Rates of evolution in ancient DNA from Adélie penguins

Evolution and biodiversity of Antarctic organisms: a molecular perspective

The Antarctic biota is highly endemic, and the diversity and abundance of taxonomic groups differ from elsewhere in the world. Such characteristics have resulted from evolution in isolation in an increasingly extreme environment over the last 100 Myr. Studies on Antarctic species represent some of the best examples of natural selection at the molecular, structural and physiological levels. Analyses of molecular genetics data are consistent with the diversity and distribution of marine and terrestrial taxa having been strongly influenced by geological and climatic cooling events over the last 70 Myr. Such events have resulted in vicariance driven by continental drift and thermal isolation of the Antarctic, and in pulses of species range contraction into refugia and subsequent expansion and secondary contact of genetically distinct populations or sister species during cycles of glaciation. Limited habitat availability has played a major role in structuring populations of species both in the past and in the present day. For these reasons, despite the apparent simplicity or homogeneity of Antarctic terrestrial and marine environments, populations of species are often geographically structured into genetically distinct lineages. In some cases, genetic studies have revealed that species defined by morphological characters are complexes of cryptic or sibling species. Climate change will cause changes in the distribution of many Antarctic and sub-Antarctic species through affecting population-level processes such as life history and dispersal.

Elevated substitution rates estimated from ancient DNA sequences

Ancient DNA sequences are able to offer valuable insights into molecular evolutionary processes, which are not directly accessible via modern DNA. They are particularly suitable for the estimation of substitution rates because their ages provide calibrating information in phylogenetic analyses, circumventing the difficult task of choosing independent calibration points. The substitution rates obtained from such datasets have typically been high, falling between the rates estimated from pedigrees and species phylogenies. Many of these estimates have been made using a Bayesian phylogenetic method that explicitly accommodates heterochronous data. Stimulated by recent criticism of this method, we present a comprehensive simulation study that validates its performance. For datasets of moderate size, it produces accurate estimates of rates, while appearing robust to assumptions about demographic history. We then analyse a large collection of 749 ancient and 727 modern DNA sequences from 19 species of animals, plants and bacteria. Our new estimates confirm that the substitution rates estimated from ancient DNA sequences are elevated above long-term phylogenetic levels.

Recent postglacial range expansion drives the rapid diversification of a songbird lineage in the genus Junco

Pleistocene glacial cycles are thought to have played a major role in the diversification of temperate and boreal species of North American birds. Given that coalescence times between sister taxa typically range from 0.1 to 2.0 Myr, it has been assumed that diversification occurred as populations were isolated in refugia over long periods of time, probably spanning one to several full glacial cycles. In contrast, the rapid postglacial range expansions and recolonization of northern latitudes following glacial maxima have received less attention as potential promoters of speciation. Here we report a case of extremely rapid diversification in the songbird genus Junco as a result of a single continent-wide range expansion within the last 10 000 years. Molecular data from 264 juncos sampled throughout their range reveal that as the yellow-eyed junco (Junco phaeonotus) of Mesoamerica expanded northward following the last glacial maximum, it speciated into the dark-eyed junco (Junco hyemalis), which subsequently diversified itself into at least five markedly distinct and geographically structured morphotypes in the USA and Canada. Patterns of low genetic structure and diversity in mitochondrial DNA and amplified fragment length polymorphism loci found in dark-eyed juncos relative to Mesoamerican yellow-eyed juncos provide support for the hypothesis of an expansion from the south, followed by rapid diversification in the north. These results underscore the role of postglacial expansions in promoting diversification and speciation through a mechanism that represents an alternative to traditional modes of Pleistocene speciation.

Large-scale mitochondrial DNA analysis of the domestic goat reveals six haplogroups with high diversity

Background

From the beginning of domestication, the transportation of domestic animals resulted in genetic and demographic processes that explain their present distribution and genetic structure. Thus studying the present genetic diversity helps to better understand the history of domestic species.

Methodology/Principal Findings

The genetic diversity of domestic goats has been characterized with 2430 individuals from all over the old world, including 946 new individuals from regions poorly studied until now (mainly the Fertile Crescent). These individuals represented 1540 haplotypes for the HVI segment of the mitochondrial DNA (mtDNA) control region. This large-scale study allowed the establishment of a clear nomenclature of the goat maternal haplogroups. Only five of the six previously defined groups of haplotypes were divergent enough to be considered as different haplogroups. Moreover a new mitochondrial group has been localized around the Fertile Crescent. All groups showed very high haplotype diversity. Most of this diversity was distributed among groups and within geographic regions. The weak geographic structure may result from the worldwide distribution of the dominant A haplogroup (more than 90% of the individuals). The large-scale distribution of other haplogroups (except one), may be related to human migration. The recent fragmentation of local goat populations into discrete breeds is not detectable with mitochondrial markers. The estimation of demographic parameters from mismatch analyses showed that all groups had a recent demographic expansion corresponding roughly to the period when domestication took place. But even with a large data set it remains difficult to give relative dates of expansion for different haplogroups because of large confidence intervals.

Conclusions/Significance

We propose standard criteria for the definition of the different haplogroups based on the result of mismatch analysis and on the use of sequences of reference. Such a method could be also applied for clarifying the nomenclature of mitochondrial haplogroups in other domestic species.

Whole-Genome Shotgun Sequencing of Mitochondria from Ancient Hair Shafts

Although the application of sequencing-by-synthesis techniques to DNA extracted from bones has revolutionized the study of ancient DNA, it has been plagued by large fractions of contaminating environmental DNA. The genetic analyses of hair shafts could be a solution: We present 10 previously unexamined Siberian mammoth (Mammuthus primigenius) mitochondrial genomes, sequenced with up to 48-fold coverage. The observed levels of damage-derived sequencing errors were lower than those observed in previously published frozen bone samples, even though one of the specimens was >50,000 14C years old and another had been stored for 200 years at room temperature. The method therefore sets the stage for molecular-genetic analysis of museum collections.

Rapid morphological and genetic change in Chicago-area Peromyscus

We report rapid change of morphology and mitochondrial genes in white-footed mice (Peromyscus leucopus) in the Chicago (Illinois, USA) region. We sequenced mitochondrial DNA COX2 from 55 museum skins of white-footed mice caught in the Chicago area since 1855 and from 44 mice recently trapped in the same locations. We found consistent directional genotype replacement at five separate collection locations. We later focused on a single one of these locations (Volo Bog State Natural Area) and sequenced mitochondrial D-loop control region from 58 museum skins of mice collected in 1903-1976 and 32 mice recently trapped there. We found complete and more recent replacement of D-loop haplotypes, apparently occurring between 1976 and 2001. We tested whether these genetic changes were mirrored by changes in morphology by comparing 15 external and cranial traits. We found no significant morphological differences between mice collected in 1903-1976; however, mice collected in 2001-2003 showed 9 of 15 measurements to be significantly changed relative to the earlier samples. Recent mice were longer in total length, with broader, longer noses, and longer but shallower skulls(1). Discriminant function analysis allowed for 100% correct classification using these traits. Principal components analysis shows variance over time is well distributed across both external and cranial measures. The sequential replacements of haplotypes and the rapid change of morphology can best be explained by replacement of the regional population with immigrants from genetically distinct neighbouring populations, likely facilitated by the large environmental changes occurring over the time period. Replacement with genotypes from external populations may be a common mechanism of evolution of newly adaptive local forms in an increasingly human-impacted world.

Ancient bacteria show evidence of DNA repair

Recent claims of cultivable ancient bacteria within sealed environments highlight our limited understanding of the mechanisms behind long-term cell survival. It remains unclear how dormancy, a favored explanation for extended cellular persistence, can cope with spontaneous genomic decay over geological timescales. There has been no direct evidence in ancient microbes for the most likely mechanism, active DNA repair, or for the metabolic activity necessary to sustain it. In this paper, we couple PCR and enzymatic treatment of DNA with direct respiration measurements to investigate long-term survival of bacteria sealed in frozen conditions for up to one million years. Our results show evidence of bacterial survival in samples up to half a million years in age, making this the oldest independently authenticated DNA to date obtained from viable cells. Additionally, we find strong evidence that this long-term survival is closely tied to cellular metabolic activity and DNA repair that over time proves to be superior to dormancy as a mechanism in sustaining bacteria viability.

Genetic variation in Holocene bowhead whales from Svalbard

Bowhead whales (Balaena mysticetus) are distributed in the Arctic in five putative stocks. All stocks have been heavily depleted due to centuries of exploitation. In the present study, nucleotide sequence variation of the mitochondrial control region was determined from bone remains of 99 bowhead whales. The bones, 14C dated from recent to more than 50,000 bp, were collected on Svalbard (Spitsbergen) and are expected to relate to ancestors of the today nearly extinct Spitsbergen stock. Fifty-eight haplotypes were found, a few being frequent but many only found in one individual. The most abundant haplotypes of the Spitsbergen stock are the same as those most abundant in the extant Bering-Chukchi-Beaufort (BCB) Seas stock of bowhead whales. Although F(ST) indicates a slight but statistically significant genetic differentiation between the Spitsbergen and the BCB stocks this was not considered informative due to the very high levels of genetic diversity of mitochondrial DNA haplotypes in both bowhead whale stocks. Other measures such as K(ST) also indicated very low genetic differentiation between the two populations. Nucleotide diversity and haplotype diversity showed only minor differences between the Spitsbergen and BCB stocks. The data suggest that the historic Spitsbergen stock--before the severe bottleneck caused by whaling--did not have substantially more genetic variation than the extant BCB stock. The similar haplotypes of the Holocene Svalbard samples and the current BCB stock indicate significant migration between these two stocks and question the current designation of five distinct stocks of bowhead whales in the Arctic.

Abrupt recent shift in delta 13C and delta 15N values in Adélie penguin eggshell in Antarctica

Stable isotope values of carbon (delta13C) and nitrogen (delta15N) in blood, feathers, eggshell, and bone have been used in seabird studies since the 1980s, providing a valuable source of information on diet, foraging patterns, and migratory behavior in these birds. These techniques can also be applied to fossil material when preservation of bone and other tissues is sufficient. Excavations of abandoned Adélie penguin (Pygoscelis adeliae) colonies in Antarctica often provide well preserved remains of bone, feathers, and eggshell dating from hundreds to thousands of years B.P. Herein we present an approximately 38,000-year time series of delta13C and delta15N values of Adélie penguin eggshell from abandoned colonies located in three major regions of Antarctica. Results indicate an abrupt shift to lower-trophic prey in penguin diets within the past approximately 200 years. We posit that penguins only recently began to rely on krill as a major portion of their diet, in conjunction with the removal of baleen whales and krill-eating seals during the historic whaling era. Our results support the "krill surplus" hypothesis that predicts excess krill availability in the Southern Ocean after this period of exploitation.

Genetic analysis of early holocene skeletal remains from Alaska and its implications for the settlement of the Americas

Mitochondrial and Y-chromosome DNA were analyzed from 10,300-year-old human remains excavated from On Your Knees Cave on Prince of Wales Island, Alaska (Site 49-PET-408). This individual's mitochondrial DNA (mtDNA) represents the founder haplotype of an additional subhaplogroup of haplogroup D that was brought to the Americas, demonstrating that widely held assumptions about the genetic composition of the earliest Americans are incorrect. The amount of diversity that has accumulated in the subhaplogroup over the past 10,300 years suggests that previous calibrations of the mtDNA clock may have underestimated the rate of molecular evolution. If substantiated, the dates of events based on these previous estimates are too old, which may explain the discordance between inferences based on genetic and archaeological evidence regarding the timing of the settlement of the Americas. In addition, this individual's Y-chromosome belongs to haplogroup Q-M3*, placing a minimum date of 10,300 years ago for the emergence of this haplogroup.

Geological Dates and Molecular Rates: Rapid Divergence of Rivers and Their Biotas

We highlight a novel molecular clock calibration system based on geologically dated river reversal and river capture events. Changes in drainage pattern may effect vicariant isolation of freshwater taxa, and thus provide a predictive framework for associated phylogeographic study. As a case in point, New Zealand's Pelorus and Kaituna rivers became geologically isolated from the larger Wairau River system 70 to 130 kyr BP. We conducted mitochondrial DNA phylogeographic analyses of two unrelated freshwater-limited fish taxa native to these river systems (Gobiomorphus breviceps, n = 63; Galaxias divergens, n = 95). Phylogenetic analysis of combined control region and cytochrome b sequences yielded reciprocally monophyletic clades of Pelorus-Kaituna and Wairau haplotypes for each species. Calibrated rates of molecular change based on this freshwater vicariant event are substantially faster than traditionally accepted rates for fishes but consistent with other recent inferences based on geologically young calibration points. A survey of freshwater phylogeographic literature reveals numerous examples in which the ages of recent evolutionary events may have been substantially overestimated through the use of "accepted" calibrations. We recommend that--wherever possible--biologists should start to reassess the conclusions of such studies by using more appropriate molecular calibrations derived from recent geological events.

Bayesian estimation of sequence damage in ancient DNA

DNA extracted from archaeological and paleontological remains is usually damaged by biochemical processes postmortem. Some of these processes lead to changes in the structure of the DNA molecule, which can result in the incorporation of incorrect nucleotides during polymerase chain reaction. These base misincorporations, or miscoding lesions, can lead to the inclusion of spurious additional mutations in ancient DNA (aDNA) data sets. This has the potential to affect the outcome of phylogenetic and population genetic analyses, including estimates of mutation rates and genetic diversity. We present a novel model, termed the delta model, which estimates the amount of damage in DNA data and accounts for its effects in a Bayesian phylogenetic framework. The ability of the delta model to estimate damage is first investigated using a simulation study. The model is then applied to 13 aDNA data sets. The amount of damage in these data sets is shown to be significant but low (about 1 damaged base per 750 nt), suggesting that precautions for limiting the influence of damaged sites, such as cloning and enzymatic treatment, are worthwhile. The results also suggest that relatively high rates of mutation previously estimated from aDNA data are not entirely an artifact of sequence damage and are likely to be due to other factors such as the persistence of transient polymorphisms. The delta model appears to be particularly useful for placing upper credibility limits on the amount of sequence damage in an alignment, and this capacity might be beneficial for future aDNA studies or for the estimation of sequencing errors in modern DNA.

Phylogeography and environmental correlates of a cap on reproduction: teat number in a small marsupial, Antechinus agilis

Natural selection should optimize litter size in response to the distribution and abundance of resources during breeding. In semelparous, litter-bearing antechinuses, teat number limits litter size. Consequently adaptation has been inferred in explaining intraspecific, geographic variability in teat number for several Antechinus spp. The phylogeography of teat number variation and associated genetic divergence were assessed in A. agilis using nine microsatellites and mitochondrial cytochrome b sequence data. Six-teat Otway Range animals were divergent in microsatellite allele identity and frequencies: samples from three Otway six-teat sites demonstrated significantly greater similarity genetically to those from six-teat animals approximately 250 km to the west, than to nearby Otway 10-teat samples, or to the six-teat animals at Wilsons Promontory. Gene flow between Otway phenotypes appears to have been limited for sufficient time to enable different microsatellite alleles to evolve. Nonetheless, nuclear genetic evidence suggested only incomplete reproductive isolation, and mitochondrial DNA (mtDNA) haplotypes showed no association with teat number. Other populations across the range were no more genetically differentiated from one another than expected from geographic separation. Principal components and distance-based redundancy analyses found an association between environmental variables and geographic distribution of A. agilis teat number - six-teat animals inhabit more temperate forests, whilst those with more teats experience greater seasonality. The apparent restricted breeding between phenotypically distinct animals, together with phylogenetically separate groups of six-teat animals in different locations with similar environments, are consistent with the hypothesis that adaptation to different habitats drives teat number variation in A. agilis.

Mitogenetic structure of brown bears (Ursus arctos L.) in northeastern Europe and a new time frame for the formation of European brown bear lineages

We estimated the phylogenetic relationships of brown bear maternal haplotypes from countries of northeastern Europe (Estonia, Finland and European Russia), using sequences of mitochondrial DNA (mtDNA) control region of 231 bears. Twenty-five mtDNA haplotypes were identified. The brown bear population in northeastern Europe can be divided into three haplogroups: one with bears from all three countries, one with bears from Finland and Russia, and the third composed almost exclusively of bears from European Russia. Four haplotypes from Finland and European Russia matched exactly with haplotypes from Slovakia, suggesting the significance of the current territory of Slovakia in ancient demographic processes of brown bears. Based on the results of this study and those from the recent literature, we hypothesize that the West Carpathian Mountains have served either as one of the northernmost refuge areas or as an important movement corridor for brown bears of the Eastern lineage towards northern Europe during or after the last ice age. Bayesian analyses were performed to investigate the temporal framework of brown bear lineages in Europe. The molecular clock was calibrated using Beringian brown bear sequences derived from radiocarbon-dated ancient samples, and the estimated mutation rate was 29.8% (13.3%-47.6%) per million years. The whole European population and Western and Eastern lineages formed about 175,000, 70,000 and 25,000 years before present, respectively. Our approach to estimating the time frame of brown bear evolution demonstrates the importance of using an appropriate mutation rate, and this has implications for other studies of Pleistocene populations.

Genetic isolation and divergence in sexual traits: evidence for the northern rockhopper penguin Eudyptes moseleyi being a sibling species

The taxonomic status of populations of rockhopper penguins (Eudyptes chrysocome) is still enigmatic. Northern populations differ from southern ones in breeding phenology, song characteristics and head ornaments used as mating signals. We conducted a molecular analysis using mitochondrial DNA sequencing to test if there is a gene flow barrier between northern (subtropical) populations and southern (subantarctic) populations in relation to the Subtropical Convergence, a major ecological boundary for marine organisms. Sequences of the control region and the ND2 gene were analysed in rockhopper penguins and in the macaroni penguin (Eudyptes chrysolophus), a closely related species. Genetic distances and phylogenetic analyses showed a clear split into three clades, two rockhopper clades and the macaroni penguin. Moreover, Theta(ST) and gene flow estimates also suggested genetic structuring within the northern rockhoppers. Our results add further support to the notion that the two rockhopper penguin taxa, often considered as two subspecies, can be recognized as two species E. chrysocome and E. moseleyi. The divergence in mating signals found between these two taxa seems to have occurred recently and relatively rapidly. Thus, the behavioural changes may have been enough to isolate these taxa without the need for morphological differentiation. The findings have important conservational implications, since E. moseleyi is far less abundant than E. chrysocome, but more populations may warrant an uplisting to endangered status if full species status should be recognized for more subpopulations.

[Biological evolution and ancient DNA]

Twenty years after the advent of ancient DNA studies, this discipline seems to have reached the maturity formerly lacking to the fulfilment of its objectives. In its early development paleogenetics, as it is now acknowledged, had to cope with very limited data due to the technical limitations of molecular biology. It led to phylogenetic assumptions often limited in their scope and sometimes non-focused or even spurious results that cast the reluctance of the scientific community. This time seems now over and huge amounts of sequences have become available which overcome the former limitations and bridge the gap between paleogenetics, genomics and population biology. The recent studies over the charismatic woolly mammoth (independent sequencing of the whole mitochondrial genome and of millions of base pairs of the nuclear genome) exemplify the growing accuracy of ancient DNA studies thanks to new molecular approaches. From the earliest publications up to now, the number of mammoth nucleotides was multiplied by 100,000. Likewise, populational approaches of ice-age taxa provide new historical scenarios about the diversification and extinction of the Pleistocene megafauna on the one hand, and about the processes of domestication of animal and vegetal species by Man on the other. They also shed light on the differential structure of molecular diversity between short-term populational research (below 2 My) and long-term (over 2 My) phylogenetic approaches. All those results confirm the growing importance of paleogenetics among the evolutionary biology disciplines.

Speciation and rapid phenotypic differentiation in the yellow-rumped warbler Dendroica coronata complex

The relative importance of the Pleistocene glacial cycles in driving avian speciation remains controversial, partly because species limits in many groups remain poorly understood, and because current taxonomic designations are often based on phenotypic characteristics of uncertain phylogenetic significance. We use mtDNA sequence data to examine patterns of genetic variation, sequence divergence and phylogenetic relationships between phenotypically distinct groups of the yellow-rumped warbler complex. Currently classified as a single species, the complex is composed of two North American migratory forms (myrtle warbler Dendroica coronata coronata and Audubon's warbler Dendroica coronata auduboni), and two largely sedentary forms: Dendroica coronata nigrifrons of Mexico, and Dendroica coronata goldmani of Guatemala. The latter are typically considered to be races of the Audubon's warbler based on plumage characteristics. However, mtDNA sequence data reveal that sedentary Mesoamerican forms are reciprocally monophyletic to each other and to migratory forms, from which they show a long history of isolation. In contrast, migratory myrtle and Audubon's warblers form a single cluster due to high levels of shared ancestral polymorphism as evidenced by widespread sharing of mtDNA haplotypes despite marked phenotypic differentiation. Sedentary and migratory forms diverged in the early Pleistocene, whereas phenotypic differentiation between the two migratory forms has occurred in the Holocene and is likely the result of geographical isolation and subsequent range expansion since the last glaciation. Our results underscore the importance of Quaternary climatic events in driving songbird speciation and indicate that plumage traits can evolve remarkably fast, thus rendering them potentially misleading for inferring systematic relationships.

Model selection and the molecular clock

A brief overview of the methods used to determine phylogenetic distances sets the stage for understanding new research published in PLoS Biology.

Genetic signatures of intermediate divergence: population history of Old and New World Holarctic ravens (Corvus corax)

Many studies of phylogeography, speciation, and species limits restrict their focus to a narrow issue: gene tree monophyly. However, reciprocal monophyly does not provide an ideal touchstone criterion of any aspect of evolutionary divergence. There is a continuum of divergence stages as isolated populations go from initial allele frequency differences to well-differentiated species. Studying intermediate stages of divergence will increase our understanding of geographical speciation, species limits, and conservation priorities. We develop a conceptual framework and terminology for thinking about the stages of 'intermediate polyphyly'. The Holarctic clade of common ravens (Corvus corax), found throughout much of Eurasia and North America, provides a case study of these stages of intermediate divergence. We used coalescent, phylogenetic, and population genetic methods to investigate the history and current status of this Old World-New World distribution using 107 mitochondrial control region sequences. Phylogenetically, New World and Old World samples are intermixed. However, most samples are grouped into small subclades that are restricted to either the New World or the Old World, and only one haplotype is shared between the hemispheres. Analysis of moleculalr variance (amova) results reflect this low haplotype sharing between hemispheres (Phi(ST) = 0.13, P < 0.01). Isolation with Migration (im) coalescent results suggest a sustained period of divergence between the hemispheres and low levels of maternal gene flow. Although there has not been sufficient time to evolve reciprocal monophyly and some gene flow may occur, New World and Old World ravens are genetically quite distinct. We use this example to demonstrate these early stages of divergence as populations go from sharing only internal haplotypes, to sharing no haplotypes, to having population specific subclades. Studies of phylogeography, speciation and systematics will benefit from increased attention to these stages of intermediate polyphyly.

Multiplex amplification of the mammoth mitochondrial genome and the evolution of Elephantidae

In studying the genomes of extinct species, two principal limitations are typically the small quantities of endogenous ancient DNA and its degraded condition, even though products of up to 1,600 base pairs (bp) have been amplified in rare cases. Using small overlapping polymerase chain reaction products, longer stretches of sequences or even whole mitochondrial genomes can be reconstructed, but this approach is limited by the number of amplifications that can be performed from rare samples. Thus, even from well-studied Pleistocene species such as mammoths, ground sloths and cave bears, no DNA sequences of more than about 1,000 bp have been reconstructed. Here we report the complete mitochondrial genome sequence of the Pleistocene woolly mammoth Mammuthus primigenius. We used about 200 mg of bone and a new approach that allows the simultaneous retrieval of multiple sequences from small amounts of degraded DNA. Our phylogenetic analyses show that the mammoth was more closely related to the Asian than to the African elephant. However, the divergence of mammoth, African and Asian elephants occurred over a short time, corresponding to only about 7% of the total length of the phylogenetic tree for the three evolutionary lineages.

Multiplex amplification of ancient DNA

This method is designed to assemble long, continuous DNA sequences using minimal amounts of fragmented ancient DNA as template. This is achieved by a two-step approach. In the first step, multiple fragments are simultaneously amplified in a single multiplex reaction. Subsequently, each of the generated fragments is amplified individually using a single primer pair, in a standard simplex (monoplex) PCR. The ability to amplify multiple fragments simultaneously in the first step allows the generation of large amounts of sequence from rare template DNA, whereas the second nested step increases specificity and decreases amplification of contaminating DNA. In contrast to current protocols using many template-consuming simplex PCRs, the method described allows amplification of several kilobases of sequence in just one reaction. It thus combines optimal template usage with a high specificity and can be performed within a day.

Microevolution and mega-icebergs in the Antarctic

Microevolution is regarded as changes in the frequencies of genes in populations over time. Ancient DNA technology now provides an opportunity to demonstrate evolution over a geological time frame and to possibly identify the causal factors in any such evolutionary event. Using nine nuclear microsatellite DNA loci, we genotyped an ancient population of Adélie penguins (Pygoscelis adeliae) aged approximately 6,000 years B.P. Subfossil bones from this population were excavated by using an accurate stratigraphic method that allowed the identification of individuals even within the same layer. We compared the allele frequencies in the ancient population with those recorded from the modern population at the same site in Antarctica. We report significant changes in the frequencies of alleles between these two time points, hence demonstrating microevolutionary change. This study demonstrates a nuclear gene-frequency change over such a geological time frame. We discuss the possible causes of such a change, including the role of mutation, genetic drift, and the effects of gene mixing among different penguin populations. The latter is likely to be precipitated by mega-icebergs that act to promote migration among penguin colonies that typically show strong natal return.

Detecting past population bottlenecks using temporal genetic data

Population bottlenecks wield a powerful influence on the evolution of species and populations by reducing the repertoire of responses available for stochastic environmental events. Although modern contractions of wild populations due to human-related impacts have been documented globally, discerning historic bottlenecks for all but the most recent and severe events remains a serious challenge. Genetic samples dating to different points in time may provide a solution in some cases. We conducted serial coalescent simulations to assess the extent to which temporal genetic data are informative regarding population bottlenecks. These simulations demonstrated that the power to reject a constant population size hypothesis using both ancient and modern genetic data is almost always higher than that based solely on modern data. The difference in power between the modern and temporal DNA approaches depends significantly on effective population size and bottleneck intensity and less significantly on sample size. The temporal approach provides more power in cases of genetic recovery (via migration) from a bottleneck than in cases of demographic recovery (via population growth). Choice of genetic region is critical, as mutation rate heavily influences the extent to which temporal sampling yields novel information regarding the demographic history of populations.

Late Quaternary loss of genetic diversity in muskox (Ovibos)

Background

The modern wildherd of the tundra muskox (Ovibos moschatus) is native only to the New World (northern North America and Greenland), and its genetic diversity is notably low. However, like several other megafaunal mammals, muskoxen enjoyed a holarctic distribution during the late Pleistocene. To investigate whether collapse in range and loss of diversity might be correlated, we collected mitochondrial sequence data (hypervariable region and cytochrome b) from muskox fossil material recovered from localities in northeastern Asia and the Arctic Archipelago of northern North America, dating from late Pleistocene to late Holocene, and compared our results to existing databases for modern muskoxen.

Results

Two classes of haplotypes were detected in the fossil material. "Surviving haplotypes" (SHs), closely similar or identical to haplotypes found in modern muskoxen and ranging in age from ~22,000 to ~160 yrbp, were found in all New World samples as well as some samples from northeastern Asia. "Extinct haplotypes" (EHs), dating between ~44,000 and ~18,000 yrbp, were found only in material from the Taimyr Peninsula and New Siberian Islands in northeastern Asia. EHs were not found in the Holocene muskoxen specimens available for this study, nor have they been found in other studies of extant muskox populations.

Conclusion

We provisionally interpret this evidence as showing that genetic variability was reduced in muskoxen after the Last Glacial Maximum but before the mid-Holocene, or roughly within the interval 18,000-4,000 yrbp. Narrowing this gap further will require the recovery of more fossils and additional genetic information from this interval.

Late Pleistocene divergence between eastern and western populations of wood ducks (Aix sponsa) inferred by the 'isolation with migration' coalescent method

During the Late Pleistocene, glaciers sundered many species into multiple glacial refugia where populations diverged in allopatry. Although deeply divergent mitochondrial DNA (mtDNA) lineages often reflect the number of refugia occupied, it is unlikely that populations that split during the recent Wisconsin glaciations will have reached reciprocal monophyly. We examined mtDNA control region sequences from eastern and western populations of wood ducks (Aix sponsa) to determine whether their current, disjunct distribution is consistent with the occupancy of two glacial refugia. We used the 'isolation with migration' coalescent method (im) to simultaneously estimate effective population sizes, maternal gene flow, and time since divergence. We found 24 unique haplotypes, none of which were shared between the eastern and western populations, but we did not find diagnostic monophyletic lineages suggestive of long-term isolation in multiple glacial refugia. However, a high Phi ST (0.31) indicates that eastern and western populations are well differentiated in mtDNA, and results from im suggest that these populations have been diverging, without extensive gene flow, for 10,000 to 124,000 years. Results from im further suggest that these populations most likely split about 34,000 years ago, and this time of divergence is consistent with the occupancy of multiple glacial refugia during the Late Wisconsin glaciation. Eastern wood ducks are characterized by high genetic diversity, a large effective population size, and a recent population expansion, while western wood ducks have much less genetic diversity, a smaller population size, and have not undergone a recent population expansion.

Ancient DNA from pollen: a genetic record of population history in Scots pine

Assessments of plant population dynamics in space and time have depended on dated records of fossil pollen synthesized on a subcontinental scale. Genetic analyses of extant populations have revealed spatial relationships that are indicative of past spatial dynamics, but lack an explicit timescale. Synthesis of these data requires genetic analyses from abundant dated fossil material, and this has hitherto been lacking. Fossil pollen is the most abundant material with which to fill this data gap. Here we report genetic analyses of fossil pollen retrieved from Holtjärnen postglacial lake sediment in Sweden and show that plastid DNA is recoverable from Scots Pine and Norway spruce pollen grains that are 100 and 10 000 years old. By sequencing clones from two short plastid PCR products and by using multiple controls we show that the ancient sequences were endogenous to the fossil grains. Comparison of ancient sequences and those obtained from an extant population of Scots pine establishes the first genetic link between extant and fossil samples in this species, providing genetic continuity through time. The finding of one common haplotype present in modern, 100-year old and 10 000-year old samples suggests that it may have persisted near Holtjärnen throughout the postglacial period. This retrieval of ancient DNA from pollen has major implications for plant palaeoecology in conifer species by allowing direct estimates of population dynamics in space and time.

Estimating a nucleotide substitution rate for maize from polymorphism at a major domestication locus

To estimate a rate for single nucleotide substitutions for maize (Zea mays ssp. mays), we have taken advantage of data from genetic and archaeological studies of the domestication of maize from its wild ancestor, teosinte (Z. mays ssp. parviglumis). Genetic studies have shown that the teosinte branched1 (tb1) gene was a major target of human selection during maize domestication, and sequence diversity in the intergenic region 5' to the tb1-coding sequence is extraordinarily low. We show that polymorphism in this region is consistent with new mutation following fixation for a small number of tb1 haplotypes during domestication. Archeological studies suggest that maize was domesticated approximately 6,250-10,000 years ago and subsequently the size of the maize population is thought to have expanded rapidly. Using the observed number of mutations within the region of selection at tb1, the approximate age of maize domestication, and approximations for the maize genealogy, we have derived estimates for the nucleotide substitution rate for the tb1 intergenic region. Using two approaches, one of which is a coalescent approach, we obtain rate estimates of approximately 2.9 x 10(-8) and 3.3 x 10(-8) substitutions per site per year. We also show that the pattern of polymorphism in the tb1 intergenic region appears to have been strongly affected by the mutagenic effect of DNA methylation. Excluding target sites of symmetric DNA methylation (CG and CNG sites) from analysis, the mutation rate estimates are reduced by approximately 50%-60%, while the rates for CG and CNG sites are nearly an order of magnitude higher. We use rate estimates from the tb1 region to estimate the timing of expansion of transposable elements in the maize genome and suggest that this expansion occurred primarily within the last million years.

Tree measures and the number of segregating sites in time-structured population samples

Background

Time-structured genetic samples are a valuable source of information in population genetics because they provide several correlated observations of the underlying evolutionary processes. In this paper we study basic properties of the genetic variation in time-structured samples as reflected in the genealogies relating individuals and the number of segregating sites observed. Our emphasis is on "measurably evolving populations" i.e. populations from which it is possible to obtain time-structured samples that span a significant interval of evolutionary time.

Results

We use results from the coalescent process to derive properties of time-structured samples. In the first section we extend existing results to attain measures on coalescent trees relating time-structured samples. These include the expected time to a most recent common ancestor, the expected total branch length and the expected length of branches subtending only ancient individuals. The effect of different sampling schemes on the latter measure is studied. In the second section we study the special case where the full sample consists of a group of contemporary extant samples and a group of contemporary ancient samples. As regards this case, we present results and applications concerning the probability distribution of the number of segregating sites where a mutation is unique to the ancient individuals and the number of segregating sites where a mutation is shared between ancient and extant individuals.

Conclusion

The methodology and results presented here is of use to the design and interpretation of ancient DNA experiments. Furthermore, the results may be useful in further development of statistical tests of e.g. population dynamics and selection, which include temporal information.

Dissemination and survival of non-indigenous bacterial genomes in pristine Antarctic environments

Continental Antarctic is perceived as a largely pristine environment, although certain localized regions (e.g., parts of the Ross Dependency Dry Valleys) are relatively heavy impacted by human activities. The procedures imposed on Antarctic field parties for the handling and disposal of both solid and liquid wastes are designed to minimise eutrofication and contamination (particularly by human enteric bacteria). However, little consideration has been given to the significance, if any, of less obvious forms of microbial contamination resulting from periodic human activities in Antarctica. The predominant commensal microorganism on human skin, Staphylococcus epidermidis, could be detected by PCR, in Dry Valley mineral soils collected from heavily impacted areas, but could not be detected in Dry Valley mineral soils collected from low impact and pristine areas. Cell viability of this non-enteric human commensal is rapidly lost in Dry Valley mineral soil. However, S. epidermidis can persist for long periods in Dry Valley mineral soil as non-viable cells and/or naked DNA.

Reconstructing the tempo and mode of evolution in an extinct clade of birds with ancient DNA: the giant moas of New Zealand

The tempo and mode of evolution of the extinct giant moas of New Zealand remain obscure because the number of lineages and their divergence times cannot be estimated reliably by using fossil bone characters only. We therefore extracted ancient DNA from 125 specimens and genetically typed them for a 658-bp mtDNA control region sequence. The sequences detected 14 monophyletic lineages, 9 of which correspond to currently recognized species. One of the newly detected lineages was a genetically divergent form of Megalapteryx originally described as a separate species, two more were lineages of Pachyornis in southern and northeastern New Zealand, and two were basal lineages of South Island Dinornis. When results from genetic typing and previous molecular sexing were combined, at least 33.6% of the specimens were incorrectly classified. We used longer sequences of the control region and nine other mtDNA genes totaling 2,814 base pairs to derive a strongly supported phylogeny of the 14 moa lineages. Molecular dating estimated the most recent common ancestor of moas existed after the Oligocene drowning of New Zealand. However, a cycle of lineage-splitting occurred approximately 4-10 million years ago, when the landmass was fragmented by tectonic and mountain-building events and general cooling of the climate. These events resulted in the geographic isolation of lineages and ecological specialization. The spectacular radiation of moa lineages involved significant changes in body size, shape, and mass and provides another example of the general influence of large-scale paleoenvironmental changes on vertebrate evolutionary history.

Ancient DNA

In the past two decades, ancient DNA research has progressed from the retrieval of small fragments of mitochondrial DNA from a few late Holocene specimens, to large-scale studies of ancient populations, phenotypically important nuclear loci, and even whole mitochondrial genome sequences of extinct species. However, the field is still regularly marred by erroneous reports, which underestimate the extent of contamination within laboratories and samples themselves. An improved understanding of these processes and the effects of damage on ancient DNA templates has started to provide a more robust basis for research. Recent methodological advances have included the characterization of Pleistocene mammal populations and discoveries of DNA preserved in ancient sediments. Increasingly, ancient genetic information is providing a unique means to test assumptions used in evolutionary and population genetics studies to reconstruct the past. Initial results have revealed surprisingly complex population histories, and indicate that modern phylogeographic studies may give misleading impressions about even the recent evolutionary past. With the advent and uptake of appropriate methodologies, ancient DNA is now positioned to become a powerful tool in biological research and is also evolving new and unexpected uses, such as in the search for extinct or extant life in the deep biosphere and on other planets.

Moa were many

Until a few hundred years ago, New Zealand hosted several species of flightless ratite birds, collectively known as the moa. We have used mitochondrial sequence data for Dinornis, the largest of the moa, and new coalescent approaches to estimate its population size prior to human arrival ca. 1000-6000 years BP. We show that, as little as 1000 years ago, Dinornis numbered between 300,000 and 1.4 million and that the standing population of all moa species was ca. 3-12 million. This estimate is an order of magnitude larger than the accepted population estimate (ca. 159,000) for all moa species at the arrival of humans and suggests that moa numbers had already declined prior to human settlement.

Beringian paleoecology inferred from permafrost-preserved fungal DNA

The diversity of fungi in permanently frozen soil from northeastern Siberia was studied by culture-independent PCR amplification of diverse environmental 18S rRNA genes. Elaborate protocols to avoid contamination during drilling, sampling, and amplification were used. A broad diversity of eukaryotic DNA sequences that were 510 bp long, including sequences of various fungi, plants, and invertebrates, could be obtained reproducibly from samples that were up to 300,000 to 400,000 years old. The sequences revealed that ancient fungal communities included a diversity of cold-adapted yeasts, dark-pigmented fungi, plant-parasitic fungi, and lichen mycobionts. DNA traces of tree-associated macrofungi in a modern tundra sample indicated that there was a shift in fungal diversity following the last ice age and supported recent results showing that there was a severe change in the plant composition in northeastern Siberia during this period. Interestingly, DNA sequences with high homology to sequences of coprophilic and keratinophilic fungi indicated that feces, hair, skin, and nails could have been sources of ancient megafauna DNA recently reported to be present in small amounts of Siberian permafrost sediments.

Time dependency of molecular rate estimates and systematic overestimation of recent divergence times

Studies of molecular evolutionary rates have yielded a wide range of rate estimates for various genes and taxa. Recent studies based on population-level and pedigree data have produced remarkably high estimates of mutation rate, which strongly contrast with substitution rates inferred in phylogenetic (species-level) studies. Using Bayesian analysis with a relaxed-clock model, we estimated rates for three groups of mitochondrial data: avian protein-coding genes, primate protein-coding genes, and primate d-loop sequences. In all three cases, we found a measurable transition between the high, short-term (< 1-2 Myr) mutation rate and the low, long-term substitution rate. The relationship between the age of the calibration and the rate of change can be described by a vertically translated exponential decay curve, which may be used for correcting molecular date estimates. The phylogenetic substitution rates in mitochondria are approximately 0.5% per million years for avian protein-coding sequences and 1.5% per million years for primate protein-coding and d-loop sequences. Further analyses showed that purifying selection offers the most convincing explanation for the observed relationship between the estimated rate and the depth of the calibration. We rule out the possibility that it is a spurious result arising from sequence errors, and find it unlikely that the apparent decline in rates over time is caused by mutational saturation. Using a rate curve estimated from the d-loop data, several dates for last common ancestors were calculated: modern humans and Neandertals (354 ka; 222-705 ka), Neandertals (108 ka; 70-156 ka), and modern humans (76 ka; 47-110 ka). If the rate curve for a particular taxonomic group can be accurately estimated, it can be a useful tool for correcting divergence date estimates by taking the rate decay into account. Our results show that it is invalid to extrapolate molecular rates of change across different evolutionary timescales, which has important consequences for studies of populations, domestication, conservation genetics, and human evolution.

Understanding differences between phylogenetic and pedigree-derived mtDNA mutation rate: a model using families from the Azores Islands (Portugal)

We analyzed the control region of the mitochondrial DNA (mtDNA) from maternally related individuals originating from the Azores Islands (Portugal) in order to estimate the mutation rate of mtDNA and to gain insights into the process by which a new mutation arises and segregates into heteroplasmy. Length and/or point heteroplasmies were found at least in one individual of 72% of the studied families. Eleven new point substitutions were found, all of them in heteroplasmy, from which five appear to be somatic mutations and six can be considered germinal, evidencing the high frequency of somatic mutations in mtDNA in healthy young individuals. Different values of the mutation rate according to different assumptions were estimated. When considering all the germinal mutations, the value of the mutation rate obtained is one of the highest reported so far in family studies. However, when corrected for gender (assuming that the mutations present in men have the same evolutionary weight of somatic mutations because they will inevitably be lost) and for the probability of intraindividual fixation, the value for the mutation rate obtained for HVRI and HVRII (0.2415 mutations/site/Myr) was in the upper end of the values provided by phylogenetic estimations. These results indicate that the discrepancy, that has been reported previously, between the human mtDNA mutation rates observed along evolutionary timescales and the estimations obtained using family pedigrees can be minimized when corrections for gender proportions in newborn individuals and for the probability of intraindividual fixation are introduced. The analyses performed support the hypothesis that (1) in a constant, tight bottleneck genetic drift alone can explain different patterns of heteroplasmy segregation and (2) in neutral conditions, the destiny of a new mutation is strictly related to the initial proportion of the new variant. Another important point arising from the data obtained is that, even in the absence of a paternal contribution of mtDNA, recombination may occur between mtDNA molecules present in an individual, which is only observable if it occurs between mtDNA types that differ at two or more positions.

Is a large-scale DNA-based inventory of ancient life possible?

A complete DNA-based inventory of the Earth's present biota using large-scale high-throughput DNA sequencing of signature region(s) (DNA barcoding) is an ambitious proposal rivaling the Human Genome Project. We examine whether this approach will also enable us to assess the past diversity of the earth's biota. To test this, we sequenced the 5' terminus of the mitochondrial cytochrome c oxidase I (COI) gene of individuals belonging to a group of extinct ratite birds, the moa of New Zealand. Moa comprised a large number of taxa that radiated in isolation on this oceanic landmass. Using a phylogenetic approach based on a large data set including protein coding and 12S DNA sequences as well as morphology, we now have precise information about the number of moa species that once existed. We show that each of the moa species detected using this extensive data set has a unique COI barcode(s) and that they all show low levels of within-species COI variation. Consequently, we conclude that COI sequences accurately identify the species discovered using the larger data set. Hence, more generally, this study suggests that DNA barcoding might also help us detect other extinct animal species and that a large-scale inventory of ancient life is possible.