The long and short of nuclear mitochondrial DNA (Numt) lineages

Se~~er,.ll t~;cvil: ~il.iiici I’IWP tICSif bed I,, t~~&:~‘i:lti,il DI’$\ trar-spostitons into the nuclrus of vart~ds antmals, or ‘Numt.DW1 I. Ihe TKE review by D-X. Zhailg and ci. l-tewitt’ gave a lttnely focus on the incltiston of Numt-DNA in evolutionary studies. Still, Tao aspects oi Numb-DNA warrant greater scrutiny: use of Nt.mt-DNA as (1) ‘o~tgrottps’ and as (2) ‘molecular fossils’. Use of t\umr-DNA sequences as serendtpitous 0utgiOups tn prtylogenetic dnalyses makes good sense. bacau$je N~tnrl DNA may lepre%!tlt ilit! GIOSesI

transition:transverston ratios in pairwise comparisons of mtDNA sequences suggest the tncluston of ‘heretical‘ mtDNA copies-’ :, and (3) before embarktng on experisive sequenctng projects. restrtction dtgesttons on suspected lalbett visibly homogeneousi PCR products can be prrfortned to screen rapidly for point tmcta\ions between Numt and cytoplasmtc tmtDNAs.

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appeared etther long or short relative to cytoptasmic homologues. For example. the Numt 12SrRNA branch was longer than tts cytoptasmtc homologue. while the cytoplastntc ND2 gene dtsplayed a faster substttutton rate (due to more thtrd codon posttton changes). The latter resembles the irse oi cytopiasmtc D-loop sequences tn thp studv of huniali origin%’ and best embodtes the usage of Numt as a molecular ‘fosstl’. Such rate hfterogenetty will have the greatest effec: on phyiogcnettc reconstructtons whar lineages are long. owing t0 the p0tenttdl systemattr error in long branch attracttonh :I. Thus, to p0tt.a; ::!%z grectseiy Ihe dtfferent evoluttonary rates tdnd btological ctrcumstdncesj as~o~ta’.~O Kttll estranged mtDNA sequences. trees should he deptcted i.v:th b~anchcs proporbon,it IO ~nlrrrrd changes. Molecttl;lt fC~st1~;dlii.i i:, God~li~~~iltc ptoctss lhc crt(l_irtd hind metho for de!ectlng Numt DNA cornpIled tn Ref. 1 can be expanded: (1) stnce many anttnal mtt0ChOr~drtal genortles range from 15 to 20 kb 1J.v. Lopez. PhD Thesis. George Mason Untversttk. ‘j4. LISA. 19%). Stlmm!ng molecular weights of all miDi%A fragments after Southern hybridtzatton may Weal stgniftcant devtattons from expected genome stzes and possibly expose ‘background bands’. (2) Obsetvaiions of lower than expected

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than their n~ttocnondrtal homologues will have ttmtted usefulness tn outgroup anal; sis. The value of nuclear integrattons as outgroup:,- ltes in the tale they play in parttcutar situations. as did the human nuclear mitochondrtal D-loop-ltke sequence r the study of Ztschler et al.“. However. tf reliable outgroup sequences can be edstly bbtatned. as for many mttochondrial coding regtons. it tndy not be wse to employ the nuclear copies ~ndtscrtnitnately lust because they are there. Some knowledge of thetr tnolecular evolution and relationships to the ingroup is necessary. In any cdse, only closely related sister or parental taxa (noi the direct or tndtrect descendants) of the ingroup should be used as outgroups to root a phylogenetic tree. The additional methods and criteria gtvt?n b\ Loper rt a/.to check for rnuclear tntegrations are

Lopez ei di ptovtde a refreshtng vten 011iI:? so-called ‘molecular fossils’ the nuclear ntttochondrlal ltke sequences (abbre\taied a~, numtDNA) III antmats’ ?. They have shown that the retattve rate of ev0tutton of numtDNA versus thett mttochonclnal counterpdtls IS qutte dtfferen! from gene to gene tn the dotnesttc cat ‘. For example. a regtoti of the nuclear ND2 pseudogene evolves 510~1 than the cotrespondtng n~itoctrnt~dt~;ll srqucnct~. wlille the reverse 15 true for o potttnn 01 the 1% rRNA gene. It then appeals that even ttt mammats. nuclear mitochottdrtai pseudogenes do not all behave ttke ‘molecular fosstts’. The retattvely faster rate of evolution of some numtDNA seetns to be mainly due to Increased funcltonal constraints on the correspondtng mtONA regions slowing down evolutionary changes. These results have clear implications for the use of numtDNA as outgroups tn phylogenetic analyses. NumtDNA with a faster substitution rate

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