Mitochondria and Evolution Research Paper

Sperm also contain mitochondria, but a chemical signal, tagging of sperm mitochondria with the protein ubiquitin, triggers its destruction. This MtDNA is eventually lost in the developing embryo, usually before the third embryonic cleavage (Sutovsky et al. 1999). The maturing embryo thus contains a mixture of both parent’s nuclear genes, but generally inherits only the mitochondrial genes of its mother.

1. Heteroplasmy Complicates Simple Uniparental Inheritance of MtDNA

Paternal transmission of MtDNA in most vertebrates is thus a rare event, mostly confined to interspecific crosses, and can be one source of the condition known as genetic heteroplasmy. A heteroplasmic individual is a genetic chimera and contains multiple MtDNA sequences. As a consequence, in species with high heteroplasmy, molecular taxonomies based on only MtDNA markers become unreliable. Instead of following a simple maternal gene genealogy, the population genetics of MtDNA transmission in heteroplasmic species can become difficult to follow.

The probability of transmission of any particular genotype in heteroplasmic taxa requires knowing the frequency of different genotypes in the sex cells of parents involved in any particular mating. Offspring from the same parents can even differ in the proportions of mixed genotypes they inherit under these circumstances, and cases illustrating this problem are known in domestic cattle herds, bovine interspecies crosses, murine hybrids, humans with complex metabolic disorders, or those babies produced as a result of fertilization assisted by spermatid or sperm microinjection (Kaneda et al. 1995, Sutovsky et al. 1999).

A second source of individual heteroplasmy is the rapid fixation of MtDNA mutations, which can result in both sequence and length differences in the mitochondrial genome within the same individual. Unlike the first case, heteroplasmy of this nature will have fewer long-term evolutionary consequences, if germline cells are unaffected. As an individual ages, mutations often accumulate in the MtDNA of somatic cells. Since differentiated cells may divide infrequently, especially if damaged; a given organ can eventually become a mixture of different MtDNA genotypes. Recombinational repair of mutations, demonstrated in vitro using rat liver mitochondrial protein extracts may counteract this (Thyagarajan et al. 1996), but the lack of nucleotide excision repair activity may limit the replication of heavily damaged MtDNA.

Mitochondria are known to be the accumulation site of highly reactive molecules and free oxygen radicals associated with ATP production during metabolic activity. A lively debate surrounds the question of whether or not MtDNA damage might be generally repaired by genetic recombination mechanisms. Evidence for mitochondrial genetic recombination is circumstantial in vertebrates and hinges on a more complete understanding of mutations at hypervariable regions within the organelle’s genome.

Recombination is known to occur in the MtDNA of numerous fungi, and MtDNA Pseudo-genes (nonfunctional MtDNA sequences) have been found transferred into the nuclear genome of most organisms studied. While mammalian mitochondria possess a recombinational DNA repair pathway, the same enzymes might not be associated with genetic recombination like in yeast. The mechanism(s) mediating the transfer of mitochondrial gene fragments into the nuclear genome are unknown at present.

1.1 Elevated MtDNA Mutation Rates Offer Opportunities

Maintenance of function often places such extreme constraints on biochemically essential pathways that mutations are incompatible with life. MtDNA contains sequences absolutely essential for producing a limited number of gene products involved in ATP synthesis (cytochrome oxidases, cytochromes, NADH dehydrogenases, and ATPases, along with specialized ribosomal and transfer rRNA elements, but they exist in high copy numbers and also contain regions within genes that are not under such tight functional constraints. MtDNA basically shows a 10-fold elevated mutation rate compared to nuclear DNAs of the same functional class (including ribosomal and transfer RNAs, and the protein coding regions).

Mitochondrial genomes as a group are specialized and streamlined, with fewer noncoding regions, compared to the numerous introns within genes in the nucleus. The noncoding regions retained by mitochondrial genomes are of interest to many evolutionary biologists, because they allow fairly personalized identification of maternal lineage groups in a nested, time-dependent fashion as new mutations rapidly accumulate on the old genetic backgrounds or haplotypes. The elevated mutation rate in noncoding MtDNA almost guarantees finding adequate polymorphism within populations such that individuals will possess unique DNA sequences. Only close maternal relatives (siblings with the same mother, maternal cousins, and maternal grandmothers) will likely carry the same MtDNA sequence.

The major noncoding region in MtDNA is commonly called the D-loop, a term borrowed from bacterial genetics and referring to a region that contains sequences for the initiation of DNA replication. Population studies within mammalian species often focus on the approximately 1,000 base-pair hyper-variable region, where substitution rates may be 10–100 times more than the average rate for the rest of the mitochondrial genome (considered about 2 percent sequence change per 1 million years of separation from the last common maternal ancestor). Mutations segregating in the noncoding regions can be used to examine sex-biased dispersal and sexual selection, the stability of specific demes contributing to biodiversity in refugia, demographic bottlenecks and founder events, as well as hybridization processes.

Local populations are often dominated by two or three MTDNA lineages that have diverged from a common ancestor less than 100,000 years ago. Mitochondrial and nuclear genetic systems such as Microsatellites, Y-chromosome markers, short tandem repeats (STRs), or variable number tandem repeats (VNTRs) may lead to different conclusions about the history of a given group. High levels of MtDNA lineage resolution may uncover unanticipated patterns of dispersal related to altered behavior within hybrid zones, previous instances of demographic catastrophes linked to environmental perturbations or disease epidemics, and also hitchhiking of nearly neutral hyper-variable MtDNA markers in linkage to coevolving haplotype sequences that convey some strong adaptive advantage to the population.

1.2 Other General Applications of Hypervariable MtDNA Markers

There are tens of thousands of individual mitochondrial sequences from different parts of the genome now reported in data banks, further evidence of the high mutation rate associated with these genes. Complete mitochondrial genomes are known for a variety of vertebrates and invertebrates, including organisms with poor taxonomic histories that are difficult to collect, breed, or maintain in a laboratory setting. Knowledge of some MtDNA sequences has stimulated the design strategy of degenerate Polymerase Chain Reaction (PCR) primers (Simon et al. 1994) that can be employed to study cryptic species, model the past population history of now-extinct organisms from museum specimens, and survey for biodiversity in barely studied ecosystems. Researchers also argue for the conservation of genetically distinct lineages with poorly differentiated morphologies but showing complex mating, foraging, or predator avoidance behaviors, tied to as yet unknown quantitative behavioral genes.

MtDNA mutations have also become important genetic markers in humans for clinical research on cancer, heart disease, neurodegenerative disorders, and other conditions. Affected populations of cells may take on distinct sets of mitochondrial substitutions at particular nucleotides after exposure to mutagens, other toxins in the environment, chemotherapy, radiation, or simple aging. Since MtDNA makes up 1–2 percent of all the DNA present in an animal’s cell, it is well suited to forensic and ancient population studies where only a few cell fragments survive.

2. Evolutionary Insights gained using MtDNA

Original enthusiasm expressed by some that the problem of speciation, Darwin’s ‘mystery of mysteries,’ would be eventually understood with molecular phylogenies based on mitochondrial markers has been tempered by the realization that even with a wellsupported MtDNA tree, species concepts, reproductive isolation, and morphological discontinuities will require broad-based research on behavioral and ecological fronts. No case perhaps illustrates this point more clearly than the continued debate over inclusion of Neanderthals in the direct line leading to modern humans. Two independent groups showed that the tree connecting the maternal ancestor of MtDNA hypervariable sequences from two different Neandertal humans to modern humans far exceeds the degree of variation found in over 5,000 modern human sequences (Ovchinnikov et al. 2000).

Mitochondrial markers have been particularly important for demonstrating the stages of genetic differentiation that many animal species show as a population evolves through paraphyly to reciprocal monophyly and complete differentiation. Indeed, discussions about molecular data and modern species origins often center on the most appropriate interpretation of these stages in speciation (Morrow et al. 2000). Patterns of allelic lineage distributions in spatially isolated subgroups have been useful for generating hypotheses concerning Pleistocene refugia, dispersal corridors, behavioral reinforcement, and incomplete barriers to gene flow in plants as well as animals. Controversy over legal protection of specific populations that show MtDNA lineage patterns, coincident with habitat disturbances disrupting ecological boundaries, often transcends dry systematic debates on the proper designation of hybrid taxa.

2.1 Intra and Intergenomic Conflicts of Interest

Hybrid taxa are of particular interest for mitochondrial genetics because hybrid dysgenesis may result when mitochondria from one taxa find themselves functioning in the company of a nuclear genome from another distinct lineage, as in the case of Mus musculus and Mus domesticus (Sage et al. 1986). Two or more genes that must interact within a single organism may display a spectrum of evolutionary responses grading from mutualism to antagonism. Speculation on why mitochondria retain some genes while shunting others into the nucleus often revolves around the idea of genomic conflicts of interest.

Mitochondrial genes normally coevolve in linkage as a uniparental chromosomal unit, and this was recognized by Hurst and Hamilton (1992) as one of two ways to prevent cytoplasmic gene conflict. In their view, sperm evolved to prevent the mixing of incompatible cytoplasmic genes. For many common species, the male sex has resigned attempts to contribute MtDNA to the next generation. Since the topic of hybrid male sterility has been so important to research on the genetics of speciation, molecular exploration of the loci controlling the ubiquitintagging pathway is likely to increase our sophistication of understanding how genomic conflicts have been solved by various species.

The suggestion that sex is an integral part of intragenomic conflict helps explain why nuclear genetic mechanisms distinct from sex but linked with incompatibility have arisen in a number of organisms, from acellular slime molds to yeast and certain ciliates. These taxa, as predicted, show unusual numbers of mating types and variations in the uniparental inheritance pattern of MtDNA. Highly inbred organisms also tend to have biparental inheritance of organelle DNA, since conflict-reducing mutations can easily spread among identical genotypic backgrounds.

2.2 Origin of Complex Cells

The prevailing view of mitochondrial genomes is that they are circular, but a large number of organisms possess linear MtDNA, including some ciliates, parasitic apicomplexan protozoa such as Plasmodium the other animal parasites Babesia and Theileria, some algae, slime molds, oomycetous fungi, many yeast, some Cnidaria species, and several Hydra species (Nosek et al. 1998). Baker’s yeast (Saccharomyces cere isiae) MtDNA is normally portrayed as circular, with linear molecules commonly found in i o, but they had been interpreted as degraded circles, as found in many plant MtDNAs. This view has now changed based on pulsed-field gel electrophoresis employed to study very large molecules, and a more sophisticated understanding of the telomeres of linear mitochondrial genomes has resulted (they are of intense interest to molecular biologists as potential sites for new drug development in diseases caused by organisms with these specialized linear structures). The question of linear vs. circular genomes is also important in order to evaluate the endosymbiont hypothesis for the origin of mitochondria, since circular genomes are widespread among hypothetical prokaryote ancestors, the purple bacteria (Wilson et al. 1987).

Do organisms with linear MtDNAs represent a separate prokaryotic lineage, compared with those with circular ones? Gene sequences as well as gene order have been examined. Phylogenetic trees of yeasts possessing both types of genomes make it clear that based on ribosomal sequences, there is not a radical difference between circles or lines. Analysis of the mechanisms that have evolved to solve the problem of replication of 5 ends of DNA are likely to reveal how linear and circular organelle genomes are related.

2.3 Adaptation, Biogeography, and Phylogeography

An extensive literature of original research dealing with the use of MtDNA markers in evolutionary biology was summarized by Avise (1994). Aside from providing phylogenetic trees for species with no fossil record, the mitochondrial marker approach is particularly useful in the mapping of organismal traits onto testable hypotheses of phylogeny based on parsimony, distance, and likelihood methods. Characters such as powered flight and the loss of it, tetrapod limb structure, brood parasitism, eusociality, melanism, endothermy, carnivory, vocal signal complexity, androdioecy, and even multicellularity have been placed on MtDNA phylogenies.

Aside from higher systematics and the phylogenetic distribution of specific adaptations, mitochondrial haplotypes can, like other single-locus markers, be analyzed as single genes with frequencies and geographic distributions that help portray population history, even in species with limited genetic variation. The relationships of the alleles in a population are informative for longer-term processes of phylogeography and population subdivision (Burke 1998), and can sometimes untangle current from historical events and reveal demographic trends.

2.4 Nonequilibrium Population Genetics

MtDNA characteristically is more sensitive to aspects of population biology and history owing to its uniparental transmission that reflects a lower effective population size (Ne). Populations not in HardyWeinberg equilibrium for genetic markers (Slatkin 1993) include many taxa of interest to conservation biologists as well as weedy or invasive species showing recent expansions of geographic range. When measured for genotype diversity, groups undergoing selection, nonrandom mating, enhanced mutation, and characterized by tiny population sizes often show deviations from expected Hardy-Weinberg allele frequencies.

MtDNA genotypes in these groups sometimes evidence ‘waves’ in the frequency distributions of particular haplotypes compared on a pairwise basis with count mismatches (Rogers and Harpending 1992). Thus, mitochondrial genotypes are particularly useful in identification of migrants and hybrid individuals, asymmetrical mating preferences, and historical effects stemming from stochastic changes in populations where an ancestral source population was polymorphic for a particular set of markers (Waser and Stroebeck 1998).

Reductions in effective population size may be the result of either population bottlenecks or selective sweeps and so mismatch distributions alone cannot be used to infer population history. However, the general shape of MtDNA trees, where a star-like pattern of alleles indicates few mutational differences between the major variants in a population, is consistent with the hypothesis of recent deme expansion. Deep branches in gene trees, in contrast, usually reflect long periods of population subdivision. Highly polymorphic nuclear genetic markers and developments of phylogenetic estimation theory will be combined with mitochondrial haplotype information to yield detailed scenarios of population history during the final stages of the Pleistocene era for some highly vagile species (Bowcock et al. 1994 Cogdon et al. 2000).

Bibliography:

1. Avise J 1994 Molecular Markers, Natural History and E olution. Chapman & Hall, New York
2. Bowcock A M, Ruiz-Linares A, Tomfohrde J, Minch E, Kidd J R, Cavalli-Sforza L L 1994 High resolution of human evolutionary trees with polymorphic microsatellites. Nature 386: 455–7
3. Burke T (ed.) 1998 Special Issue: Phylogeography. Molecular Ecology 7: 367–545
4. Cogdon B C, Piatt J F, Martin K, Friesen V L 2000 Mechanisms of population differentiation in marbled murrelets: Historical versus contemporary processes. E olution 54: 974–86
5. Hurst L D, Hamilton W 1992 Cytoplasmic fusion and the nature of sexes. Proceedings of the Royal Society, London B 247: 189–94
6. Kaneda H, Hayashi J-I, Takahama S, Taya C, Fischer-Lindahl K, Yonekawa H 1995 Elimination of paternal mitochondrial DNA in intrasepcific crosses during early mouse embryogenesis. Proceedings of the National Academy of Sciences USA 92: 4542–6
7. Morrow J, Scott L, Cogdon B, Yeates D, Frommer M, Sved J 2000 Close genetic similarity between two symatric species of Tephritid fruit fly reproductively isolated by mating time. E olution 54: 899–910
8. Nosek J, Tomaska L, Fukuhara H, Suyama Y, Kovac L 1998 Linear mitochondrial genomes: 30 years down the line. Trends in Genetics 14: 184–8
9. Ovchinnikov I V, Gotherstrom A, Romanova G P, Kharitonov V M, Liden K, Goodwin W 2000 Molecular analysis of Neanderthal DNA from the northern Caucasus. Nature 404: 490–3
10. Rogers A R, Harpending H C 1992 Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and E olution 9: 552–69
11. Sage R D, Heyneman D, Lim K-C, Wilson A C 1986 Wormy mice in a hybrid zone. Nature 324: 60–3
12. Simon C, Frati F, Beckenbach A, Crespi B, Liu H, Flook P 1994 Evolution, weighting, and phylogenetic utility of mitochondrial gene sequences and a compilation of conserved polymerase chain reaction primers. Annals of the Entomological Society of America 87: 651–701
13. Slatkin M 1993 Isolation by distance in equilibrium and nonequilibrium populations. E olution 47: 264–79
14. Sutovsky P, Moreno R D, Ramalho-Santos J, Dominko T, Simerly C, Schatten G 1999 Ubiquitin tag for sperm mitochondria. Nature 402: 371–2
15. Thyagarajan B, Padua R A, Campbell C 1996 Mammalian mitochondria possess homologous recombination activity. The Journal of Biological Chemistry 271: 27536–43
16. Waser P M, Stroebeck C 1998 Genetic signatures of interpopulational dispersal. Trends in Ecology and E olution 13: 33–4
17. Wilson A C, Ochman H, Prager E M 1987 Molecular time scale for evolution. Trends in Genetics 3: 241–7
18. Wolstenholme D R 1992 Animal mitochondrial DNA: Structure and evolution. International Review of Cytology 141: 173–216