Genotype transmitters

class GenoTransmitter

class GenoTransmitter

This during mating operator is the base class of all genotype transmitters. It is made available to users because it provides a few member functions that can be used by derived transmitters, and by customized Python during mating operators.

GenoTransmitter(output="", begin=0, end=-1, step=1, at=[], reps=ALL_AVAIL, subPops=ALL_AVAIL, infoFields=[])

Create a base genotype transmitter.

clearChromosome(ind, ploidy, chrom)

Clear (set alleles to zero) chromosome chrom on the ploidy- th homologous set of chromosomes of individual ind. It is equivalent to ind.setGenotype([0], ploidy, chrom), except that it also clears allele lineage if it is executed in a module with lineage allele type.

copyChromosome(parent, parPloidy, offspring, ploidy, chrom)

Transmit chromosome chrom on the parPloidy set of homologous chromosomes from parent to the ploidy set of homologous chromosomes of offspring. It is equivalent to offspring.setGenotype(parent.genotype(parPloidy, chrom), polidy, chrom), except that it also copies allelic lineage when it is executed in a module with lineage allele type.

copyChromosomes(parent, parPloidy, offspring, ploidy)

Transmit the parPloidy set of homologous chromosomes from parent to the ploidy set of homologous chromosomes of offspring. Customized chromosomes are not copied. It is equivalent to offspring.setGenotype(parent.genotype(parPloidy), ploidy), except that it also copies allelic lineage when it is executed in a module with lineage allele type.

class CloneGenoTransmitter

class CloneGenoTransmitter

This during mating operator copies parental genotype directly to offspring. This operator works for all mating schemes when one or two parents are involved. If both parents are passed, maternal genotype are copied. In addition to genotypes on all non-customized or specified chromosomes, sex and information fields are by default also coped copied from parent to offspring.

CloneGenoTransmitter(output="", chroms=ALL_AVAIL, begin=0, end=-1, step=1, at=[], reps=ALL_AVAIL, subPops=ALL_AVAIL, infoFields=ALL_AVAIL)

Create a clone genotype transmitter (a during-mating operator) that copies genotypes from parents to offspring. If two parents are specified, genotypes are copied maternally. After genotype transmission, offspring sex and affection status is copied from the parent even if sex has been determined by an offspring generator. All or specified information fields (parameter infoFields, default to ALL_AVAIL) will also be copied from parent to offspring. Parameters subPops is ignored. This operator by default copies genotypes on all autosome and sex chromosomes (excluding customized chromosomes), unless a parameter chroms is used to specify which chromosomes to copy. This operator also copies allelic lineage when it is executed in a module with lineage allele type.

class MendelianGenoTransmitter

class MendelianGenoTransmitter

This Mendelian offspring generator accepts two parents and pass their genotypes to an offspring following Mendel’s laws. Sex chromosomes are handled according to the sex of the offspring, which is usually determined in advance by an offspring generator. Customized chromosomes are not handled.

MendelianGenoTransmitter(output="", begin=0, end=-1, step=1, at=[], reps=ALL_AVAIL, subPops=ALL_AVAIL, infoFields=[])

Create a Mendelian genotype transmitter (a during-mating operator) that transmits genotypes from parents to offspring following Mendel’s laws. Autosomes and sex chromosomes are handled but customized chromosomes are ignored. Parameters subPops and infoFields are ignored. This operator also copies allelic lineage when it is executed in a module with lineage allele type.

transmitGenotype(parent, offspring, ploidy)

Transmit genotype from parent to offspring, and fill the ploidy homologous set of chromosomes. This function does not set genotypes of customized chromosomes and handles sex chromosomes properly, according to offspring sex and ploidy.

class SelfingGenoTransmitter

class SelfingGenoTransmitter

A genotype transmitter (during-mating operator) that transmits parental genotype of a parent through self-fertilization. That is to say, the offspring genotype is formed according to Mendel’s laws, only that a parent serves as both maternal and paternal parents.

SelfingGenoTransmitter(output="", begin=0, end=-1, step=1, at=[], reps=ALL_AVAIL, subPops=ALL_AVAIL, infoFields=[])

Create a self-fertilization genotype transmitter that transmits genotypes of a parent to an offspring through self- fertilization. Cutsomized chromosomes are not handled. Parameters subPops and infoFields are ignored. This operator also copies allelic lineage when it is executed in a module with lineage allele type.

class HaplodiploidGenoTransmitter

class HaplodiploidGenoTransmitter

A genotype transmitter (during-mating operator) for haplodiploid populations. The female parent is considered as diploid and the male parent is considered as haploid (only the first homologous copy is valid). If the offspring is FEMALE, she will get a random copy of two homologous chromosomes of her mother, and get the only paternal copy from her father. If the offspring is MALE, he will only get a set of chromosomes from his mother.

HaplodiploidGenoTransmitter(output="", begin=0, end=-1, step=1, at=[], reps=ALL_AVAIL, subPops=ALL_AVAIL, infoFields=[])

Create a haplodiploid genotype transmitter (during-mating operator) that transmit parental genotypes from parents to offspring in a haplodiploid population. Parameters subPops and infoFields are ignored. This operator also copies allelic lineage when it is executed in a module with lineage allele type.

class MitochondrialGenoTransmitter

class MitochondrialGenoTransmitter

This geno transmitter transmits the first homologous copy of a Mitochondrial chromosome. If no mitochondrial chromosome is present, it assumes that the first homologous copy of several (or all) Customized chromosomes are copies of mitochondrial chromosomes. This operator transmits the mitochondrial chromosome from the female parent to offspring for sexsual reproduction, and any parent to offspring for asexual reproduction. If there are multiple chromosomes, the organelles are selected randomly. If this transmitter is applied to populations with more than one homologous copies of chromosomes, it transmits the first homologous copy of chromosomes and clears alleles (set to zero) on other homologous copies.

MitochondrialGenoTransmitter(output="", chroms=ALL_AVAIL, begin=0, end=-1, step=1, at=[], reps=ALL_AVAIL, subPops=ALL_AVAIL, infoFields=[])

Createa a mitochondrial genotype transmitter that treats the Mitochondiral chromosome, or Customized chromosomes if no Mitochondrial chromosome is specified, or a list of chromosomes specified by chroms, as human mitochondrial chromosomes. These chromosomes should have the same length and the same number of loci. This operator transmits these chromosomes randomly from the female parent to offspring of both sexes. It also copies allelic lineage when it is executed in a module with lineage allele type.

class Recombinator

class Recombinator

A genotype transmitter (during-mating operator) that transmits parental chromosomes to offspring, subject to recombination and gene conversion. This can be used to replace MendelianGenoTransmitter and SelfingGenoTransmitter. It does not work in haplodiploid populations, although a customized genotype transmitter that makes uses this operator could be defined. Please refer to the simuPOP user’s guide or online cookbook for details.

Recombination could be applied to all adjacent markers or after specified loci. Recombination rate between two adjacent markers could be specified directly, or calculated using physical distance between them. In the latter case, a recombination intensity is multiplied by physical distance between markers.

Gene conversion is interpreted as double-recombination events. That is to say, if a recombination event happens, it has a certain probability (can be 1) to become a conversion event, namely triggering another recombination event down the chromosome. The length of the converted chromosome can be controlled in a number of ways.

Note

simuPOP does not assume any unit to loci positions so recombination intensity could be explained differntly (e.g. cM/Mb, Morgan/Mb) depending on your intepretation of loci positions. For example, if basepair is used for loci position, intensity=10^-8 indicates 10^-8 per basepair, which is equivalent to 10^-2 per Mb or 1 cM/Mb. If Mb is used for physical positions, the same recombination intensity could be achieved by intensity=0.01.

Recombinator(rates=[], intensity=-1, loci=ALL_AVAIL, convMode=NO_CONVERSION, output="", begin=0, end=-1, step=1, at=[], reps=ALL_AVAIL, subPops=ALL_AVAIL, infoFields=[])

Create a Recombinator (a mendelian genotype transmitter with recombination and gene conversion) that passes genotypes from parents (or a parent in case of self-fertilization) to offspring.

Recombination happens by default between all adjacent markers but can be limited to a given set of loci, which can be a list of loci indexes, names, list of chromosome position pairs, ALL_AVAIL, or a function with optional parameter pop that will be called at each ganeeration to determine indexes of loci. Each locus in this list specifies a recombination point between the locus and the locus immediately after it. Loci that are the last locus on each chromosome are ignored.

If a single recombination rate (parameter rates) is specified, it will used for all loci (all loci or loci specified by parameter loci), regardless of physical distances between adjacent loci.

If a list of recombination rates are specified in rates, different recombination rates could be applied after a list of specified loci (between loci and their immediate neighbor to the right). The loci should be specified by parameter loci as a list with the same length as rates, or ALL_AVAIL (default) in which case the length of rates should equal to the total number of loci. Note that recombination rates specified for the last locus on each chromosome are ignored because simuPOP assumes free recombination between chromosomes.

A recombination intensity (intensity) can be used to specify recombination rates that are proportional to physical distances between adjacent markers. If the physical distance between two markers is d, the recombination rate between them will be intensity * d. No unit is assume for loci position and recombination intensity.

Gene conversion is controlled using parameter convMode, which can be

• NoConversion: no gene conversion (default).
• (NUM_MARKERS, prob, n): With probability prob, convert a fixed number (n) of markers if a recombination event happens.
• (GEOMETRIC_DISTRIBUTION, prob, p): With probability prob, convert a random number of markers if a recombination event happens. The number of markes converted follows a geometric distribution with probability p.
• (TRACT_LENGTH, prob, n): With probability prob, convert a region of fixed tract length (n) if a recombination event happens. The actual number of markers converted depends on loci positions of surrounding loci. The starting position of this tract is the middle of two adjacent markers. For example, if four loci are located at 0, 1, 2, 3 respectively, a conversion event happens between 0 and 1, with a tract length 2 will start at 0.5 and end at 2.5, covering the second and third loci.
• (EXPONENTIAL_DISTRIBUTION, prob, p): With probability prob, convert a region of random tract length if a recombination event happens. The distribution of tract length follows a exponential distribution with probability p. The actual number of markers converted depends on loci positions of surrounding loci.

simuPOP uses this probabilistic model of gene conversion because when a recombination event happens, it may become a recombination event if the if the Holliday junction is resolved/repaired successfully, or a conversion event if the junction is not resolved/repaired. The probability, however, is more commonly denoted by the ratio of conversion to recombination events in the literature. This ratio varies greatly from study to study, ranging from 0.1 to 15 (Chen et al, Nature Review Genetics, 2007). This translate to 0.1/0.9~0.1 to 15/16~0.94 of the gene conversion probability.

A Recombinator usually does not send any output. However, if an information field is given (parameter infoFields), this operator will treat this information field as an unique ID of parents and offspring and output all recombination events in the format of offspring_id parent_id starting_ploidy loc1 loc2 ... `` where ``starting_ploidy indicates which homologous copy genotype replication starts from (0 or 1), loc1, loc2 etc are loci after which recombination events happens. If there are multiple chromosomes on the genome, you will see a lot of (fake) recombination events because of independent segregation of chromosomes. Such a record will be generated for each set of homologous chromosomes so an diploid offspring will have two lines of output. Note that individual IDs need to be set (using a IdTagger operator) before this Recombinator is applied.

In addition to genotypes, this operator also copies alleleic lineage if it is executed in a module with lineage allele type.

Note

There is no recombination between sex chromosomes (Chromosomes X and Y), although recombination is possible between pesudoautosomal regions on these chromosomes. If such a feature is required, you will have to simulate the pesudoautosomal regions as separate chromosomes.

transmitGenotype(parent, offspring, ploidy)

This function transmits genotypes from a parent to the ploidy-th homologous set of chromosomes of an offspring. It can be used, for example, by a customized genotype transmitter to use sex-specific recombination rates to transmit parental genotypes to offspring.