Exceptional cryptic diversity and multiple origins of parthenogenesis in a freshwater ostracod

When it only takes one to tango: assessing the impact of apomixis in the fern genus Pteris

PREMISE

Apomixis (asexual reproduction by seed, spore, or egg) has evolved repeatedly across the tree of life. Studies of animals and angiosperms show that apomictic lineages are often evolutionarily short-lived and frequently exhibit different distributions than their sexual relatives. However, apomixis is rare in these groups. Less is known about the role of apomixis in the evolution and biogeography of ferns, in which ~10% of species are apomictic. Apomixis is especially common in the fern genus Pteris (34-39% of species); however, because of the limited taxonomic and geographic sampling of previous studies, the true frequency of apomixis and its associations with geography and phylogeny in this lineage remain unclear.

METHODS

We used spore analyses of herbarium specimens to determine reproductive mode for 127 previously unsampled Pteris species. Then we leveraged biogeographic and phylogenetic analyses to estimate the global distribution and evolution of apomixis in Pteris.

RESULTS

Among all Pteris species examined, we found that 21% are exclusively apomictic, 71% are exclusively sexual, and 8% have conflicting reports. Apomixis is unevenly distributed across the range of the genus, with the Paleotropics exhibiting the highest frequency, and has evolved numerous times across the Pteris phylogeny, with predominantly East Asian and South Asian clades containing the most apomictic species.

CONCLUSIONS

Apomixis arises frequently in Pteris, but apomictic species do not appear to diversify. Species that encompass both apomictic and sexual populations have wider ranges than exclusively sexual or apomictic species, which suggests that sexual and apomictic ferns could occupy separate ecological niches.

Repeated convergent evolution of parthenogenesis in Acariformes (Acari)

The existence of old species-rich parthenogenetic taxa is a conundrum in evolutionary biology. Such taxa point to ancient parthenogenetic radiations resulting in morphologically distinct species. Ancient parthenogenetic taxa have been proposed to exist in bdelloid rotifers, darwinulid ostracods, and in several taxa of acariform mites (Acariformes, Acari), especially in oribatid mites (Oribatida, Acari). Here, we investigate the diversification of Acariformes and their ancestral mode of reproduction using 18S rRNA. Because parthenogenetic taxa tend to be more frequent in phylogenetically old taxa of Acariformes, we sequenced a wide range of members of this taxon, including early-derivative taxa of Prostigmata, Astigmata, Endeostigmata, and Oribatida. Ancestral character state reconstruction indicated that (a) Acariformes as well as Oribatida evolved from a sexual ancestor, (b) the primary mode of reproduction during evolution of Acariformes was sexual; however, species-rich parthenogenetic taxa radiated independently at least four times (in Brachychthonioidea (Oribatida), Enarthronota (Oribatida), and twice in Nothrina (Oribatida), (c) parthenogenesis additionally evolved frequently in species-poor taxa, for example, Tectocepheus, Oppiella, Rostrozetes, Limnozetes, and Atropacarus, and (d) sexual reproduction likely re-evolved at least three times from species-rich parthenogenetic clusters, in Crotonia (Nothrina), in Mesoplophora/Apoplophora (Mesoplophoridae, Enarthronota), and in Sphaerochthonius/Prototritia (Protoplophoridae, Enarthronota). We discuss possible reasons that favored the frequent diversification of parthenogenetic taxa including the continuous long-term availability of dead organic matter resources as well as generalist feeding of species as indicated by natural variations in stable isotope ratios.

Molecular and Morphological Diversity of Heterodesmus Brady and Its Phylogenetic Position within Cypridinidae (Ostracoda)

Ostracod genus Heterodesmus Brady, 1866 is known thus far to contain only three species: H. adamsii Brady, 1866; H. apriculus Hiruta, 1992; and H. naviformis (Poulsen, 1962). This genus has been recorded from the Sea of Japan, and the coastal areas of Thailand and Vietnam. The main generic character is the presence of antero-dorsal and postero-dorsal tube-like processes on the rostrum on both valves. The three species mostly differ in the shell lateral projections. Their relationship and the position of Heterodesmus within family Cypridinidae are poorly understood, partly due to the lack of publication of DNA data so far. We study Heterodesmus collected from several localities in the Northwest Pacific, namely Tsushima and Iki Islands in Japan and Maemul Island in Korea. Besides morphological characters, we also use two mitochondrial markers (16S rRNA and mtCOI) and three nuclear regions (18S rRNA, 28S rRNA, and internal transcribed spacer - ITS) in the samples to detect the biodiversity of this genus. Our phylogenetic tree based on molecular data coupled with morphology reveals the presence of two species, H. adamsii and H. apriculus. We report on their morphological variability, molecular diversity, and phylogenetic position within Cypridinidae based on 16S, 28S and 18S rRNAs, and provide a taxonomic key for all living genera of this family. For the first time, we give an overview of the intrageneric and intrafamily DNA distances of the above markers for the entire subclass Myodocopa.

Phylogenetic relationships and cryptic species in the genus Sthenoteuthis (Cephalopoda: Ommastrephidae) in the South China Sea

Large squids of the genus Sthenoteuthis are commercially relevant species that include two truly oceanic squids. They are large nektonic predators being widely distributed throughout tropical and subtropical waters of the Atlantic and Indo-Pacific Ocean. The present study investigates different morphs varying in size at maturity, and assesses the genetic divergence in Sthenotheutis in relation to geographic patterns in the South China Sea. We obtained sequences using a mitochondrial (cytochrome c oxidase subunit I) and a nuclear (Histone H3) gene marker from 111 individuals in 23 locations of the South China Sea. In combination with sequences available in public databases, we performed tests on DNA taxonomy, mostly based on molecular phylogenies. Our results suggest that the genus Sthenoteuthis includes at least three species. The Indo-Pacific purpleback squid Sthenoteuthis oualaniensis contains at least two genetically distinct lineages that can be considered separate species, a dwarf species and a medium-sized species, separated by both the mitochondrial marker and the more conserved nuclear marker. We also assessed whether the few cases of mitonuclear discordance could be the result of genetic introgression and past hybridization or incongruence lineage sorting. The medium-sized species is more widely distributed and dominant in the South China Sea than the dwarf species. The medium-sized species inhabits the whole South China Sea, whereas the dwarf species is restricted to the equatorial waters of the South China Sea. The medium-sized species has two further genetic clades, one distributed in the East Pacific Ocean and the other in the South China Sea. This high level of genetic differentiation is in agreement with the discriminant analysis on the morphological measurements, clearly separating the dwarf and medium-sized species, indicating the presence of a complex of pseudo-cryptic species in S. oualaniensis, clearly identifiable by differences in DNA sequences and in body size, and statistically differentiated in their body measurements.

Novel Cardinium strains in non-marine ostracod (Crustacea) hosts from natural populations

Endosymbiotic bacteria are known from many metazoan taxa, where they manipulate host biology and reproduction. Here, we used classic PCR amplification and direct DNA sequencing with universal primers for four different endosymbionts to test for their presence in more than 300 specimens of three recent non-marine ostracod superfamilies from different geographic areas and aquatic habitats. We verified these results with "high throughput" amplicon sequencing of 16S of nine selected specimens and evolutionary placement algorithms. The phylogenetic position of endosymbionts detected in ostracod hosts was compared to known endosymbionts from other metazoans. While Wolbachia, Spiroplasma and Rickettsia are absent, we find evidence for the general presence of Cardinium bacteria in natural populations of various non-marine ostracod species. Phylogenetic reconstructions based on Cardinium 16S data and estimates of genetic distances both indicate that Cardinium from ostracods are distantly related to Cardinium from Diptera and Nematoda but represent novel strains with a monophyletic origin. Cardinium bacteria from different ostracod hosts have genetic distances of up to 3.8%, providing evidence against recent and frequent horizontal transmissions amongst the three ostracod superfamilies. High throughput sequencing reveals more than 400 different 16S amplicon sequence variants in the investigated ostracods as well as the presence of different Cardinium strains within individual Eucypris virens and Heterocypris hosts. These results call for future, more in-depth investigations. Mapping Cardinium infections on COI trees of non-marine ostracod hosts shows that the occurrence of these endosymbionts is not linked to genetic species identity or phylogenetic host groups and, except for one ostracod morphospecies, prevalence never reaches 100%.

Diversity of marine planktonic ostracods in South China Sea: a DNA taxonomy approach

Ostracods (Crustacea, Ostracoda) are small bivalved crustaceans, contributing over 200 described species to the marine zooplankton community. They are widely distributed and are relatively abundant components of the mesozooplankton, playing an important role in the transport of organic matter to deep layers. However, identification of ostracods based on micro-morphological characters is extremely difficult and time-consuming. Previous fragmentary taxonomic studies of ostracods in the South China Sea (SCA), were based solely on morphology. Here, by analysing the mitochondrial COI gene, we explore the taxa across the SCA using molecular tools for the first time. Our results show that sequence divergence among species varies within a large range, from 12.93% to 35.82%. Sixteen of the taxonomic units recovered by DNA taxonomy agree well with morphology, but Paraconchoecia oblonga, Conchoecia magna and Halocypris brevirostris split into two clades each, each of which contains cryptic species.

Karyotype Variability and Inter-Population Genomic Differences in Freshwater Ostracods (Crustacea) Showing Geographical Parthenogenesis

Transitions from sexual to asexual reproduction are often associated with polyploidy and increased chromosomal plasticity in asexuals. We investigated chromosomes in the freshwater ostracod species Eucypris virens (Jurine, 1820), where sexual, asexual and mixed populations can be found. Our initial karyotyping of multiple populations from Europe and North Africa, both sexual and asexual, revealed a striking variability in chromosome numbers. This would suggest that chromosomal changes are likely to be accelerated in asexuals because the constraints of meiosis are removed. Hence, we employed comparative genomic hybridization (CGH) within and among sexual and asexual populations to get insights into E. virens genome arrangements. CGH disclosed substantial genomic imbalances among the populations analyzed, and three patterns of genome arrangement between these populations: 1. Only putative ribosomal DNA (rDNA)-bearing regions were conserved in the two populations compared indicating a high sequence divergence between these populations. This pattern is comparable with our findings at the interspecies level of comparison; 2. Chromosomal regions were shared by both populations to a varying extent with a distinct copy number variation in pericentromeric and presumable rDNA-bearing regions. This indicates a different rate of evolution in repetitive sequences; 3. A mosaic pattern of distribution of genomic material that can be explained as non-reciprocal genetic introgression and evidence of a hybrid origin of these individuals. We show an overall increased chromosomal dynamics in E. virens that is complementary with available phylogenetic and population genetic data reporting highly differentiated diploid sexual and asexual lineages with a wide variety of genetic backgrounds.

Aquatic long-distance dispersal and vicariance shape the evolution of an ostracod species complex (Crustacea) in four major Brazilian floodplains

Cladogenesis is often driven by the interplay of dispersal and vicariance. The importance of long-distance dispersal in biogeography and speciation is increasingly recognised, but still ill-understood. Here, we study faunal interconnectivity between four large Brazilian floodplains, namely the Amazon, Araguaia, Pantanal (on Paraguay River) and Upper Paraná River floodplains, investigating a species complex of the non-marine ostracod genus Strandesia. We use DNA sequence data from the mitochondrial COI and the nuclear Elongation Factor 1 alpha genes to construct molecular phylogenies and minimum spanning networks, to identify genetic species, analyse biogeographic histories and provide preliminary age estimates of this species complex. The Strandesia species complex includes five morphological and eleven genetic species, which doubles the known diversity in this lineage. The evolutionary history of this species complex appears to comprise sequences of dispersal and vicariance events. Faunal and genetic patterns of connectivity between floodplains in some genetic species are mirrored in modern hydrological connections. This could explain why we find evidence for (aquatic) long-distance dispersal between floodplains, thousands of kilometres apart. Our phylogenetic reconstructions seem to mostly indicate recent dispersal and vicariance events, but the evolution of the present Strandesia species complex could span up to 25 Myr, which by far exceeds the age of the floodplains and the rivers in their current forms.

Is meiosis a fundamental cause of inviability among sexual and asexual plants and animals?

Differences in viability between asexually and sexually generated offspring strongly influence the selective advantage and therefore the prevalence of sexual reproduction (sex). However, no general principle predicts when sexual offspring will be more viable than asexual offspring. We hypothesize that when any kind of reproduction is based on a more complex cellular process, it will encompass more potential failure points, and therefore lower offspring viability. Asexual reproduction (asex) can be simpler than sex, when offspring are generated using only mitosis. However, when asex includes meiosis and meiotic restitution, gamete production is more complex than in sex. We test our hypothesis by comparing the viability of asexual and closely related sexual offspring across a wide range of plants and animals, and demonstrate that meiotic asex does result in lower viability than sex; without meiosis, asex is mechanistically simple and provides higher viability than sex. This phylogenetically robust pattern is supported in 42 of 44 comparisons drawn from diverse plants and animals, and is not explained by the other variables included in our model. Other mechanisms may impact viability, such as effects of reproductive mode on heterozygosity and subsequent viability, but we propose the complexity of cellular processes of reproduction, particularly meiosis, as a fundamental cause of early developmental failure and mortality. Meiosis, the leading cause of inviability in humans, emerges as a likely explanation of offspring inviability among diverse eukaryotes.

Checklist de ostrácodes (Crustacea, Ostracoda) dulcícolas do Pantanal Sul Mato-grossense, Brasil

RESUMO Atualmente existem cerca de 2.000 espécies de Ostracoda dulcícolas descritas em diversos ambientes aquáticos do mundo, das quais cerca de 117 espécies em aproximadamente 37 gêneros são conhecidas no Brasil. O presente levantamento de ostrácodes do Pantanal Sul Mato-grossense, registrou 35 espécies pertencentes às famílias Cyprididae, Candonidae, Limnocytheridae e Darwinulidae. A fauna de ostrácodes do Brasil ainda é pouco conhecida e a biodiversidade de ostrácodes de vários habitats (por exemplo, instersticial) ainda permanecem desconhecidos. Neste sentido, existe grande probabilidade de se encontrar novos registros e novos táxons de ostrácodes no Pantanal, assim como em todo território brasileiro.

Sperm length variations in five species of cypridoidean non-marine ostracods (Crustacea)

Spermatozoa of the ostracod superfamily Cypridoidea include some of the longest in the animal kingdom, but unlike other so-called giant spermatozoa, they are aflagellate, probably evolved only once, and represent an exceptionally old trait. Sperm length variations within cypridoidean species remain poorly known, a lack that hinders the development of hypotheses to explain their length and variation. For this study, the lengths of 500 spermatozoa from each of five species of freshwater cypridoidean ostracods, Candonopsis tenuis (Brady, 1886), Fabaeformiscandona subacuta (Yang, 1982), Heterocypris rotundata (Bronshtein, 1928), Ilyocypris japonica Okubo, 1990, and Notodromas trulla Smith and Kamiya, 2014, were measured, including the lengths of the posterior and anterior regions. No overall pattern in sperm variation was discernible. Length variations between species, between males of the same species, and within individual males varied from low (Candonopsis tenuis) to extraordinarily large (Notodromas trulla and Fabaeformiscandona subacuta). Sperm competition, cryptic female choice, sperm heteromorphism, and testis size are unlikely to explain all of the variations observed. Age structures of the populations sampled might play a role in explaining some intraspecific variation. The differing amounts of variation in sperm characters revealed in this study suggest that multiple evolutionary trends and pressures shape sperm lengths in this superfamily.

Ostracod (Ostracoda, Crustacea) genomics - Promises and challenges

Ostracods are well-suited model organisms for evolutionary research. Classic genetic techniques have mostly been used for phylogenetic studies on Ostracoda and were somewhat affected by the lack of large numbers of suitable markers. Genomic methods with their huge potential have so far rarely been applied to this group of crustaceans. We provide relevant examples of genomic studies on other organisms to propose future avenues of genomic ostracod research. At the same time, we suggest solutions to the potential problems in ostracods that the application of genomic techniques might present.

Barcoding of ancient lake ostracods (crustacea) reveals cryptic speciation with extremely low distances

Ostracods are drastically reduced crustaceans, with never more than eight appendages enclosed between two valves, leaving only a limited number of morphological characters for species delineation. Conservative morphology of characters used to define genera, along with high variability of characters used to define species are creating problems in applying a morphospecies concept. A high intraspecific variability in a Lake Biwa (Japan) endemic, Physocypria biwaensis (Okubo, 1990), has been observed previously but was never studied in detail. Two sympatric forms, differing in pigmentation and size, suggest a presence of reproductive isolation. The aim of this study is to employ molecular and morphometric tools to aid in species delineation within P. biwaensis complex and reconstruct their phylogenetic relationships. A fragment of the mtCOI gene was amplified from 30 specimens, and an additional 37 specimens were studied for morphological characters. Resulting phylogenies showed that each morphologically distinct form is associated with a distinct phylogenetic group based on mtDNA. The average pairwise distance is very low (5%), indicating a recent divergence time. I speculate that there is a possibility that one of them originated in the lake, while the other probably colonized it afterwards. This seems to be supported with an apparent niche partitioning at different depths. In spite of the fact that traditionally used sexual characters are highly variable in these two species, the morphometric analysis of shell and soft part related characters clearly delineates them and suggests that such characters may be useful for future detection of seemingly cryptic ostracod species.

Extensive variation in chromosome number and genome size in sexual and parthenogenetic species of the jumping-bristletail genus Machilis (Archaeognatha)

Parthenogenesis in animals is often associated with polyploidy and restriction to extreme habitats or recently deglaciated areas. It has been hypothesized that benefits conferred by asexual reproduction and polyploidy are essential for colonizing these habitats. However, while evolutionary routes to parthenogenesis are manifold, study systems including polyploids are scarce in arthropods. The jumping-bristletail genus Machilis (Insecta: Archaeognatha) includes both sexual and parthenogenetic species, and recently, the occurrence of polyploidy has been postulated. Here, we applied flow cytometry, karyotyping, and mitochondrial DNA sequencing to three sexual and five putatively parthenogenetic Eastern-Alpine Machilis species to investigate whether (1) parthenogenesis originated once or multiply and (2) whether parthenogenesis is strictly associated with polyploidy. The mitochondrial phylogeny revealed that parthenogenesis evolved at least five times independently among Eastern-Alpine representatives of this genus. One parthenogenetic species was exclusively triploid, while a second consisted of both diploid and triploid populations. The three other parthenogenetic species and all sexual species were diploid. Our results thus indicate that polyploidy can co-occur with parthenogenesis, but that it was not mandatory for the emergence of parthenogenesis in Machilis. Overall, we found a weak negative correlation of monoploid genome size (Cx) and chromosome base number (x), and this connection is stronger among parthenogenetic species alone. Likewise, monoploid genome size decreased with elevation, and we therefore hypothesize that genome downsizing could have been crucial for the persistence of alpine Machilis species. Finally, we discuss the evolutionary consequences of intraspecific chromosomal rearrangements and the presence of B chromosomes. In doing so, we highlight the potential of Alpine Machilis species for research on chromosomal and genome-size alterations during speciation.

Genetic uniformity and long-distance clonal dispersal in the invasive androgenetic Corbicula clams

The clam genus Corbicula is an interesting model system to study the evolution of reproductive modes as it includes both sexual and asexual (androgenetic) lineages. While the sexual populations are restricted to the native Asian areas, the androgenetic lineages are widely distributed being also found in America and Europe where they form a major aquatic invasive pest. We investigated the genetic diversity of native and invasive Corbicula populations through a worldwide sampling. The use of mitochondrial and nuclear (microsatellite) markers revealed an extremely low diversity in the invasive populations with only four, undiversified, genetic lineages distributed across Europe and America. On the contrary, in the native populations, both sexual and androgenetic lineages exhibited much higher genetic diversity. Remarkably, the most abundant and widely distributed invasive forms, the so-called form A and form R found in America and Europe respectively, are fixed for the same single COI (cytochrome c oxydase subunit I) haplotype and same multilocus genotype. This suggests that form R, observed in Europe since the 1980s, derived directly from form A found in America since the 1920s. In addition, this form shares alleles with some Japanese populations, indicating a Japanese origin for this invasive lineage. Finally, our study suggests that few androgenetic Corbicula individuals successfully invaded the non-native range and then dispersed clonally. This is one striking case of genetic paradox raising the issue of invasive and evolutionary success of genetically undiversified populations.

Morphotypes of Cytheridella Ilosvayi (Ostracoda) Detected by Soft and Hard Part Analyses

Quantitative approaches dealing with soft- and hard-part morphological variability of ostracods are very rare for most species. Here we present intraspecific limb and shell variability of the Neotropical freshwater ostracod species assumed as Cytheridella ilosvayi. For the first time such an analysis considered adult females and males, as well as juveniles. Variability of the appendages included the antennule, second antenna as well as the first and second thoracopod and was analysed in terms of ratios of podomeres, setae and limbs. Limb variability of adult and juvenile individuals (down to A-3) is generally low. The highest variation is shown in podomere proportions of the antennas, while thoracopods and setae provide minor and/or non-significant influence on the variability. Based on discrimination analyses shell parameters (i.e., shell length, position of the transversal sulcus) emerge to be more important for differentiation of groups than limb ratios. Adult females exhibit a large size range in which two clearly separated morphotypes exist. Although differences in limbs are small their existence can be proven also on the basis of proportions between podomeres of the antennas. Males and juveniles, however, do not display a separation into corresponding subgroups or morphotypes. The presence of two morphologically similar females and only one type of males indicates the coexistence of female morphotypes which may represent either two (cryptic) species or a mixed reproduction population in which parthenogenetic and sexual reproduction coexists.

Multiple lines of evidence on the genetic relatedness of the parthenogenetic and bisexual Haemaphysalis longicornis (Acari: Ixodidae)

As an obligate hematophagous ectoparasite, the hard tick Haemaphysalis longicornis exhibits two reproductive strategies, bisexual reproduction, and obligate parthenogenesis, which have attracted a widespread attention. However, the speciation of parthenogenetic population remained ambiguous due to its similarity in morphology but the remarkable differences in cytogenetics as compared with those of the bisexual ones. In the present study, we explored several new lines of genetic evidence to resolve this controversial issue. The number of the chromosomes in two lineages was checked by classical methods and their total DNA levels were determined utilizing flowcytometry. In addition, the sequences of 12S rDNA, 16S rDNA, cytochrome c oxidase I and II (COI, COII) and internal transcribed spacer-2 (ITS-2) genes were used to assess their phylogenetic relationship. We observed that the chromosome ploidy of bisexual and parthenogenetic H. longicornis collected by our laboratory was diploid and triploid, respectively. Flowcytometry analysis indicated a ratio close to 2:3 in the DNA contents of bisexual to parthenogenetic H. longicornis. Although the chromosome ploidy is different, their gene sequences are extremely similar. Analogous to the intra-species genetic difference of other invertebrates, sequence differences of all loci examined are below 2%. Phylogenetic trees constructed from 12S rDNA, 16S rDNA, COI, and ITS-2 genes revealed that they were all in the same monophyletic clade instead of splitting independently into evolutional branches. Moreover, according to 4× Rule, the K/θ ratio of two reproductive populations calculated based on COI was much smaller than four, strongly supporting that they belong to the same species. Therefore, we conclude that the evolutionary process just disturbs the chromosome ploidy and the sexual determination of parthenogenetic population and that it would be better to consider parthenogenetic H. longicornis as a metapopulation rather than a cryptic species.

The distribution of sexual reproduction of the geographic parthenogen Eucypris virens (Crustacea: Ostracoda) matches environmental gradients in a temporary lake

Niche segregation may prevent competitive exclusion and promote local coexistence. This typically results in the occupation of different habitats. In the freshwater ostracod Eucypris virens (Jurine, 1820), the distribution of sexual and parthenogenetic populations in the temporary Lake Caracuel, central Spain, was not homogeneous. Parthenogens were found everywhere including the littoral, whereas sexuals were restricted to the centre. We investigated the hypothesis that spatial distribution responded to ecological differences. We studied the ecological significance of this segregation by linking environmental data to male presence, sexual fraction, ploidy, and genetic structure of our model organism in 12 ponds in the lake basin. Hydro-chemical and biological data indicated that the observed segregation is not only spatial but also ecological, with sexual E. virens occurring in ponds with shorter and probably more unpredictable hydroperiod. The correlations between environmental gradients and E. virens population structure suggest that sexual and parthenogenetic lineages are ecologically segregated. Sexual populations appeared restricted to sufficiently unpredictable environments, while parthenogens dominated environments with longer hydroperiods. Local coexistence seems mediated by spatial heterogeneity in habitat stability.

Comparative transcriptome analysis of obligately asexual and cyclically sexual rotifers reveals genes with putative functions in sexual reproduction, dormancy, and asexual egg production

BACKGROUND

Sexual reproduction is a widely studied biological process because it is critically important to the genetics, evolution, and ecology of eukaryotes. Despite decades of study on this topic, no comprehensive explanation has been accepted that explains the evolutionary forces underlying its prevalence and persistence in nature. Monogonont rotifers offer a useful system for experimental studies relating to the evolution of sexual reproduction due to their rapid reproductive rate and close relationship to the putatively ancient asexual bdelloid rotifers. However, little is known about the molecular underpinnings of sex in any rotifer species.

RESULTS

We generated mRNA-seq libraries for obligate parthenogenetic (OP) and cyclical parthenogenetic (CP) strains of the monogonont rotifer, Brachionus calyciflorus, to identify genes specific to both modes of reproduction. Our differential expression analysis identified receptors with putative roles in signaling pathways responsible for the transition from asexual to sexual reproduction. Differential expression of a specific copy of the duplicated cell cycle regulatory gene CDC20 and specific copies of histone H2A suggest that such duplications may underlie the phenotypic plasticity required for reproductive mode switch in monogononts. We further identified differential expression of genes involved in the formation of resting eggs, a process linked exclusively to sex in this species. Finally, we identified transcripts from the bdelloid rotifer Adineta ricciae that have significant sequence similarity to genes with higher expression in CP strains of B. calyciflorus.

CONCLUSIONS

Our analysis of global gene expression differences between facultatively sexual and exclusively asexual populations of B. calyciflorus provides insights into the molecular nature of sexual reproduction in rotifers. Furthermore, our results offer insight into the evolution of obligate asexuality in bdelloid rotifers and provide indicators important for the use of monogononts as a model system for investigating the evolution of sexual reproduction.

Insights into biodiversity sampling strategies for freshwater microinvertebrate faunas through bioblitz campaigns and DNA barcoding

BACKGROUND

Biodiversity surveys have long depended on traditional methods of taxonomy to inform sampling protocols and to determine when a representative sample of a given species pool of interest has been obtained. Questions remain as to how to design appropriate sampling efforts to accurately estimate total biodiversity. Here we consider the biodiversity of freshwater ostracods (crustacean class Ostracoda) from the region of Churchill, Manitoba, Canada. Through an analysis of observed species richness and complementarity, accumulation curves, and richness estimators, we conduct an a posteriori analysis of five bioblitz-style collection strategies that differed in terms of total duration, number of sites, protocol flexibility to heterogeneous habitats, sorting of specimens for analysis, and primary purpose of collection. We used DNA barcoding to group specimens into molecular operational taxonomic units for comparison.

RESULTS

Forty-eight provisional species were identified through genetic divergences, up from the 30 species previously known and documented in literature from the Churchill region. We found differential sampling efficiency among the five strategies, with liberal sorting of specimens for molecular analysis, protocol flexibility (and particularly a focus on covering diverse microhabitats), and a taxon-specific focus to collection having strong influences on garnering more accurate species richness estimates.

CONCLUSIONS

Our findings have implications for the successful design of future biodiversity surveys and citizen-science collection projects, which are becoming increasingly popular and have been shown to produce reliable results for a variety of taxa despite relying on largely untrained collectors. We propose that efficiency of biodiversity surveys can be increased by non-experts deliberately selecting diverse microhabitats; by conducting two rounds of molecular analysis, with the numbers of samples processed during round two informed by the singleton prevalence during round one; and by having sub-teams (even if all non-experts) focus on select taxa. Our study also provides new insights into subarctic diversity of freshwater Ostracoda and contributes to the broader "Barcoding Biotas" campaign at Churchill. Finally, we comment on the associated implications and future research directions for community ecology analyses and biodiversity surveys through DNA barcoding, which we show here to be an efficient technique enabling rapid biodiversity quantification in understudied taxa.

Sex produces as numerous and long-lived offspring as parthenogenesis in a new parthenogenetic insect

Sex is a costly form of reproduction compared with parthenogenesis, but sex persists because of the more resistant and competitive descendants that it produces. We obtained thelytokous offspring from unmated female Doru lineare (Eschscholtz, 1822) earwigs, a species of insect in which parthenogenesis has never before been reported, and found that their number and survival rate did not differ from offspring of mated females. Current hypotheses support advantages of sex or parthenogenesis, but never equilibrium between them like the one reported in this paper. We suggest that parthenogenesis is how females multiply their entire genome and renew themselves.

Cryptic species in putative ancient asexual darwinulids (Crustacea, Ostracoda)

BACKGROUND

Fully asexually reproducing taxa lack outcrossing. Hence, the classic Biological Species Concept cannot be applied.

METHODOLOGY/PRINCIPAL FINDINGS

We used DNA sequences from the mitochondrial COI gene and the nuclear ITS2 region to check species boundaries according to the evolutionary genetic (EG) species concept in five morphospecies in the putative ancient asexual ostracod genera, Penthesilenula and Darwinula, from different continents. We applied two methods for detecting cryptic species, namely the K/θ method and the General Mixed Yule Coalescent model (GMYC). We could confirm the existence of species in all five darwinulid morphospecies and additional cryptic diversity in three morphospecies, namely in Penthesilenula brasiliensis, Darwinula stevensoni and in P. aotearoa. The number of cryptic species within one morphospecies varied between seven (P. brasiliensis), five to six (D. stevensoni) and two (P. aotearoa), respectively, depending on the method used. Cryptic species mainly followed continental distributions. We also found evidence for coexistence at the local scale for Brazilian cryptic species of P. brasiliensis and P. aotearoa. Our ITS2 data confirmed that species exist in darwinulids but detected far less EG species, namely two to three cryptic species in P. brasiliensis and no cryptic species at all in the other darwinulid morphospecies.

CONCLUSIONS/SIGNIFICANCE

Our results clearly demonstrate that both species and cryptic diversity can be recognized in putative ancient asexual ostracods using the EG species concept, and that COI data are more suitable than ITS2 for this purpose. The discovery of up to eight cryptic species within a single morphospecies will significantly increase estimates of biodiversity in this asexual ostracod group. Which factors, other than long-term geographic isolation, are important for speciation processes in these ancient asexuals remains to be investigated.

Rare gene capture in predominantly androgenetic species

The long-term persistence of completely asexual species is unexpected. Although asexuality has short-term evolutionary advantages, a lack of genetic recombination leads to the accumulation over time of deleterious mutations. The loss of individual fitness as a result of accumulated deleterious mutations is expected to lead to reduced population fitness and possible lineage extinction. Persistent lineages of asexual, all-female clones (parthenogenetic and gynogenetic species) avoid the negative effects of asexual reproduction through the production of rare males, or otherwise exhibit some degree of genetic recombination. Another form of asexuality, known as androgenesis, results in offspring that are clones of the male parent. Several species of the Asian clam genus Corbicula reproduce via androgenesis. We compared gene trees of mitochondrial and nuclear loci from multiple sexual and androgenetic species across the global distribution of Corbicula to test the hypothesis of long-term clonality of the androgenetic species. Our results indicate that low levels of genetic capture of maternal nuclear DNA from other species occur within otherwise androgenetic lineages of Corbicula. The rare capture of genetic material from other species may allow androgenetic lineages of Corbicula to mitigate the effects of deleterious mutation accumulation and increase potentially adaptive variation. Models comparing the relative advantages and disadvantages of sexual and asexual reproduction should consider the possibility of rare genetic recombination, because such events seem to be nearly ubiquitous among otherwise asexual species.

Toward a DNA taxonomy of Alpine Rhithrogena (Ephemeroptera: Heptageniidae) using a mixed Yule-coalescent analysis of mitochondrial and nuclear DNA

Aquatic larvae of many Rhithrogena mayflies (Ephemeroptera) inhabit sensitive Alpine environments. A number of species are on the IUCN Red List and many recognized species have restricted distributions and are of conservation interest. Despite their ecological and conservation importance, ambiguous morphological differences among closely related species suggest that the current taxonomy may not accurately reflect the evolutionary diversity of the group. Here we examined the species status of nearly 50% of European Rhithrogena diversity using a widespread sampling scheme of Alpine species that included 22 type localities, general mixed Yule-coalescent (GMYC) model analysis of one standard mtDNA marker and one newly developed nDNA marker, and morphological identification where possible. Using sequences from 533 individuals from 144 sampling localities, we observed significant clustering of the mitochondrial (cox1) marker into 31 GMYC species. Twenty-one of these could be identified based on the presence of topotypes (expertly identified specimens from the species' type locality) or unambiguous morphology. These results strongly suggest the presence of both cryptic diversity and taxonomic oversplitting in Rhithrogena. Significant clustering was not detected with protein-coding nuclear PEPCK, although nine GMYC species were congruent with well supported terminal clusters of nDNA. Lack of greater congruence in the two data sets may be the result of incomplete sorting of ancestral polymorphism. Bayesian phylogenetic analyses of both gene regions recovered four of the six recognized Rhithrogena species groups in our samples as monophyletic. Future development of more nuclear markers would facilitate multi-locus analysis of unresolved, closely related species pairs. The DNA taxonomy developed here lays the groundwork for a future revision of the important but cryptic Rhithrogena genus in Europe.

Evolutionary criteria outperform operational approaches in producing ecologically relevant fungal species inventories

Analyses of the structure and function of microbial communities are highly constrained by the diversity of organisms present within most environmental samples. A common approach is to rely almost entirely on DNA sequence data for estimates of microbial diversity, but to date there is no objective method of clustering sequences into groups that is grounded in evolutionary theory of what constitutes a biological lineage. The general mixed Yule-coalescent (GMYC) model uses a likelihood-based approach to distinguish population-level processes within lineages from processes associated with speciation and extinction, thus identifying a distinct point where extant lineages became independent. Using two independent surveys of DNA sequences associated with a group of ubiquitous plant-symbiotic fungi, we compared estimates of species richness derived using the GMYC model to those based on operational taxonomic units (OTUs) defined by fixed levels of sequence similarity. The model predicted lower species richness in these surveys than did traditional methods of sequence similarity. Here, we show for the first time that groups delineated by the GMYC model better explained variation in the distribution of fungi in relation to putative niche-based variables associated with host species identity, edaphic factors, and aspects of how the sampled ecosystems were managed. Our results suggest the coalescent-based GMYC model successfully groups environmental sequences of fungi into clusters that are ecologically more meaningful than more arbitrary approaches for estimating species richness.