Colonization of America by Drosophila subobscura: Experiment in natural populations that supports the adaptive role of chromosomal-inversion polymorphism

North America and South America have recently been colonized by the Palearctic species Drosophila subobscura. This double colonization offers a rare opportunity for evolutionary studies. Correlations between chromosomal arrangement frequencies and latitude were calculated for the colonizing populations. Signs of these correlations are highly coincident with those found in the Old World. These results provide experimental support for the adaptive value of the chromosomal-inversion polymorphism; historical and other nonadaptive explanations are thus excluded or relegated to a secondary role.     

Selective loss of polymorphic mating types is associated with rapid phenotypic evolution during morphic speciation

Polymorphism may play an important role in speciation because new species could originate from the distinctive morphs observed in polymorphic populations. However, much remains to be understood about the process by which morphs found new species. To detail the steps of this mode of speciation, we studied the geographic variation and evolutionary history of a throat color polymorphism that distinguishes the “rock-paper-scissors” mating strategies of the side-blotched lizard, Uta stansburiana. We found that the polymorphism is geographically widespread and has been maintained for millions of years. However, there are many populations with reduced numbers of throat color morphs. Phylogenetic reconstruction showed that the polymorphism is ancestral, but it has been independently lost eight times, often giving rise to morphologically distinct subspecies/species. Changes to the polymorphism likely involved selection because the allele for one particular male strategy, the “sneaker” morph, has been lost in all cases. Polymorphism loss was associated with accelerated evolution of male size, female size, and sexual dimorphism, which suggests that polymorphism loss can promote rapid divergence among populations and aid species formation.     

Unique insights into maternal mitochondrial inheritance in mice

In animals, mtDNA is always transmitted through the female and this is termed “maternal inheritance.” Recently, autophagy was reported to be involved in maternal inheritance by elimination of paternal mitochondria and mtDNA in Caenorhabditis elegans; moreover, by immunofluorescence, P62 and LC3 proteins were also found to colocalize to sperm mitochondria after fertilization in mice. Thus, it has been speculated that autophagy may be an evolutionary conserved mechanism for paternal mitochondrial elimination. However, by using two transgenic mouse strains, one bearing GFP-labeled autophagosomes and the other bearing red fluorescent protein-labeled mitochondria, we demonstrated that autophagy did not participate in the postfertilization elimination of sperm mitochondria in mice. Although P62 and LC3 proteins congregated to sperm mitochondria immediately after fertilization, sperm mitochondria were not engulfed and ultimately degraded in lysosomes until P62 and LC3 proteins disengaged from sperm mitochondria. Instead, sperm mitochondria unevenly distributed in blastomeres during cleavage and persisted in several cells until the morula stages. Furthermore, by using single sperm mtDNA PCR, we observed that most motile sperm that had reached the oviduct for fertilization had eliminated their mtDNA, leaving only vacuolar mitochondria. However, if sperm with remaining mtDNA entered the zygote, mtDNA was not eliminated and could be detected in newborn mice. Based on these results, we conclude that, in mice, maternal inheritance of mtDNA is not an active process of sperm mitochondrial and mtDNA elimination achieved through autophagy in early embryos, but may be a passive process as a result of prefertilization sperm mtDNA elimination and uneven mitochondrial distribution in embryos.     

A detailed picture of the origin of the Australian dingo, obtained from the study of mitochondrial DNA

To determine the origin and time of arrival to Australia of the dingo, 582 bp of the mtDNA control region were analyzed in 211 Australian dingoes sampled in all states of Australia, 676 dogs from all continents, and 38 Eurasian wolves, and 263 bp were analyzed in 19 pre-European archaeological dog samples from Polynesia. We found that all mtDNA sequences among dingoes were either identical to or differing by a single substitution from a single mtDNA type, A29. This mtDNA type, which was present in >50% of the dingoes, was found also among domestic dogs, but only in dogs from East Asia and Arctic America, whereas 18 of the 19 other types were unique to dingoes. The mean genetic distance to A29 among the dingo mtDNA sequences indicates an origin approximately 5,000 years ago. From these results a detailed scenario of the origin and history of the dingo can be derived: dingoes have an origin from domesticated dogs coming from East Asia, possibly in connection with the Austronesian expansion into Island Southeast Asia. They were introduced from a small population of dogs, possibly at a single occasion, and have since lived isolated from other dog populations.     

Expanding the functional human mitochondrial DNA database by the establishment of primate xenomitochondrial cybrids

The nuclear and mitochondrial genomes coevolve to optimize approximately 100 different interactions necessary for an efficient ATP-generating system. This coevolution led to a species-specific compatibility between these genomes. We introduced mitochondrial DNA (mtDNA) from different primates into mtDNA-less human cells and selected for growth of cells with a functional oxidative phosphorylation system. mtDNA from common chimpanzee, pigmy chimpanzee, and gorilla were able to restore oxidative phosphorylation in the context of a human nuclear background, whereas mtDNA from orangutan, and species representative of Old-World monkeys, New-World monkeys, and lemurs were not. Oxygen consumption, a sensitive index of respiratory function, showed that mtDNA from chimpanzee, pigmy chimpanzee, and gorilla replaced the human mtDNA and restored respiration to essentially normal levels. Mitochondrial protein synthesis was also unaltered in successful “xenomitochondrial cybrids.” The abrupt failure of mtDNA from primate species that diverged from humans as recently as 8–18 million years ago to functionally replace human mtDNA suggests the presence of one or a few mutations affecting critical nuclear–mitochondrial genome interactions between these species. These cellular systems provide a demonstration of intergenus mtDNA transfer, expand more than 20-fold the number of mtDNA polymorphisms that can be analyzed in a human nuclear background, and provide a novel model for the study of nuclear–mitochondrial interactions.     

Evidence for Pleistocene Population Divergence and Expansion of Anopheles albimanus in Southern Central America

The micro-geographic structure of Anopheles albimanus was studied in southern Central America using partial sequences of the mtDNA cytochrome oxidase subunit I gene (COI). Analysis of molecular variance supported significant genetic structure between populations from Costa Rica and western Panama versus those from central-eastern Panama (Φ_CT = 0.33), whereas the within group divergence was shallow and statistically insignificant (Φ_ST = 0.08). Furthermore, a statistical parsimony network depicted three divergent groups of haplotypes that were not evenly distributed across the study area. Our findings are in partial agreement with previous studies, yet they do not support physical barriers to gene flow or contemporary isolation by distance in this region. Instead, three co-occurring groups of An. albimanus may be the result of multiple introductions, most likely caused by historical fragmentation and subsequent secondary contact. In addition, the molecular signature of population expansion of An. albimanus was detected in central-eastern Panama approximately 22,000 years ago (95% confidence interval [CI] 10,183–38,169). We hypothesize that the population structure of An. albimanus, as determined by our COI locus analysis, is the result of late Pleistocene climatic changes in northern South America.     

Mitochondrial DNA "clock" for the Amerinds and its implications for timing their entry into North America.

Students of the time of entry of the ancestors of the Amerinds into the New World are divided into two camps, one favoring an "early" entry [more than approximately 30,000 years before the present (YBP)], the other favoring a "late" entry (less than approximately 13,000 YBP). An "intermediate" date is unlikely for geological reasons. The correlation of the appropriate data on mtDNA variation in Amerinds with linguistic, archaeological, and genetic data offers the possibility of establishing a time frame for mtDNA evolution in Amerinds. In this paper, we estimate that the separation of the Chibcha-speaking tribes of Central America from other linguistic groups/nascent tribes began approximately 8000-10,000 YBP. Characterization of the mtDNA of 110 Chibcha speakers with 14 restriction enzymes leads on the basis of their time depth to an estimated mtDNA nucleotide substitution rate for Amerinds of 0.022-0.029% per 10,000 years. As a first application of this rate, we consider the mtDNA variation observed in 18 Amerind tribes widely dispersed throughout the Americas and studied by ourselves with the same techniques, and we estimate that if the Amerinds entered the New World as a single group, that entry occurred approximately 22,000-29,000 YBP. This estimate carries a large but indeterminate error. The mtDNA data are thus at present equivocal with respect to the most likely times of entry of the Amerind into the New World mentioned above but favor the "early" entry hypothesis.     

An independent evaluation of the Younger Dryas extraterrestrial impact hypothesis

Based on elevated concentrations of a set of “impact markers” at the onset of the Younger Dryas stadial from sedimentary contexts across North America, Firestone, Kennett, West, and others have argued that 12.9 ka the Earth experienced an impact by an extraterrestrial body, an event that had devastating ecological consequences for humans, plants, and animals in the New World [Firestone RB, et al. (2007) Proc. Natl. Acad. Sci. USA 104:16016–16021]. Herein, we report the results of an independent analysis of magnetic minerals and microspherules from seven sites of similar age, including two examined by Firestone et al. We were unable to reproduce any results of the Firestone et al. study and find no support for Younger Dryas extraterrestrial impact.     

Test of Martin’s overkill hypothesis using radiocarbon dates on extinct megafauna

Following Martin [Martin PS (1973) Science 179:969–974], we propose the hypothesis that the timing of human arrival to the New World can be assessed by examining the ecological impacts of a small population of people on extinct Pleistocene megafauna. To that end, we compiled lists of direct radiocarbon dates on paleontological specimens of extinct genera from North and South America with the expectation that the initial decline of extinct megafauna should correspond in time with the initial evidence for human colonization and that those declines should occur first in eastern Beringia, next in the contiguous United States, and last in South America. Analyses of spacings and frequency distributions of radiocarbon dates for each region support the idea that the extinction event first commenced in Beringia, roughly 13,300–15,000 BP. For the United States and South America, extinctions commenced considerably later but were closely spaced in time. For the contiguous United States, extinction began at ca. 12,900–13,200 BP, and at ca. 12,600–13,900 BP in South America. For areas south of Beringia, these estimates correspond well with the first significant evidence for human presence and are consistent with the predictions of the overkill hypothesis.Just over 42 y ago, Paul Martin (1) proposed that humans entered the contiguous United States via the Ice Free Corridor at ∼13,500 BP and there encountered almost three dozen genera of now-extinct megafaunal mammals. Hunting of these naïve prey fueled rapid human population growth, he argued, resulting in both the colonization of the landmass stretching from the southern terminus of the North American ice sheets to the far tip of South America in 1,000 y, and the extinction of the mammoths, mastodons, camels, horses, ground sloths, and other large mammal taxa that had inhabited the Western Hemisphere for hundreds of thousands to millions of years before human arrival. Martin (p. 973) closed his paper with the statement, “Should the model survive future findings, it will mean that the extinction chronology of the Pleistocene megafauna can be used to map the spread of Homo sapiens through the New World.”Central to this hypothesis is the idea that small numbers of humans can have large ecological impacts and that those impacts should be directly observable in the paleontological record. If we accept that premise as true, then as Martin argues, it is possible to assess the timing of human arrival independently of direct archaeological evidence by examining when megafaunal decline occurred across time and space. In this paper, we use databases of radiocarbon dates on extinct megafauna from Eastern Beringia (EB), the contiguous United States (CUSA), and South America (SA) to estimate the timing of initial population declines that ultimately resulted in extinction. We intend this exercise to be both a direct test of the timing of extinction as proposed by Martin (1) and as an independent means of estimating the timing of human arrival to each region. Similar approaches using paleoecological proxy records as possible indicators of human arrival have been applied elsewhere, particularly on islands (2–7).From this premise, we make two complementary arguments pertaining to New World colonization. First, we expect initial megafaunal declines for each region to correspond temporally with the first evidence of human presence. Second, we expect that the timing of megafaunal declines should be geographically patterned according to Martin’s (1) model in which the founding population moved through EB and then south into the CUSA and SA. When Martin published his classic work, radiocarbon calibration was not possible, so by necessity, he worked within the radiocarbon time scale. For the CUSA, Martin estimated a mean colonization age of ca. 11,200 ¹⁴C y BP, or ca. 13,100 BP, and for SA, ca. 10,700 ¹⁴C y BP, or ca. 12,700 BP. Martin did not specify a human arrival date for EB, except to suggest his model required that “the time of human entry into Alaska need be no older than 11,700 [radiocarbon] years ago,” or roughly 13,600 BP.Importantly, the expectation of a north to south spatiotemporal extinction trend across the Western Hemisphere should be largely unique to the overkill hypothesis. There is no single climatic (8, 9) or catastrophic (10) extinction hypothesis that shares this prediction. Therefore, this kind of analysis is not only capable of testing the overkill hypothesis, but of posing legitimate challenges to other extinction hypotheses, with the possible exception of multifactor models that also invoke “first contact” effects, such as the keystone herbivore (11), habitat modification (12), and hyperdisease hypotheses (13).We use two analytical techniques to identify dates of initial megafaunal decline: for technical precision, an approach based on spacings (time lags between consecutive ordered dates), and, for simple understanding, an approach based on histograms of observed dates. The key property of spacings is that mean spacings are inversely proportional to population levels. For spacings, individual spacing values are regressed onto the midtime (t_i+1 + t_i)/2 of the spacing interval using a generalized linear model with estimated breakpoints (representing times of onset of extinction). Decline dates are identified as the time before extinction for which waiting times between dates begin to increase, implying population declines. This method produces both a likely date for extinction onset and an associated approximate 95% CI (confidence interval). For histogram creation, we first apply a jackknife method to identify optimal binning parameters for histogram creation (14) to create frequency distributions of calibrated radiocarbon dates, which are then corrected for taphonomic bias following Surovell et al. (15). Taphonomic correction adjusts frequency distributions of radiocarbon dates to account for the loss of sedimentary contexts through time due to erosion and weathering. Decline dates are estimated as occurring within the last mode before extinction. Spacings are also taphonomically corrected (SI Materials and Methods).Both spacings and frequency analyses rest on three assumptions: (i) our radiocarbon datasets are representative of the relative frequencies of megafauna in the paleontological records of each region; (ii) after taphonomic correction, temporal frequency distributions positively correlate with population densities of megafaunal taxa through time; and (iii) the same taphonomic correction model characterizes each region.^*     

Isolation and amino acid sequences of opossum vasoactive intestinal polypeptide and cholecystokinin octapeptide.

Evolutionary history suggests that the marsupials entered South America from North America about 75 million years ago and subsequently dispersed into Australia before the separation between South America and Antarctica-Australia. A question of interest is whether marsupial peptides resemble the corresponding peptides of Old or New World mammals. Previous studies had shown that "little" gastrin of the North American marsupial, the opossum, is identical in length to that of the New World mammals, the guinea pig and chinchilla. In this report, we demonstrate that opossum cholecystokinin octapeptide, like that of the Australian marsupials, the Eastern quoll and the Tamar wallaby, is identical to the cholecystokinin octapeptide of Old World mammals and differs from that of the guinea pig and chinchilla. However, opossum vasoactive intestinal polypeptide differs from the usual Old World mammalian vasoactive intestinal polypeptide in five sites: [sequence; see text].     

An odyssey of the green sea turtle: Ascension Island revisited

Green turtles (Chelonia mydas) that nest on Ascension Island, in the south-central Atlantic, utilize feeding grounds along the coast of Brazil, more than 2000 km away. To account for the origins of this remarkable migratory behavior, Carr and Coleman [Carr, A. & Coleman, P. J. (1974) Nature (London) 249, 128-130] proposed a vicariant biogeographic scenario involving plate tectonics and natal homing. Under the Carr-Coleman hypothesis, the ancestors of Ascension Island green turtles nested on islands adjacent to South America in the late Cretaceous, soon after the opening of the equatorial Atlantic Ocean. Over the last 70 million years, these volcanic islands have been displaced from South America by sea-floor spreading, at a rate of about 2 cm/year. A population-specific instinct to migrate to Ascension Island is thus proposed to have evolved gradually over tens of millions of years of genetic isolation. Here we critically test the Carr-Coleman hypothesis by assaying genetic divergence among several widely separated green turtle rookeries. We have found fixed or nearly fixed mitochondrial DNA (mtDNA) restriction site differences between some Atlantic rookeries, suggesting a severe restriction on contemporary gene flow. Data are consistent with a natal homing hypothesis. However, an extremely close similarity in overall mtDNA sequences of surveyed Atlantic green turtles from three rookeries is incompatible with the Carr-Coleman scenario. The colonization of Ascension Island, or at least extensive gene flow into the population, has been evolutionarily recent.     

Revealing the prehistoric settlement of Australia by Y chromosome and mtDNA analysis

Published and new samples of Aboriginal Australians and Melanesians were analyzed for mtDNA (n=172) and Y variation (n=522), and the resulting profiles were compared with the branches known so far within the global mtDNA and the Y chromosome tree. (i) All Australian lineages are confirmed to fall within the mitochondrial founder branches M and N and the Y chromosomal founders C and F, which are associated with the exodus of modern humans from Africa approximately 50-70,000 years ago. The analysis reveals no evidence for any archaic maternal or paternal lineages in Australians, despite some suggestively robust features in the Australian fossil record, thus weakening the argument for continuity with any earlier Homo erectus populations in Southeast Asia. (ii) The tree of complete mtDNA sequences shows that Aboriginal Australians are most closely related to the autochthonous populations of New Guinea/Melanesia, indicating that prehistoric Australia and New Guinea were occupied initially by one and the same Palaeolithic colonization event approximately 50,000 years ago, in agreement with current archaeological evidence. (iii) The deep mtDNA and Y chromosomal branching patterns between Australia and most other populations around the Indian Ocean point to a considerable isolation after the initial arrival. (iv) We detect only minor secondary gene flow into Australia, and this could have taken place before the land bridge between Australia and New Guinea was submerged approximately 8,000 years ago, thus calling into question that certain significant developments in later Australian prehistory (the emergence of a backed-blade lithic industry, and the linguistic dichotomy) were externally motivated.     

The origins and precolonial epidemiology of tuberculosis in the Americas: can we figure them out?

Paleologic evidence of tuberculosis in the precolonial Americas is reviewed to cast light on its origins and subsequent epidemiology. The genus Mycobacterium is an ancient one, and M. tuberculosis may have differentiated 20,400 to 15,300 years ago. The Americas were peopled by migrants from Asia in two major migrations, one occurring more than 20,000 years ago and the other 12,000 to 11,000 years ago. Tuberculosis reached the Americas with these migrants, persisting at a low level of endemnicity in small, dispersed population groups. Beginning about 1500 years ago, an epidemic of tuberculosis began, probably in the Andean region of South America. It did not reach or subsided in time to leave highly susceptible indigenous American populations at the time of European colonization.     

Mitochondrial heteroplasmy and the evolution of insecticide resistance: Non-Mendelian inheritance in action

Genes encoded by mitochondrial DNA (mtDNA) exist in large numbers per cell but can be selected very rapidly as a result of unequal partitioning of mtDNA between germ cells during embryogenesis. However, empirical studies of this “bottlenecking” effect are rare because of the apparent scarcity of heteroplasmic individuals possessing more than one mtDNA haplotype. Here, we report an example of insecticide resistance in an arthropod pest (Tetranychus urticae) being controlled by mtDNA and on its inheritance in a heteroplasmic mite strain. Resistance to the insecticide bifenazate is highly correlated with remarkable mutations in cytochrome b, a mitochondrially encoded protein in the respiratory pathway. Four sites in the Q_o site that are absolutely conserved across fungi, protozoa, plants, and animals are mutated in resistant mite strains. Despite the unusual nature of these mutations, resistant mites showed no fitness costs in the absence of insecticide. Partially resistant strains, consisting of heteroplasmic individuals, transmit their resistant and susceptible haplotypes to progeny in highly variable ratios consistent with a sampling bottleneck of ≈180 copies. Insecticide selection on heteroplasmic individuals favors those carrying resistant haplotypes at a frequency of 60% or more. This combination of factors enables very rapid evolution and accounts for mutations being fixed in most field-collected resistant strains. The results provide a rare insight into non-Mendelian mechanisms of mitochondrial inheritance and evolution, relevant to anticipating and understanding the development of other mitochondrially encoded adaptations in arthropods. They also provide strong evidence of cytochrome b being the target site for bifenazate in spider mites.     

Evolutionary lag times and recent origin of the biota of an ancient desert (Atacama–Sechura)

The assembly of regional biotas and organismal responses to anthropogenic climate change both depend on the capacity of organisms to adapt to novel ecological conditions. Here we demonstrate the concept of evolutionary lag time, the time between when a climatic regime or habitat develops in a region and when it is colonized by a given clade. We analyzed the time of colonization of four clades (three plant genera and one lizard genus) into the Atacama–Sechura Desert of South America, one of Earth’s driest and oldest deserts. We reconstructed time-calibrated phylogenies for each clade and analyzed the timing of shifts in climatic distributions and biogeography and compared these estimates to independent geological estimates of the time of origin of these deserts. Chaetanthera and Malesherbia (plants) and Liolaemus (animal) invaded arid regions of the Atacama–Sechura Desert in the last 10 million years, some 20 million years after the initial onset of aridity in the region. There are also major lag times between when these clades colonized the region and when they invaded arid habitats within the region (typically 4–14 million years). Similarly, hyperarid climates developed ∼8 million years ago, but the most diverse plant clade in these habitats (Nolana) only colonized them ∼2 million years ago. Similar evolutionary lag times may occur in other organisms and habitats, but these results are important in suggesting that many lineages may require very long time scales to adapt to modern desertification and climatic change.     

Microsatellites provide evidence for Y chromosome diversity among the founders of the New World

Recently, Y chromosome markers have begun to be used to study Native American origins. Available data have been interpreted as indicating that the colonizers of the New World carried a single founder haplotype. However, these early studies have been based on a few, mostly complex polymorphisms of insufficient resolution to determine whether observed diversity stems from admixture or diversity among the colonizers. Because the interpretation of Y chromosomal variation in the New World depends on founding diversity, it is important to develop marker systems with finer resolution. Here we evaluate the hypothesis of a single-founder Y haplotype for Amerinds by using 11 Y-specific markers in five Colombian Amerind populations. Two of these markers (DYS271, DYS287) are reliable indicators of admixture and detected three non-Amerind chromosomes in our sample. Two other markers (DYS199, M19) are single-nucleotide polymorphisms mostly restricted to Native Americans. The relatedness of chromosomes defined by these two markers was evaluated by constructing haplotypes with seven microsatellite loci (DYS388 to 394). The microsatellite backgrounds found on the two haplogroups defined by marker DYS199 demonstrate the existence of at least two Amerind founder haplotypes, one of them (carrying allele DYS199 T) largely restricted to Native Americans. The estimated age and distribution of these haplogroups places them among the founders of the New World.     

Two kinds of theta constants and period relations on a riemann surface

It was recognized in Riemann's work more than one hundred years ago and proved recently by Rauch (cf. Bull. Am. Math. Soc., 71, 1-39 (1965) that the g(g + 1)/2 unnormalized periods of the normal differentials of first kind on a compact Riemann surface S of genus g ≥ 2 with respect to a canonical homology basis are holomorphic functions of 3g - 3 complex variables, “the” moduli, which parametrize the space of Riemann surfaces near S and, hence, that there are (g - 2)(g - 3)/2 holomorphic relations among those periods. Eighty years ago, Schottky exhibited the one relation for g = 4 as the vanishing of an explicit homogeneous polynomial in the Riemann theta constants. Sixty years ago, Schottky and Jung conjectured a result which implies Schottky's earlier one and some generalizations for higher genera.

Here, we formulate Schottky and Jung's conjecture precisely and, on the basis of a recent result of Farkas (these PROCEEDINGS, 62, 320 (1969)), prove it. We then derive Schottky's result (we believe for the first time correctly) and exhibit a typical relation of this kind for g = 5 (we can do this for any genus). We do not prove that our relations imply all relations, but there are some indications that they do.

     

Mitochondrial genomes and exceptional longevity in a Chinese population: the Rugao longevity study

Genetic variants of whole mitochondrial DNA (mtDNA) that predispose to exceptional longevity need to be systematically identified and appraised. Here, we conducted a case-control study with 237 exceptional longevity subjects (aged 95–107) and 444 control subjects (aged 40–69) randomly recruited from a “longevity town”—the city of Rugao in China—to investigate the effects of mtDNA variants on exceptional longevity. We sequenced the entire mtDNA genomes of the 681 subjects using a next-generation platform and employed a complete mtDNA phylogenetic analytical strategy. We identified T3394C as a candidate that counteracts longevity, and we observed a higher load of private nonsynonymous mutations in the COX1 gene predisposing to female longevity. Additionally, for the first time, we identified several variants and new subhaplogroups related to exceptional longevity. Our results provide new clues for genetic mechanisms of longevity and shed light on strategies for evaluating rare mitochondrial variants that underlie complex traits.

Electronic supplementary material

The online version of this article (doi:10.1007/s11357-015-9750-8) contains supplementary material, which is available to authorized users.     

Apparent mtDNA heteroplasmy in Alzheimer’s disease patients and in normals due to PCR amplification of nucleus-embedded mtDNA pseudogenes

In an unprecedented finding, Davis et al. [Davis, R. E., Miller, S., Herrnstadt, C., Ghosh, S. S., Fahy, E., Shinobu, L. A., Galasko, D., Thal, L. J., Beal, M. F., Howell, N. & Parker, W. D., Jr. (1997) Proc. Natl. Acad. Sci. USA 94, 4526–4531] used an unusual DNA isolation method to show that healthy adults harbor a specific population of mutated mitochondrial cytochrome c oxidase (COX) genes that coexist with normal mtDNAs. They reported that this heteroplasmic population was present at a level of 10–15% in the blood of normal individuals and at a significantly higher level (20–30%) in patients with sporadic Alzheimer’s disease. We provide compelling evidence that the DNA isolation method employed resulted in the coamplification of authentic mtDNA-encoded COX genes together with highly similar COX-like sequences embedded in nuclear DNA (“mtDNA pseudogenes”). We conclude that the observed heteroplasmy is an artifact.     

Phylogeographic population structure of Red-winged Blackbirds assessed by mitochondrial DNA

A continent-wide survey of restriction-site variation in mitochondrial DNA (mtDNA) of the Red-winged Blackbird (Agelaius phoeniceus) was conducted to assess the magnitude of phylogeographic population structure in an avian species. A total of 34 mtDNA genotypes was observed among the 127 specimens assayed by 18 restriction endonucleases. Nonetheless, population differentiation was minor, as indicated by (i) small genetic distances in terms of base substitutions per nucleotide site between mtDNA genotypes (maximum P ≈ 0.008) and by (ii) the widespread geographic distributions of particular mtDNA clones and phylogenetic arrays of clones. Extensive morphological differentiation among redwing populations apparently has occurred in the context of relatively little phylogenetic separation. A comparison between mtDNA data sets for Red-winged Blackbirds and deermice (Peromyscus maniculatus) also sampled from across North America shows that intraspecific population structures of these two species differ dramatically. The lower phylogeographic differentiation in redwings is probably due to historically higher levels of gene flow.