Molecular phylogenies in the genus Mus: Comparative analysis of electrophoretic, scnDNA hybridization, and mtDNA RFLP data

She, Jin‐Xiong; Bonhomme, François; Boursot, Pierre; Thaler, L.; Catzeflis, François

doi:10.1111/j.1095-8312.1990.tb00823.x

Cited by 179 publications

(158 citation statements)

References 31 publications

(27 reference statements)

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“…There appears to be substantial geographic structure to the variation, as discussed in detail elsewhere (16 (23), these divergence estimates (3.7% and 11.7%, respectively) are similar to those obtained from the entire molecule based on restriction fragment length polymorphism data (4.3% and 10.0%6, respectively) (27). Table 2 summarizes the numbers of replacement and silent differences observed within and between species.…”

Section: Resultssupporting

confidence: 70%

Nonneutral evolution at the mitochondrial NADH dehydrogenase subunit 3 gene in mice.

Nachman

Boyer

Aquadro

1994

Proc. Natl. Acad. Sci. U.S.A.

139

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The neutral theory of molecular evolution asserts that while many mutations are deleterious and rapidly ellminated from populations, those that we observe as polymorphisms within populations are functionally equivalent to each other and thus neutral with respect to fitness. Mitochondrial DNA (mtDNA) is widely used as a genetic marker in evolutionary studies and is generally assumed to evolve according to a strictly neutral model of molecular evolution. One prediction of the neutral theory is that the ratio of replacement (nonsynonymous) to silent (synonymous) nucleotide substitutions will be the same within and between species. We To understand the genetic basis of evolutionary change, we must understand the extent to which selection governs the amount and distribution of genetic variation in natural populations. Considerable debate has centered on whether most naturally occurring genetic variants are strictly neutral (1), slightly deleterious (2), or advantageous (3). While these different views imply relatively small differences in selection coefficients, these differences can still have profound consequences for how molecular evolution occurs.The neutral theory, in its strictest form, asserts that while many mutations are strongly deleterious and therefore rapidly eliminated from populations, those that we observe within populations are equivalent with respect to fitness (1). The level of genetic variation within populations is determined by the neutral mutation rate and the effective population size. The amount of divergence between species is determined by the neutral mutation rate and the time since divergence. Under strict neutrality, the amount of variation within species is expected to be correlated with the rate of divergence between species for different genes or gene regions.A modification of the strictly neutral model, known as the nearly neutral or slightly deleterious model (2, 4), proposes that observed variants have a distribution of selective effects focused around neutrality. The extent to which these nearly neutral variants are affected by selection is a function of population size. Variants will behave as neutral if their effect on fitness is less than 1/2N in a diploid population of N individuals. Thus, in a large population, a larger fraction of nearly neutral mutations will be affected by selection. According to this model, the level of polymorphism within species and the rate ofdivergence between species depend on the population size.In addition to these two views, there are a variety ofmodels that describe how balancing selection can maintain variability within populations (e.g., ref. 5) and how directional selection can fix substitutions within populations (e.g., ref. 6).

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Section: Resultssupporting

confidence: 70%

Nonneutral evolution at the mitochondrial NADH dehydrogenase subunit 3 gene in mice.

Nachman

Boyer

Aquadro

1994

Proc. Natl. Acad. Sci. U.S.A.

139

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“…For example, in the European hybrid zone between M. m. musculus and M. m. domesticus (diverged 4700 000 generations ago; She et al, 1990) the transition of sex chromosomes is similar in width to M. arvalis (for example, o4 km) and mtDNA clines are also wider (for example, Dod et al, 1993;Raufaste et al, 2005;Macholan et al, 2007;. This is likely a consequence of Haldane's rule in place in the hybrid zone, which may-among other factors-prevent the mouse Y-chromosome cline width to increase (Britton-Davidian et al, 2005; but see Turner et al, 2012).…”

Section: Evidence For Selectionmentioning

confidence: 99%

Sex-specific clines support incipient speciation in a common European mammal

2013

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Hybrid zones provide excellent opportunities to study processes and mechanisms underlying reproductive isolation and speciation. Here we investigated sex-specific clines of molecular markers in hybrid zones of morphologically cryptic yet genetically highly-diverged evolutionary lineages of the European common vole (Microtus arvalis). We analyzed the position and width of four secondary contact zones along three independent transects in the region of the Alps using maternally (mitochondrial DNA) and paternally (Y-chromosome) inherited genetic markers. Given male-biased dispersal in the common vole, a selectively neutral secondary contact would show broader paternal marker clines than maternal ones. In a selective case, for example, involving a form of Haldane's rule, Y-chromosomal clines would not be expected to be broader than maternal markers because they are transmitted by the heterogametic sex and thus gene flow would be restricted. Consistent with the selective case, paternal clines were significantly narrower or at most equal in width to maternal clines in all contact zones. In addition, analyses using maximum likelihood cline-fitting detected a shift of paternal relative to maternal clines in three of four contact zones. These patterns suggest that processes at the contact zones in the common vole are not selectively neutral, and that partial reproductive isolation is already established between these evolutionary lineages. We conclude that hybrid zone movement, sexual selection and/or genetic incompatibilities are likely associated with an unusual unidirectional manifestation of Haldane's rule in this common European mammal.

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“…DNA/DNA hybridization and allozyme data have been useful (Catzeflis et aL, 1987;She et al, 1990), but lack the resolution necessary to determine conclusively a phylogeny in closely related rodent species.…”

Section: Rodent Phylogenymentioning

confidence: 99%

“…The phylogenetic relationships of some or all of the eight rodent species used in this paper have been studied using morphological (Marshall, 1986), DNA/DNA hybridization (She et al 1990), electrophoretic data (She et al, 1990), mtDNA (Ferris et al, 1983;She et a!., 1990), Ig heavy chain (Morgado et al, 1993), Y chromosome repetitive elements (Nishioka et a!., 1994) and the Siy locus (Lundrigan & Tucker, 1994 The existence of an accurate molecular clock, although desirable, cannot be assumed to exist in all genes and regions of the genome. There are many different mutational and selective forces acting on the sequences that depend on a multitude of factors such as the sequence itself and the sequence context.…”

Section: Rodent Phylogenymentioning

confidence: 99%

“…For these reasons we have sequenced the APRT gene of five closely related rodent species and analysed these sequences along with three other rodent APRTs available from GenBank. These species range in divergence times from an estimated 1-3 MYA between the two closest species (M spicilegus and M musculus) up to 16-46 MYA between the most divergent species (M spicilegus and Mesocricetus auratus) (She et al, 1990;O'hUigin & Li, 1992;Hammer & Silver, 1993). This provides sequences having from 1 to 12 per cent nucleotide sequence divergence in the APRT coding region between the closest and most divergent species, respectively, and up to 26 per cent sequence divergence in the intronic regions.…”

Section: Introductionmentioning

confidence: 99%

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Substitution rate variation in closely related rodent species

Fieldhouse

Yazdani

1997

Heredity

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The existence of evolutionary rate variation has previously been demonstrated between different orders, different species and even between different regions of the same gene. To examine rate variation between closely related species of rodents we have sequenced the adenine phosphorybosyltransferase (APRT) gene from Mus spicilegus, Mus pahari, Mastomys hildebrandtii, Stochomys longicaudatus and Gerbillus campestris and compared these sequences with the previously published Mus musculus, Rattus norvegicus and Mesocricetus auratus APRT sequences. The alignment of these eight rodent APRT sequences reveals two large insertions within the introns: an insertion with sequence similar to a Bi repetitive element is found within Mastomys and an insertion with sequence similar to a B2 repetitive element is found within M. pahari. A phylogeny for the rodent APRTs agrees with the previously published rodent phylogeny based on other molecular and morphological data. The relative rate test which is often used to test for variation in rates of evolution in different lineages is shown here to be sensitive to the choice of outgroup and therefore should be used with great caution. This sensitivity is detectable only with closely related species and results from the prevalence of homoplastic substitutions. Rate variation is demonstrated within the APRT exons and introns and between the rodent species (with the most significant difference being a rate difference in M. spicilegus). In addition, some third codon positions are shown to be more prone to substitution than others. This clearly demonstrates that even between very closely related species there is ample evidence of major differences in rates of evolution among species, among regions of the gene and among different positions within the gene. We also demonstrate that standard methods of analysis might not detect this variation.

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Molecular phylogenies in the genus Mus: Comparative analysis of electrophoretic, scnDNA hybridization, and mtDNA RFLP data

Cited by 179 publications

References 31 publications

Nonneutral evolution at the mitochondrial NADH dehydrogenase subunit 3 gene in mice.

Nonneutral evolution at the mitochondrial NADH dehydrogenase subunit 3 gene in mice.

Sex-specific clines support incipient speciation in a common European mammal

Substitution rate variation in closely related rodent species

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