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.     

Ancient hyaenas highlight the old problem of estimating evolutionary rates

Phylogenetic analyses of ancient DNA data can provide a timeline for evolutionary change even in the absence of fossils. The power to infer the evolutionary rate is, however, highly dependent on the number and age of samples, the information content of the sequence data and the demographic history of the sampled population. In this issue of Molecular Ecology, Sheng et al. ( 2014 ) analysed mitochondrial DNA sequences isolated from a combination of ancient and present‐day hyaenas, including three Pleistocene samples from China. Using an evolutionary rate inferred from the ages of the ancient sequences, they recalibrated the timing of hyaena diversification and suggest a much more recent evolutionary history than was believed previously. Their results highlight the importance of accurately estimating the evolutionary rate when inferring timescales of geographical and evolutionary diversification.     

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.     

Reconstructing the evolutionary history of China: a caveat about inferences drawn from ancient DNA

The decipherment of the meager information provided by short fragments of ancient mitochondrial DNA (mtDNA) is notoriously difficult but is regarded as a most promising way toward reconstructing the past from the genetic perspective. By haplogroup-specific hypervariable segment (HVS) motif search and matching or near-matching with available modern data sets, most of the ancient mtDNAs can be tentatively assigned to haplogroups, which are often subcontinent specific. Further typing for mtDNA haplogroup-diagnostic coding region polymorphisms, however, is indispensable for establishing the geographic/genetic affinities of ancient samples with less ambiguity. In the present study, we sequenced a fragment (approximately 982 bp) of the mtDNA control region in 76 Han individuals from Taian, Shandong, China, and we combined these data with previously reported samples from Zibo and Qingdao, Shandong. The reanalysis of two previously published ancient mtDNA population data sets from Linzi (same province) then indicates that the ancient populations had features in common with the modern populations from south China rather than any specific affinity to the European mtDNA pool. Our results highlight that ancient mtDNA data obtained under different sampling schemes and subject to potential contamination can easily create the impression of drastic spatiotemporal changes in the genetic structure of a regional population during the past few thousand years if inappropriate methods of data analysis are employed.     

Inferring the ancient population structure of the vulnerable albatross Phoebastria albatrus, combining ancient DNA, stable isotope, and morphometric analyses of archaeological samples

The history of population structure is a key to effective wildlife management and conservation. However, inferring the history of population structure using present genetic structures is problematic when the method is applied to species that have experienced severe population bottlenecks. Ancient DNA analysis seemed to be a promising, direct method for inferring ancient population structures. However, the usual methods for inferring modern population structure, i.e. the phylogeographic approach using mitochondrial DNA and the Bayesian approach using microsatellite DNA, are often unsuitable for ancient samples. In this study, we combined ancient DNA obtained from zooarchaeological bones with carbon/nitrogen stable isotope ratios and morphological variations to infer ancient population structure of the short-tailed albatross Phoebastria albatrus. The results showed that the bird existed in two populations, between which the genetic distance was greater than that of distinct sister albatross species, although no subspecies of P. albatrus have been proposed. Our results suggest that the birds at the present two breeding regions (Torishima in the Izu Islands and two islets of the Senkaku Islands) are descended from these two ancient populations, and that reevaluation of the status and conservation strategy for the species is required. Our results also indicate that lineage breeding on the Senkaku Islands has drastically reduced genetic diversity, while that on Torishima has not. The approach proposed in this study would be useful for inferring ancient population structure, using samples of highly mobile animals and/or samples from archaeological sites, and the reconstructed ancient population structure would be useful for conservation and management recommendations.     

Ancient genomics

The past decade has witnessed a revolution in ancient DNA (aDNA) research. Although the field''s focus was previously limited to mitochondrial DNA and a few nuclear markers, whole genome sequences from the deep past can now be retrieved. This breakthrough is tightly connected to the massive sequence throughput of next generation sequencing platforms and the ability to target short and degraded DNA molecules. Many ancient specimens previously unsuitable for DNA analyses because of extensive degradation can now successfully be used as source materials. Additionally, the analytical power obtained by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans, archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when testing specific hypotheses related to the past.     

Bayesian estimation of the timing and severity of a population bottleneck from ancient DNA

In this first application of the approximate Bayesian computation approach using the serial coalescent, we demonstrated the estimation of historical demographic parameters from ancient DNA. We estimated the timing and severity of a population bottleneck in an endemic subterranean rodent, Ctenomys sociabilis, over the last 10,000 y from two cave sites in northern Patagonia, Argentina. Understanding population bottlenecks is important in both conservation and evolutionary biology. Conservation implications include the maintenance of genetic variation, inbreeding, fixation of mildly deleterious alleles, and loss of adaptive potential. Evolutionary processes are impacted because of the influence of small populations in founder effects and speciation. We found a decrease from a female effective population size of 95,231 to less than 300 females at 2,890 y before present: a 99.7% decline. Our study demonstrates the persistence of a species depauperate in genetic diversity for at least 2,000 y and has implications for modes of speciation in the incredibly diverse rodent genus Ctenomys. Our approach shows promise for determining demographic parameters for other species with ancient and historic samples and demonstrates the power of such an approach using ancient DNA.     

Genome-wide signatures of population bottlenecks and diversifying selection in European wolves

Genomic resources developed for domesticated species provide powerful tools for studying the evolutionary history of their wild relatives. Here we use 61K single-nucleotide polymorphisms (SNPs) evenly spaced throughout the canine nuclear genome to analyse evolutionary relationships among the three largest European populations of grey wolves in comparison with other populations worldwide, and investigate genome-wide effects of demographic bottlenecks and signatures of selection. European wolves have a discontinuous range, with large and connected populations in Eastern Europe and relatively smaller, isolated populations in Italy and the Iberian Peninsula. Our results suggest a continuous decline in wolf numbers in Europe since the Late Pleistocene, and long-term isolation and bottlenecks in the Italian and Iberian populations following their divergence from the Eastern European population. The Italian and Iberian populations have low genetic variability and high linkage disequilibrium, but relatively few autozygous segments across the genome. This last characteristic clearly distinguishes them from populations that underwent recent drastic demographic declines or founder events, and implies long-term bottlenecks in these two populations. Although genetic drift due to spatial isolation and bottlenecks seems to be a major evolutionary force diversifying the European populations, we detected 35 loci that are putatively under diversifying selection. Two of these loci flank the canine platelet-derived growth factor gene, which affects bone growth and may influence differences in body size between wolf populations. This study demonstrates the power of population genomics for identifying genetic signals of demographic bottlenecks and detecting signatures of directional selection in bottlenecked populations, despite their low background variability.     

Using pre- and postexploitation samples to assess the impact of commercial whaling on the genetic characteristics of eastern North Pacific gray and humpback whales and to compare methods used to infer historic demography

Many species of whales went through recent bottlenecks due to commercial whaling. These declines were rapid and recent relative to the life spans and generation times of these species, raising questions regarding to what degree commercial whaling influenced the genetic characteristics of these populations. We analyzed mitochondrial and nuclear DNA from pre- and postwhaling samples from two populations that have arguably shown the greatest degree of recovery: eastern North Pacific gray and humpback whales. We also compare the performance of different methods to test for historic bottlenecks and infer past demography based on genetic data. We found substantially higher levels of genetic diversity in gray than in humpback whales (for both time periods), likely due to recent connectivity between Atlantic and Pacific gray whale populations. Other than mitochondrial diversity in humpback whales, levels of diversity were not lower in contemporary samples relative to prewhaling samples, indicating that commercial whaling had a minimal impact on metrics of genetic diversity themselves. However, it did have large impacts on the patterns of diversity, as evidenced by all coalescent-based methods showing clear evidence of a bottleneck for both populations, whereas all but one method not based on the coalescent failed to detect a bottleneck.     

Mitochondrial and Nuclear DNA Diversity in the Choco and Chibcha Amerinds of Panama

Mitochondrial and nuclear DNA diversities were determined for two Choco-speaking Amerind populations, the Embera and Wounan, sampled widely across their geographic range in eastern Panama. These data were compared with mitochondrial and nuclear diversities determined here and previously for neighboring Chibcha-speaking Ngobe and Kuna populations. Chocoan groups exhibited mitochondrial diversity levels typical for Amerind populations while Chibchan groups revealed reduced mitochondrial diversity. A slight reduction in autosomal levels of heterozygosity was determined for the Chibcha while X and Y variation appeared equivalent in all populations. Genetic distinctiveness of the two linguistic groups contradicts the anthropological theory that Paleoindians migrated repeatedly through the isthmian region and, instead, supports the idea of cultural adaptation by endogenous populations. Reduced genetic diversity in Chibchan populations has been proposed to represent a population bottleneck dating to Chibchan ethnogenesis. The relative sensitivities of haplotype pairwise difference distributions and Tajima's D to detect demographic events such as population bottlenecks are examined. Also, the potential impact of substitution rate heterogeneity, population subdivision, and genetic selection on pairwise difference distributions are discussed. Evidence is presented suggesting that a larger effective population size may obscure the historical signal obtained from nuclear genes while the single mitochondrial locus may provide a moderately strong signal.     

Mitochondrial introgressive hybridization following a demographic expansion in the tomato frogs of Madagascar,genus Dyscophus

Madagascar is a biodiversity hotspot with a unique fauna and flora largely endemic at the species level and highly threatened by habitat destruction. The processes underlying population‐level differentiation in Madagascar's biota are poorly understood and have been proposed to be related to Pleistocene climatic cycles, yet the levels of genetic divergence observed are often suggestive of ancient events. We combined molecular markers of different variability to assess the phylogeography of Madagascar's emblematic tomato frogs (Dyscophus guineti and D. antongilii) and interpret the observed pattern as resulting from ancient and recent processes. Our results suggest that the initial divergence between these taxa is probably old as reflected by protein‐coding nuclear genes and by a strong mitochondrial differentiation of the southernmost population. Dramatic changes in their demography appear to have been triggered by the end of the last glacial period and possibly by the short return of glacial conditions known as the 8K event. This dramatic change resulted in an approximately 50‐fold reduction of the effective population size in various populations of both species. We hypothesize these species' current mitochondrial DNA diversity distribution reflects a swamping of the mitochondrial genetic diversity of D. guineti by that of D. antongilii previous to the populations' bottlenecks during the Holocene, and probably as a consequence of D. antongilii demographic expansion approximately 1 million years ago. Our data support the continued recognition of D. antongilii and D. guineti as separate species and flag D. guineti as the more vulnerable species to past and probably also future environmental changes.     

Multiple SNP Markers Reveal Fine-Scale Population and Deep Phylogeographic Structure in European Anchovy (Engraulis encrasicolus L.)

Geographic surveys of allozymes, microsatellites, nuclear DNA (nDNA) and mitochondrial DNA (mtDNA) have detected several genetic subdivisions among European anchovy populations. However, these studies have been limited in their power to detect some aspects of population structure by the use of a single or a few molecular markers, or by limited geographic sampling. We use a multi-marker approach, 47 nDNA and 15 mtDNA single nucleotide polymorphisms (SNPs), to analyze 626 European anchovies from the whole range of the species to resolve shallow and deep levels of population structure. Nuclear SNPs define 10 genetic entities within two larger genetically distinctive groups associated with oceanic variables and different life-history traits. MtDNA SNPs define two deep phylogroups that reflect ancient dispersals and colonizations. These markers define two ecological groups. One major group of Iberian-Atlantic populations is associated with upwelling areas on narrow continental shelves and includes populations spawning and overwintering in coastal areas. A second major group includes northern populations in the North East (NE) Atlantic (including the Bay of Biscay) and the Mediterranean and is associated with wide continental shelves with local larval retention currents. This group tends to spawn and overwinter in oceanic areas. These two groups encompass ten populations that differ from previously defined management stocks in the Alboran Sea, Iberian-Atlantic and Bay of Biscay regions. In addition, a new North Sea-English Channel stock is defined. SNPs indicate that some populations in the Bay of Biscay are genetically closer to North Western (NW) Mediterranean populations than to other populations in the NE Atlantic, likely due to colonizations of the Bay of Biscay and NW Mediterranean by migrants from a common ancestral population. Northern NE Atlantic populations were subsequently established by migrants from the Bay of Biscay. Populations along the Iberian-Atlantic coast appear to have been founded by secondary waves of migrants from a southern refuge.     

High Potential for Using DNA from Ancient Herring Bones to Inform Modern Fisheries Management and Conservation

Pacific herring (Clupea pallasi) are an abundant and important component of the coastal ecosystems for the west coast of North America. Current Canadian federal herring management assumes five regional herring populations in British Columbia with a high degree of exchange between units, and few distinct local populations within them. Indigenous traditional knowledge and historic sources, however, suggest that locally adapted, distinct regional herring populations may have been more prevalent in the past. Within the last century, the combined effects of commercial fishing and other anthropogenic factors have resulted in severe declines of herring populations, with contemporary populations potentially reflecting only the remnants of a previously more abundant and genetically diverse metapopulation. Through the analysis of 85 archaeological herring bones, this study attempted to reconstruct the genetic diversity and population structure of ancient herring populations using three different marker systems (mitochondrial DNA (mtDNA), microsatellites and SNPs). A high success rate (91%) of DNA recovery was obtained from the extremely small herring bone samples (often <10 mg). The ancient herring mtDNA revealed high haplotype diversity comparable to modern populations, although population discrimination was not possible due to the limited power of the mtDNA marker. Ancient microsatellite diversity was also similar to modern samples, but the data quality was compromised by large allele drop-out and stuttering. In contrast, SNPs were found to have low error rates with no evidence for deviations from Hardy-Weinberg equilibrium, and simulations indicated high power to detect genetic differentiation if loci under selection are used. This study demonstrates that SNPs may be the most effective and feasible approach to survey genetic population structure in ancient remains, and further efforts should be made to screen for high differentiation markers.This study provides the much needed foundation for wider scale studies on temporal genetic variation in herring, with important implications for herring fisheries management, Aboriginal title rights and herring conservation.     

Robust Demographic Inference from Genomic and SNP Data

We introduce a flexible and robust simulation-based framework to infer demographic parameters from the site frequency spectrum (SFS) computed on large genomic datasets. We show that our composite-likelihood approach allows one to study evolutionary models of arbitrary complexity, which cannot be tackled by other current likelihood-based methods. For simple scenarios, our approach compares favorably in terms of accuracy and speed with , the current reference in the field, while showing better convergence properties for complex models. We first apply our methodology to non-coding genomic SNP data from four human populations. To infer their demographic history, we compare neutral evolutionary models of increasing complexity, including unsampled populations. We further show the versatility of our framework by extending it to the inference of demographic parameters from SNP chips with known ascertainment, such as that recently released by Affymetrix to study human origins. Whereas previous ways of handling ascertained SNPs were either restricted to a single population or only allowed the inference of divergence time between a pair of populations, our framework can correctly infer parameters of more complex models including the divergence of several populations, bottlenecks and migration. We apply this approach to the reconstruction of African demography using two distinct ascertained human SNP panels studied under two evolutionary models. The two SNP panels lead to globally very similar estimates and confidence intervals, and suggest an ancient divergence (>110 Ky) between Yoruba and San populations. Our methodology appears well suited to the study of complex scenarios from large genomic data sets.     

Historical demography, selection, and coalescence of mitochondrial and nuclear (genes in Prochilodus species of northern South America

Fishes of the genus Prochilodus are ecologically and commercially important, ubiquitous constituents of large river biota in South America. Recent ecologic and demographic studies indicate that these fishes exist in large, stable populations with adult census numbers exceeding one million individuals. Abundance data present a stark contrast to very low levels of genetic diversity (theta) and small effective population sizes (Ne) observed in a mitochondrial (mt) DNA dataset obtained for two species, Prochilodus mariae, and its putative sister taxon, Prochilodus rubrotaeniatus. Both species occupy major river drainages (Orinoco, Essequibo, and Negro) of northeastern South America. Disparity between expectations based on current abundance and life history information and observed genetic data in these lineages could result from historical demographic bottlenecks, or alternatively, natural selection (i.e., a mtDNA selective sweep). To ascertain underlying processes that affect mtDNA diversity in these species we compared theta and Ne estimates obtained from two, unlinked nuclear loci (calmodulin intron-4 and elongation factor-1alpha intron-6) using an approach based on coalescent theory. Genetic diversity and Ne estimated from mtDNA and nuclear sequences were uniformly low in P. rubrotaeniatus from the Rio Negro, suggesting that this population has encountered a historical bottleneck. For all P. mariae populations, theta and Ne based on nuclear sequences were comparable to expectations based on current adult census numbers and were significantly greater than mtDNA estimates, suggesting that a selective mtDNA sweep has occurred in this species. Comparative genetic analysis indicates that a suite of evolutionary processes involving historical demography and natural selection have influenced patterns of genetic variation and speciation in this important Neotropical fish group.     

A Recent Shift from Polygyny to Monogamy in Humans Is Suggested by the Analysis of Worldwide Y-Chromosome Diversity

Molecular genetic data contain information on the history of populations. Evidence of prehistoric demographic expansions has been detected in the mitochondrial diversity of most human populations and in a Y-chromosome STR analysis, but not in a previous study of 11 Y-chromosome SNPs in Europeans. In this paper, we show that mismatch distributions and tests of mutation/drift equilibrium based on up to 166 Y-chromosome SNPs, in 46 samples from all continents, also fail to support an increase of the male effective population size. Computer simulations show that the low nuclear versus mitochondrial mutation rates cannot explain these results. However, ascertainment bias, i.e., when only highly variable SNP sites are typed, may be concealing any Y SNPs evidence for a recent, but not an ancient, increase in male effective population sizes. The results of our SNP analyses can be reconciled with the expansion of male effective population sizes inferred from STR loci, and with mitochondrial evidence, by admitting that humans were essentially polygynous during much of their history. As a consequence, until recently only a few men may have contributed a large fraction of the Y-chromosome pool at every generation. The number of breeding males may have increased, and the variance of their reproductive success may have decreased, through a recent shift from polygyny to monogamy, which is supported by ethnological data and possibly accompanied the shift from mobile to sedentary communities.     

Using ancient DNA and coalescent-based methods to infer extinction

DNA sequences extracted from preserved remains can add considerable resolution to inference of past population dynamics. For example, coalescent-based methods have been used to correlate declines in some arctic megafauna populations with habitat fragmentation during the last ice age. These methods, however, often fail to detect population declines preceding extinction, most likely owing to a combination of sparse sampling, uninformative genetic markers, and models that cannot account for the increasingly structured nature of populations as habitats decline. As ancient DNA research expands to include full-genome analyses, these data will provide greater resolution of the genomic consequences of environmental change and the genetic signatures of extinction.     

High mitochondrial and nuclear genetic diversity in one of the world’s most endangered seabirds,the Chatham Island Taiko (<Emphasis Type="Italic">Pterodroma magentae</Emphasis>)

Interpreting the levels of genetic diversity in organisms with diverse life and population histories can be difficult. The processes and mechanisms regulating this diversity are complex and still poorly understood. However, endangered species typically have low genetic variation as a consequence of the effects of genetic drift in small populations. In this study we examine genetic variation in the critically endangered Chatham Island Taiko (Tchaik, Pterodroma magentae), one of the world’s rarest seabirds. The Taiko has a very small population size of between 120 and 150 individuals, including just 8–15 breeding pairs. We report surprisingly high mitochondrial and nuclear genetic diversity in this critically endangered long-lived species. We hypothesise that the present Taiko population has retained a significant proportion of its past genetic diversity. However, it is also possible that undiscovered birds are breeding in unknown areas, which could increase the population size estimate. Importantly, from a conservation perspective, we show that the high level of variation is unlikely to be maintained in the future since chicks currently being born have only a limited number of the mitochondrial DNA haplotypes found in adults. Reduced genetic variation will mean that our ability to infer past events and the population history of Taiko using genetics could soon be lost and the power to determine, for example, parentage and other close order relationships will be diminished. Therefore, the maintenance of genetic diversity in future generations is an important consideration for conservation management of the Taiko.     

Mitochondrial DNA and Y-chromosomal diversity in ancient populations of domestic sheep (Ovis aries) in Finland: comparison with contemporary sheep breeds

Background

Several molecular and population genetic studies have focused on the native sheep breeds of Finland. In this work, we investigated their ancestral sheep populations from Iron Age, Medieval and Post-Medieval periods by sequencing a partial mitochondrial DNA D-loop and the 5’-promoter region of the SRY gene. We compared the maternal (mitochondrial DNA haplotypes) and paternal (SNP oY1) genetic diversity of ancient sheep in Finland with modern domestic sheep populations in Europe and Asia to study temporal changes in genetic variation and affinities between ancient and modern populations.

Results

A 523-bp mitochondrial DNA sequence was successfully amplified for 26 of 36 sheep ancient samples i.e. five, seven and 14 samples representative of Iron Age, Medieval and Post-Medieval sheep, respectively. Genetic diversity was analyzed within the cohorts. This ancient dataset was compared with present-day data consisting of 94 animals from 10 contemporary European breeds and with GenBank DNA sequence data to carry out a haplotype sharing analysis. Among the 18 ancient mitochondrial DNA haplotypes identified, 14 were present in the modern breeds. Ancient haplotypes were assigned to the highly divergent ovine haplogroups A and B, haplogroup B being the major lineage within the cohorts. Only two haplotypes were detected in the Iron Age samples, while the genetic diversity of the Medieval and Post-Medieval cohorts was higher. For three of the ancient DNA samples, Y-chromosome SRY gene sequences were amplified indicating that they originated from rams. The SRY gene of these three ancient ram samples contained SNP G-oY1, which is frequent in modern north-European sheep breeds.

Conclusions

Our study did not reveal any sign of major population replacement of native sheep in Finland since the Iron Age. Variations in the availability of archaeological remains may explain differences in genetic diversity estimates and patterns within the cohorts rather than demographic events that occurred in the past. Our ancient DNA results fit well with the genetic context of domestic sheep as determined by analyses of modern north-European sheep breeds.