No evidence of Neandertal admixture in the mitochondrial genomes of early European modern humans and contemporary Europeans

Neandertals, the archaic human form documented in Eurasia until 29,000 years ago, share no mitochondrial haplotype with modern Europeans. Whether this means that the two groups were reproductively isolated is controversial, and indeed nuclear data have been interpreted as suggesting that they admixed. We explored the range of demographic parameters that may have generated the observed mitochondrial diversity, simulating 3.0 million genealogies under six models differing as for the relationships among contemporary Europeans, Neandertals, and Upper Palaeolithic European early modern humans (EEMH), who coexisted with Neandertals for millennia. We compared by Approximate Bayesian Computations the simulation results with mitochondrial diversity in 7 Neandertals, 3 EEMH, and 150 opportunely chosen modern Europeans. A model of genealogical continuity between EEMH and contemporary Europeans, with no Neandertal contribution, received overwhelming support from the analyses. The maximum degree of Neandertal admixture, under the model of gene flow supported by nuclear data, was estimated at 1.5%, but this model proved 20-32 times less likely than a model without any gene flow. Nuclear and mitochondrial evidence might be reconciled if smaller population sizes led to faster lineage sorting for mitochondrial DNA, and Neandertals shared a longer period of common ancestry with the non-African's than with the African's ancestors.     

CoMuS: simulating coalescent histories and polymorphic data from multiple species

The simultaneous analysis of intra‐ and interspecies variation is challenging mainly because our knowledge about patterns of polymorphisms where both intra‐ and interspecies samples coexist is limited. In this study, we present CoMuS (Coalescent of Multiple Species), a multispecies coalescent software that can simulate intra‐ and interspecies polymorphisms. CoMuS supports a variety of speciation models and demographic scenarios related to the history of each species. In CoMuS, speciation can be accompanied by either instant or gradual isolation between sister species. Sampling may also occur in the past, and thus, we can study simultaneously extinct and extant species. Our software supports both the infinite‐ and the finite‐site model, with substitution rate heterogeneity among sites and a user‐defined proportion of invariable sites. We demonstrate the usage of CoMuS in various applications: species delimitation, software testing, model selection and parameter inference involving present‐day and ancestral samples, comparison between gradual and instantaneous isolation models, estimation of speciation time between human and chimpanzee using both intra‐ and interspecies variation. We expect that CoMuS will be particularly useful for studies where species have been separated recently from their common ancestor and phenomena such as incomplete lineage sorting or introgression still occur.     

Genetic population structure and demography of an apex predator,the tiger shark Galeocerdo cuvier

Population genetics has been increasingly applied to study large sharks over the last decade. Whilst large shark species are often difficult to study with direct methods, improved knowledge is needed for both population management and conservation, especially for species vulnerable to anthropogenic and climatic impacts. The tiger shark, Galeocerdo cuvier, is an apex predator known to play important direct and indirect roles in tropical and subtropical marine ecosystems. While the global and Indo‐West Pacific population genetic structure of this species has recently been investigated, questions remain over population structure and demographic history within the western Indian (WIO) and within the western Pacific Oceans (WPO). To address the knowledge gap in tiger shark regional population structures, the genetic diversity of 286 individuals sampled in seven localities was investigated using 27 microsatellite loci and three mitochondrial genes (CR, COI, and cytb). A weak genetic differentiation was observed between the WIO and the WPO, suggesting high genetic connectivity. This result agrees with previous studies and highlights the importance of the pelagic behavior of this species to ensure gene flow. Using approximate Bayesian computation to couple information from both nuclear and mitochondrial markers, evidence of a recent bottleneck in the Holocene (2,000–3,000 years ago) was found, which is the most probable cause for the low genetic diversity observed. A contemporary effective population size as low as 111 [43,369] was estimated during the bottleneck. Together, these results indicate low genetic diversity that may reflect a vulnerable population sensitive to regional pressures. Conservation measures are thus needed to protect a species that is classified as Near Threatened.     

Testing hypotheses of mitochondrial gene‐tree paraphyly: unravelling mitochondrial capture of the Streak‐breasted Scimitar Babbler (Pomatorhinus ruficollis) by the Taiwan Scimitar Babbler (Pomatorhinus musicus)

Species‐level paraphyly inferred from mitochondrial gene trees is a prevalent phenomenon in taxonomy and systematics, but there are several potential causes that are not easily explained by currently used methods. This study aimed to test the underlying causes behind the observed paraphyly of Streak‐breasted Scimitar Babbler (Pomatorhinus ruficollis) via statistical analyses of four mitochondrial (mtDNA) and nine nuclear (nuDNA) genes. Mitochondrial gene trees show paraphyly of P. ruficollis with respect to the Taiwan Scimitar Babbler (Pomatorhinus musicus), but nuclear genealogies support a sister‐group relationship. Predictive coalescent simulations imply several hypothetical explanations, the most likely being mitochondrial capture of P. ruficollis by P. musicus for the observed cyto‐nuclear incongruence. Further approximate Bayesian computation suggests a unidirectional introgression model with substantial level of gene flow from P. ruficollis to P. musicus during their initial divergence during the Late Pleistocene. This specific observation frames several potential causes for incongruent outcomes of mitochondrial and nuclear introgression in general, and on the whole, our results underscore the strength of multiple independent loci for species delimitation and importance of testing hypotheses that explain disparate causes of mitochondrial gene‐tree paraphyly.     

Exploring Approximate Bayesian Computation for inferring recent demographic history with genomic markers in nonmodel species

Approximate Bayesian computation (ABC) is widely used to infer demographic history of populations and species using DNA markers. Genomic markers can now be developed for nonmodel species using reduced representation library (RRL) sequencing methods that select a fraction of the genome using targeted sequence capture or restriction enzymes (genotyping‐by‐sequencing, GBS). We explored the influence of marker number and length, knowledge of gametic phase, and tradeoffs between sample size and sequencing depth on the quality of demographic inferences performed with ABC. We focused on two‐population models of recent spatial expansion with varying numbers of unknown parameters. Performing ABC on simulated data sets with known parameter values, we found that the timing of a recent spatial expansion event could be precisely estimated in a three‐parameter model. Taking into account uncertainty in parameters such as initial population size and migration rate collectively decreased the precision of inferences dramatically. Phasing haplotypes did not improve results, regardless of sequence length. Numerous short sequences were as valuable as fewer, longer sequences, and performed best when a large sample size was sequenced at low individual depth, even when sequencing errors were added. ABC results were similar to results obtained with an alternative method based on the site frequency spectrum (SFS) when performed with unphased GBS‐type markers. We conclude that unphased GBS‐type data sets can be sufficient to precisely infer simple demographic models, and discuss possible improvements for the use of ABC with genomic data.     

The impact of past climate change on genetic variation and population connectivity in the Icelandic arctic fox

Previous studies have suggested that the presence of sea ice is an important factor in facilitating migration and determining the degree of genetic isolation among contemporary arctic fox populations. Because the extent of sea ice is dependent upon global temperatures, periods of significant cooling would have had a major impact on fox population connectivity and genetic variation. We tested this hypothesis by extracting and sequencing mitochondrial control region sequences from 17 arctic foxes excavated from two late-ninth-century to twelfth-century AD archaeological sites in northeast Iceland, both of which predate the Little Ice Age (approx. sixteenth to nineteenth century). Despite the fact that five haplotypes have been observed in modern Icelandic foxes, a single haplotype was shared among all of the ancient individuals. Results from simulations within an approximate Bayesian computation framework suggest that the rapid increase in Icelandic arctic fox haplotype diversity can only be explained by sea-ice-mediated fox immigration facilitated by the Little Ice Age.     

Molecular evidence for introgressive hybridization in New Zealand masked gulls

We used mitochondrial DNA (mtDNA) gene sequences and nuclear microsatellite loci to investigate the extent and outcome of hybridization between the Black-billed Gull Chroicocephalus bulleri and the Red-billed Gull Chroicocephalus novaehollandiae scopulinus in New Zealand. Six of 26 sampled Black-billed Gulls possessed mtDNA typical of Red-billed Gulls, but allele frequencies at six polymorphic microsatellites provided little evidence of mixed ancestry expected in very recent hybrids. None of the Red-billed Gulls sampled from different colonies possessed Black-billed Gull mtDNA expected in the reciprocal cross, suggesting that hybridization in the two species typically occurs between female Red-billed Gulls and Black-billed Gull males. The lack of any hybrid signal in the nuclear loci indicates that there has been extensive backcrossing with Black-billed Gulls, effectively diluting the Red-billed Gull nuclear DNA contribution. Divergence of Red-billed Gulls and Black-billed Gulls occurred approximately 250 000 years ago, indicating that unsorted ancestral polymorphism is an unlikely alternative to hybridization. Comparing demographic models within an approximate Bayesian computation (ABC) framework, we confirm that the observed patterns cannot result from incomplete lineage sorting. Using an ABC random forest approach, we determined that the most likely model explaining the data is a recent introgression scenario, whereby unidirectional gene flow is re-established following a period of strict isolation. The ability of Black-billed and Red-billed Gulls to successfully interbreed shows that despite significant differentiation (F_ST > 0.3), there has been insufficient time for the two species to develop complete reproductive isolation. The apparent one-way transfer of Red-billed Gull mtDNA into Black-billed Gulls and extensive backcrossing argues against cytoplasmic–nuclear genome incompatibilities between the two species. We hypothesize that the specific mate recognition system cued on colours of soft parts normally functions to prevent hybridization, but that it can break down under demographic conditions where there is a shortage of available mates and a surplus of females in the Red-billed Gull population. The high incidence of introgression in Black-billed Gulls conflicts with field observations that interbreeding is extremely rare.     

Lack of support for the time‐dependent molecular evolution hypothesis

There is increasing momentum surrounding the hypothesis that rates of molecular evolution between individuals within contemporary populations are high, and that these rates decrease as a function of time, perhaps over several millions of years, before reaching stationarity. The implications of this are powerful, potentially reshaping our view of how climate history impacts upon both species distribution patterns and the geographic structuring of genetic variation within species. However, our assessment of the hypothesis reveals a lack of theoretical support and empirical evidence for hypothesized magnitudes of time‐dependent rates of molecular evolution, with much of the apparent rate changes coming from artefacts and biases inherent in the methods of rate estimation. Our assessment also reveals a problem with how serial sampling is implemented for mutation rate estimation using ancient DNA samples, rendering published estimates unreliable.     

Widespread primary,but geographically restricted secondary,human introductions of wall lizards,Podarcis muralis

Establishing the introduction pathways of alien species is a fundamental task in invasion biology. The common wall lizard, Podarcis muralis, has been widely introduced outside of its native range in both Europe and North America, primarily through escaped pets or deliberate release of animals from captive or wild populations. Here, we use Bayesian clustering, approximate Bayesian computation (ABC) methods and network analyses to reconstruct the origin and colonization history of 23 non‐native populations of wall lizards in England. Our analyses show that established populations in southern England originate from at least nine separate sources of animals from native populations in France and Italy. Secondary introductions from previously established non‐native populations were supported for eleven (47%) populations. In contrast to the primary introductions, secondary introductions were highly restricted geographically and appear to have occurred within a limited time frame rather than being increasingly common. Together, these data suggest that extant wall lizard populations in England are the result of isolated accidental and deliberate releases of imported animals since the 1970s, with only local translocation of animals from established non‐native populations. Given that populations introduced as recently as 25 years ago show evidence of having adapted to cool climate, discouraging further translocations may be important to prevent more extensive establishment on the south coast of England.     

Rapid increase in southern elephant seal genetic diversity after a founder event

Genetic diversity provides the raw material for populations to respond to changing environmental conditions. The evolution of diversity within populations is based on the accumulation of mutations and their retention or loss through selection and genetic drift, while migration can also introduce new variation. However, the extent to which population growth and sustained large population size can lead to rapid and significant increases in diversity has not been widely investigated. Here, we assess this empirically by applying approximate Bayesian computation to a novel ancient DNA dataset that spans the life of a southern elephant seal (Mirounga leonina) population, from initial founding approximately 7000 years ago to eventual extinction within the past millennium. We find that rapid population growth and sustained large population size can explain substantial increases in population genetic diversity over a period of several hundred generations, subsequently lost when the population went to extinction. Results suggest that the impact of diversity introduced through migration was relatively minor. We thus demonstrate, by examining genetic diversity across the life of a population, that environmental change could generate the raw material for adaptive evolution over a very short evolutionary time scale through rapid establishment of a large, stable population.     

2BAD: an application to estimate the parental contributions during two independent admixture events

Several approaches have been developed to calculate the relative contributions of parental populations in single admixture event scenarios, including Bayesian methods. In many breeds and populations, it may be more realistic to consider multiple admixture events. However, no approach has been developed to date to estimate admixture in such cases. This report describes a program application, 2BAD (for 2-event Bayesian ADmixture), which allows the consideration of up to two independent admixture events involving two or three parental populations and a single admixed population, depending on the number of populations sampled. For each of these models, it is possible to estimate several parameters (admixture, effective sizes, etc.) using an approximate Bayesian computation approach. In addition, the program allows comparing pairs of admixture models, determining which is the most likely given data. The application was tested through simulations and was found to provide good estimates for the contribution of the populations at the two admixture events. We were also able to determine whether an admixture model was more likely than a simple split model.     

Can the Site-Frequency Spectrum Distinguish Exponential Population Growth from Multiple-Merger Coalescents?

The ability of the site-frequency spectrum (SFS) to reflect the particularities of gene genealogies exhibiting multiple mergers of ancestral lines as opposed to those obtained in the presence of population growth is our focus. An excess of singletons is a well-known characteristic of both population growth and multiple mergers. Other aspects of the SFS, in particular, the weight of the right tail, are, however, affected in specific ways by the two model classes. Using an approximate likelihood method and minimum-distance statistics, our estimates of statistical power indicate that exponential and algebraic growth can indeed be distinguished from multiple-merger coalescents, even for moderate sample sizes, if the number of segregating sites is high enough. A normalized version of the SFS (nSFS) is also used as a summary statistic in an approximate Bayesian computation (ABC) approach. The results give further positive evidence as to the general eligibility of the SFS to distinguish between the different histories.     

Bayesian coalescent inference of major human mitochondrial DNA haplogroup expansions in Africa

Past population size can be estimated from modern genetic diversity using coalescent theory. Estimates of ancestral human population dynamics in sub-Saharan Africa can tell us about the timing and nature of our first steps towards colonizing the globe. Here, we combine Bayesian coalescent inference with a dataset of 224 complete human mitochondrial DNA (mtDNA) sequences to estimate effective population size through time for each of the four major African mtDNA haplogroups (L0-L3). We find evidence of three distinct demographic histories underlying the four haplogroups. Haplogroups L0 and L1 both show slow, steady exponential growth from 156 to 213kyr ago. By contrast, haplogroups L2 and L3 show evidence of substantial growth beginning 12-20 and 61-86kyr ago, respectively. These later expansions may be associated with contemporaneous environmental and/or cultural changes. The timing of the L3 expansion--8-12kyr prior to the emergence of the first non-African mtDNA lineages--together with high L3 diversity in eastern Africa, strongly supports the proposal that the human exodus from Africa and subsequent colonization of the globe was prefaced by a major expansion within Africa, perhaps driven by some form of cultural innovation.     

Ancient DNA suggests modern wolves trace their origin to a Late Pleistocene expansion from Beringia

Grey wolves (Canis lupus) are one of the few large terrestrial carnivores that have maintained a wide geographical distribution across the Northern Hemisphere throughout the Pleistocene and Holocene. Recent genetic studies have suggested that, despite this continuous presence, major demographic changes occurred in wolf populations between the Late Pleistocene and early Holocene, and that extant wolves trace their ancestry to a single Late Pleistocene population. Both the geographical origin of this ancestral population and how it became widespread remain unknown. Here, we used a spatially and temporally explicit modelling framework to analyse a data set of 90 modern and 45 ancient mitochondrial wolf genomes from across the Northern Hemisphere, spanning the last 50,000 years. Our results suggest that contemporary wolf populations trace their ancestry to an expansion from Beringia at the end of the Last Glacial Maximum, and that this process was most likely driven by Late Pleistocene ecological fluctuations that occurred across the Northern Hemisphere. This study provides direct ancient genetic evidence that long‐range migration has played an important role in the population history of a large carnivore, and provides insight into how wolves survived the wave of megafaunal extinctions at the end of the last glaciation. Moreover, because Late Pleistocene grey wolves were the likely source from which all modern dogs trace their origins, the demographic history described in this study has fundamental implications for understanding the geographical origin of the dog.     

Genetic variation reveals large-scale population expansion and migration during the expansion of Bantu-speaking peoples

The majority of sub-Saharan Africans today speak a number of closely related languages collectively referred to as ‘Bantu’ languages. The current distribution of Bantu-speaking populations has been found to largely be a consequence of the movement of people rather than a diffusion of language alone. Linguistic and single marker genetic studies have generated various hypotheses regarding the timing and the routes of the Bantu expansion, but these hypotheses have not been thoroughly investigated. In this study, we re-analysed microsatellite markers typed for large number of African populations that—owing to their fast mutation rates—capture signatures of recent population history. We confirm the spread of west African people across most of sub-Saharan Africa and estimated the expansion of Bantu-speaking groups, using a Bayesian approach, to around 5600 years ago. We tested four different divergence models for Bantu-speaking populations with a distribution comprising three geographical regions in Africa. We found that the most likely model for the movement of the eastern branch of Bantu-speakers involves migration of Bantu-speaking groups to the east followed by migration to the south. This model, however, is only marginally more likely than other models, which might indicate direct movement from the west and/or significant gene flow with the western Branch of Bantu-speakers. Our study use multi-loci genetic data to explicitly investigate the timing and mode of the Bantu expansion and it demonstrates that west African groups rapidly expanded both in numbers and over a large geographical area, affirming the fact that the Bantu expansion was one of the most dramatic demographic events in human history.     

Colonization of the Mediterranean basin by the vector biting midge species Culicoides imicola: an old story

Understanding the demographic history and genetic make‐up of colonizing species is critical for inferring population sources and colonization routes. This is of main interest for designing accurate control measures in areas newly colonized by vector species of economically important pathogens. The biting midge Culicoides imicola is a major vector of orbiviruses to livestock. Historically, the distribution of this species was limited to the Afrotropical region. Entomological surveys first revealed the presence of C. imicola in the south of the Mediterranean basin by the 1970s. Following recurrent reports of massive bluetongue outbreaks since the 1990s, the presence of the species was confirmed in northern areas. In this study, we addressed the chronology and processes of C. imicola colonization in the Mediterranean basin. We characterized the genetic structure of its populations across Mediterranean and African regions using both mitochondrial and nuclear markers, and combined phylogeographical analyses with population genetics and approximate Bayesian computation. We found a west/east genetic differentiation between populations, occurring both within Africa and within the Mediterranean basin. We demonstrated that three of these groups had experienced demographic expansions in the Pleistocene, probably because of climate changes during this period. Finally, we showed that C. imicola could have colonized the Mediterranean basin in the Late Pleistocene or Early Holocene through a single event of introduction; however, we cannot exclude the hypothesis involving two routes of colonization. Thus, the recent bluetongue outbreaks are not linked to C. imicola colonization event, but rather to biological changes in the vector or the virus.     

Model misspecification confounds the estimation of rates and exaggerates their time dependency

While welcoming the comment of Ho et al. ( 2015 ), we find little that undermines the strength of our criticism, and it would appear they have misunderstood our central argument. Here we respond with the purpose of reiterating that we are (i) generally critical of much of the evidence presented in support of the time‐dependent molecular rate (TDMR) hypothesis and (ii) specifically critical of estimates of μ derived from tip‐dated sequences that exaggerate the importance of purifying selection as an explanation for TDMR over extended timescales. In response to assertions put forward by Ho et al. ( 2015 ), we use panmictic coalescent simulations of temporal data to explore a fundamental assumption for tip‐dated tree shape and associated mutation rate estimates, and the appropriateness and utility of the date randomization test. The results reveal problems for the joint estimation of tree topology, effective population size and μ with tip‐dated sequences using beast . Given the simulations, beast consistently obtains incorrect topological tree structures that are consistent with the substantial overestimation of μ and underestimation of effective population size. Data generated from lower effective population sizes were less likely to fail the date randomization test yet still resulted in substantially upwardly biased estimates of rates, bringing previous estimates of μ from temporally sampled DNA sequences into question. We find that our general criticisms of both the hypothesis of time‐dependent molecular evolution and Bayesian methods to estimate μ from temporally sampled DNA sequences are further reinforced.     

Elevated substitution rate estimates from ancient DNA: model violation and bias of Bayesian methods

The increasing ability to extract and sequence DNA from noncontemporaneous tissue offers biologists the opportunity to analyse ancient DNA (aDNA) together with modern DNA (mDNA) to address the taxonomy of extinct species, evolutionary origins, historical phylogeography and biogeography. Perhaps more exciting are recent developments in coalescence-based Bayesian inference that offer the potential to use temporal information from aDNA and mDNA for the estimation of substitution rates and divergence dates as an alternative to fossil and geological calibration. This comes at a time of growing interest in the possibility of time dependency for molecular rate estimates. In this study, we provide a critical assessment of Bayesian Markov chain Monte Carlo (MCMC) analysis for the estimation of substitution rate using simulated samples of aDNA and mDNA. We conclude that the current models and priors employed in Bayesian MCMC analysis of heterochronous mtDNA are susceptible to an upward bias in the estimation of substitution rates because of model misspecification when the data come from populations with less than simple demographic histories, including sudden short-lived population bottlenecks or pronounced population structure. However, when model misspecification is only mild, then the 95% highest posterior density intervals provide adequate frequentist coverage of the true rates.     

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.