Highlight: Comparative Population Genomics—Answering Old Questions with New Data

0.13 MB·English

by  Casey McGrath

GBE
Highlight: Comparative Population Genomics—Answering
Old Questions with New Data
Casey McGrath *
*Correspondingauthor:E-mail:[email protected].
Accepted: 9 December 2021
Highlightseditor:GeorgeZhang
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Thefundamentalprinciplesofpopulationgenetics—including patternsofpurifyingselectionacrossapproximately40species fro
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theroleofmutation,selection,migration,andgeneticdrift— prevalent in the human gut microbiome, identifying func- h
were established by evolutionary biologists such as Sewall tional categories that may be under more or less constraint ttp
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Wright, J. B. S. Haldane, and Ronald Fisher in the first few inthemicrobiome. ://a
decadesofthe20thcentury.Nearlyacenturylater,thefield The second review article discusses the link between the ca
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of population genomics leverages advances in genome se- newer field of comparative population genomics and the em
quencing,datastorage,andbioinformaticstodissectthein- muchmoreestablishedfieldofphylogeography.Inaninter- ic
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fluenceofthesepopulation-levelforcesatagenomicscale.At national partnership, Scott Edwards at Harvard University up
a higher level, comparative population genomics is now a teamed up with collaborators from India, Portugal, and .co
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growingfieldofstudythatinvolvesinvestigatingtheseforces Australia to review the history of comparative phylogeogra- /g
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at various taxonomic scales—frompopulationstospeciesor phy and its intersection with population genomics (Edwards e
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evenmoredistantgroups—tounderstandthedifferencesand etal.2022).Theauthorsarguethat“comparativephylogeog- rtic
commonalitiesinthesepatternsacrosslineages.Theseques- raphyoffersanimportantperspectiveonevolutionaryhistory le
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tions/topics are addressed in the Special Section titled thatsucceedsinintegratinggenomicswithlandscapeevolu- 4/1
“ComparativePopulationGenomics”andcompiledbyguest tioninwaysthatcomplementthesuprageographicperspec- /e
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editors Tim Sackton, Director of Bioinformatics at Harvard tiveofcomparativepopulationgenomics.” b
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University, and Russell Corbett-Detig, Assistant Professor of In addition to the above reviews, Sackton and Corbett- 78
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Biomolecular Engineering at the University of California Detig “wanted to highlight some of the emerging areas of 4
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SantaCruz. research that comparative population genetic data enables, 83
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AccordingtoSackton,thisSpecialSectionhasbeeninthe especiallyasitbecomeseasierandeasiertogeneratepopu- 0
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worksforoverayear.HeandCorbett-Detigoriginallyorga- lationvariationdatasetsfrommanyspecies.”Forexample,a y g
nizedasymposiumonComparativePopulationGenomicsfor studyincludedintheSpecialSectionbyGoldbergandHarris ue
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the2020SocietyforMolecularBiologyandEvolution(SMBE) (2022)fromtheUniversityofWashingtonlooksatmutational t o
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meeting that was canceled due to the coronavirus disease signaturesfromacrossthegreatapephylogeny.Usingwhole- 0
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2019pandemic.Sacktonnotesthat,withtheencouragement genome variation data from 88 great apes, Goldberg and F
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ofEditor-in-ChiefsAdamEyre-WalkerandLauraA.Katz,“we Harrisfindthatmutationspectrumevolutionislargelydriven bru
thoughtthataspecialsectionofGBEwouldbeagoodformat by“trans-actingmutationalmodifiersthataffectmutagenesis ary
tohighlightsomeoftheresearchinthisemergingfieldthat acrossthewholegenomefairlyuniformly.” 20
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wasnotabletobepresented”duetothecancelation. In another study, again led by Scott Edwards, a team in- 2
TheSpecialSectionincludestworeviewarticlesthathelpto vestigated cryptic speciation and adaptive divergence in
put the emerging fieldof comparative populationgenomics Bicknell’s and gray-cheeked thrushes (Termignoni-Garcia
into context. A review by Shoemaker et al. (2022) at the etal.2022).Thesetwobirdspeciesaredifficulttodistinguish
UniversityofCaliforniaLosAngeleshighlightsrecentfindings innature,exhibitingonlyminordifferencesinsongandcol-
from the human gut microbiome, “a system with unparal- oration.Usingnewlyassembledreferencegenomesforeach
leledpotentialforcomparativepopulationgenomicsstudies” speciesaswellassequencedpopulationsamples,Termignoni-
accordingtotheauthors.Thearticleincludesareanalysisof Garciaandcolleaguesconfirmthegeneticdifferentiationand
(cid:2)TheAuthor(s)2022.PublishedbyOxfordUniversityPressonbehalfoftheSocietyforMolecularBiologyandEvolution.
ThisisanOpenAccessarticledistributedunderthetermsoftheCreativeCommonsAttributionLicense(https://creativecommons.org/licenses/by/4.0/),whichpermitsunrestrictedreuse,
distribution,andreproductioninanymedium,providedtheoriginalworkisproperlycited.
GenomeBiol.Evol.14(1) https://doi.org/10.1093/gbe/evab278 1
GBE
McGrath
lowgeneflowbetweenthetwospecies,whilealsosuggest- highlighting the emerging power of comparative analysis of
ingamorerecentsplitbetweenthetwolineagesthanwhat multispeciespopulationvariationdatasetswillstimulatenew
had been previously inferred. The researchers also identify ideasinthefieldandencourageagrowingemphasisonmulti-
potential mechanisms driving and/or reinforcing this diver- speciescomparisonsinpopulationgenetics.”
gence, including transposable element proliferation, rapid
evolutionoftheZ-chromosome,andpositiveselectionacting
LiteratureCited
ongenesinvolvedinneuronalprocessesinBicknell’sthrush.
ChenJ,BataillonT,Gl(cid:2)eminS,LascouxM.2022.Huntingforbeneficial
GuesteditorsSacktonandCorbett-Detigalsosoughttohigh-
mutations:conditioningonSIFTscoreswhenestimatingthedistribu-
lightnewapproachesforanalyzingcomparativepopulationge-
tionoffitnesseffectofnewmutations.GenomeBiolEvol.evab151.
nomicdatasetsintheSpecialSection.Amultinationalteamof doi:10.1093/gbe/evab151.
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researchersfromChina,Denmark,France,andSwedenledby EdwardsSV,RobinV,FerrandN,MoritzC.2022.Theevolutionofcom- o
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Martin Lascoux investigates how the distribution of fitness parativephylogeography:puttingthegeography(andmore)intocom- nlo
parative population genomics. Genome Biol Evol. evab176. a
effects(DFE)ofnewmutations,akeyparameterofmolecular d
doi:10.1093/gbe/evab176. e
evolution(Chenetal.2022)variesaccordingtohowconserved GoldbergME,HarrisK.2022.Mutationalsignaturesofreplicationtiming d fro
thesiteisinotherspecies.ThiscanhelptocharacterizetheDFE andepigeneticmodificationpersistthroughtheglobaldivergenceof m
ofbeneficialmutations,aparameterthatisnotoriouslydifficult mutationspectraacrossthegreatapephylogeny.GenomeBiolEvol. http
toestimateduetotherarityofthesetypesofmutations. evab104.doi:10.1093/gbe/evab104. s
Together,thearticlesintheSpecialSectionhighlightnew ShoemakerWR,ChenD,GarudNR.2022.Comparativepopulationge- ://ac
netics in the human gut microbiome. Genome Biol Evol. evab116. a
findings,aswell as new approaches and avenues for explo- d
doi:10.1093/gbe/evab116. e
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rationincomparativepopulationgenomics.Inaddition,they Termignoni-Garcia F, Kirchman JJ, Clark J, Edwards SV. 2022. ic
showhowtheseapproachescanbeusedtolinkthisemerging Comparativepopulationgenomicsofcrypticspeciationandadaptive .ou
field to older disciplines that have historically relied on data divergenceinBicknell’sandGray-CheekedThrushes(Aves:Catharus p.c
frommorelimitedmarkers.AccordingtoSackton,thiswasa bicknelliandC.minimus).GenomeBiolEvol.evab255.doi:10.1093/ om
gbe/evab255. /g
major motivation behind the Special Section: “I hope that b
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2 GenomeBiol.Evol.14(1) https://doi.org/10.1093/gbe/evab278