parallel evolution - senecio7の日記

Ralph P & Coop G 2010 Parallel adaptation: one or many waves of advance of an advantageous allele? Genetics 186:647-668.

we study various models of parallel mutation in a continuous, geographically spread population adapting to a global selection pressure
when these different selected alleles meet, their spread can slow dramatically and so initially form a geographic patchwork, a random tessellation, which could be mistaken for a signal of local adaptation
this spatial tessellation will dissipate over time due to mixing by migration, leaving a set of partial sweeps within the global population
the spatial tessellation initially formed by mutational types is closely connected to Poisson process models of crystallization
the spatial scale on which parallel mutation occurs are captured by a single compound parameter, a characteristic length, which reflects the expected distance a spreading allele travels before it encounters a different spreading allele
this characteristic length depends on the mutation rate, the dispersal parameter, the effective local density of individuals, and to a much lesser extent the strength of selection
as more data become available, many more examples of intraspecies parallel adaptation will be uncovered

there are many dramatic examples of convergent evolution across distantly related species
indicating that adaptation can be strongly shaped by pleiotropic constraints
there are also a growing number of examples of the parallel evolution of a phenotype within a species due to independent mutations at the same gene
which are sometimes referred to as genetically redundant

there are also a number of examples of parallel evolution within our own species
various G6PD mutations have spread in parallel in response to malaria
lactase persistence has evolved independently in at least three different pastoral populations
a particularly impressive example in humans is offered by the sickle cell allele at the β-globin gene that confers malaria resistance, where multiple changes have putatively occurred at a single base pair
in each of these examples, multiple, independent mutations have led to the same or a functionally equivalent adaptive phenotype
repeated adaptive evolution via similar changes within a species, which we term parallel adaptation, may therefore be common
as we also address repeated evolution of a similar phenotype via changes at different genetic loci, this could more broadly be termed "convergent adaptation"
in many of these examples the selection pressure is patchy and rates of gene flow are low, increasing the chance of parallel adaptation
parallel adaptation can occur even in a panmictic population
adaptation may occur from multiple independent copies of the selected allele present in standing variation at mutation–selection balance within the population
even when there is no standing variation for a trait in a panmictic population, a selected allele could arise independently several times during the course of a selective sweep, if mutation is sufficiently fast relative to the spread of the selected allele
such soft sweeps may be expected when the population scaled mutation rate (the product of the effective population size and mutation rate) toward the adaptive allele is >1
repeated mutation may be quite common for species with large populations or where the mutation target is large
Pennings and Hermisson (2006a) showed that the number of independently arisen selected alleles in a sample has approximately a Ewens distribution

if parallel mutations can occur during adaptation in a large panmictic population, then limited dispersal should further increase the chance of parallel adaptation, as other mutations can arise and spread during the time it takes one to move across the species range
intuitively, a low rate of dispersal and a large mutational target should increase the chance of parallel adaptation
but it is unclear exactly how other dispersal, population, and mutational parameters play into the probability of parallel adaptation

we study parallel adaptation in a homogeneous, geographically spread population
a population is exposed to a novel selection regime throughout a homogeneous species range
the population is initially entirely devoid of standing variation for the trait
assumptions that favor the fixation of only a single new allele in the population

modeling assumptions:
we assume each mutation under consideration confers a selective advantage such that, upon appearing in the population, it quickly rises locally to some equilibrium frequency
there is significant spatial structure
migration is weak enough that the selected trait reaches an equilibrium frequency locally before spreading to the entire population
the parallel mutations are distinguishable and confer the same selective benefit
these mutations are neutral relative to each other, in the sense that in a population at equilibrium frequency (e.g., fixation) for any collection of these mutations, the dynamics of their relative proportions occur on a longer timescale than their dynamics in the original background
we call this last assumption allelic exclusion
by our assumption of allelic exclusion, the dynamics are slower than the spread of the selected alleles
this allows us to neglect the slower mixing of types and genetic drift that will happen in this phase, instead focusing on the first process by which independently arisen alleles partition the population

why are there so few recent Eurasian-wide sweeps in Humans?
Coop et al. (2009) and Pickrell et al. (2009) argued that few selected alleles have recently swept to fixation across Eurasia
there are at least three possible explanations for this pattern:
(1) there has not been sufficient time for these alleles to spread
(2) the selection pressures are at a local scale, not Eurasia-wide
(3) the selection pressures are shared across Eurasia and different populations have adapted in parallel

as human population densities have increased dramatically over time, so too has the probability of parallel adaptation
it is interesting therefore to note that a number of recent human adaptations (e.g., sickle cell alleles) involve repeated changes at very small mutational targets in relatively small geographic areas, while older adaptations from single changes (e.g., skin pigmentation) are more broadly spread

the regions occupied by distinct types have dimensions on the order of the characteristic length
if the species range is at least as large as the characteristic length, then parallel adaptation is likely

the expected number of parallel mutations is a simple function that, as intuition would predict, decreases with dispersal rate and increases with mutation rate
somewhat counterintuitively, the results are relatively insensitive to the strength of selection
selection both hastens the spread of an allele and conversely increases the chances that a new mutation escapes drift

the likelihood of parallel adaptation depends on dispersal strength relative to population density
geographic parallel adaptation may be an important factor even in species that appear panmictic at neutral markers
increasing population density (ρ) increases the chance of parallel adaptation

our results apply equally well to selected alleles of similar phenotypic effect that have arisen in parallel at different genetic loci

the boundaries between selected types will tend to occur at geographic barriers to migration, as selected alleles will temporarily be slowed there

parallel mutation would allow a population to maintain a higher level of heterozygosity at the selected loci than would sweeps from a single mutational origin
a related argument has been made by Goldstein and Holsinger (1992)

the spatial density of individuals within a population is likely to fluctuate dramatically over time
the long-term effective population size for the species is likely to be a very poor estimate for the rate at which selected mutations arise
especially in populations that have experienced recent rapid growth

if migration is not spatially restricted (e.g., the fully connected "island" model), then we expect the dynamics to be significantly different