This essay reviews comparative studies of animal mitochondrial DNA (mtDNA), with emphasis on findings made and ideas developed at Berkeley. It argues that such studies are bringing together two previous paths of progress in evolutionary biology. One path is that of those who worked far above the species level and were concerned with genealogical trees, time scales and the accumulation of new mutations on surviving molecular lineages. The other path is that of those who worked at and below the species level and were concerned mainly with population structure, migration and the frequencies of alleles that existed in an ancestral population. This fusion of paths is made possible by the high rate at which mutations accumulate on mtDNA lineages and by this molecule's uniparental and apparently haploid mode of inheritance. These properties make mtDNA a superb tool for building trees and time scales relating molecular lineages at and below the species level. In addition, owing to its mode of inheritance, mtDNA is more sensitive to bottlenecks in population size and to population subdivision than are nuclear genes. Joint comparative studies of both mtDNA and nuclear DNA variability give us valuable insights into how effective population size has varied through time. Such studies also give insight into the conditions under which mtDNA from one species can colonize another species.

Mitochondrial DNA and two perspectives on evolutionary genetics

THE mouse H19 gene encodes one of the most abundant RNAs in the developing mouse embryo It is expressed at the blastocyst stage of development, and accumulates to high levels in tissues of endodermal and mesodermal origin (H Kim, unpublished result) After birth the gene is expressed in all tissues except skeletal muscle It lacks a common open reading frame in the 25-kilobase RNA, but has considerable nucleotide sequence similarity between the genes of rodents and humans Expression of the gene in transgenic mice results in late prenatal lethality, suggesting that the dosage of its gene product is strictly controlled The H19 gene maps to the distal segment of mouse chromosome 7, in a region that is parentally imprinted, a process by which genes are differentially expressed on the maternal and paternal chromosomes We have now used an RNase protection assay that can distinguish between H19 alleles in four subspecies of Mus, to demonstrate that the H19 gene is parentally imprinted, with the active copy derived from the mother This assay will be of general use in assaying allele-specific gene expression

Parental imprinting of the mouse H19 gene.

The evolutionary significance of genetic diversity of proteins in nature remains controversial despite the numerous protein studies conducted electrophoretically during the last two decades. Ironically, the discovery of extensive protein polymorphisms in nature (reviewed by Lewontin, 1974; Powell, 1975; Selander, 1976; Nevo 1978, 1983b; Hamrick et al., 1979; Nelson and Hedgecock, 1980), did not resolve the disagreement between the die ho torn ou s explanatory models of selection (e.g., Ayala, 1977; Milkman, 1978; Clarke, 1979; Wills, 1981) versus neutrality (Kimura, 1968; Kimura and Chta, 1971; Nei, 1975; and modifications in Kimura, 1979atb). The more general problem of the relative importance of the evolutionary forces interacting in genetic population differentiation at the molecular levels of proteins and DNA, i.e., mutation, migration, natural selection and genetic drift, remains now as enigmatic as ever.

The Evolutionary Significance of Genetic Diversity: Ecological, Demographic and Life History Correlates

Theory and Methods: An Idiosyncratic History of Early Morphometrics R.A. Reyment. Multivariate Allometry C.P. Klingenberg. Data Acquisition: Introduction to Data Acquisition L.F. Marcus. Three-dimensional Data Capture and Acquisition D. Dean. Two-dimensional Imaging: An Update A. GarciaValdecasas. Imagina: A Direct Tool for Image Analysis in Systematics J.M. Becerra. Landmark Methods: Introduction to Landmark Methods D. Slice. Morphometric Spaces, Shape Components and the Effects of Linear Transformations F.J. Rohlf. Combining the Tools of Geometric Morphometrics F.L. Bookstein. Standard Formula for the Uniform Shape Component in Landmark Data F.L. Bookstein. Affine Transformations as a Modelof Virtual Form Change for Generating Morphospaces D. Russkin-Gutman, A.D. Buscalioni. Outlines: With and without Landmarks: Introduction to Outlines F.J. Rohlf. Eigenshape Analysis of Left Ventricular Outlines from Contrast Ventriculograms P.D. Sampson, et al. Chisquare Test of Biological Space Curve Affinities D. Dean, et al. Comparing Shapes of Organisms: Geographic Comparisons: Introduction to Geometric Morphometrics and Intraspecific Variation: A Fascinating Adventure A. Loy. Fluctuating Asymmetry in Mus musculus Subspecific Hybridization: Traditional and Procrustes Comparative Approach J.C. Auffray, et al. Wing Venation Variability in Monarthropalpus buxi (Diptera, Cecidomyiidae) and the Quaternary Coevolution of Box (Buxus sempervirens L.) and Its Midge: A Geometrical Morphometric Analysis M. Baylac, T. Daufresne. Size and Shape Variation in the Mandible of the Fossorial Rodent Spalax ehrenbergi: A Procrustes Analysis of Three Dimensions M. Corti, et al. Principal Components of Body Shape Variation within an Endemic Radiation of Threespine Stickleback J. Walker. Low Taxonomic Level and Intraspecific Comparisons: Introduction to Comparison of Similar Objects Whose Group Identity Is Known M. Corti. Identification of House Mice Musmusculus, and Mound Building Mice, M. spicilegus, Based on Distance and Landmark Data A. Demeter et al. Correspondence between Interlandmark Distances and Caliper Measurements S. Reig. Some Applications of Geometric Morphometrics to Ostracoda R.A. Reyment. Shape Changes during the Growth of the Sea Bass, Dicentrarchus labrax (Teleostea: Perciformes), in Relation to Different Rearing Conditions: An Application of Thinplate Spline Regression Analysis A. Loy, et al. Higher Taxonomic Level Comparisons: Introduction to Comparisons amongTaxa at the Level of Species, Genus and Family G. Naylor. The Evolution and Growth of the Hominid Pelvis: A Preliminary Thinplate Spline Study of Ilium Shape C. Berge. Stephanodonty in Fossil Murids: A Landmark based Morphometric Approach J. van Dam. 16 additional articles. Appendixes. Index.

Advances in morphometrics

Genomic scans of multiple populations often reveal marker loci with greatly increased differentiation between populations. Often this differentiation coincides in space with contrasts in ecological factors, forming a genetic–environment association (GEA). GEAs imply a role for local adaptation, and so it is tempting to conclude that the strongly differentiated markers are themselves under ecologically based divergent selection, or are closely linked to loci under such selection. Here, we highlight an alternative and neglected explanation: intrinsic (i.e. environment-independent) pre- or post-zygotic genetic incompatibilities rather than local adaptation can be responsible for increased differentiation. Intrinsic genetic incompatibilities create endogenous barriers to gene flow, also known as tension zones, whose location can shift over time. However, tension zones have a tendency to become trapped by, and therefore to coincide with, exogenous barriers due to ecological selection. This coupling of endogenous and exogenous barriers can occur easily in spatially subdivided populations, even if the loci involved are unlinked. The result is that local adaptation explains where genetic breaks are positioned, but not necessarily their existence, which can be best explained by endogenous incompatibilities. More precisely, we show that (i) the coupling of endogenous and exogenous barriers can easily occur even when ecological selection is weak; (ii) when environmental heterogeneity is fine-grained, GEAs can emerge at incompatibility loci, but only locally, in places where habitats and gene pools are sufficiently intermingled to maintain linkage disequilibria between genetic incompatibilities, local-adaptation genes and neutral loci. Furthermore, the association between the locally adapted and intrinsically incompatible alleles (i.e. the sign of linkage disequilibrium between endogenous and exogenous loci) is arbitrary and can form in either direction. Reviewing results from the literature, we find that many predictions of our model are supported, including endogenous genetic barriers that coincide with environmental boundaries, local GEA in mosaic hybrid zones, and inverted or modified GEAs at distant locations. We argue that endogenous genetic barriers are often more likely than local adaptation to explain the majority of Fst-outlying loci observed in genome scan approaches – even when these are correlated to environmental variables. (Resume d'auteur)

The coupling hypothesis: why genome scans may fail to map local adaptation genes.

Thirteen biochemical groups of wild mice from Europe, Asia, and Africa belonging to the genus Mus are analyzed at 22–42 protein loci. Phylogenetic trees are proposed and patterns of biochemical evolution are discussed, as well as the possible contribution of wild mice to the genetic diversity of laboratory stocks.

Biochemical diversity and evolution in the genus Mus.

In this paper, we present data on murid rodents obtained by three major techniques used in biochemical systematics today: protein electrophoresis, scnDNA hybridization and mtDNA RFLP. The data have been analysed by both phenetic and cladistic methods and results of the three techniques were compared with one another. Four clear major levels of divergence (or nodes) can be recognized by all methods. Node 1 groups four subspecies of M. musculus (domesticus, bactrianus, castaneus and musculus). Node 2 groups four species: M. musculus, M. spretus, M. spicilegus and M. spretoides. Node 3 groups the stem of node 2 and three strictly Oriental species (M. caroli, M. cervicolor and M. cookii) Node 4 groups the previous lineages with Oriental Pyromys and Coelomys and the Ethiopian Nannomys. However, the relationships within each level cannot be resolved without ambiguity. We argue that this is not due to the resolutive power of our methods, but to a biological reality, that is successive adaptive radiations marked by quasi-simultaneous speciation events linked with geographical colonization. Our estimation of divergence time between different taxa showed that the genus Mus is very young. The youngest ‘bona fide’ species are 1.1 Myr old, or even less than 0.3 Myr if one takes into consideration the two sibling species M. spicilegus and M. spretoides. It appears that mtDNA evolves three to six times faster than scnDNA. The zoogeographical history of the genus can be reconstructed as a series of adaptative radiations leading to the present day distribution of the Palaearctic, Oriental, and Ethiopian groups of taxa.

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

This paper examines the relation between chromosomal and nuclear-gene divergence in 28 wild populations of the house mouse semi-species, Mus musculus domesticus, in Western Europe and North Africa. Besides describing the karyotypes of 15 of these populations and comparing them to those of 13 populations for which such information was already known, it reports the results of an electrophoretic survey of proteins encoded by 34 nuclear loci in all 28 populations. Karyotypic variation in this taxon involves only centric (or Robertsonian) fusions which often differ in arm combination and number between chromosomal races. The electrophoretic analysis showed that the amount of genic variation within Robertsonian (Rb) populations was similar to that for all-acrocentric populations, i.e. bearing the standard karyotype. Moreover, divergence between the two types of populations was extremely low. These results imply that centric fusions in mice have not modified either the level or the nature of genic variability. The genetic similarity between Rb and all-acrocentric populations is not attributed to the persistence of gene flow, since multiple fusions cause marked reproductive isolation. Rather, we attribute this extreme similarity to the very recent origin of chromosomal races in Europe. Furthermore, genic diversity measures suggest that geographically separated Rb populations have in situ and independent origins. Thus, Rb translocations are probably not unique events, but originated repeatedly. Two models are presented to explain how the rapid fixation of a series of chromosomal rearrangements can occur in a population without lowering variability in the nuclear genes. The first model assumes that chromosomal mutation rates are between 10(-3) and 10(-4) and that populations underwent a series of transient bottlenecks in which the effective population size did not fall below 35. In the second model, genic variability is restored following severe bottlenecks, through gene flow and recombination.

/pdf/genic-differentiation-and-origin-of-robertsonian-populations-2uc75btt7r.pdf

Genic differentiation and origin of Robertsonian populations of the house mouse (Mus musculus domesticus Rutty).

Self-fertilization depression of fitness in the freshwater hermaphroditic snail Bulinus globosus, an intermediate host of the parasitic trematode Schistosoma, has been studied in a strain originating from Niger. B. globosus is an outcrosser that can self-fertilize when isolated before any copulation has occurred. The self-fertilization depression has been estimated during two successive generations. In the first generation, selfing was compared to outcrossing. Within each mating system group, selfing and outcrossing were compared again in the second generation. A striking difference was shown in favor of cross-fertilization for the number of eggs laid, the survival at birth of young snails and the number of snails reaching sexual maturity. The overall self-fertilization depression is 0.920 after two generations of selfing. We discuss the relative role of selfing and outcrossing in the evolution of freshwater snail populations.

Self-fertilization versus cross-fertilization in the hermaphroditic freshwater snail bulinus globosus.

Populations of mice established outdoors as well as indoors have been investigated at 24 loci using starch gel electrophoresis. Two reproductively isolated groups are recognized, one of which is referable to a house mouse subspecies, Mus musculus brevirostris, and the other to a different species. Mus spretus, contrary to the view of Schwarz and Schwarz that only one species of Mus is present in the Mediterranean Basin. The genetic distance between these two groups is larger than between any pair of investigated subspecies of M. musculus. M. m. brevirostris is biochemically almost indistinguishable from M. m. domesticus. On the other hand, M. spretus exhibits several allelic variants unknown or at most very infrequent in M. musculus, as for instance at the lactate dehydrogenase B-chain locus.

Louis Thaler

Papers

Biochemical diversity and evolution in the genus Mus.

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

Genic differentiation and origin of Robertsonian populations of the house mouse (Mus musculus domesticus Rutty).

Self-fertilization versus cross-fertilization in the hermaphroditic freshwater snail bulinus globosus.

Evidence for the presence of two sympatric species of mice (genus mus l.) In southern france based on biochemical genetics.