Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

Sequencing of the genome of the butterfly Heliconius melpomene shows that closely related Heliconius species exchange protective colour-pattern genes promiscuously.

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Butterfly genome reveals promiscuous exchange of mimicry adaptations among species

The metaphor of ‘genomic islands of speciation’ was first used to describe heterogeneous differentiation among loci between the genomes of closely related species. The biological model proposed to explain these differences was that the regions showing high levels of differentiation were resistant to gene flow between species, while the remainder of the genome was being homogenized by gene flow and consequently showed lower levels of differentiation. However, the conditions under which such differentiation can occur at multiple unlinked loci are restrictive; additionally, essentially, all previous analyses have been carried out using relative measures of divergence, which can be misleading when regions with different levels of recombination are compared. Here, we test the model of differential gene flow by asking whether absolute divergence is also higher in the previously identified ‘islands’. Using five species pairs for which full sequence data are available, we find that absolute measures of divergence are not higher in genomic islands. Instead, in all cases examined, we find reduced diversity in these regions, a consequence of which is that relative measures of divergence are abnormally high. These data therefore do not support a model of differential gene flow among loci, although islands of relative divergence may represent loci involved in local adaptation. Simulations using the program IMa2 further suggest that inferences of any gene flow may be incorrect in many comparisons. We instead present an alternative explanation for heterogeneous patterns of differentiation, one in which postspeciation selection generates patterns consistent with multiple aspects of the data.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.12796

Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow

This Review distinguishes between three distinct routes by which similar genetic changes contribute to convergent evolution and discusses examples from diverse taxa. Convergent genetic evolution might result from the fact that some mutations both minimize pleiotropic effects and maximize adaptation.

The genetic causes of convergent evolution.

Adaptive genetic variation has been thought to originate primarily from either new mutation or standing variation. Another potential source of adaptive variation is adaptive variants from other (donor) species that are introgressed into the (recipient) species, termed adaptive introgression. Here, the various attributes of these three potential sources of adaptive variation are compared. For example, the rate of adaptive change is generally thought to be faster from standing variation, slower from mutation and potentially intermediate from adaptive introgression. Additionally, the higher initial frequency of adaptive variation from standing variation and lower initial frequency from mutation might result in a higher probability of fixation of the adaptive variants for standing variation. Adaptive variation from introgression might have higher initial frequency than new adaptive mutations but lower than that from standing variation, again making the impact of adaptive introgression variation potentially intermediate. Adaptive introgressive variants might have multiple changes within a gene and affect multiple loci, an advantage also potentially found for adaptive standing variation but not for new adaptive mutants. The processes that might produce a common variant in two taxa, convergence, trans-species polymorphism from incomplete lineage sorting or from balancing selection and adaptive introgression, are also compared. Finally, potential examples of adaptive introgression in animals, including balancing selection for multiple alleles for major histocompatibility complex (MHC), S and csd genes, pesticide resistance in mice, black colour in wolves and white colour in coyotes, Neanderthal or Denisovan ancestry in humans, mimicry genes in Heliconius butterflies, beak traits in Darwin's finches, yellow skin in chickens and non-native ancestry in an endangered native salamander, are examined.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.12415

Adaptive introgression in animals: examples and comparison to new mutation and standing variation as sources of adaptive variation.

Adaptive Introgression of Anticoagulant Rodent Poison Resistance by Hybridization between Old World Mice

To determine whether Norway rats contribute to the risk of human Lyme disease in a central European city park, densities of endemic rodents were compared as were feeding densities of vector ticks and prevalence of infection by the Lyme disease spirochete. Only Norway rats and yellow-necked mice were abundant, and three times as many mice as rats were present. More larval ticks fed on rats than on mice, and far more nymphs engorged on the rats. All rats but only about half of the mice infected ticks. Each rat was more infectious than each infectious mouse. Infected rats were distributed throughout the city. Spirochetes infected about a quarter of the questing nymphal ticks. The capacity of rats to serve as reservoir hosts for the Lyme disease spirochete, therefore, increases risk of infection among visitors to this and other urban parks.

Risk of Urban Lyme Disease Enhanced by the Presence of Rats

This paper presents a reappraisal of the blood clotting response (BCR) tests for anticoagulant rodenticides, and proposes a standardised methodology for identifying and quantifying physiological resistance in populations of rodent species. The standardisation is based on the International Normalised Ratio, which is standardised against a WHO international reference preparation of thromboplastin, and allows comparison of data obtained using different thromboplastin reagents. The methodology is statistically sound, being based on the 50% response, and has been validated against the Norway rat (Rattus norvegicus) and the house mouse (Mus domesticus). Susceptibility baseline data are presented for warfarin, diphacinone, chlorophacinone and coumatetralyl against the Norway rat, and for bromadiolone, difenacoum, difethialone, flocoumafen and brodifacoum against the Norway rat and the house mouse. A ‘test dose’ of twice the ED50 can be used for initial identification of resistance, and will provide a si...

A standardised BCR resistance test for all anticoagulant rodenticides

To determine whether particular Borrelia burgdorferi s.l. genospecies associate solely with rodent reservoir hosts, we compared the genospecies prevalence in questing nymphal Ixodes ticks with that in xenodiagnostic ticks that had fed as larvae on rodents captured in the same site. No genospecies was more prevalent in rodent-fed ticks than in questing ticks. The three main spirochete genospecies, therefore, share common rodent hosts.

Stefan Endepols

Papers

Adaptive Introgression of Anticoagulant Rodent Poison Resistance by Hybridization between Old World Mice

Risk of Urban Lyme Disease Enhanced by the Presence of Rats

A standardised BCR resistance test for all anticoagulant rodenticides

Genospecies diversity of Lyme disease spirochetes in rodent reservoirs.

A scheme for the placement of rodenticide baits for rat eradication on confinement livestock farms.