Population genomics of rapid adaptation by soft selective sweeps

Messer, Philipp W.; Petrov, Dmitri A.

doi:10.1016/j.tree.2013.08.003

Cited by 495 publications

(599 citation statements)

References 97 publications

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“…Another alternative is fixation by selection through a process analogous to soft sweeps. As often reported in mammalian genome analyses 77 , multiple alleles at a locus can be swept to fixation in a 'soft' event that evades detection by ordinary criteria. In our example, tandem CNVs among individuals would comprise the alternative (exploratory) 'allelic' states, perhaps maintained in populations by balancing selection 75 .…”

Section: Candidate Gene Adaptation Correlates With Environmentmentioning

confidence: 96%

Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

Salojärvi¹,

Smolander²,

Nieminen³

et al. 2017

Nat Genet

246

253

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Forest ecosystems maintain a large share of Northern Hemisphere biodiversity. Boreal forests comprise roughly 30% of global forest area 1 and contain the highest tree density among climate zones 2 . Moreover, boreal regions are undergoing extensive climate change. Annual temperature increases exceeding 1.5 °C are projected to result in a warming of 4-11 °C by the end of this century, with little concomitant increase in precipitation 1 . At this pace, climate zones will shift northward at a greater speed than trees can migrate 3 . To understand how future populations of forest trees may respond to climate change, it is essential to uncover past and present signatures of molecular adaptation in their genomes. Silver birch, B. pendula, is a pioneer species in boreal forests of Eurasia. Flowering of the species can be artificially accelerated 4 , giving it an advantage over other tree species with published genome sequences (such as poplar 5 , spruce 6 , and pine 7 ) for the optimization of fiber and biomass production.Here we sequenced 150 birch individuals and assembled a B. pendula reference genome from a fourth-generation inbred line, resulting in a high-quality assembly of 435 Mb that was linked to chromosomes using a dense genetic map. We analyzed SNPs in the genomes of 80 birch individuals spanning most of the geographic range of B. pendula, as well as seven other members of Betulaceae. Population genomic analyses of these data provide insights into the deep-time evolution of the birch family and on recent natural selection acting on silver birch.Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch Silver birch (Betula pendula) is a pioneer boreal tree that can be induced to flower within 1 year. Its rapid life cycle, small (440-Mb) genome, and advanced germplasm resources make birch an attractive model for forest biotechnology. We assembled and chromosomally anchored the nuclear genome of an inbred B. pendula individual. Gene duplicates from the paleohexaploid event were enriched for transcriptional regulation, whereas tandem duplicates were overrepresented by environmental responses. Population resequencing of 80 individuals showed effective population size crashes at major points of climatic upheaval. Selective sweeps were enriched among polyploid duplicates encoding key developmental and physiological triggering functions, suggesting that local adaptation has tuned the timing of and cross-talk between fundamental plant processes. Variation around the tightlylinked light response genes PHYC and FRS10 correlated with latitude and longitude and temperature, and with precipitation for PHYC. Similar associations characterized the growth-promoting cytokinin response regulator ARR1, and the wood development genes KAK and MED5A.A full list of affiliations appears at the end of the paper.

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Section: Candidate Gene Adaptation Correlates With Environmentmentioning

confidence: 96%

Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

Salojärvi¹,

Smolander²,

Nieminen³

et al. 2017

Nat Genet

246

253

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“…It is becoming increasingly clear that classic hard selective sweeps (where a new advantageous mutation arises and spreads quickly to fixation, causing large reductions in genetic diversity in its vicinity due to hitchhiking effects) are relatively rare in natural populations of species surveyed so far (Pritchard et al, 2010;Messer and Petrov, 2013). Instead, adaptation often happens through minor shifts in allele frequency at many loci (polygenic selection) or through soft selective sweeps in which multiple adaptive haplotypes sweep through the population simultaneously and the effects on linked genetic variation are less pronounced than under hard sweeps (Hermisson and Pennings, 2005;Hancock et al, 2010;Pritchard et al, 2010).…”

Section: Complex Architecture and Mechanism Of Adaptationmentioning

confidence: 99%

Population Genomics of Marine Fishes: Next-Generation Prospects and Challenges

Hemmer‐Hansen

Therkildsen

Pujolar

2014

The Biological Bulletin

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“…of homozygosity are expected to be the more powerful methods applied to detect these signatures (Yi et al, 2010;Garud et al, 2013;Messer and Petrov, 2013).…”

Section: Moving Towards An Autosomal and Paternal Marker-based Definimentioning

confidence: 99%

Mining the pig genome to investigate the domestication process

et al. 2014

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Pig domestication began around 9000 YBP in the Fertile Crescent and Far East, involving marked morphological and genetic changes that occurred in a relatively short window of time. Identifying the alleles that drove the behavioural and physiological transformation of wild boars into pigs through artificial selection constitutes a formidable challenge that can only be faced from an interdisciplinary perspective. Indeed, although basic facts regarding the demography of pig domestication and dispersal have been uncovered, the biological substrate of these processes remains enigmatic. Considerable hope has been placed on new approaches, based on next-generation sequencing, which allow whole-genome variation to be analyzed at the population level. In this review, we provide an outline of the current knowledge on pig domestication by considering both archaeological and genetic data. Moreover, we discuss several potential scenarios of genome evolution under the complex mixture of demography and selection forces at play during domestication. Finally, we highlight several technical and methodological approaches that may represent significant advances in resolving the conundrum of livestock domestication.

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Population genomics of rapid adaptation by soft selective sweeps

Cited by 495 publications

References 97 publications

Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

Population Genomics of Marine Fishes: Next-Generation Prospects and Challenges

Mining the pig genome to investigate the domestication process

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