Asexual Species Research Articles

Microsatellite markers revealed moderate genetic diversity and population differentiation of moso bamboo (Phyllostachys edulis)—a primarily asexual reproduction species in China

As an ecologically and economically important endemic bamboo species, moso (Phyllostachys edulis) has been widely distributed in Southern China. In the paper, 20 fluorescently labeled microsatellite markers were used to evaluate the genetic structure of Ph. edulis including 34 representative populations (803 individuals) covering the geographic range in China. Moderate genetic diversity (H = 0.376) and differentiation (Gst = 0.162) were detected at the species level, with the majority of genetic diversity occurring within populations (84.55%). Bayesian model-based structure analysis and sNMF/ANLS-AS method revealed the presence of two and three clusters. When K = 2, majority of populations (except SX) were clustered together (C1). It implied that SX, known as an introduced and isolated founder population, significantly differed from other populations for distinct environmental selection and allele mutation with the proof of scarce outcrossing and relatively high frequency of private allele. While K = 3, two subgroups (C1a of 18 populations and C1b of 14 populations) were detected within C1. The C1b displayed as a belt-shape region with an east-west direction. It coincided with the extremely high artificial selection in C1b (lower genetic diversity than that of C1a) due to the intensive plantation in the last four decades. Our results implied that the population protection and germplasm collection of moso bamboo should be not only from representative populations in Zhejiang, Jiangxi, Fujian, and other places with intensive cultivation in the east of China, but from populations with high level of gene and genotypic diversity in the west (e.g., HN5, GD1, GZ2, YN1, and SX).

Imitating the cost of males: A hypothesis for coexistence of all-female sperm-dependent species and their sexual host.

All‐female sperm‐dependent species are particular asexual organisms that must coexist with a closely related sexual host for reproduction. However, demographic advantages of asexual over sexual species that have to produce male individuals could lead both to extinction. The unresolved question of their coexistence still challenges and fascinates evolutionary biologists. As an alternative hypothesis, we propose those asexual organisms are afflicted by a demographic cost analogous to the production of males to prevent exclusion of the host. Previously proposed hypotheses stated that asexual individuals relied on a lower fecundity than sexual females to cope with demographic advantage. In contrast, we propose that both sexual and asexual species display the same number of offspring, but half of asexual individuals imitate the cost of sex by occupying ecological niches but producing no offspring. Simulations of population growth in closed systems under different demographic scenarios revealed that only the presence of nonreproductive individuals in asexual females can result in long‐term coexistence. This hypothesis is supported by the fact that half of the females in some sperm‐dependent organisms did not reproduce clonally.

Recombination: the good, the bad and the variable.

Recombination, the process by which DNA strands are broken and repaired, producing new combinations of alleles, occurs in nearly all multicellular organisms and has important implications for many evolutionary processes. The effects of recombination can be good, as it can facilitate adaptation, but also bad when it breaks apart beneficial combinations of alleles, and recombination is highly variable between taxa, species, individuals and across the genome. Understanding how and why recombination rate varies is a major challenge in biology. Most theoretical and empirical work has been devoted to understanding the role of recombination in the evolution of sex—comparing between sexual and asexual species or populations. How recombination rate evolves and what impact this has on evolutionary processes within sexually reproducing organisms has received much less attention. This Theme Issue focusses on how and why recombination rate varies in sexual species, and aims to coalesce knowledge of the molecular mechanisms governing recombination with our understanding of the evolutionary processes driving variation in recombination within and between species. By integrating these fields, we can identify important knowledge gaps and areas for future research, and pave the way for a more comprehensive understanding of how and why recombination rate varies.

Marginal distribution and high heterozygosity of asexual Caloglossa vieillardii (Delesseriaceae, Rhodophyta) along the Australian coasts.

In animals and land plants, many asexual species originate through inter- or intraspecific crosses, and such heterozygous asexuals frequently are more abundant than their sexual relatives in marginal habitats. Although asexual species have been reported in various macroalgal taxa, detailed information regarding their distribution, heterozygosity, and origin is limited. Because many asexual tetrasporophyte strains of Caloglossa vieillardii have been isolated from South Australia, far from their core tropical habitats, we re-examined the distribution range of asexual C.vieillardii and genotyped these and other western Pacific strains using an actin gene marker. We confirmed the marginal distribution of the asexuals; however, a small patch of sexual thalli was newly discovered 450km further west from asexual populations in South Australia. Three heterozygous genotypes and one homozygous genotypes were detected from nine asexual populations; 21 heterozygous strains were obligately asexual, but one homozygous strain suddenly produced sexual gametophytes after several years of culture. We hypothesized that the most abundant heterozygous genotype (defined as type 3/4) in asexual populations occurred by a cross between type 3 and type 4 allele gametophytes, both of which were isolated from the Australian coasts. In the crossing experiments, certain combinations between type 3 females and type 4 males produced tetrasporophytes, which recycled successive tetrasporophytes. In the culture experiments, whereas both sexual and asexual strains successfully produced tetraspores at 12°C, no sexual strains released carpospores below 14°C. However, it is uncertain whether this slight difference of maturation temperature was related to the marginal distribution of asexual C.vieillardii.

Genome Architecture and Evolution of a Unichromosomal Asexual Nematode

Asexual reproduction in animals, though rare, is the main or exclusive mode of reproduction in some long-lived lineages. The longevity of asexual clades may be correlated with the maintenance of heterozygosity by mechanisms that rearrange genomes and reduce recombination. Asexual species thus provide an opportunity to gain insight into the relationship between molecular changes, genome architecture, and cellular processes. Here we report the genome sequence of the parthenogenetic nematode Diploscapter pachys with only one chromosome pair. We show that this unichromosomal architecture is shared by a long-lived clade of asexual nematodes closely related to the genetic model organism Caenorhabditis elegans. Analysis of the genome assembly reveals that the unitary chromosome arose through fusion of six ancestral chromosomes, with extensive rearrangement among neighboring regions. Typical nematode telomeres and telomeric protection-encoding genes are lacking. Most regions show significant heterozygosity; homozygosity is largely concentrated to one region and attributed to gene conversion. Cell-biological and molecular evidence is consistent with the absence of key features of meiosis I, including synapsis and recombination. We propose that D.pachys preserves heterozygosity and produces diploid embryos without fertilization through a truncated meiosis. As a prelude to functional studies, we demonstrate that D.pachys is amenable to experimental manipulation by RNA interference.

Analysis of simple sequence repeat (SSR) structure and sequence within Epichloë endophyte genomes reveals impacts on gene structure and insights into ancestral hybridization events.

Epichloë grass endophytes comprise a group of filamentous fungi of both sexual and asexual species. Known for the beneficial characteristics they endow upon their grass hosts, the identification of these endophyte species has been of great interest agronomically and scientifically. The use of simple sequence repeat loci and the variation in repeat elements has been used to rapidly identify endophyte species and strains, however, little is known of how the structure of repeat elements changes between species and strains, and where these repeat elements are located in the fungal genome. We report on an in-depth analysis of the structure and genomic location of the simple sequence repeat locus B10, commonly used for Epichloë endophyte species identification. The B10 repeat was found to be located within an exon of a putative bZIP transcription factor, suggesting possible impacts on polypeptide sequence and thus protein function. Analysis of this repeat in the asexual endophyte hybrid Epichloë uncinata revealed that the structure of B10 alleles reflects the ancestral species that hybridized to give rise to this species. Understanding the structure and sequence of these simple sequence repeats provides a useful set of tools for readily distinguishing strains and for gaining insights into the ancestral species that have undergone hybridization events.

Sex and the Imperfect Fungi.

Approximately 20% of species in the fungal kingdom are only known to reproduce by asexual means despite the many supposed advantages of sexual reproduction. However, in recent years, sexual cycles have been induced in a series of emblematic "asexual" species. We describe how these discoveries were made, building on observations of evidence for sexual potential or "cryptic sexuality" from population genetic analyses; the presence, distribution, and functionality of mating-type genes; genome analyses revealing the presence of genes linked to sexuality; the functionality of sex-related genes; and formation of sex-related developmental structures. We then describe specific studies that led to the discovery of mating and sex in certain Candida, Aspergillus, Penicillium, and Trichoderma species and discuss the implications of sex including the beneficial exploitation of the sexual cycle. We next consider whether there might be any truly asexual fungal species. We suggest that, although rare, imperfect fungi may genuinely be present in nature and that certain human activities, combined with the genetic flexibility that is a hallmark of the fungal kingdom, might favor the evolution of asexuality under certain conditions. Finally, we argue that fungal species should not be thought of as simply asexual or sexual, but rather as being composed of isolates on a continuum of sexual fertility.

Aging asexual lineages and the evolutionary maintenance of sex.

Finite populations of asexual and highly selfing species suffer from a reduced efficacy of selection. Such populations are thought to decline in fitness over time due to accumulating slightly deleterious mutations or failing to adapt to changing conditions. These within-population processes that lead nonrecombining species to extinction may help maintain sex and outcrossing through species level selection. Although inefficient selection is proposed to elevate extinction rates over time, previous models of species selection for sex assumed constant diversification rates. For sex to persist, classic models require that asexual species diversify at rates lower than sexual species; the validity of this requirement is questionable, both conceptually and empirically. We extend past models by allowing asexual lineages to decline in diversification rates as they age, that is nonrecombining lineages "senesce" in diversification rates. At equilibrium, senescing diversification rates maintain sex even when asexual lineages, at young ages, diversify faster than their sexual progenitors. In such cases, the age distribution of asexual lineages contains a peak at intermediate values rather than showing the exponential decline predicted by the classic model. Coexistence requires only that the average rate of diversification in asexuals be lower than that of sexuals.

Species delimitation in asexual insects of economic importance: The case of black scale (Parasaissetia nigra), a cosmopolitan parthenogenetic pest scale insect.

Asexual lineages provide a challenge to species delimitation because species concepts either have little biological meaning for them or are arbitrary, since every individual is monophyletic and reproductively isolated from all other individuals. However, recognition and naming of asexual species is important to conservation and economic applications. Some scale insects are widespread and polyphagous pests of plants, and several species have been found to comprise cryptic species complexes. Parasaissetia nigra (Nietner, 1861) (Hemiptera: Coccidae) is a parthenogenetic, cosmopolitan and polyphagous pest that feeds on plant species from more than 80 families. Here, we implement multiple approaches to assess the species status of P. nigra, including coalescence-based analyses of mitochondrial and nuclear genes, and ecological niche modelling. Our results indicate that the sampled specimens of P. nigra should be considered to comprise at least two ecotypes (or "species") that are ecologically differentiated, particularly in relation to temperature and moisture. The presence of more than one ecotype under the current concept of P. nigra has implications for biosecurity because the geographic extent of each type is not fully known: some countries may currently have only one of the biotypes. Introduction of additional lineages could expand the geographic extent of damage by the pest in some countries.

Four new species of Tubeufia (Tubeufiaceae, Tubeufiales) from Thailand

Tubeufia was named for a sexual morph taxon. However, several asexual morph species have been accommodated in this genus as well. In our study, four new species of Tubeufia, viz. T. filiformis, T. latispora, T. laxispora and T. mackenziei, are described and illustrated. The phylogenetic placement of the new species is confirmed by analysis of combined ITS, LSU and TEF1α sequence data. A key to Tubeufia species is provided and the new species are compared with similar fungal taxa.

Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus

BackgroundThe fungal genus Aspergillus is of critical importance to humankind. Species include those with industrial applications, important pathogens of humans, animals and crops, a source of potent carcinogenic contaminants of food, and an important genetic model. The genome sequences of eight aspergilli have already been explored to investigate aspects of fungal biology, raising questions about evolution and specialization within this genus.ResultsWe have generated genome sequences for ten novel, highly diverse Aspergillus species and compared these in detail to sister and more distant genera. Comparative studies of key aspects of fungal biology, including primary and secondary metabolism, stress response, biomass degradation, and signal transduction, revealed both conservation and diversity among the species. Observed genomic differences were validated with experimental studies. This revealed several highlights, such as the potential for sex in asexual species, organic acid production genes being a key feature of black aspergilli, alternative approaches for degrading plant biomass, and indications for the genetic basis of stress response. A genome-wide phylogenetic analysis demonstrated in detail the relationship of the newly genome sequenced species with other aspergilli.ConclusionsMany aspects of biological differences between fungal species cannot be explained by current knowledge obtained from genome sequences. The comparative genomics and experimental study, presented here, allows for the first time a genus-wide view of the biological diversity of the aspergilli and in many, but not all, cases linked genome differences to phenotype. Insights gained could be exploited for biotechnological and medical applications of fungi.

Frequency and maintenance of unreduced gametes in natural plant populations: associations with reproductive mode, life history and genome size.

Fertilization involving unreduced (2n) gametes is considered the dominant mechanism of polyploid formation in angiosperms; however, our knowledge of the prevalence of and evolutionary mechanisms maintaining 2n gametes in natural populations is limited. We hypothesize that 2n gametes are deleterious consequences of meiotic errors maintained by mutation-selection balance and should increase in species with relaxed opportunities for selection on sexual processes (asexuality), reduced efficacy of selection (asexuality, selfing) and increased genome instability (high chromosome number). We used flow cytometry to estimate male 2n gamete production in 60 populations from 24 species of Brassicaceae. We quantified variation in 2n gamete production within and among species, and examined associations with life history, reproductive mode, genome size and chromosomal number while accounting for phylogeny. Most individuals produced <2% 2n male gametes, whereas a small number had >5% (up to 85%) production. Variation in 2n gamete production was significant among species and related to reproductive system; asexual species produced significantly more 2n gametes than mixed-mating and outcrossing species. Our results, unique in their multi-species perspective, are consistent with 2n gametes being deleterious but maintained when opportunities for selection are limited. Rare individuals with elevated 2n gamete production may be key contributors to polyploid formation.

Haplotyping a Non-meiotic Diploid Fungal Pathogen Using Induced Aneuploidies and SNP/CGH Microarray Analysis.

The generation of haplotype information has recently become very attractive due to its utility for identifying mutations associated with human disease and for the development of personalized medicine. Haplotype information also is crucial for studying recombination mechanisms and genetic diversity, and for analyzing allele-specific gene expression. Classic haplotyping methods require the analysis of hundreds of meiotic progeny. To facilitate haplotyping in the non-meiotic human fungal pathogen Candida albicans, we exploited trisomic heterozygous chromosomes generated via the UAU1 selection strategy. Using this system, we obtained phasing information from allelic biases, detected by SNP/CGH microarray analysis. This strategy has the potential to be applicable to other diploid, asexual Candida species that are important causes of human disease.

Environment not dispersal limitation drives clonal composition of Arctic Daphnia in a recently deglaciated area

One of the most prominent manifestations of the ongoing climate warming is the retreat of glaciers and ice sheets around the world. Retreating glaciers result in the formation of new ponds and lakes, which are available for colonization. The gradual appearance of these new habitat patches allows us to determine to what extent the composition of asexual Daphnia (water flea) populations is affected by environmental drivers vs. dispersal limitation. Here, we used a landscape genetics approach to assess the processes structuring the clonal composition of species in the D.pulex species complex that have colonized periglacial habitats created by ice-sheet retreat in western Greenland. We analysed 61 populations from a young (<50years) and an old cluster (>150years) of lakes and ponds. We identified 42 asexual clones that varied widely in spatial distribution. Beta-diversity was higher among older than among younger systems. Lineage sorting by the environment explained 14% of the variation in clonal composition whereas the pure effect of geographical distance was very small and statistically insignificant (Radj2=0.010, P=0.085). Dispersal limitation did not seem important, even among young habitat patches. The observation of several tens of clones colonizing the area combined with environmentally driven clonal composition of populations illustrates that population assembly of asexual species in the Arctic is structured by environmental gradients reflecting differences in the ecology of clones.

Population genetics and dispersal of the flatworm, Polycelis coronata: a test of the habitat stability hypothesis

ABSTRACTThe habitat stability hypothesis states that species in spring-like habitats have little reason to disperse compared to species in temporary habitats. Planarians commonly inhabit springs around the world and they have long been considered poor dispersers. Recently, however, genetic analyses have shown contradictory results on the dispersal of planarians. Asexual planarians that can establish a new population by colonization of a single individual showed little genetic differentiation between sites separated by hundreds of kilometers, whereas species inhabiting springs showed deep differentiation between sites separated by hundreds of meters. The latter results are consistent with the habitat stability hypothesis. We used the cytochrome oxidase subunit I gene from 468 individuals of Polycelis coronata, an asexual species, collected from 50 sites, nested in 26 tributaries, in 4 catchments of the Wasatch Mountains of Utah, USA, to explore the dispersal capabilities of P. coronata. The longest distance between sites was 66 km. Despite this small spatial extent, we found that 77% of the 130 haplotypes were collected from a single site and 89% from a single catchment. FST values between local populations in the same tributary (0.221, 0.266, 0.389) were similar to the average FST values in different catchments for other headwater taxa. Also, variation among individuals accounted for the majority of genetic structuring with little differentiation beyond the scale of a single site. Dispersal is very slow in this species which is consistent with the habitat stability hypothesis. However, we suggest that other explanations also warrant consideration. We also identified two potential cryptic species suggesting a high degree of hidden variation at the level of species in this genus.

Joint Prediction of the Effective Population Size and the Rate of Fixation of Deleterious Mutations.

Mutation, genetic drift, and selection are considered the main factors shaping genetic variation in nature. There is a lack, however, of general predictions accounting for the mutual interrelation between these factors. In the context of the background selection model, we provide a set of equations for the joint prediction of the effective population size and the rate of fixation of deleterious mutations, which are applicable both to sexual and asexual species. For a population of N haploid individuals and a model of deleterious mutations with effect s appearing with rate U in a genome L Morgans long, the asymptotic effective population size (Ne) and the average number of generations (T) between consecutive fixations can be approximated by [Formula: see text] and [Formula: see text] The solution is applicable to Muller's ratchet, providing satisfactory approximations to the rate of accumulation of mutations for a wide range of parameters. We also obtain predictions of the effective size accounting for the expected nucleotide diversity. Predictions for sexual populations allow for outlining the general conditions where mutational meltdown occurs. The equations can be extended to any distribution of mutational effects and the consideration of hotspots of recombination, showing that Ne is rather insensitive and not proportional to changes in N for many combinations of parameters. This could contribute to explain the observed small differences in levels of polymorphism between species with very different census sizes.

Mating-Type Gene Structure and Spatial Distribution of Didymella tanaceti in Pyrethrum Fields.

Tan spot of pyrethrum (Tanacetum cinerariifolium) is caused by the ascomycete Didymella tanaceti. To assess the evolutionary role of ascospores in the assumed asexual species, the structure and arrangement of mating-type (MAT) genes were examined. A single MAT1-1 or MAT1-2 idiomorph was identified in all isolates examined, indicating that the species is heterothallic. The idiomorphs were flanked upstream and downstream by regions encoding pyridoxamine phosphate oxidase-like and DNA lyase-like proteins, respectively. A multiplex MAT-specific polymerase chain reaction assay was developed and used to genotype 325 isolates collected within two transects in each of four fields in Tasmania, Australia. The ratio of isolates of each mating-type in each transect was consistent with a 1:1 ratio. The spatial distribution of the isolates of the two mating-types within each transect was random for all except one transect for MAT1-1 isolates, indicating that clonal patterns of each mating-type were absent. However, evidence of a reduced selection pressure on MAT1-1 isolates was observed, with a second haplotype of the MAT1-1-1 gene identified in 4.4% of MAT1-1 isolates. In vitro crosses between isolates with opposite mating-types failed to produce ascospores. Although the sexual morph could not be induced, the occurrence of both mating-types in equal frequencies suggested that a cryptic sexual mode of reproduction may occur within field populations.

Picking holes in traditional species delimitations: an integrative taxonomic reassessment of theParmotrema perforatumgroup (Parmeliaceae, Ascomycota)

Accurate species delimitation is important as species are a fundamental unit in ecological, evolutionary and conservation biology research. In lichenized fungi, species delimitation has been difficult due to a lack of taxonomically important characteristics and due to the limits of traditional, morphology-based species concepts. In this study we reassess the current taxonomy of the Parmotrema perforatum group, which recognizes six closely related species divided into three species pairs, each pair comprising one apotheciate (sexual) and one sorediate (asexual) species. Each pair is further characterized by a distinct combination of secondary metabolites. It was hypothesized that the three apotheciate species are reproductively isolated sibling species and that each sorediate species evolved once from the chemically identical apotheciate species. In this study, species boundaries were re-examined using an integrative approach incorporating morphological, chemical and molecular sequence data to delimit species boundaries. Phylogenetic trees were inferred from a seven-locus DNA sequence dataset using concatenated gene tree and coalescent-based species-tree inference methods. Furthermore, we employed a multi-species coalescent method to validate candidate species. Micromorphological measurements of conidia were found to be congruent with phylogenetic clusters. Each approach that we applied to the P. perforatum group consistently recovered four of the currently circumscribed species (P. perforatum, P. hypotropum, P. subrigidum and P. louisianae), whereas P. preperforatum and P. hypoleucinum were consistently combined and are thus interpreted as conspecific.

Hidden Genetic Diversity in an Asexually Reproducing Lichen Forming Fungal Group.

Asexual species with vegetative propagation of both symbiont partners (soredia) in lichens may harbor lower species diversity because they may indeed represent evolutionary dead ends or clones. In this study we aim to critically examine species boundaries in the sorediate lichen forming fungi Parmotrema reticulatum–Parmotrema pseudoreticulatum complex applying coalescent-based approaches and other recently developed DNA-based methods. To this end, we gathered 180 samples from Africa, Asia, Australasia, Europe, North and South America and generated sequences of internal transcribed spacer of nuclear ribosomal DNA (ITS) and DNA replication licensing factor MCM7 (MCM7). The dataset was analysed using different approaches such as traditional phylogeny–maximum likelihood and Bayesian–genetic distances, automatic barcode gap discovery and coalescent-based methods–PTP, GMYC, spedeSTEM and *Beast–in order to test congruence among results. Additionally, the divergence times were also estimated to elucidate diversification events. Delimitations inferred from the different analyses are comparable with only minor differences, and following a conservative approach we propose that the sampled specimens of the P. reticulatum–P. pseudoreticulatum complex belong to at least eight distinct species-level lineages. Seven are currently classified under P. reticulatum and one as P. pseudoreticulatum. In this work we discuss one of only few examples of cryptic species that have so far been found in sorediate reproducing lichen forming fungi. Additionally our estimates suggest a recent origin of the species complex–during the Miocene. Consequently, the wide distribution of several of the cryptic species has to be explained by intercontinental long-distance dispersal events.

Effects of Cushion Plants on High-Altitude Soil Microarthropod Communities: Cushions Increase Abundance and Diversity of Mites (Acari), but not Springtails (Collembola)

ABSTRACTCushion plants in alpine ecosystems act as nurse species, which modify and alleviate environmental conditions and positively influence the diversity and abundance of other organisms. Soil fauna in alpine environments should benefit from nurse plant facilitation, but this has not been investigated. We compared diversity, abundance, and community structure of soil microarthropods (Collembola, Oribatida, Mesostigmata, Prostigmata, Endeostigmata, and Astigmata) under cushion plants and in adjacent open microsites in high altitude patterned ground landscapes in New Zealand. We investigated how cushion plants influence environmental factors, and how environmental factors and species traits contribute to microarthropod community structure. The results show that cushion plants are a key in maintaining the biodiversity of soil microarthropods in the high alpine. Cushion plants maintain higher moisture and organic matter content in the soil, provide productive and structurally complex habitat, and mitigate disturbance. Abundance and species richness of Oribatida, Mesostigmata, and Prostigmata were higher under cushion plants. In contrast, abundance of Collembola was higher in open microsites, while their species richness similar in and out of cushions. Oribatida assemblages were dominated by small asexual species, indicating a disturbed environment. Oribatida community structure was significantly related to the microhabitat in two out of three mountain ranges. Collembola assemblages were similar in and out of cushions. Higher soil moisture and organic matter content under cushion plants were significant in explaining patterns in microarthropod assemblages, although high percentage of variability was not explained by environmental variables. There was no effect of cushions on soil temperatures. Species identity of the cushion plant did not influence abundance, species richness, or community assemblages of mites and springtails; however, some species were associated with either Dracophyllum or Raoulia cushions.