that mitochondrial genome capture enrichment is a powerful tool for excluding direct maternal relationship in ancient individuals.

A new quill mite Syringophiloidus plocei sp. nov. (Prostigmata: Syringophilidae) parasitizing ploceid birds (Passeriformes) in Gabon - a combined description using morphology and DNA barcoding

A new species of quill mites (Syringophilidae) Syringophiloidus plocei sp. nov. parasitizing Ploceus cucullatus (St. Muller) (type host), P. aurantius (Vieillot) and P. nigerrimus (Vieillot) (Ploceidae: Passeriformes) in Gabon is described using external morphology and DNA barcode data (the mitochondrial cytochrome c oxidase subunit I sequences (COI) and D1-D3 region of the nuclear 28S rRNA gene). Females of S. plocei sp. nov. differ from S. pseudonigritae Glowska, Dragun-Damian and Dabert, 2012 by the length of setae ag3 190-230 (vs 145-160). The genetic distances (K2P) between COI haplotypes of S. plocei sp. nov. individuals (from P. cucullatus, P. nigerrimus and P. aurantius) and S. pseudonigritae ranges from 13.1-13.7%.

Aulonastus similis n. sp., a new quill mite species (Syringophilidae) parasitising passeriform birds (Tyrannidae and Cardinalidae) in Mexico

A new quill mite species, Aulonastus similis n. sp. (Acariformes: Syringophilidae), parasitising Myiozetetes similis (Spix) (Tyrannidae) and Habia fuscicauda (Cabanis) (Cardinalidae) in Mexico is described and DNA barcode sequences of the mitochondrial cytochrome c oxidase subunit I (cox1) and D1-D3 region of the nuclear 28S rRNA gene are provided. Morphologically, females of A. similis are close to A. euphagus Skoracki, Hendricks & Spicer, 2010 but differ from this species in the length ratios of the idiosomal setae: ve:si (2-2.3:1 vs 1:1) and f2:f1 (4.7-6.3:1 vs 3.3:1).

Bifidochaetus, a new Arctic genus of freshwater Chaetonotida (Gastrotricha) from Spitsbergen revealed by an integrative taxonomic approach

Gastrotricha is a cosmopolitan phylum of aquatic and semi-terrestrial invertebrates that comprises ~820 described species. To date, freshwater gastrotrichs have not been the subject of faunistic or taxonomic research in the polar regions. In this paper, we present the first species-level description of a freshwater gastrotrich from the Arctic (Svalbard Archipelago). Evidence from morphology, morphometry and molecular analyses reveals that the species represents a new genus in Chaetonotidae: Bifidochaetus arcticus, gen. et sp. nov. Taking into consideration many morphological similarities to Chaetonotus (Primochaetus) veronicae Kånneby, 2013 we propose to include C. (P.) veronicae in the newly established genus under the new combination Bifidochaetus veronicae (Kånneby, 2013), comb. nov. In the phylogenetic analysis based on nuclear 18S rRNA, 28S rRNA and mitochondrial cytochrome c oxidase subunit I sequence data, B. arcticus, gen. et sp. nov. is nested within the family Chaetonotidae, as the sister group to the genus Lepidochaetus Kisielewski, 1991. In this paper we also present new taxonomic characters useful for gastrotrich taxonomy: the pharynx-to-intestine length ratio (I) and the spine bifurcation ratio (B).

Differences in speciation progress in feather mites (Analgoidea) inhabiting the same host: the case of Zachvatkinia and Alloptes living on arctic and long-tailed skuas

Recent molecular phylogenetic analyses have revealed that some apparently oligoxenous feather mite species are in fact monoxenous cryptic species with little morphological differentiation. In this study we analyzed two species, Zachvatkinia isolata (Avenzoariidae) and Alloptes (Sternalloptes) stercorarii (Alloptidae) which prefer different parts of the plumage of two sister species of birds: arctic skua (Stercorarius parasiticus) and long-tailed skua (S. longicaudus) breeding on tundra in the High Arctic archipelago of Svalbard. Given that there are no reports about hybridization events between the host species, we expected that both skuas would have a species-specific acarofauna. The genetic distances among DNA-barcode sequences (COI and 28S rDNA), phylogenetic tree topologies, and haplotype networks of the COI sequences of mites suggested extensive gene flow in Z. isolata between and within populations inhabiting both skua species, whereas the Alloptes populations were host specific and sufficiently genetically separated as to warrant species-level status. The discrepancy in the genetic structure of Alloptes and Zachvatkinia populations suggests frequent but transient contacts between the two skua species in which the probability of mite exchange is much higher for Zachvatkinia, which is present in high numbers and inhabits exposed parts of primary flight feathers, than for the less abundant Alloptes that lives primarily in more protected and inaccessible parts of the plumage. We discuss the possible nature of these contacts between host species and the area(s) where they might take place. The star-like structures in the haplotype network as well as high haplotype diversity and low nucleotide diversity observed in Z. isolata are concordant with the known dispersal strategy of feather mites: vertical colonization of new host individuals followed by rapid growth of founder populations.

Ancient DNA reveals matrilineal continuity in present-day Poland over the last two millennia

While numerous ancient human DNA datasets from across Europe have been published till date, modern-day Poland in particular, remains uninvestigated. Besides application in the reconstruction of continent-wide human history, data from this region would also contribute towards our understanding of the history of the Slavs, whose origin is hypothesized to be in East or Central Europe. Here, we present the first population-scale ancient human DNA study from the region of modern-day Poland by establishing mitochondrial DNA profiles for 23 samples dated to 200 BC – 500 AD (Roman Iron Age) and for 20 samples dated to 1000–1400 AD (Medieval Age). Our results show that mitochondrial DNA sequences from both periods belong to haplogroups that are characteristic of contemporary West Eurasia. Haplotype sharing analysis indicates that majority of the ancient haplotypes are widespread in some modern Europeans, including Poles. Notably, the Roman Iron Age samples share more rare haplotypes with Central and Northeast Europeans, whereas the Medieval Age samples share more rare haplotypes with East-Central and South-East Europeans, primarily Slavic populations. Our data demonstrates genetic continuity of certain matrilineages (H5a1 and N1a1a2) in the area of present-day Poland from at least the Roman Iron Age until present. As such, the maternal gene pool of present-day Poles, Czechs and Slovaks, categorized as Western Slavs, is likely to have descended from inhabitants of East-Central Europe during the Roman Iron Age.

DNA barcodes reveal female dimorphism in syringophilid mites (Actinotrichida: Prostigmata: Cheyletoidea): Stibarokris phoeniconaias and Ciconichenophilus phoeniconaias are conspecific

Here we present the first evidence of female dimorphism in ectoparasitic quill mites of the family Syringophilidae (Actinotrichida: Prostigmata: Cheyletoidea). Stibarokris phoeniconaias Skoracki et OConnor, 2010 and Ciconichenophilus phoeniconaias Skoracki et OConnor, 2010 so far have been treated as two distinct species cohabiting inside the quills of feathers of the lesser flamingo Phoeniconaias minor (Geoffroy Saint-Hilaire) and the American flamingo Phoenicopterus ruber Linnaeus. Although females of these species differ morphologically by the extent of body sclerotisation, presence/absence of lateral hypostomal teeth, and shape of dorsal setae, their important common features are the lack of leg setae vs II, and both stylophore and peritremes shape. Here, we apply the DNA barcode markers to test whether the differences between S. phoeniconaias and C. phoeniconaias have a genetic basis, indicating that they really are distinct taxa, or whether they just represent two morphs of a single species. All analysed sequences (616 bp for COI and 1159 bp for 28S rDNA) obtained for specimens representing females of both studied taxa as well as male, tritonymph, protonymph and larva of S. phoeniconaias were identical, which indicates that S. phoeniconaias and C. phoeniconaias are conspecific. The formal taxonomic consequence of our results is denial of the genus status of Ciconichenophilus Skoracki et OConnor, 2010 and species status of C. phoeniconaias, and recommendation that they should be treated as junior synonyms of Stibarokris Kethley, 1970 and S. phoeniconaias, respectively.

Multidisciplinary analysis of Knemidocoptes jamaicensis parasitising the Common Chaffinch, Fringilla coelebs: proofs for a multispecies complex?

The number of studies discussing the pathology and host specificity in Knemidocoptinae is very limited. In Knemidocoptes jamaicensis, the host specificity seems to be very broad, and there is a clear morphological variability in individuals originating from various bird species; hence, serious doubts appear about the species status of this mite. We report a multidisciplinary approach to the taxonomy, morphology, ecology, and pathology of K. jamaicensis. The source of the mites in our study was a second year aged female of the Common Chaffinch, Fringilla coelebs, which accidentally died in the mist net during a field study in Dumbrava, Cluj County, Romania in March 2011. Comparisons of the biometrical data regarding the body dimensions, length of certain setae, and distances between bases of dorsal setae with other published data showed a great variability of certain measurements between populations infecting various hosts and localities and sometimes even within single populations. Gross and histologic lesions consisted in severe bilateral orthokeratotic hyperkeratosis and epidermal spongiosis. Lesions also involved the skin of the joints. Skin inflammation was absent, and no lesions were noticed in the metatarsus bone. Following molecular analysis, the 518-base-long sequence differed from the published 18S rDNA in nine positions. Additionally, our paper reports for the first time the DNA barcode sequences of K. jamaicensis and, together with the synoptic analysis of host spectrum, geographical distribution and morphological variability it brings important evidences to sustain the hypothesis of multispecies complex for K. jamaicensis.

The cereal rust mite Abacarus hystrix (Acari: Eriophyoidea) is a complex of species: evidence from mitochondrial and nuclear DNA sequences

The cereal rust mite Abacarus hystrix (Nalepa), a significant pest of grasses, has been regarded as one of a few exceptions among eriophyoid mites with reference to the pattern of host plant utilization. At least 60 grass species have been recorded as its hosts. Thus, the mite has long been considered as a host generalist in which host specialization would not be likely to evolve. However, recent studies have revealed that host-associated specialization is possible in A. hystrix. Here, we aimed to discriminate between the three populations of A. hystrix associated with the different hosts (namely quackgrass, ryegrass and smooth brome) on the basis of mitochondrial (COI) and nuclear (D2 region of 28S rDNA) DNA sequences. The phylogenetic trees obtained with the maximum likelihood analysis of both COI and D2 region data sets showed that host-adapted strains of A. hystrix form distinct clades. Furthermore, on the COI nucleotide tree, the quackgrass- and brome-associated strains were internally divided each into two well-supported monophyletic clusters. The nucleotide D2 region data set tree showed that brome-associated strain is polyphyletic in origin. There is clear co-variation of DNA results with earlier morphological and ecological traits, as well as the results of crossing experiments. We showed that reproductively incompatible strains of A. hystrix exhibit more than 20% sequence divergence in the COI gene and 0.2% sequence divergence in the D2 28S rDNA. Our results did not confirm the placement of three host-associated strains of A. hystrix within one, ostensibly generalist, species.

Genetic diversity of naturally established ectomycorrhizal fungi on Norway spruce seedlings under nursery conditions

We have assessed ectomycorrhizal fungi colonizing Norway spruce (Picea abies L.) seedlings in nine forest nurseries using restriction fragment length polymorphism (RFLP) and sequencing analyses of the internal transcribed spacers (ITS1-5.8S-ITS2) amplicons. Restriction analysis of the amplified DNA fragments with HinfI, MboI, and TaqI enzymes allowed the definition of 17 RFLP genotypes; five of them could be unambiguously assigned to Thelephora terrestris, Hebeloma longicaudum, H. crustuliniforme, Tricharina ochroleuca, and Cenococcum geophilum species by comparison with the sporocarp RFLP-pattern database. The remaining genotypes have been sequenced and compared with sequences deposited in the GenBank database. The phylogenetic analysis of resulting sequences and their identified matches indicated that isolated genotypes have formed seven clades. The ascomycetes were predominant: we have determined eight species--Wilcoxina mikolae, Phialophora finlandia, Tuber sp., Cenococcum geophilum, Tricharina ochroleuca, Pulvinula constellatio, and two unidentified ascomycetes--whereas the basidiomycetes were less common (four species denoted: Amphinema byssoides, Hebeloma crustuliniforme, H. longicaudum, and Thelephora terrestris). Wilcoxina mikolae and Phialophora finlandia were the most frequent fungi. Analysis of variance revealed that ascomycetes abundance was higher in nurseries that used organic fertilizer.

Phylogeny of feather mite subfamily Avenzoariinae (Acari: Analgoidea: Avenzoariidae) inferred from combined analyses of molecular and morphological data

Phylogenetic relationships among feather mites of the subfamily Avenzoariinae (Acari: Analgoidea: Avenzoariidae) were reconstructed by parsimony analysis of a combined data matrix. We analyzed 41 morphological characters and 246 molecular characters from a fragment of the 16S rDNA. Morphological trees were well supported at deep branches (genera and above), but showed much less support and resolution within genera. Molecular analyses produced trees with better resolution and support on terminal branches and worse support on basal branches. I(MF) index for the combined matrix pointed to the significant congruence of both data subsets with the whole of the data. The topology of the combined tree was close to the morphological tree in the deep branches and had well-resolved terminal branches as in the molecular tree. This suggests a considerable level of complimentarity between the two data sets. An analysis of association patterns of the mites and their hosts was conducted based on the results of the combined analyses for the Avenzoariinae and a phylogeny of their charadriiform hosts (compiled from various bird phylogeny hypotheses). The trees could be reconciled by the invoking of 12-13 cospeciation events, 6-7 duplications, 2 host shifts, and 26-29 sorting events. This suggests a high degree of cospeciation.