Origin and genetic diversity of diploid parthenogenetic Artemia in Eurasia

There is wide interest in understanding how genetic diversity is generated and maintained in parthenogenetic lineages, as it will help clarify the debate of the evolution and maintenance of sexual reproduction. There are three mechanisms that can be responsible for the generation of genetic diversity of parthenogenetic lineages: contagious parthenogenesis, repeated hybridization and microorganism infections (e.g. Wolbachia). Brine shrimps of the genus Artemia (Crustacea, Branchiopoda, Anostraca) are a good model system to investigate evolutionary transitions between reproductive systems as they include sexual species and lineages of obligate parthenogenetic populations of different ploidy level, which often co-occur. Diploid parthenogenetic lineages produce occasional fully functional rare males, interspecific hybridization is known to occur, but the mechanisms of origin of asexual lineages are not completely understood. Here we sequenced and analysed fragments of one mitochondrial and two nuclear genes from an extensive set of populations of diploid parthenogenetic Artemia and sexual species from Central and East Asia to investigate the evolutionary origin of diploid parthenogenetic Artemia, and geographic origin of the parental taxa. Our results indicate that there are at least two, possibly three independent and recent maternal origins of parthenogenetic lineages, related to A. urmiana and Artemia sp. from Kazakhstan, but that the nuclear genes are very closely related in all the sexual species and parthenogegetic lineages except for A. sinica, who presumable took no part on the origin of diploid parthenogenetic strains. Our data cannot rule out either hybridization between any of the very closely related Asiatic sexual species or rare events of contagious parthenogenesis via rare males as the contributing mechanisms to the generation of genetic diversity in diploid parthenogenetic Artemia lineages

A new molecular diagnostic tool for surveying and monitoring Triops cancriformis populations

© 2017 Sellers et al. The tadpole shrimp, Triops cancriformis, is a freshwater crustacean listed as endangered in the UK and Europe living in ephemeral pools. Populations are threatened by habitat destruction due to land development for agriculture and increased urbanisation. Despite this, there is a lack of efficient methods for discovering and monitoring populations. Established macroinvertebrate monitoring methods, such as net sampling, are unsuitable given the organism's life history, that include long lived diapausing eggs, benthic habits and ephemerally active populations. Conventional hatching methods, such as sediment incubation, are both time consuming and potentially confounded by bet-hedging hatching strategies of diapausing eggs. Here we develop a new molecular diagnostic method to detect viable egg banks of T. cancriformis, and compare its performance to two conventional monitoring methods involving diapausing egg hatching. We apply this method to a collection of pond sediments from the Wildfowl & Wetlands Trust Caerlaverock National Nature Reserve, which holds one of the two remaining British populations of T. cancriformis. DNA barcoding of isolated eggs, using newly designed species-specific primers for a large region of mtDNA, was used to estimate egg viability. These estimates were compared to those obtained by the conventional methods of sediment and isolation hatching. Our method outperformed the conventional methods, revealing six ponds holding viable T. cancriformis diapausing egg banks in Caerlaverock. Additionally, designed species-specific primers for a short region of mtDNA identified degraded, inviable eggs and were used to ascertain the levels of recent mortality within an egg bank. Together with efficient sugar flotation techniques to extract eggs from sediment samples, our molecular method proved to be a faster and more powerful alternative for assessing the viability and condition of T. cancriformis diapausing egg banks

Isolation mediates persistent founder effects on zooplankton colonisation in new temporary ponds

Understanding the colonisation process in zooplankton is crucial for successful restoration of aquatic ecosystems. Here, we analyzed the clonal and genetic structure of the cyclical parthenogenetic rotifer Brachionus plicatilis by following populations established in new temporary ponds during the first three hydroperiods. Rotifer populations established rapidly after first flooding, although colonisation was ongoing throughout the study. Multilocus genotypes from 7 microsatellite loci suggested that most populations (10 of 14) were founded by few clones. The exception was one of the four populations that persisted throughout the studied hydroperiods, where high genetic diversity in the first hydroperiod suggested colonisation from a historical egg bank and, no increase in allelic diversity was detected with time. In contrast, in another of these four populations, we observed a progressive increase of allelic diversity. This population became less differentiated from the other populations suggesting effective gene flow soon after its foundation. Allelic diversity and richness remained low in the remaining two, more isolated, populations, suggesting little gene flow. Our results highlight the complexity of colonisation dynamics, with evidence for persistent founder effects in some ponds, but not in others, and with early immigration both from external source populations, and from residual, historical diapausing egg banks

Colonization and dispersal patterns of the invasive American brine shrimp Artemia franciscana (Branchiopoda: Anostraca) in the Mediterranean region

Cysts of the brine shrimp Artemia franciscana are harvested from the Great Salt Lake (GSL) and San Francisco Bay (SFB) saltworks in the USA, and marketed worldwide to provide live food for aquaculture. This species has become invasive across several countries. We investigated (1) if the introduced populations in the Mediterranean region could have originated from these USA populations, (2) how the genetic diversity of Mediterranean compares to that at GSL and SFB, and (3) if genetic patterns in the Mediterranean can shed light on colonization routes. We sequenced a fragment of the cytochrome c oxidase subunit I and screened microsatellites loci from Mediterranean populations and the two putative USA sources. Haplotypes from Mediterranean populations were identical or closely related to those from SFB and GSL, and not related to other available American populations. Microsatellite analyses showed a reduced population diversity for most Mediterranean populations suggesting bottleneck effects, but few populations were showing similar or higher genetic diversity than native ones, which are likely to be admixed from both GSL and SFB because of multiple introductions. Results suggest natural dispersal, potentially via flamingos, between two Spanish populations. Our analyses show that all invaded populations could have originated from those commercialized USA populations. © 2013 Springer Science+Business Media Dordrecht

Global isolation by distance despite strong regional phylogeography in a small metazoan

<p>Abstract</p> <p>Background</p> <p>Small vagile eukaryotic organisms, which comprise a large proportion of the Earth's biodiversity, have traditionally been thought to lack the extent of population structuring and geographic speciation observed in larger taxa. Here we investigate the patterns of genetic diversity, amongst populations of the salt lake microscopic metazoan <it>Brachionus plicatilis s. s</it>. (sensu stricto) (Rotifera: Monogononta) on a global scale. We examine the phylogenetic relationships of geographic isolates from four continents using a 603 bp fragment of the mitochondrial <it>COI </it>gene to investigate patterns of phylogeographic subdivision in this species. In addition we investigate the relationship between genetic and geographic distances on a global scale to try and reconcile the paradox between the high vagility of this species and the previously reported patterns of restricted gene flow, even over local spatial scales.</p> <p>Results</p> <p>Analysis of global sequence diversity of <it>B. plicatilis s. s</it>. reveals the presence of four allopatric genetic lineages: North American-Far East Asian, Western Mediterranean, Australian, and an Eastern Mediterranean lineage represented by a single isolate. Geographically orientated substructure is also apparent within the three best sampled lineages. Surprisingly, given this strong phylogeographic structure, <it>B. plicatilis s. s</it>. shows a significant correlation between geographic and genetic distance on a global scale ('isolation by distance' – IBD).</p> <p>Conclusion</p> <p>Despite its cosmopolitan distribution and potential for high gene flow, <it>B. plicatilis s. s</it>. is strongly structured at a global scale. IBD patterns have traditionally been interpreted to indicate migration-drift equilibrium, although in this system equilibrium conditions are incompatible with the observed genetic structure. Instead, we suggest the pattern may have arisen through persistent founder effects, acting in a similar fashion to geographic barriers for larger organisms. Our data indicates that geographic speciation, contrary to historical views, is likely to be very important in microorganisms. By presenting compelling evidence for geographic speciation in a small eukaryote we add to the growing body of evidence that is forcing us to rethink our views of global biodiversity.</p

Widespread secondary contact and new glacial refugia in the Halophilic Rotifer Brachionus Plicatilis in the Iberian Peninsula

Small aquatic organisms harbour deep phylogeographic patterns and highly structured populations even at local scales. These patterns indicate restricted gene flow, despite these organisms' high dispersal abilities, and have been explained by a combination of (1) strong founder effects due to rapidly growing populations and very large population sizes, and (2) the development of diapausing egg banks and local adaptation, resulting in low effective gene flow, what is known as the Monopolization hypothesis. In this study, we build up on our understanding of the mitochondrial phylogeography of the halophilic rotifer Brachionus plicatilis in the Iberian Peninsula by both increasing the number of sampled ponds in areas where secondary contact is likely and doubling sample sizes. We analyzed partial mitochondrial sequences of 252 individuals. We found two deep mitochondrial DNA lineages differing in both their genetic diversity and the complexity of their phylogeographic structure. Our analyses suggest that several events of secondary contact between clades occurred after their expansion from glacial refugia. We found a pattern of isolation-by-distance, which we interpret as being the result of historical colonization events. We propose the existence of at least one glacial refugium in the SE of the Iberian Peninsula. Our findings challenge predictions of the Monopolization hypothesis, since coexistence (i.e., secondary contact) of divergent lineages in some ponds in the Iberian Peninsula is common. Our results indicate that phylogeographic structures in small organisms can be very complex and that gene flow between diverse lineages after population establishment can indeed occur

Long-Term Coexistence of Rotifer Cryptic Species

Despite their high morphological similarity, cryptic species often coexist in aquatic habitats presenting a challenge in the framework of niche differentiation theory and coexistence mechanisms. Here we use a rotifer species complex inhabiting highly unpredictable and fluctuating salt lakes to gain insights into the mechanisms involved in stable coexistence in cryptic species. We combined molecular barcoding surveys of planktonic populations and paleogenetic analysis of diapausing eggs to reconstruct the current and historical coexistence dynamics of two highly morphologically similar rotifer species, B. plicatilis and B. manjavacas. In addition, we carried out laboratory experiments using clones isolated from eight lakes where both species coexist to explore their clonal growth responses to salinity, a challenging, highly variable and unpredictable condition in Mediterranean salt lakes. We show that both species have co-occurred in a stable way in one lake, with population fluctuations in which no species was permanently excluded. The seasonal occurrence patterns of the plankton in two lakes agree with laboratory experiments showing that both species differ in their optimal salinity. These results suggest that stable species coexistence is mediated by differential responses to salinity and its fluctuating regime. We discuss the role of fluctuating salinity and a persistent diapausing egg banks as a mechanism for species coexistence in accordance with the ‘storage effect’

Mu-DNA: a modular universal DNA extraction method adaptable for a wide range of sample types

Efficient DNA extraction is fundamental to molecular studies. However, commercial kits are expensive when a large number of samples need to be processed. Here we present a simple, modular and adaptable DNA extraction ‘toolkit’ for the isolation of high purity DNA from multiple sample types (modular universal DNA extraction method or Mu-DNA). We compare the performance of our method to that of widely used commercial kits across a range of soil, stool, tissue and water samples. Mu-DNA produced DNA extractions of similar or higher yield and purity to that of the commercial kits. As a proof of principle, we carried out replicate fish metabarcoding of aquatic eDNA extractions, which confirmed that the species detection efficiency of our method is similar to that of the most frequently used commercial kit. Our results demonstrate the reliability of Mu-DNA along with its modular adaptability to challenging sample types and sample collection methods. Mu-DNA can substantially reduce the costs and increase the scope of experiments in molecular studies

Morphological Characterization of Indoor Airborne Particles in Seven Primary Schools

This paper focuses on a study of fine (less than 2.5 µm) airborne particles collected inside seven primary schools located on a coastal Mediterranean area which has a significant industrial hub for the processing of clays and other minerals as raw materials. Of the seven schools, three are located in an urban area 20 km away from the main industrial hub, three are in a town located next to the industrial estate, and one is in a rural location, 30 km from the industrial area. The objective of this study is to identify the main types of particles found in the three examined environments. The particle matter identified in the fine particle samples is grouped into three main groups: mineral compounds, particles from combustion processes and phases emitted in high-temperature industrial processes. The mineral particles, which can come from natural or anthropogenic emissions, have been classified depending on their morphology as isometric allotriomorphs or subidiomorphs, with a tabular habit; acicular forms; or pure crystalline forms. Compounds from combustion processes have two types of morphologies: spheroid and dendritic soot particles. Additionally, in smaller quantities, spherical particles associated with high-temperature industrial processes, such as the emissions of ceramic tile-firing and frit-melting processes, are identified. A summary table is shown, which lists the characteristics, as well as the most significant origin of the main particles identified in the fine (<2.5 μm) airborne particles collected inside primary schools located in three different environments (urban, industrial and rural). A visual scale has been established based on the number of particles observed in the samples of the atmospheric particulate fraction between the sizes of 2.5 and 10 µm collected inside the schools. The ratios Ca/Si, S/Si, S/Ca and (Si+Ca)/S have been established. Results obtained may be useful in epidemiological studies in the ceramic cluster area in order to estimate children’s exposure to different indoor primary school microenvironments. Effective policies and mitigation measurements for the protection of children’s health should be carried out in this highly industrialized area

Distribution Levels of Particulate Matter Fractions (<2.5 µm, 2.5–10 µm and >10 µm) at Seven Primary Schools in a European Ceramic Cluster

This study addresses the concentration of particulate matter and their size using a statistical analysis of data obtained inside seven schools located in the towns of Castellón (S1, S2, and S3), Alcora (S4, S5, and S6) and Lucena (S7) in northeast Spain. Samples were taken for five to eight hours, depending on school hours, to obtain a monthly sample for each school. The main goal of this study is to assess the differences depending on the type of location and the sampling point to be able to design corrective measures that improve the habitability and safety of the teaching spaces analyzed. The lowest concentrations of fine particulate matter, less than 2.5 µm, were registered at the rural location. The values of these particles found in industrial and urban locations were not substantially different. In the case of particulate matter between 2.5 and 10 µm, significant differences were observed between the three types of locations. The lowest concentrations of particles larger than 10 µm were registered at the rural location, and the highest concentrations were found at the industrial locations. Among the urban stations, the particle concentration of this fraction in station S2 was significantly higher than that in stations S1 and S3, which had similar concentrations. These values are also similar to those registered at school S6, which is at an industrial location. The resuspension of particles from both indoor sources as well as those transported from the outside is an important factor in the concentrations of particles inside classrooms