Editing Brown rat (section)

== Evolution ==
Brown rats’ ancestors diverged from the black rat lineage approximately 2.9 million years ago.<ref>{{Cite journal |last1=Robins |first1=Judith H. |last2=McLenachan |first2=Patricia A. |last3=Phillips |first3=Matthew J. |last4=Craig |first4=Lauren |last5=Ross |first5=Howard A. |last6=Matisoo-Smith |first6=Elizabeth |date=November 2008 |title=Dating of divergences within the Rattus genus phylogeny using whole mitochondrial genomes |url=https://linkinghub.elsevier.com/retrieve/pii/S1055790308003837 |journal=Molecular Phylogenetics and Evolution |language=en |volume=49 |issue=2 |pages=460–466 |doi=10.1016/j.ympev.2008.08.001|pmid=18725306 |bibcode=2008MolPE..49..460R }}</ref>  Evidence collected from mitochondrial genomes suggests that they emerged as a separate species anywhere from 0.5 to 2.9 million years ago.<ref>{{Cite journal |last1=Song |first1=Ying |last2=Lan |first2=Zhenjiang |last3=Kohn |first3=Michael H. |date=2014-02-28 |editor-last=Janke |editor-first=Axel |title=Mitochondrial DNA Phylogeography of the Norway Rat |journal=PLOS ONE |language=en |volume=9 |issue=2 |pages=e88425 |doi=10.1371/journal.pone.0088425 |doi-access=free |pmid=24586325 |pmc=3938417 |bibcode=2014PLoSO...988425S |issn=1932-6203}}</ref> Brown rats have two sister species within the ''norvegicus'' group. The [[Himalayan field rat]] (''Rattus nitidus'') has recently been identified as closely related, with mitochondrial DNA suggesting divergence around 700 thousand years ago.<ref>{{Cite journal |last1=Wei |first1=Haixue |last2=Li |first2=Fengjun |last3=Wang |first3=Xuming |last4=Wang |first4=Qiong |last5=Chen |first5=Guiying |last6=Zong |first6=Hao |last7=Chen |first7=Shunde |date=April 2017 |title=The characterization of complete mitochondrial genome and phylogenetic relationship within Rattus genus (Rodentia: Muridae) |url=https://linkinghub.elsevier.com/retrieve/pii/S0305197817300121 |journal=Biochemical Systematics and Ecology |language=en |volume=71 |pages=179–186 |doi=10.1016/j.bse.2017.01.012|bibcode=2017BioSE..71..179W }}</ref> However, genetic intermixing between these species is believed to have continued after this separation.<ref name=":9">{{Cite journal |last1=Teng |first1=Huajing |last2=Zhang |first2=Yaohua |last3=Shi |first3=Chengmin |last4=Mao |first4=Fengbiao |last5=Cai |first5=Wanshi |last6=Lu |first6=Liang |last7=Zhao |first7=Fangqing |last8=Sun |first8=Zhongsheng |last9=Zhang |first9=Jianxu |date=2017-09-01 |title=Population Genomics Reveals Speciation and Introgression between Brown Norway Rats and Their Sibling Species |url=https://academic.oup.com/mbe/article/34/9/2214/3804551 |journal=Molecular Biology and Evolution |language=en |volume=34 |issue=9 |pages=2214–2228 |doi=10.1093/molbev/msx157 |issn=0737-4038|pmc=5850741 }}</ref> Re-encounters between Himalayan and brown rat populations led to the [[introgression]] of genes from the former into the latter. This allowed for adaptations in olfactory receptors to be spread to brown rats.<ref name=":9" /> Another sister species, the [[Turkestan rat]], has been found close to the brown rat’s ancestral range in Nepal.<ref>{{Cite web |title=Rattus pyctoris • Himalayan Rat |url=https://www.mammaldiversity.org/taxon/1003657/ |access-date=2025-05-08 |website=www.mammaldiversity.org}}</ref> No such cases of genetic mixing between Turkestan and brown rats have been documented thus far. 

=== Adaptations in Laboratory Populations ===
{{main|Laboratory rat}}
Brown rats’ interactions with human environments have resulted in a number of identifiable changes in traits. This is especially well documented in laboratory rats. Despite significant levels of inbreeding through [[Selective breeding|artificial selection]], domesticated laboratory rats maintain higher genetic diversity than [[Laboratory mouse|laboratory mice]].<ref>{{Cite journal |last=Canzian |first=F |date=March 1997 |title=Phylogenetics of the laboratory rat Rattus norvegicus. |url=http://genome.cshlp.org/lookup/doi/10.1101/gr.7.3.262 |journal=Genome Research |language=en |volume=7 |issue=3 |pages=262–267 |doi=10.1101/gr.7.3.262 |pmid=9074929 |issn=1088-9051|doi-access=free }}</ref> [[Population structure (genetics)|Population structure]] among strains of domesticated rats is so powerful that distinctions are detectable between rats bred in different rooms of the same facilities.<ref>{{Cite journal |last1=Gileta |first1=Alexander F. |last2=Fitzpatrick |first2=Christopher J. |last3=Chitre |first3=Apurva S. |last4=St. Pierre |first4=Celine L. |last5=Joyce |first5=Elizabeth V. |last6=Maguire |first6=Rachael J. |last7=McLeod |first7=Africa M. |last8=Gonzales |first8=Natalia M. |last9=Williams |first9=April E. |last10=Morrow |first10=Jonathan D. |last11=Robinson |first11=Terry E. |last12=Flagel |first12=Shelly B. |last13=Palmer |first13=Abraham A. |date=2022-05-31 |editor-last=Kukekova |editor-first=Anna V. |title=Genetic characterization of outbred Sprague Dawley rats and utility for genome-wide association studies |journal=PLOS Genetics |language=en |volume=18 |issue=5 |pages=e1010234 |doi=10.1371/journal.pgen.1010234 |doi-access=free |pmid=35639796 |pmc=9187121 |issn=1553-7404}}</ref> The earliest evidence of differentiation from wild populations is the early proliferation of color variants among domesticated strains. This was documented in the 18th century in Japan and by the 19th century in Europe.<ref>{{Cite journal |last=Kuramoto |first=Takashi |date=2011 |title=Yoso-Tama-No-Kakehashi; The First Japanese Guidebook on Raising Rats |url=http://www.jstage.jst.go.jp/article/expanim/60/1/60_1_1/_article |journal=Experimental Animals |language=en |volume=60 |issue=1 |pages=1–6 |doi=10.1538/expanim.60.1 |pmid=21325747 |issn=1341-1357}}</ref><ref name="Hulme-Beaman" />

Today’s laboratory rats exhibit physical and behavioral adaptations. Rats bred for laboratory use develop smaller testes and have smaller neocortexes.<ref>{{Cite journal |last=Richter |first=Curt P. |date=January 1959 |title=Rats, man, and the welfare state. |url=https://doi.apa.org/doi/10.1037/h0043834 |journal=American Psychologist |language=en |volume=14 |issue=1 |pages=18–28 |doi=10.1037/h0043834 |issn=1935-990X}}</ref><ref>{{Cite journal |last1=Welniak-Kaminska |first1=Marlena |last2=Fiedorowicz |first2=Michal |last3=Orzel |first3=Jaroslaw |last4=Bogorodzki |first4=Piotr |last5=Modlinska |first5=Klaudia |last6=Stryjek |first6=Rafel |last7=Chrzanowska |first7=Anna |last8=Pisula |first8=Wojciech |last9=Grieb |first9=Pawel |date=April 11, 2019 |title=Volumes of brain structures in captive wild-type and laboratory rats: 7T magnetic resonance in vivo automatic atlas-based study |journal=PLOS ONE |volume=14 |issue=4 |pages=e0215348 |doi=10.1371/journal.pone.0215348 |doi-access=free |pmid=30973956 |bibcode=2019PLoSO..1415348W }}</ref> They struggle significantly more with digging and swimming than wild rats when placed under identical conditions.[17] This latter difference results in an aversion in domesticated rats that allows researchers to test memory using the [[Morris water navigation task|Morris water maze]].[19] Rats will recall an unseen platform’s location in a pool and swim to it to avoid swimming.  Other differences contribute to testing in more direct fashions; domesticated rats are able to learn faster and have lower resting levels of stress hormones.[19] On the other hand, laboratory rats’ increased agonistic behavior is less beneficial and not intentionally selected for.[19] A mixture of artificial selection and random variation through [[genetic drift]] is likely responsible for these differences. 

Unique adaptations have been observed in [[Albinism|albino]] strains of laboratory rats. Albinos have smaller [[Visual cortex|visual cortices]] and are less active during the day than their pigmented counterparts.<ref name=":10">{{Cite journal |last1=Stryjek |first1=Rafał |last2=Modlińska |first2=Klaudia |last3=Turlejski |first3=Krzysztof |last4=Pisula |first4=Wojciech |date=2013-06-07 |title=Circadian Rhythm of Outside-Nest Activity in Wild (WWCPS), Albino and Pigmented Laboratory Rats |journal=PLOS ONE |language=en |volume=8 |issue=6 |pages=e66055 |doi=10.1371/journal.pone.0066055 |doi-access=free |issn=1932-6203 |pmc=3676357 |pmid=23762462|bibcode=2013PLoSO...866055S }}</ref><ref name="Modlinska" /> Both of these adaptations are believed to be connected to their diminished visual acuity.

Differences between laboratory rats and wild populations have led to increasing concerns over the representativeness of psychological studies using inbred strains. Some researchers point to the effects of selective breeding on fear response and brain size as warping the results’ applicability to human fear mechanisms.<ref>{{Cite journal |last1=Stryjek |first1=Rafal |last2=Parsons |first2=Michael H. |last3=Fendt |first3=Markus |last4=Święcicki |first4=Jan |last5=Bębas |first5=Piotr |date=October 2021 |title=Let's get wild: A review of free-ranging rat assays as context-enriched supplements to traditional laboratory models |url=https://linkinghub.elsevier.com/retrieve/pii/S0165027021002387 |journal=Journal of Neuroscience Methods |language=en |volume=362 |pages=109303 |doi=10.1016/j.jneumeth.2021.109303|pmid=34352335 |doi-access=free }}</ref>

=== Adaptations in Wild Populations ===
Like laboratory strains, wild populations in human-occupied environments show significant genetic variation. Urban environments present substantial barriers to movement that may restrict brown rat populations to single city blocks.<ref>{{Cite journal |last1=Feng |first1=Alice Y. T. |last2=Himsworth |first2=Chelsea G. |date=March 2014 |title=The secret life of the city rat: a review of the ecology of urban Norway and black rats (Rattus norvegicus and Rattus rattus) |url=http://link.springer.com/10.1007/s11252-013-0305-4 |journal=Urban Ecosystems |language=en |volume=17 |issue=1 |pages=149–162 |doi=10.1007/s11252-013-0305-4 |bibcode=2014UrbEc..17..149F |issn=1083-8155}}</ref>  These lead to differentiated population structures between regions of the same city, as demonstrated in New York, Vancouver, and Salvador.<ref name="Combs" /> Roadways and districts with low levels of garbage were found to separate populations and restrict [[gene flow]] among groups.<ref name="Combs" />

Particular attention has been given to the adaptations found in the New York City population. New York rats have longer noses and shorter molar rows than the Chinese population; these are hypothesized to be adaptations to a colder climate and a diet including human food, respectively.<ref>{{Cite journal |last1=Puckett |first1=Emily E. |last2=Sherratt |first2=Emma |last3=Combs |first3=Matthew |last4=Carlen |first4=Elizabeth J. |last5=Harcourt-Smith |first5=William |last6=Munshi-South |first6=Jason |date=June 2020 |title=Variation in brown rat cranial shape shows directional selection over 120 years in New York City |journal=Ecology and Evolution |language=en |volume=10 |issue=11 |pages=4739–4748 |doi=10.1002/ece3.6228 |pmid=32551057 |pmc=7297766 |bibcode=2020EcoEv..10.4739P |issn=2045-7758}}</ref> Genetic markers also show differences in regions associated with the metabolism and diet of New York rats.<ref>{{Cite journal |last1=Harpak |first1=Arbel |last2=Garud |first2=Nandita |last3=Rosenberg |first3=Noah A |last4=Petrov |first4=Dmitri A |last5=Combs |first5=Matthew |last6=Pennings |first6=Pleuni S |last7=Munshi-South |first7=Jason |date=2021-01-07 |editor-last=Eyre-Walker |editor-first=Adam |title=Genetic Adaptation in New York City Rats |url=https://academic.oup.com/gbe/article/doi/10.1093/gbe/evaa247/5991490 |journal=Genome Biology and Evolution |language=en |volume=13 |issue=1 |doi=10.1093/gbe/evaa247 |pmid=33211096 |issn=1759-6653|pmc=7851592 }}</ref> However, metabolic differences have also been connected to migrating populations prior to relocation in urban settlements.<ref name=":9" /> Immune response changes from this period are suspected to have enabled the eventual domestication of brown rats in Europe.<ref name="Hulme-Beaman" />

Population [[Population bottleneck|bottlenecks]] are a significant source of adaptation. Such a bottleneck is theorized to have occurred 20,000 years ago in the ancestral Chinese population, and similar reductions due to founder effects have been observed as invasive populations spread to new areas.<ref>{{Cite journal |last1=Deinum |first1=Eva E. |last2=Halligan |first2=Daniel L. |last3=Ness |first3=Rob W. |last4=Zhang |first4=Yao-Hua |last5=Cong |first5=Lin |last6=Zhang |first6=Jian-Xu |last7=Keightley |first7=Peter D. |date=October 2015 |title=Recent Evolution in Rattus norvegicus Is Shaped by Declining Effective Population Size |url=https://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/msv126 |journal=Molecular Biology and Evolution |language=en |volume=32 |issue=10 |pages=2547–2558 |doi=10.1093/molbev/msv126 |pmid=26037536 |pmc=4576703 |issn=0737-4038}}</ref><ref name=":11">{{Cite journal |last1=Chen |first1=Yi |last2=Zhao |first2=Lei |last3=Teng |first3=Huajing |last4=Shi |first4=Chengmin |last5=Liu |first5=Quansheng |last6=Zhang |first6=Jianxu |last7=Zhang |first7=Yaohua |date=December 2021 |title=Population genomics reveal rapid genetic differentiation in a recently invasive population of Rattus norvegicus |journal=Frontiers in Zoology |language=en |volume=18 |issue=1 |page=6 |doi=10.1186/s12983-021-00387-z |doi-access=free |pmid=33499890 |pmc=7836188 |issn=1742-9994}}</ref> A notable recent instance of bottleneck-induced adaptation is the rise of rodenticide resistance among wild brown rats. Resistance to [[warfarin]] was discovered in urban populations in the mid-20th century, prompting the synthesis of new forms of rodenticide.<ref name=":11" /> Some populations in the United Kingdom have also been found to resist the second-generation rodenticides developed.<ref>{{Cite journal |last=Buckle |first=Alan |date=March 2013 |title=Anticoagulant resistance in the United Kingdom and a new guideline for the management of resistant infestations of Norway rats ( Rattus norvegicus Berk.) |url=https://onlinelibrary.wiley.com/doi/10.1002/ps.3309 |journal=Pest Management Science |language=en |volume=69 |issue=3 |pages=334–341 |doi=10.1002/ps.3309 |pmid=22730379 |issn=1526-498X}}</ref> Behavioral adaptations have also made effective rodenticide more difficult to provide; fear of new stimuli in wild populations has been linked to the widespread presence of rodenticide.<ref name="Combs" /> This fear is markedly reduced in domesticated populations.<ref name=":10" />