Many microbial, fungal, or oomcyete populations violate assumptions for population genetic analysis because these populations are clonal, admixed, partially clonal, and/or sexual. Furthermore, few tools exist that are specifically designed for analyzing data from clonal populations, making analysis difficult and haphazard. We developed the R package poppr providing unique tools for analysis of data from admixed, clonal, mixed, and/or sexual populations. Currently, poppr can be used for dominant/codominant and haploid/diploid genetic data. Data can be imported from several formats including GenAlEx formatted text files and can be analyzed on a user-defined hierarchy that includes unlimited levels of subpopulation structure and clone censoring. New functions include calculation of Bruvo’s distance for microsatellites, batch-analysis of the index of association with several indices of genotypic diversity, and graphing including dendrograms with bootstrap support and minimum spanning networks. While functions for genotypic diversity and clone censoring are specific for clonal populations, several functions found in poppr are also valuable to analysis of any populations. A manual with documentation and examples is provided. Poppr is open source and major releases are available on CRAN: http://cran.r-project.org/package=poppr. More supporting documentation and tutorials can be found under ‘resources’ at: http://grunwaldlab.cgrb.oregonstate.edu/.

/pdf/poppr-an-r-package-for-genetic-analysis-of-populations-with-24k9jtq97d.pdf

Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction.

We redescribe the only previously known species of Myrsidea from bulbuls, M. pycnonoti Eichler. Sixteen new species are described; they and their type hosts are: M. phillipsi ex Pycnonotus goiavier goiavier (Scopoli), M. gieferi ex P. goiavier suluensis Mearns, M. kulpai ex P. flavescens Blyth, M. finlaysoni ex P. finlaysoni Strickland, M. kathleenae ex P. cafer (L.), M. warwicki ex Ixos philippinus (J. R. Forster), M. mcclurei ex Microscelis amaurotis (Temminck), M. zeylanici ex P. zeylanicus (Gmelin), M. plumosi ex P. plumosus Blyth, M. eutiloti ex P. eutilotus (Jardine and Selby), M. adamsae ex P. urostictus (Salvadori), M. ochracei ex Criniger ochraceus F. Moore, M. borbonici ex Hypsipetes borbonicus (J. R. Forster), M. johnsoni ex P. atriceps (Temminck), M. palmai ex C. ochraceus, and M. claytoni ex P. eutilotus. A key is provided for the identification of these 17 species.

A new species

Sexual reproduction is an ancient feature of life on earth, and the familiar X and Y chromo- somes in humans and other model species have led to the impression that sex determination mecha- nisms are old and conserved. In fact, males and females are deter- mined by diverse mechanisms that evolve rapidly in many taxa. Yet this diversity in primary sex-deter- mining signals is coupled with conserved molecular pathways that trigger male or female develop- ment. Conflicting selection on dif- ferent parts of the genome and on the two sexes may drive many of these transitions, but few systems with rapid turnover of sex determi- nation mechanisms have been rig- orously studied. Here we survey our current understanding of how and why sex determination evolves in animals and plants and identify important gaps in our knowledge that present exciting research op- portunities to characterize the evo- lutionary forces and molecular pathways underlying the evolution of sex determination.

/pdf/sex-determination-why-so-many-ways-of-doing-it-ivb1ovfz8c.pdf

Sex Determination: Why So Many Ways of Doing It?

Plastic debris is widespread in the environment, but information on the effects of microplastics on terrestrial fauna is completely lacking. Here, we studied the survival and fitness of the earthworm Lumbricus terrestris (Oligochaeta, Lumbricidae) exposed to microplastics (Polyethylene, <150 μm) in litter at concentrations of 7, 28, 45, and 60% dry weight, percentages that, after bioturbation, translate to 0.2 to 1.2% in bulk soil. Mortality after 60 days was higher at 28, 45, and 60% of microplastics in the litter than at 7% w/w and in the control (0%). Growth rate was significantly reduced at 28, 45, and 60% w/w microplastics, compared to the 7% and control treatments. Due to the digestion of ingested organic matter, microplastic was concentrated in cast, especially at the lowest dose (i.e., 7% in litter) because that dose had the highest proportion of digestible organic matter. Whereas 50 percent of the microplastics had a size of <50 μm in the original litter, 90 percent of the microplastics in the casts was <50 μm in all treatments, which suggests size-selective egestion by the earthworms. These concentration-transport and size-selection mechanisms may have important implications for fate and risk of microplastic in terrestrial ecosystems.

Microplastics in the Terrestrial Ecosystem: Implications for Lumbricus terrestris (Oligochaeta, Lumbricidae)

To gain a detailed understanding of how plant microbes evolve and adapt to hosts, pesticides, and other factors, knowledge of the population dynamics and evolutionary history of populations is crucial. Plant pathogen populations are often clonal or partially clonal which requires different analytical tools. With the advent of high throughput sequencing technologies, obtaining genome-wide population genetic data has become easier than ever before. We previously contributed the R package poppr specifically addressing issues with analysis of clonal populations. In this paper we provide several significant extensions to poppr with a focus on large, genome-wide SNP data. Specifically, we provide several new functionalities including the new function mlg.filter to define clone boundaries allowing for inspection and definition of what is a clonal lineage, minimum spanning networks with reticulation, a sliding-window analysis of the index of association, modular bootstrapping of any genetic distance, and analyses across any level of hierarchies.

/pdf/novel-r-tools-for-analysis-of-genome-wide-population-genetic-5fu08kqf09.pdf

Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality.

Microsatellites are powerful molecular markers, used commonly to estimate intraspecific genetic distances. With the exception of band sharing similarity index, available distance measures were developed specifically for diploid organisms and are unsuited for comparisons of polyploids. Here, we present a simple method for calculation of microsatellite genotype distances, which takes into account mutation processes and permits comparison of individuals with different ploidy levels. This method should provide a valuable tool for intraspecific analyses of polyploid organisms, which are widespread among plants and some animal taxa. An illustration is given using data from the planarian flatworm Schmidtea polychroa (Platyhelminthes).

A simple method for the calculation of microsatellite genotype distances irrespective of ploidy level.

Differences in objectives between males and females are a driving force in the evolution of copulatory mechanisms. Hermaphrodites can also have sexual conflicts, but caused by opposing sexual interests within rather than between individuals. One consequence seems to be that physically damaging sex, as occurs with the marine flatworm Pseudoceros bifurcus, might be favoured more in hermaphrodites than in species with separate sexes.

/pdf/sex-and-violence-in-hermaphrodites-1ol39o3n7y.pdf

Sex and violence in hermaphrodites

The intensity of sperm competition determines how much reproductive effort should be invested in sperm. One important factor affecting sperm competition in internally fertilizing organisms is the mating frequency of females, since it determines the extent of competition between ejaculates. In simultaneous hermaphrodites, energy spent on sperm has to be traded off against energy expended on ova production. By extending an existing model, we consider how the number of matings affects sperm competition and, thus, sex allocation in internally fertilizing simultaneous hermaphrodites. We then go on to explore the consequences of two common characteristics of hermaphroditic mating systems, namely, sperm digestion and reciprocal insemination. Since sperm digestion reduces the competitive ability of a given ejaculate, it selects for increased sperm investment. As a result, the amount of sperm digested and male allocation can enter a coevolutionary cycle in which both will increase up to the point of equa...

https://www.jstor.org/stable/10.1086/303184

Sperm Digestion and Reciprocal Sperm Transfer Can Drive Hermaphrodite Sex Allocation to Equality

Models of the maintenance of sex predict that one reproductive strategy, sexual or parthenogenetic, should outcompete the other. Distribution patterns may reflect the outcome of this competition as well as the effect of chance and historical events. We review the distribution data of sexual and parthenogenetic biotypes of the planarian Schmidtea polychroa. S. polychroa lives in allopatry or sympatry across Europe except for Central and North-Western Europe, where sexual individuals have never been reported. A phylogenetic relationship between 36 populations based on a 385 bp fragment of the mitochondrial cytochrome oxidase I gene revealed that haplotypes were often similar over large geographic distances. In North Italian lakes, however, diversity was extreme, with sequence differences of up to 5% within the same lake in both sexuals and parthenogens. Mixed populations showed "endemic" parthenogenetic lineages that presumably originated from coexisting sexuals, and distantly related ones that probably result from colonization by parthenogens independent from sexuals. Parthenogens originated repeatedly from sexuals, mainly in Italy, but the same may apply to other Mediterranean regions (Spain, Greece). The degree of divergence between populations suggests that S. polychroa survived the ice ages in separate ice-free areas in Central, Eastern and Southern Europe and re-colonised Europe after the retreat of the major glaciers. Combining these results with those based on nuclear markers, the data suggest that repeated hybridisation between sexuals and parthenogenetic lineages in mixed populations maintains high levels of genetic diversity in parthenogens. This can explain why parthenogens persist in populations that were originally sexual. Exclusive parthenogenesis in central and western populations suggests better colonisation capacity, possibly because of inbreeding costs as well as hybridisation of sexuals with parthenogens.

/pdf/phylogeography-of-competing-sexual-and-parthenogenetic-forms-dmzfj98hsu.pdf

Phylogeography of competing sexual and parthenogenetic forms of a freshwater flatworm: patterns and explanations

In the earthworm Lumbricus terrestris L., mating occurs on the soil surface, but partners remain anchored in their burrow and mating is preceded by repeated mutual burrow visits between neighbors. This study focuses on body size as one possible trait that earthworms may assess during these burrow visits. Size-related mate choice is predicted to result in size-assortative mating, which we found in one field sample (n 90 pairs), but not in a second (n 102). We discovered that when mates separate, one of them can be pulled out of its burrow. This was more likely for small individuals or those mating across wide distances. In a subsequent greenhouse experiment, we allowed focal individuals to mate with two neighbors of different sizes. Relative size affected neither mating rate nor primary preference, but focals mated sooner with the same-sized neighbor than with a differently sized one. Small focals visited large neighbors more often than small ones. We conclude that size influences mate choice as well as the outcome of mating and discuss how the ‘‘tug-of-war’’ that ends a mating contributes to this result. Precopulatory visits may involve assessment as well as enticement to lure the partner closer to the individual’s own burrow, in order to minimize the risk when mating with a partner that is large or far away.

/pdf/precopulatory-mate-assessment-in-relation-to-body-size-in-59qi5axy6z.pdf

Nicolaas K. Michiels

Papers

A simple method for the calculation of microsatellite genotype distances irrespective of ploidy level.

Sex and violence in hermaphrodites

Sperm Digestion and Reciprocal Sperm Transfer Can Drive Hermaphrodite Sex Allocation to Equality

Phylogeography of competing sexual and parthenogenetic forms of a freshwater flatworm: patterns and explanations

Precopulatory mate assessment in relation to body size in the earthworm Lumbricus terrestris: Avoidance of dangerous liaisons?