Parallel adaptation of rabbit populations to myxoma virus

Alves, Joel M.; Carneiro, Miguel; Cheng, Jade Yu; Matos, Ana Lemos de; Rahman, Masmudur M.; Loog, Liisa; Campos, Paula F.; Wales, Nathan; Eriksson, Anders; Manica, Andrea; Strive, Tanja; Graham, Stephen C.; Afonso, Sandra; Bell, Diana; Belmont, Laura; Day, Jonathan P.; Fuller, Susan; Marchandeau, Stéphane; Palmer, William J.; Queney, Guillaume; Surridge, Alison K.; Vieira, Filipe Garrett; McFadden, Grant; Nielsen, Rasmus; Gilbert, M. Thomas P.; Esteves, Pedro J.; Ferrand, Nuno; Jiggins, Francis M.

doi:10.1126/science.aau7285

Cited by 140 publications

(146 citation statements)

References 56 publications

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“…1). Moreover, we found that allele reuse (repeated selection of the same haplotype, shared either via gene flow or from standing genetic variation) frequently underlies parallel adaptation between closely related lineages [29][30][31][32] , while parallelism from de-novo mutations dominates between distantly related taxa 13 . This suggests that the degree of allele reuse may be the primary mechanism behind the hypothesized divergence-dependency of parallel genome evolution, possibly reflecting either genetic (weak hybridization barriers, widespread ancestral polymorphism between closely related lineages 33 ) or ecological reasons (lower niche differentiation and geographical proximity 34,35 ).…”

Section: Introductionmentioning

confidence: 93%

Genomic basis of parallel adaptation varies with divergence inArabidopsisand its relatives

Bohutínská

Vlček

Yair

et al. 2020

Preprint

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Understanding the predictability of evolutionary change is of major importance in biology.Parallel adaptation provides unique insights through replicated natural experiments, yet mechanisms governing the ample variation in genomic parallelism remain unknown. Here, we investigate them using multi-scale genomic analyses of parallel evolution across populations, species and genera. By resequencing genomes of seven independent alpine lineages from two Arabidopsis species, we found that the degree of gene reuse decreases with increasing divergence between lineages. This relationship is well predicted by decreasing frequency of allele reuse, suggesting that availability of preexisting genetic variation is the prime mechanism. A meta-analysis demonstrated that the relationship further continues within the Brassicaceae family. Thus, we found empirical support for a longstanding hypothesis that the genetic basis of adaptive evolution is more predictable in closely related lineages while it becomes more contingent over larger evolutionary distances.

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Section: Introductionmentioning

confidence: 93%

Genomic basis of parallel adaptation varies with divergence inArabidopsisand its relatives

Bohutínská

Vlček

Yair

et al. 2020

Preprint

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“…; Alves et al. ). Previous research has shown that the correlation between selection coefficients of a given allele in each of two populations inhabiting different environments is expected to increase with the similarity in the direction of selection (eq.…”

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confidence: 98%

Parallel genetic evolution and speciation from standing variation

2019

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Adaptation often proceeds from standing variation, and natural selection acting on pairs of populations is a quantitative continuum ranging from parallel to divergent. Yet, it is unclear how the extent of parallel genetic evolution during adaptation from standing variation is affected by the difference in the direction of selection between populations. Nor is it clear whether the availability of standing variation for adaptation affects progress toward speciation in a manner that depends on the difference in the direction of selection. We conducted a theoretical study investigating these questions and have two primary findings. First, the extent of parallel genetic evolution between two populations rapidly declines as selection changes from fully parallel toward divergent, and this decline is steeper in organisms with more traits (i.e., greater dimensionality). This rapid decline happens because small differences in the direction of selection greatly reduce the fraction of alleles that are beneficial in both populations. For example, populations adapting to optima separated by an angle of 33° might have only 50% of potentially beneficial alleles in common. Second, relative to when adaptation is from only new mutation, adaptation from standing variation improves hybrid fitness under parallel selection and reduces hybrid fitness under divergent selection. Under parallel selection, genetic parallelism from standing variation reduces the phenotypic segregation variance in hybrids, thereby increasing mean fitness in the parental environment. Under divergent selection, larger pleiotropic effects of alleles fixed from standing variation cause maladaptive transgressive phenotypes when combined in hybrids. Adaptation from standing genetic variation therefore slows progress toward speciation under parallel selection and facilitates progress toward speciation under divergent selection.

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“…Several viruses, including cytomegalovirus 70 and herpesvirus 71 manipulated the CD200-CD200R pathway as a means of immune evasion. Interestingly, in one of the longest running and most in-depth studies of host-pathogen coevolution, CD200R was shown to be under selection in rabbits in response to myxoma virus biocontrol agent 72 . As DFT1 and DFT2 have been circulating in devils for more than 20 years and 5 years, respectively, it will be important to monitor CD200/R expression and the potential evolution of paired activating and inhibitory receptors in these natural disease models 73 .…”

Section: Discussionmentioning

confidence: 99%

A novel system to map protein interactions reveals evolutionarily conserved immune evasion pathways on transmissible cancers

Flies

Darby

Lennard

et al. 2019

Preprint

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Immune checkpoint immunotherapy has revolutionized medicine, but translational success for new treatments remains low. Around 40% of humans and Tasmanian devils (Sarcophilus harrisii) develop cancer in their lifetime, compared to less than 10% for most species. Additionally, devils are affected by two of the three known transmissible cancers in mammals. Unfortunately, little is known about of immune checkpoints in devils and other non-model species, largely due to a lack of species-specific reagents. We developed a simple cut-and-paste reagent development method applicable to any vertebrate species and show that immune checkpoint interactions are conserved across 160 million years of evolution. The inhibitory checkpoint molecule CD200 is highly expressed on devil facial tumor cells. We are the first to demonstrate that co-expression of CD200R1 can block CD200 expression. The evolutionarily conserved pathways suggest that naturally occurring cancers in devils and other species can serve as models for understanding cancer and immunological tolerance.GRAPHICAL ABSTRACT

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Parallel adaptation of rabbit populations to myxoma virus

Cited by 140 publications

References 56 publications

Genomic basis of parallel adaptation varies with divergence inArabidopsisand its relatives

Genomic basis of parallel adaptation varies with divergence inArabidopsisand its relatives

Parallel genetic evolution and speciation from standing variation

A novel system to map protein interactions reveals evolutionarily conserved immune evasion pathways on transmissible cancers

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