Quantum-enhanced sensing on optical transitions through finite-range interactions.

The control over quantum states in atomic systems has led to the most precise optical atomic clocks so far1-3. Their sensitivity is bounded at present by the standard quantum limit, a fundamental floor set by quantum mechanics for uncorrelated particles, which can-nevertheless-be overcome when operated with entangled particles. Yet demonstrating a quantum advantage in real-world sensors is extremely challenging. Here we illustrate a pathway for harnessing large-scale entanglement in an optical transition using 1D chains of up to 51 ions with interactions that decay as a power-law function of the ion separation. We show that our sensor can emulate many features of the one-axis-twisting (OAT) model, an iconic, fully connected model known to generate scalable squeezing4 and Greenberger-Horne-Zeilinger-like states5-8. The collective nature of the state manifests itself in the preservation of the total transverse magnetization, the reduced growth of the structure factor, that is, spin-wave excitations (SWE), at finite momenta, the generation of spin squeezing comparable with OAT (a Wineland parameter9,10 of -3.9 ± 0.3 dB for only N = 12 ions) and the development of non-Gaussian states in the form of multi-headed cat states in the Q-distribution. We demonstrate the metrological utility of the states in a Ramsey-type interferometer, in which we reduce the measurement uncertainty by -3.2 ± 0.5 dB below the standard quantum limit for N = 51 ions.

Exploring large-scale entanglement in quantum simulation.

Entanglement is a distinguishing feature of quantum many-body systems, and uncovering the entanglement structure for large particle numbers in quantum simulation experiments is a fundamental challenge in quantum information science1. Here we perform experimental investigations of entanglement on the basis of the entanglement Hamiltonian (EH)2 as an effective description of the reduced density operator for large subsystems. We prepare ground and excited states of a one-dimensional XXZ Heisenberg chain on a 51-ion programmable quantum simulator3 and perform sample-efficient 'learning' of the EH for subsystems of up to 20 lattice sites4. Our experiments provide compelling evidence for a local structure of the EH. To our knowledge, this observation marks the first instance of confirming the fundamental predictions of quantum field theory by Bisognano and Wichmann5,6, adapted to lattice models that represent correlated quantum matter. The reduced state takes the form of a Gibbs ensemble, with a spatially varying temperature profile as a signature of entanglement2. Our results also show the transition from area- to volume-law scaling7 of von Neumann entanglement entropies from ground to excited states. As we venture towards achieving quantum advantage, we anticipate that our findings and methods have wide-ranging applicability to revealing and understanding entanglement in many-body problems with local interactions including higher spatial dimensions.

Phylogenomics Reveals High Levels of Incomplete Lineage Sorting at the Ancestral Nodes of the Macaque Radiation.

The genus Macaca includes 23 species assigned into 4 to 7 groups. It exhibits the largest geographic range and represents the most successful example of adaptive radiation of nonhuman primates. However, intrageneric phylogenetic relationships among species remain controversial and have not been resolved so far. In this study, we conducted a phylogenomic analysis on 16 newly generated and 8 published macaque genomes. We found strong evidence supporting the division of this genus into 7 species groups. Incomplete lineage sorting (ILS) was the primary factor contributing to the discordance observed among gene trees; however, we also found evidence of hybridization events, specifically between the ancestral arctoides/sinica and silenus/nigra lineages that resulted in the hybrid formation of the fascicularis/mulatta group. Combined with fossil data, our phylogenomic data were used to establish a scenario for macaque radiation. These findings provide insights into ILS and potential ancient introgression events that were involved in the radiation of macaques, which will lead to a better understanding of the rapid speciation occurring in nonhuman primates.

Complex Evolutionary History With Extensive Ancestral Gene Flow in an African Primate Radiation.

Understanding the drivers of speciation is fundamental in evolutionary biology, and recent studies highlight hybridization as an important evolutionary force. Using whole-genome sequencing data from 22 species of guenons (tribe Cercopithecini), one of the world's largest primate radiations, we show that rampant gene flow characterizes their evolutionary history and identify ancient hybridization across deeply divergent lineages that differ in ecology, morphology, and karyotypes. Some hybridization events resulted in mitochondrial introgression between distant lineages, likely facilitated by cointrogression of coadapted nuclear variants. Although the genomic landscapes of introgression were largely lineage specific, we found that genes with immune functions were overrepresented in introgressing regions, in line with adaptive introgression, whereas genes involved in pigmentation and morphology may contribute to reproductive isolation. In line with reports from other systems that hybridization might facilitate diversification, we find that some of the most species-rich guenon clades are of admixed origin. This study provides important insights into the prevalence, role, and outcomes of ancestral hybridization in a large mammalian radiation.

Observing the Quantum Mpemba Effect in Quantum Simulations.

The nonequilibrium physics of many-body quantum systems harbors various unconventional phenomena. In this Letter, we experimentally investigate one of the most puzzling of these phenomena-the quantum Mpemba effect, where a tilted ferromagnet restores its symmetry more rapidly when it is farther from the symmetric state compared to when it is closer. We present the first experimental evidence of the occurrence of this effect in a trapped-ion quantum simulator. The symmetry breaking and restoration are monitored through entanglement asymmetry, probed via randomized measurements, and postprocessed using the classical shadows technique. Our findings are further substantiated by measuring the Frobenius distance between the experimental state and the stationary thermal symmetric theoretical state, offering direct evidence of subsystem thermalization.

A New World Monkey Resembles Human in Bitter Taste Receptor Evolution and Function via a Single Parallel Amino Acid Substitution.

Bitter taste receptors serve as a vital component in the defense system against toxin intake by animals, and the family of genes encoding these receptors has been demonstrated, usually by family size variance, to correlate with dietary preference. However, few systematic studies of specific Tas2R to unveil their functional evolution have been conducted. Here, we surveyed Tas2R16 across all major clades of primates and reported a rare case of a convergent change to increase sensitivity to ß-glucopyranosides in human and a New World monkey, the white-faced saki. Combining analyses at multiple levels, we demonstrate that a parallel amino acid substitution (K172N) shared by these two species is responsible for this functional convergence of Tas2R16. Considering the specialized feeding preference of the white-faced saki, the K172N change likely played an important adaptive role in its early evolution to avoid potentially toxic cyanogenic glycosides, as suggested for the human TAS2R16 gene.

Population Genomics Reveals Incipient Speciation, Introgression, and Adaptation in the African Mona Monkey (Cercopithecus mona).

Guenons (tribe Cercopithecini) are the most widely distributed nonhuman primate in the tropical forest belt of Africa and show considerable phenotypic, taxonomic, and ecological diversity. However, genomic information for most species within this group is still lacking. Here, we present a high-quality de novo genome (total 2.90 Gb, contig N50 equal to 22.7 Mb) of the mona monkey (Cercopithecus mona), together with genome resequencing data of 13 individuals sampled across Nigeria. Our results showed differentiation between populations from East and West of the Niger River ∼84 ka and potential ancient introgression in the East population from other mona group species. The PTPRK, FRAS1, BNC2, and EDN3 genes related to pigmentation displayed signals of introgression in the East population. Genomic scans suggest that immunity genes such as AKT3 and IL13 (possibly involved in simian immunodeficiency virus defense), and G6PD, a gene involved in malaria resistance, are under positive natural selection. Our study gives insights into differentiation, natural selection, and introgression in guenons.

Molecular phylogeny and systematics of bald uakaris, genus Cacajao (Primates: Pitheciidae), with the description of a new species.

Bald uakaris, genus Cacajao, are Amazonian primates currently classified as one species and four subspecies based on the patterns of pelage coloration. In this study, we test if their current taxonomy is represented by the phylogenetic relationship of the main lineages retrieved from molecular data. We included, for the first time, all bald uakari taxa in a mitochondrial (cytochrome b) and genome-wide (ddRAD) phylogenetic analyses. We also examined the pattern of pelage colouration in specimens from zoological collections. Having determined the number of lineages using Maximum Likelihood and the species tree using coalescent analyses, we test their divergence time using a Bayesian approach. While the cytochrome b analysis only recovered two clades, the ddRAD analysis supported the reciprocal monophyly of five lineages of bald uakaris, with all clades including only individuals with distinct and exclusive diagnostic phenotypic characters. We found that species diversification in Cacajao occurred during the last 300 Kya and may have been influenced by the formation of rivers and flooded forests in western Amazonia. We propose that the four bald uakari subspecies currently recognised can be upgraded to species level and we describe the white uakaris from the basin of the Rio Tarauacá as a new species.

Increasing dental zirconia micro-retentive aspect through ultra-short pulsed laser microstructuring: study on flexural strength and crystal phase characterization.

OBJECTIVES: Although ultra-short pulsed laser (USPL) microstructuring has previously improved zirconia bond-strength, it is yet unclear how different laser-machined surface microstructures and patterns may influence the material's mechanical properties. Therefore, the aim of this study was to assess the flexural strength of zirconia after different USPL settings creating three different geometrical patterns with structures in micrometer scale. METHODS: One hundred sixty zirconia bars (3Y-TZP, 21 × 4 × 2.1 mm) were prepared and randomly divided into five groups (n = 32): no surface treatment (negative control-NC); sandblasting with Al2O3 (SB); and three laser groups irradiated with USPL (Nd:YVO4/1064 nm/2-34 J/cm2/12 ps): crossed-lines (LC), random-hatching (LR), and parallel-waves (LW). Bars were subjected to a four-point flexural test (1 mm/min) and crystal phase content changes were identified by X-ray diffraction. Surface roughness and topography were analyzed through 3D-laser-profilometry and SEM. Data were analyzed with parametric tests for roughness and Weibull for flexural strength (α = 5%). RESULTS: LR (Mean[95%CI]: 852.0 MPa, [809.2-894.7]) was the only group that did not show a significantly different flexural strength than NC (819.8 MPa, [796.6-842.9]), (p > 0.05). All laser groups exhibited higher Weibull moduli than NC and SB, indicating higher reliability and homogeneity of the strength data. An increase of monoclinic phase peak was only observed for SB. CONCLUSION: In conclusion, USPL created predictable, homogeneous, highly reproducible, and accurate surface microstructures on zirconia ceramic. The laser-settings of random-hatching (12 ps pulses) increased 3Y-TZP average surface roughness similarly to SB, while not causing deleterious crystal phase transformation or loss of flexural strength of the material. Furthermore, it has increased the Weibull modulus and consequently material's reliability. CLINICAL SIGNIFICANCE: Picosecond laser microstructuring (LR conditions) of 3Y-TZP ceramic does not decrease its flexural strength, while increasing materials realiability and creating highly reproducible and accurate microstructures. These features may be of interest both for improving clinical survival of zirconia restorations as well as enhancing longevity of zirconia implants.

Mitogenomic phylogeny of Callithrix with special focus on human transferred taxa.

BACKGROUND: Callithrix marmosets are a relatively young primate radiation, whose phylogeny is not yet fully resolved. These primates are naturally para- and allopatric, but three species with highly invasive potential have been introduced into the southeastern Brazilian Atlantic Forest by the pet trade. There, these species hybridize with each other and endangered, native congeners. We aimed here to reconstruct a robust Callithrix phylogeny and divergence time estimates, and identify the biogeographic origins of autochthonous and allochthonous Callithrix mitogenome lineages. We sequenced 49 mitogenomes from four species (C. aurita, C. geoffroyi, C. jacchus, C. penicillata) and anthropogenic hybrids (C. aurita x Callithrix sp., C. penicillata x C. jacchus, Callithrix sp. x Callithrix sp., C. penicillata x C. geoffroyi) via Sanger and whole genome sequencing. We combined these data with previously published Callithrix mitogenomes to analyze five Callithrix species in total. RESULTS: We report the complete sequence and organization of the C. aurita mitogenome. Phylogenetic analyses showed that C. aurita was the first to diverge within Callithrix 3.54 million years ago (Ma), while C. jacchus and C. penicillata lineages diverged most recently 0.5 Ma as sister clades. MtDNA clades of C. aurita, C. geoffroyi, and C. penicillata show intraspecific geographic structure, but C. penicillata clades appear polyphyletic. Hybrids, which were identified by phenotype, possessed mainly C. penicillata or C. jacchus mtDNA haplotypes. The biogeographic origins of mtDNA haplotypes from hybrid and allochthonous Callithrix were broadly distributed across natural Callithrix ranges. Our phylogenetic results also evidence introgression of C. jacchus mtDNA into C. aurita. CONCLUSION: Our robust Callithrix mitogenome phylogeny shows C. aurita lineages as basal and C. jacchus lineages among the most recent within Callithrix. We provide the first evidence that parental mtDNA lineages of anthropogenic hybrid and allochthonous marmosets are broadly distributed inside and outside of the Atlantic Forest. We also show evidence of cryptic hybridization between allochthonous Callithrix and autochthonous C. aurita. Our results encouragingly show that further development of genomic resources will allow to more clearly elucidate Callithrix evolutionary relationships and understand the dynamics of Callithrix anthropogenic introductions into the Brazilian Atlantic Forest.

Genomic Mechanisms of Physiological and Morphological Adaptations of Limestone Langurs to Karst Habitats.

Knowledge of the physiological and morphological evolution and adaptation of nonhuman primates is critical to understand hominin origins, physiological ecology, morphological evolution, and applications in biomedicine. Particularly, limestone langurs represent a direct example of adaptations to the challenges of exploiting a high calcium and harsh environment. Here, we report a de novo genome assembly (Tfra_2.0) of a male François's langur (Trachypithecus francoisi) with contig N50 of 16.3 Mb and resequencing data of 23 individuals representing five limestone and four forest langur species. Comparative genomics reveals evidence for functional evolution in genes and gene families related to calcium signaling in the limestone langur genome, probably as an adaptation to naturally occurring high calcium levels present in water and plant resources in karst habitats. The genomic and functional analyses suggest that a single point mutation (Lys1905Arg) in the α1c subunit of the L-type voltage-gated calcium channel Cav1.2 (CACNA1C) attenuates the inward calcium current into the cells in vitro. Population genomic analyses and RNA-sequencing indicate that EDNRB is less expressed in white tail hair follicles of the white-headed langur (T. leucocephalus) compared with the black-colored François's langur and hence might be responsible for species-specific differences in body coloration. Our findings contribute to a new understanding of gene-environment interactions and physiomorphological adaptative mechanisms in ecologically specialized primate taxa.

Corrigendum: A Severe Lack of Evidence Limits Effective Conservation of the World's Primates.

[This corrects the article DOI: 10.1093/biosci/biaa082.].

New mitogenomic lineages in Papio baboons and their phylogeographic implications.

OBJECTIVES: Incomplete and/or biased sampling either on a taxonomic or geographic level can lead to delusive phylogenetic and phylogeographic inferences. However, a complete taxonomic and geographical sampling is often and for various reasons impossible, particularly for widespread taxa such as baboons (Papio spp.). Previous studies on baboon phylogeography identified several sampling gaps, some of which we fill by investigating additional material including samples from museum specimens. MATERIALS AND METHODS: We generated 10 new mitochondrial genomes either via conventional PCR and subsequent Sanger sequencing from two blood samples or via high-throughput shotgun sequencing from degraded DNA extracted from eight museum specimens. Phylogenetic relationships and divergence times among baboon lineages were determined using maximum-likelihood and Bayesian inferences. RESULTS: We identified new mitochondrial lineages in baboons from Central Africa (Chad, the Central African Republic), from the Mahale, and the Udzungwa Mountains (Tanzania), with the latter likely representing a case of mitochondrial capture from sympatric kipunjis (Rungwecebus kipunji). We also found that the mitochondrial clades of olive baboons found in Ivory Coast and Tanzania extend into Niger and the Democratic Republic of Congo, respectively. Moreover, an olive baboon from Sierra Leone carries a mitochondrial haplotype usually found in Guinea baboons, suggesting gene flow between these two species. DISCUSSION: The extension of the geographic sampling by including samples from areas difficult to visit or from populations that are most likely extirpated has improved the geographic and temporal resolution of the mitochondrial phylogeny of baboons considerably. Our study also shows the great value of museum material for genetic analyses even when DNA is highly degraded.

Environmental and anthropogenic effects on the nesting patterns of Nigeria-Cameroon chimpanzees in North-West Cameroon.

Environmental conditions and human activity influence the selection of nest sites by chimpanzees and may have serious conservation implications. We examined the characteristics of nesting trees preferred by chimpanzees, investigated the effect of vegetation composition and topography on nest site locations and seasonality on nesting heights of chimpanzees, and verified the effect of predator occurrence and human activity on the nesting behavior of the Nigeria-Cameroon chimpanzee (Pan troglodytes ellioti) in Kom-Wum Forest Reserve (KWFR) and surrounding unprotected forest in Cameroon. We recorded 923 nests, 502 signs of human activity, and 646 nesting trees along line transects and recces (reconnaissance) for two seasons. We found that chimpanzees constructed more arboreal nests on tall primary trees with high lowest branch height and large diameter at breast height. Moreover, they oriented their nests within trees in the slope direction when the nesting trees were located on slopes. Additionally, the occurrence of chimpanzee nests was positively related to increasing elevation and slope and decreased with distance to primary forest. In contrast, the number of nests increased with distance to secondary forest, open land, and villages, and nesting height was not influenced by seasons. While we recorded no signs of large nocturnal chimpanzee predators at nesting trees, we found signs of hunting activity at nesting locations. Nesting high in trees is likely a way of avoiding hunting, while nest orientation within trees in slope direction shortens escape routes from human hunters. Our findings suggest that chimpanzees select safe trees (tall trees with high lowest branch height) located in nesting areas (primary forest, high elevation, and steep slopes) that are not easily accessible by humans. Therefore, conservation efforts should focus on protecting primary forests at high elevation and steep slopes and reducing human impact.

Variation in predicted COVID-19 risk among lemurs and lorises.

The novel coronavirus SARS-CoV-2, which in humans leads to the disease COVID-19, has caused global disruption and more than 2 million fatalities since it first emerged in late 2019. As we write, infection rates are at their highest point globally and are rising extremely rapidly in some areas due to more infectious variants. The primary target of SARS-CoV-2 is the cellular receptor angiotensin-converting enzyme-2 (ACE2). Recent sequence analyses of the ACE2 gene predict that many nonhuman primates are also likely to be highly susceptible to infection. However, the anticipated risk is not equal across the Order. Furthermore, some taxonomic groups show high ACE2 amino acid conservation, while others exhibit high variability at this locus. As an example of the latter, analyses of strepsirrhine primate ACE2 sequences to date indicate large variation among lemurs and lorises compared to other primate clades despite low sampling effort. Here, we report ACE2 gene and protein sequences for 71 individual strepsirrhines, spanning 51 species and 19 genera. Our study reinforces previous results while finding additional variability in other strepsirrhine species, and suggests several clades of lemurs have high potential susceptibility to SARS-CoV-2 infection. Troublingly, some species, including the rare and endangered aye-aye (Daubentonia madagascariensis), as well as those in the genera Avahi and Propithecus, may be at high risk. Given that lemurs are endemic to Madagascar and among the primates at highest risk of extinction globally, further understanding of the potential threat of COVID-19 to their health should be a conservation priority. All feasible actions should be taken to limit their exposure to SARS-CoV-2.

The Origin and Population History of the Endangered Golden Snub-Nosed Monkey (Rhinopithecus roxellana).

The origin and population history of the endangered golden snub-nosed monkey (Rhinopithecus roxellana) remain largely unavailable and/or controversial. We here integrate analyses of multiple genomic markers, including mitochondrial (mt) genomes, Y-chromosomes, and autosomes of 54 golden monkey individuals from all three geographic populations (SG, QL, and SNJ). Our results reveal contrasting population structures. Mt analyses suggest a division of golden monkeys into five lineages: one in SNJ, two in SG, and two in QL. One of the SG lineages (a mixed SG/QL lineage) is basal to all other lineages. In contrast, autosomal analyses place SNJ as the most basal lineage and identify one QL and three SG lineages. Notably, Y-chromosome analyses bear features similar to mt analyses in placing the SG/QL-mixed lineage as the first diverging lineage and dividing SG into two lineages, while resembling autosomal analyses in identifying one QL lineage. We further find bidirectional gene flow among all three populations at autosomal loci, while asymmetric gene flow is suggested at mt genomes and Y-chromosomes. We propose that different population structures and gene flow scenarios are the result of sex-linked differences in the dispersal pattern of R. roxellana. Moreover, our demographic simulation analyses support an origin hypothesis suggesting that the ancestral R. roxellana population was once widespread and then divided into SNJ and non-SNJ (SG and QL) populations. This differs from previous mt-based "mono-origin (SG is the source population)" and "multiorigin (SG is a fusion of QL and SNJ)" hypotheses. We provide a detailed and refined scenario for the origin and population history of this endangered primate species, which has a broader significance for Chinese biogeography. In addition, this study highlights the importance to investigate multiple genomic markers with different modes of inheritance to trace the complete evolutionary history of a species, especially for those exhibiting differential or mixed patterns of sex dispersal.

Bonds of bros and brothers: Kinship and social bonding in postdispersal male macaques.

Group-living animals often maintain a few very close affiliative relationships-social bonds-that can buffer them against many of the inevitable costs of gregariousness. Kinship plays a central role in the development of such social bonds. The bulk of research on kin biases in sociality has focused on philopatric females, who typically live in deeply kin-structured systems, with matrilineal dominance rank inheritance and life-long familiarity between kin. Closely related males, in contrast, are usually not close in rank or familiar, which offers the opportunity to test the importance of kinship per se in the formation of social bonds. So far, however, kin biases in male social bonding have only been tested in philopatric males, where familiarity remains a confounding factor. Here, we studied bonds between male Assamese macaques, a species in which males disperse from their natal groups and in which male bonds are known to affect fitness. Combining extensive behavioural data on 43 adult males over a 10-year period with DNA microsatellite relatedness analyses, we find that postdispersal males form stronger relationships with the few close kin available in the group than with the average nonkin. However, males form the majority of their bonds with nonkin and may choose nonkin over available close kin to bond with. Our results show that kinship facilitates bond formation, but is not a prerequisite for it, which suggests that strong bonds are not restricted to kin in male mammals and that animals cooperate for both direct and indirect fitness benefits.

A Severe Lack of Evidence Limits Effective Conservation of the World's Primates.

Threats to biodiversity are well documented. However, to effectively conserve species and their habitats, we need to know which conservation interventions do (or do not) work. Evidence-based conservation evaluates interventions within a scientific framework. The Conservation Evidence project has summarized thousands of studies testing conservation interventions and compiled these as synopses for various habitats and taxa. In the present article, we analyzed the interventions assessed in the primate synopsis and compared these with other taxa. We found that despite intensive efforts to study primates and the extensive threats they face, less than 1% of primate studies evaluated conservation effectiveness. The studies often lacked quantitative data, failed to undertake postimplementation monitoring of populations or individuals, or implemented several interventions at once. Furthermore, the studies were biased toward specific taxa, geographic regions, and interventions. We describe barriers for testing primate conservation interventions and propose actions to improve the conservation evidence base to protect this endangered and globally important taxon.

Quantum Information Scrambling in a Trapped-Ion Quantum Simulator with Tunable Range Interactions.

In ergodic many-body quantum systems, locally encoded quantum information becomes, in the course of time evolution, inaccessible to local measurements. This concept of "scrambling" is currently of intense research interest, entailing a deep understanding of many-body dynamics such as the processes of chaos and thermalization. Here, we present first experimental demonstrations of quantum information scrambling on a 10-qubit trapped-ion quantum simulator representing a tunable long-range interacting spin system, by estimating out-of-time ordered correlators (OTOCs) through randomized measurements. We also analyze the role of decoherence in our system by comparing our measurements to numerical simulations and by measuring Rényi entanglement entropies.

Cross-Platform Verification of Intermediate Scale Quantum Devices.

We describe a protocol for cross-platform verification of quantum simulators and quantum computers. We show how to measure directly the overlap Tr[ρ_{1}ρ_{2}] and the purities Tr[ρ_{1,2}^{2}], and thus a fidelity of two, possibly mixed, quantum states ρ_{1} and ρ_{2} prepared in separate experimental platforms. We require only local measurements in randomized product bases, which are communicated classically. As a proof of principle, we present the measurement of experiment-theory fidelities for entangled 10-qubit quantum states in a trapped ion quantum simulator.