Palaeo-Eskimo genetic ancestry and the peopling of Chukotka and North America.

Much of the American Arctic was first settled 5,000 years ago, by groups of people known as Palaeo-Eskimos. They were subsequently joined and largely displaced around 1,000 years ago by ancestors of the present-day Inuit and Yup'ik1-3. The genetic relationship between Palaeo-Eskimos and Native American, Inuit, Yup'ik and Aleut populations remains uncertain4-6. Here we present genomic data for 48 ancient individuals from Chukotka, East Siberia, the Aleutian Islands, Alaska, and the Canadian Arctic. We co-analyse these data with data from present-day Alaskan Iñupiat and West Siberian populations and published genomes. Using methods based on rare-allele and haplotype sharing, as well as established techniques4,7-9, we show that Palaeo-Eskimo-related ancestry is ubiquitous among people who speak Na-Dene and Eskimo-Aleut languages. We develop a comprehensive model for the Holocene peopling events of Chukotka and North America, and show that Na-Dene-speaking peoples, people of the Aleutian Islands, and Yup'ik and Inuit across the Arctic region all share ancestry from a single Palaeo-Eskimo-related Siberian source.

The population history of northeastern Siberia since the Pleistocene.

Northeastern Siberia has been inhabited by humans for more than 40,000 years but its deep population history remains poorly understood. Here we investigate the late Pleistocene population history of northeastern Siberia through analyses of 34 newly recovered ancient genomes that date to between 31,000 and 600 years ago. We document complex population dynamics during this period, including at least three major migration events: an initial peopling by a previously unknown Palaeolithic population of 'Ancient North Siberians' who are distantly related to early West Eurasian hunter-gatherers; the arrival of East Asian-related peoples, which gave rise to 'Ancient Palaeo-Siberians' who are closely related to contemporary communities from far-northeastern Siberia (such as the Koryaks), as well as Native Americans; and a Holocene migration of other East Asian-related peoples, who we name 'Neo-Siberians', and from whom many contemporary Siberians are descended. Each of these population expansions largely replaced the earlier inhabitants, and ultimately generated the mosaic genetic make-up of contemporary peoples who inhabit a vast area across northern Eurasia and the Americas.

Stone Age Yersinia pestis genomes shed light on the early evolution, diversity, and ecology of plague.

The bacterial pathogen Yersinia pestis gave rise to devastating outbreaks throughout human history, and ancient DNA evidence has shown it afflicted human populations as far back as the Neolithic. Y. pestis genomes recovered from the Eurasian Late Neolithic/Early Bronze Age (LNBA) period have uncovered key evolutionary steps that led to its emergence from a Yersinia pseudotuberculosis-like progenitor; however, the number of reconstructed LNBA genomes are too few to explore its diversity during this critical period of development. Here, we present 17 Y. pestis genomes dating to 5,000 to 2,500 y BP from a wide geographic expanse across Eurasia. This increased dataset enabled us to explore correlations between temporal, geographical, and genetic distance. Our results suggest a nonflea-adapted and potentially extinct single lineage that persisted over millennia without significant parallel diversification, accompanied by rapid dispersal across continents throughout this period, a trend not observed in other pathogens for which ancient genomes are available. A stepwise pattern of gene loss provides further clues on its early evolution and potential adaptation. We also discover the presence of the flea-adapted form of Y. pestis in Bronze Age Iberia, previously only identified in in the Caucasus and the Volga regions, suggesting a much wider geographic spread of this form of Y. pestis. Together, these data reveal the dynamic nature of plague's formative years in terms of its early evolution and ecology.

A minimally destructive protocol for DNA extraction from ancient teeth.

Ancient DNA sampling methods-although optimized for efficient DNA extraction-are destructive, relying on drilling or cutting and powdering (parts of) bones and teeth. As the field of ancient DNA has grown, so have concerns about the impact of destructive sampling of the skeletal remains from which ancient DNA is obtained. Due to a particularly high concentration of endogenous DNA, the cementum of tooth roots is often targeted for ancient DNA sampling, but destructive sampling methods of the cementum often result in the loss of at least one entire root. Here, we present a minimally destructive method for extracting ancient DNA from dental cementum present on the surface of tooth roots. This method does not require destructive drilling or grinding, and, following extraction, the tooth remains safe to handle and suitable for most morphological studies, as well as other biochemical studies, such as radiocarbon dating. We extracted and sequenced ancient DNA from 30 teeth (and nine corresponding petrous bones) using this minimally destructive extraction method in addition to a typical tooth sampling method. We find that the minimally destructive method can provide ancient DNA that is of comparable quality to extracts produced from teeth that have undergone destructive sampling processes. Further, we find that a rigorous cleaning of the tooth surface combining diluted bleach and UV light irradiation seems sufficient to minimize external contaminants usually removed through the physical removal of a superficial layer when sampling through regular powdering methods.

Ultra-broadband spectroscopy using a 2-11.5 µm IDFG-based supercontinuum source.

Supercontinuum sources based on intrapulse difference frequency generation (IDFG) from mode-locked lasers open new opportunities in mid-infrared gas spectroscopy. These sources provide high power and ultra-broadband spectral coverage in the molecular fingerprint region with very low relative intensity noise. Here, we demonstrate the performance of such a light source in combination with a multipass cell and a custom-built Fourier transform spectrometer (FTS) for multispecies trace gas detection. The light source provides a low-noise, ultra-broad spectrum from 2-11.5 µm with ∼3 W output power, outperforming existing mid-infrared supercontinuum sources in terms of noise, spectral coverage, and output power. This translates to an excellent match for spectroscopic applications, establishing (sub-)ppb sensitivity for molecular hydrocarbons (e.g., CH4, C2H4), oxides (e.g., SO2, NOx), and small organic molecules (e.g., acetone, ethyl acetate) over the spectral range of the supercontinuum source with a measurement time varying from seconds to minutes. We demonstrate a practical application by measuring the off-gas composition of a bioreactor containing an acidic ammonia-oxidizing culture with the simultaneous detection of multiple nitrogen oxides (NO, NO2, N2O, etc.). As the different species absorb various parts of the spectrum, these results highlight the functionality of this spectroscopic system for biological and environmental applications.

Human auditory ossicles as an alternative optimal source of ancient DNA.

DNA recovery from ancient human remains has revolutionized our ability to reconstruct the genetic landscape of the past. Ancient DNA research has benefited from the identification of skeletal elements, such as the cochlear part of the osseous inner ear, that provides optimal contexts for DNA preservation; however, the rich genetic information obtained from the cochlea must be counterbalanced against the loss of morphological information caused by its sampling. Motivated by similarities in developmental processes and histological properties between the cochlea and auditory ossicles, we evaluate the ossicles as an alternative source of ancient DNA. We show that ossicles perform comparably to the cochlea in terms of DNA recovery, finding no substantial reduction in data quantity and minimal differences in data quality across preservation conditions. Ossicles can be sampled from intact skulls or disarticulated petrous bones without damage to surrounding bone, and we argue that they should be used when available to reduce damage to human remains. Our results identify another optimal skeletal element for ancient DNA analysis and add to a growing toolkit of sampling methods that help to better preserve skeletal remains for future research while maximizing the likelihood that ancient DNA analysis will produce useable results.

Longwave infrared (6.6-11.4†µm) dual-comb spectroscopy with 240,000 comb-mode-resolved data points at video rate.

Using sub-3-cycle pulses from mode-locked Cr:ZnS lasers at λ ≈ 2.4 µm as a driving source, we performed high-resolution dual-frequency-comb spectroscopy in the longwave infrared (LWIR) range. A duo of highly coherent broadband (6.6-11.4 µm) frequency combs were produced via intrapulse difference frequency generation in zinc germanium phosphide (ZGP) crystals. Fast (up to 0.1 s per spectrum) acquisition of 240,000 comb-mode-resolved data points, spaced by 80 MHz and referenced to a Rb clock, was demonstrated, resulting in metrology grade molecular spectra of N2O (nitrous oxide) and CH3OH (methane). The key to high-speed massive spectral data acquisition was low intensity and phase noise of the LWIR combs and high (7.5%) downconversion efficiency, resulting in a LWIR power of 300 mW for each comb.

Kerr-lens mode-locked Cr:ZnS oscillator reaches the spectral span of an optical octave.

We report, to the best of our knowledge, the first super-octave femtosecond polycrystalline Cr:ZnS laser at the central wavelength 2.4 µm. The laser is based on a non-polarizing astigmatic X-folded resonator with normal incidence mounting of the gain element. The chromatic dispersion of the resonator is controlled with a set of dispersive mirrors within one third of an optical octave over 2.05-2.6 µm range. The resonator's optics is highly reflective in the range 1.8-2.9 µm. The components of the oscillator's output spectrum at the wavelengths 1.6 µm and 3.2 µm are detected at -60 dB with respect to the main peak. Average power of few-cycle Kerr-lens mode-locked laser is 1.4 W at the pulse repetition frequency 79 MHz. That corresponds to 22% conversion of cw radiation of Er-doped fiber laser, which we used for optical pumping of the Cr:ZnS oscillator.

Middle-IR frequency comb based on Cr:ZnS laser.

We report, to the best of our knowledge, the first fully referenced Cr:ZnS optical frequency comb. The comb features few cycle output pulses with 3.25 W average power at 80 MHz repetition rate, spectrum spanning 60 THz in the middle-IR range 1.79-2.86 µm, and a small footprint (0.1 m2), The spectral components used for the measurement of the comb's carrier envelope offset frequency were obtained directly inside the polycrystalline Cr:ZnS laser medium via intrinsic nonlinear interferometry. Using this scheme we stabilized the offset frequency of the comb with the residual phase noise of 75 mrads.

Multi-octave visible to long-wave IR femtosecond continuum generated in Cr:ZnS-GaSe tandem.

We report a technique for generation of broad and coherent femtosecond (fs) continua that span several octaves from visible to long-wave IR parts of the spectrum (0.4-18 µm). The approach is based on simultaneous amplification of few-cycle pulses at 2.5 µm central wavelength at 80 MHz repetition rate, and augmentation of their spectrum via three-wave mixing in a tandem arrangement of polycrystalline Cr:ZnS and single crystal GaSe. The obtained average power levels include several mW in the 0.4-0.8 µm visible, 0.23 W in the 0.8-2 µm near-IR, up to 4 W in the 2-3 µm IR, and about 17 mW in the 3-18 µm long-wave IR bands, respectively. High brightness and mutual coherence of all parts of the continuum was confirmed by direct detections of the carrier envelope offset frequency of the master oscillator.

Characterization of high-harmonic emission from ZnO up to 11 eV pumped with a Cr:ZnS high-repetition-rate source.

We report the measurement of high-order harmonics from a ZnO crystal with photon energies up to 11 eV generated by a high-repetition-rate femtosecond Cr:ZnS laser operating in the mid-infrared at 2-3 µm, delivering few-cycle pulses with multi-watt average power and multi-megawatt peak power. High-focus intensity is achieved in a single pass through the crystal without a buildup cavity or nanostructued pattern for field enhancement. We measure in excess of 108 high-harmonic photons/second.

Multi-Watt mid-IR femtosecond polycrystalline Cr(2+):ZnS and Cr(2+):ZnSe laser amplifiers with the spectrum spanning 2.0-2.6 µm.

We demonstrate efficient amplification of few-optical-cycle mid-IR pulses in single-pass continuously pumped laser amplifiers based on polycrystalline Cr(2+):ZnS and Cr(2+):ZnSe. The 1.7 W output of a Kerr-lens mode-locked master oscillator at 2.4 µm central wavelength, 79 MHz repetition rate was amplified to 7.1 W and 2.7 W in Cr(2+):ZnS and Cr(2+):ZnSe, respectively. High peak power of the input pulses (0.5 MW) and high nonlinearity of the amplifiers' gain media resulted in a significant shortening of the output pulses and in spectral broadening. Transform-limited 40 fs pulses of the master oscillator were compressed to about 27-30 fs. The spectrum of the pulses was broadened from 136 nm to 450 nm (at -3 dB level); the span of the spectra exceeds 600 nm at -10 dB level.

140 W Cr:ZnSe laser system.

We report a significant breakthrough in the development of fiber-pumped high-power CW laser systems based on Cr2+:ZnS and Cr2+:ZnSe gain media. We demonstrate output power levels of up to 140 W near 2500 nm, and 32 W at 2940 nm with corresponding optical efficiencies of 62% and 29%. Our novel approach is based on rapid simultaneous scanning of the collinear laser mode and pump beam across the Cr:ZnS/Se gain element which allows us to virtually eliminate thermal lensing effects and obtain unprecedented levels of output power with very high optical-to-optical efficiency.

Three optical cycle mid-IR Kerr-lens mode-locked polycrystalline Cr(2+):ZnS laser.

We report Kerr-lens mode-locked polycrystalline Cr(2+):ZnS lasers at 2.4 µm central wavelength optimized for short pulse duration. By control of the second- and third-order dispersion within 500 nm bandwidth we obtained pulses of three optical cycles (<29 fs) at 100 MHz repetition rate with 0.44 W average power. The emission spectrum is 240 nm broad at -3 dB level and spans 950 nm at -30 dB level. Transform-limited 38 fs pulses were obtained at 300 MHz repetition rate with 700 mW average power. To the best of our knowledge these are the shortest reported to-date pulses from Cr(2+):ZnS and Cr(2+):ZnSe lasers.

Kerr-lens mode-locked femtosecond polycrystalline Cr2+:ZnS and Cr2+:ZnSe lasers.

We report the first Kerr-lens mode-locked polycrystalline Cr(2+):ZnS and Cr(2+):ZnSe lasers, with pulse duration of 125 fs at a pulse repetition rate of 160 MHz, emitting around 2.3 - 2.4 µm. The mode-locked lasers were pumped by a radiation of 1550 nm Er-fiber amplifier seeded by semiconductor laser. The long-term stable Kerr-lens mode-locked laser operation with the output power of 30 mW (Cr(2+):ZnS) and 60 mW (Cr(2+):ZnSe) was obtained. We also demonstrate amplification of the fs laser pulse train in a cw pumped single-pass polycrystalline Cr(2+):ZnS laser amplifier.

Dietary 14C reservoir effects and the chronology of prehistoric burials at Sakhtysh, central European Russia.

We present a robust radiocarbon (14C) chronology for burials at Sakhtysh, in European Russia, where nearly 180 inhumations of Lyalovo and Volosovo pottery-using hunter-gatherer-fishers represent the largest known populations of both groups. Past dating attempts were restricted by poor understanding of dietary 14C reservoir effects (DREs). We developed a DRE correction approach that uses multiple linear regression of differences in 14C, δ13C, and δ15N between bones and teeth of the same individuals to predict DREs of up to approximately 900 years. Our chronological model dates Lyalovo burials to the early fifth millennium BCE, and Volosovo burials to the mid-fourth to early third millennium. It reveals a change in the subsistence economy at approximately 3300 BCE, coinciding with a reorientation of trade networks, and dates the final burial to the early Fatyanovo period, the regional expression of the Yamnaya/Corded Ware expansion. Our approach is applicable when freshwater 14C reservoir effects are poorly constrained and grave goods cannot be dated directly.

Robust, frequency-stable and accurate mid-IR laser spectrometer based on frequency comb metrology of quantum cascade lasers up-converted in orientation-patterned GaAs.

We demonstrate a robust and simple method for measurement, stabilization and tuning of the frequency of cw mid-infrared (MIR) lasers, in particular of quantum cascade lasers. The proof of principle is performed with a quantum cascade laser at 5.4 µm, which is upconverted to 1.2 µm by sum-frequency generation in orientation-patterned GaAs with the output of a standard high-power cw 1.5 µm fiber laser. Both the 1.2 µm and the 1.5 µm waves are measured by a standard Er:fiber frequency comb. Frequency measurement at the 100 kHz-level, stabilization to sub-10 kHz level, controlled frequency tuning and long-term stability are demonstrated.

Spectrally narrow, long-term stable optical frequency reference based on a Eu3+:Y2SiO5 crystal at cryogenic temperature.

Using an ultrastable continuous-wave laser at 580 nm we performed spectral hole burning of Eu(3+):Y(2)SiO(5) at a very high spectral resolution. The essential parameters determining the usefulness as a macroscopic frequency reference, linewidth, temperature sensitivity, and long-term stability, were characterized using a H-maser stabilized frequency comb. Spectral holes with a linewidth as low as 6 kHz were observed and the upper limit of the drift of the hole frequency was determined to be 5±3 mHz/s. We discuss the necessary requirements for achieving ultrahigh stability in laser frequency stabilization to these spectral holes.

Respiratory adaptation to climate in modern humans and Upper Palaeolithic individuals from Sungir and Mladec.

As our human ancestors migrated into Eurasia, they faced a considerably harsher climate, but the extent to which human cranial morphology has adapted to this climate is still debated. In particular, it remains unclear when such facial adaptations arose in human populations. Here, we explore climate-associated features of face shape in a worldwide modern human sample using 3D geometric morphometrics and a novel application of reduced rank regression. Based on these data, we assess climate adaptations in two crucial Upper Palaeolithic human fossils, Sungir and Mladec, associated with a boreal-to-temperate climate. We found several aspects of facial shape, especially the relative dimensions of the external nose, internal nose and maxillary sinuses, that are strongly associated with temperature and humidity, even after accounting for autocorrelation due to geographical proximity of populations. For these features, both fossils revealed adaptations to a dry environment, with Sungir being strongly associated with cold temperatures and Mladec with warm-to-hot temperatures. These results suggest relatively quick adaptative rates of facial morphology in Upper Palaeolithic Europe.

Genetic ancestry changes in Stone to Bronze Age transition in the East European plain.

The transition from Stone to Bronze Age in Central and Western Europe was a period of major population movements originating from the Ponto-Caspian Steppe. Here, we report new genome-wide sequence data from 30 individuals north of this area, from the understudied western part of present-day Russia, including 3 Stone Age hunter-gatherers (10,800 to 4250 cal BCE) and 26 Bronze Age farmers from the Corded Ware complex Fatyanovo Culture (2900 to 2050 cal BCE). We show that Eastern hunter-gatherer ancestry was present in northwestern Russia already from around 10,000 BCE. Furthermore, we see a change in ancestry with the arrival of farming-Fatyanovo Culture individuals were genetically similar to other Corded Ware cultures, carrying a mixture of Steppe and European early farmer ancestry. Thus, they likely originate from a fast migration toward the northeast from somewhere near modern-day Ukraine-the closest area where these ancestries coexisted from around 3000 BCE.