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Patterns of epistasis and shapes of fitness landscapes are of wide interest because of their bearings on a number of evolutionary theories. The common phenomena of slowing fitness increases during adaptations and diminishing returns from beneficial mutations are believed to reflect a concave fitness landscape and a preponderance of negative epistasis. Paradoxically, fitness decreases tend to decelerate and harm from deleterious mutations shrinks during the accumulation of random mutations—patterns thought to indicate a convex fitness landscape and a predominance of positive epistasis. Current theories cannot resolve this apparent contradiction. Here, we show that the phenotypic effect of a mutation varies substantially depending on the specific genetic background and that this idiosyncrasy in epistasis creates all of the above trends without requiring a biased distribution of epistasis. The idiosyncratic epistasis theory explains the universalities in mutational effects and evolutionary trajectories as emerging from randomness due to biological complexity. Theory, simulations and empirical data are used to show that the phenotypic effect of a mutation varies substantially depending on the specific genetic background, thereby resolving an apparent contradiction between predictions of convex and concave fitness landscapes.

Both tunable and passively mode-locked laser oscillators based on an efficient Yb,Gd:SrF2 crystal are reported for the first time. Charge compensation ions of Gd3+ enhanced the emission and absorption cross section of Yb,Gd:SrF2 crystal markedly. With the aid of birefringent filter, a 61.1-nm continuous-wavelength-tunable laser from 1020.2 to 1081.3 nm was obtained, making it a potential candidate for ultrafast lasers. Based on a semiconductor saturable absorber mirror, a diode-pumped passively mode-locked laser with the pulse width of 951 fs was realized. The oscillator operated at a repetition rate of 92 MHz.

The avian eye color, generally referred to the color of the iris, results from both pigments and structural coloration. Avian iris colors exhibit striking interspecific and, in some domestic species, intraspecific variations, suggesting unique evolutionary and ecological histories. Here we tackled the genetic basis of the pearl (white) iris color in domestic pigeons (Columba livia), to elucidate the largely unknown genetic mechanism underlying the evolution of avian iris coloration. Using a genome-wide association study (GWAS) in 92 pigeons, we mapped the pearl iris trait to a 9 kb region and a facilitative glucose transporter gene SLC2A11B. A nonsense mutation W49X leading to a premature stop codon in SLC2A11B was identified as the causal variant. Transcriptome analysis suggested that SLC2A11B loss-of-function may downregulate the xanthophore-differentiation gene CSF1R, and a key gene GCH1 involved in biosynthesis of pteridine, whose absence results in pearl iris. Coalescence and phylogenetic analyses indicated the mutation originated about 5,400 years ago coinciding with the onset of pigeon domestication, while positive selection was detected likely associated with artificial breeding. Within Aves, potentially impaired SLC2A11B was found in 10 species from six distinct lineages correlated to their signature brown or blue eyes. Analysis of vertebrate SLC2A11B orthologs revealed relaxed selection in the avian clade, consistent with the scenario that, during and after avian divergence from reptile ancestor, the SLC2A11B-involved development of dermal chromatophores likely degenerated due to feather coverage. Our findings provide new insight into the mechanism of avian iris color variations and the evolution of pigmentation in vertebrates.

Yb,Nd:Sc2SiO5 crystal was investigated by co-doping Nd3+ ions into Yb:Sc2SiO5 crystal. The emission cross section was systematically enquired under different excitation wavelengths at 808, 915, and 980 nm. The emission cross section was enhanced by 18.9% at an excitation wavelength of 980 nm due to energy transfer between Nd3+ ions and Yb3+ ions when comparing with Yb:Sc2SiO5 crystal. The continuous-wave tunable Yb,Nd:Sc2SiO5 laser ranging over 58 nm was achieved from 1030.4 to 1088.4 nm. Mode-locking Yb,Nd:Sc2SiO5 femtosecond laser was obtained with output power of 240 mW, pulse duration of 367 fs, and peak power of 11.5 kW.

In this paper, we have demonstrated an efficient intra-cavity pumped Ho:SSO laser based on a cascaded in-band pumping scheme for the first time. The laser diode at 1.6 µm was used to pump the Tm:YAG crystal. At an incident LD pump power of 18.7 W, dual end-pumped Tm:YAG laser provides the maximum output power of 9.7 W with a slope efficiency of 55.9%. With the same incident LD power, a maximum output power of 4.9 W at 2116.5 nm was achieved with a slope efficiency of 31.6% in the Ho:SSO laser intra-cavity pumped by a Tm:YAG laser. The beam quality factor of the Ho:SSO laser at maximum output level was measured to be 1.1 and 1.2 in the horizontal and vertical directions, respectively.

Spectroscopic features and laser performance of a novel thulium-doped scandium yttrium silicate crystal Tm 3+ :ScYSiO 5 (Tm:SYSO) are presented. The experimental lifetime of luminescence related to the 3 F 4 – 3 H 6 laser transition of Tm 3+ amounts to 1.1 ms, which is smaller by a factor of three than the calculated radiative lifetime value due to the contribution of nonradiative relaxation. As a consequence of the internal disordered structure of the SYSO host crystal, the luminescence bands of 3 F 4 – 3 H 6 and 3 H 4 - 3 H 6 show significant inhomogeneous spectral broadening as compared with that of SSO. The laser performances were evaluated in an end-pumped cavity using a CW semiconductor laser as a pump source. In a free run regime, the Tm:SYSO laser delivered a maximum output power of 580 mW at 2022 nm, corresponding to a slope efficiency of 17.4%. With a birefringent quartz plate inserted into laser cavity, the laser output wavelength was continuously tuned from 1950 nm to 2057 nm and dual wavelength operations at 2011 nm and 2020 nm, 1987 nm and 2045 nm, 2022 nm and 2044 nm were observed.

Several authors reported lower frequencies of protein sequence convergence between more distantly related evolutionary lineages and attributed this trend to epistasis, which renders the acceptable amino acids at a site more different and convergence less likely in more divergent lineages. A recent primate study, however, suggested that this trend is at least partially and potentially entirely an artifact of gene tree discordance (GTD). Here, we demonstrate in a genome-wide data set from 17 mammals that the temporal trend remains (1) upon the control of the GTD level, (2) in genes whose genealogies are concordant with the species tree, and (3) for convergent changes, which are extremely unlikely to be caused by GTD. Similar results are observed in a comparable data set of 12 fruit flies in some but not all of these tests. We conclude that, at least in some cases, the temporal decline of convergence is genuine, reflecting an impact of epistasis on protein evolution.

Phylogenetic inference is of fundamental importance to evolutionary as well as other fields of biology, and molecular sequences have emerged as the primary data for this task. Although many phylogenetic methods have been developed to explicitly take into account substitution models of sequence evolution, such methods could fail due to model misspecification and insufficiency, especially in the face of heterogeneities in substitution processes across sites and among lineages. In this study, we propose to infer topologies of four-taxon trees using deep residual neural networks, a machine learning approach needing no explicit modeling of the subject system and having a record of success in solving complex non-linear inference problems. We train residual networks on simulated protein sequence data with extensive amino acid substitution heterogeneities. We show that the well-trained residual network predictors can outperform existing state-of-the-art inference methods such as the maximum likelihood method on diverse simulated test data, especially under extensive substitution heterogeneities. Reassuringly, residual network predictors generally agree with existing methods in the trees inferred from real phylogenetic data with known or widely believed topologies. We conclude that deep learning represents a powerful new approach to phylogenetic reconstruction, especially when sequences evolve via heterogeneous substitution processes. We present our best trained predictor in a freely available program named Phylogenetics by Deep Learning (PhyDL, https://gitlab.com/ztzou/phydl).

The male specific regions of primate Y-chromosomes (MSY) are enriched for multi-copy genes highly expressed in the testis. These genes are located in large repetitive sequences arranged as palindromes, inverted-, and tandem-repeats termed amplicons. In humans, these genes have critical roles in male fertility and are essential for the production of sperm. The structure of human and chimpanzee amplicon sequences show remarkable difference relative to the remainder of the genome, a difference that may be the result of intense selective pressure on male fertility. Four populations of common chimpanzees have undergone extended periods of isolation and appear to be in the early process of speciation. A recent study found amplicons enriched for testis-expressed genes on the primate X-chromosome the target of hard selective sweeps, and male-fertility genes on the Y-chromosome may also be the targets of selection. However, little is understood about Y-chromosome amplicon diversity within and across chimpanzee populations. Here, we analyze 9 common chimpanzee (representing three subspecies: Pan troglodytes schweinfurthii, Pan troglodytes ellioti, and Pan troglodytes verus) and two bonobo (Pan paniscus) male whole-genome sequences to assess Y ampliconic copy-number diversity across the Pan genus. We observe that the copy-number of Y chromosome amplicons is variable amongst chimpanzees and bonobos, and identify several lineage-specific patterns, including variable copy-number of azoospermia candidates RBMY and DAZ. We detect recurrent switchpoints of copy-number change along the ampliconic tracts across chimpanzee populations, which may be the result of localized genome instability or selective forces.

The South China tiger (Panthera tigris amoyensis) is endemic to China and also the most critically endangered subspecies of living tigers. It is considered extinct in the wild and only about 150 individuals survive in captivity to date, whose genetic heritage, however, is ambiguous and controversial. Here, we conducted an explicit genetic assessment of 92 studbook-registered South China tigers from 14 captive facilities using a subspecies-diagnostic system in the context of comparison with other voucher specimens to evaluate the genetic ancestry and level of distinctiveness of the last surviving P. t. amoyensis. Three mtDNA haplotypes were identified from South China tigers sampled in this study, including a unique P. t. amoyensis AMO1 haplotype not found in other subspecies, a COR1 haplotype that is widespread in Indochinese tigers (P. t. corbetti), and an ALT haplotype that is characteristic of Amur tigers (P. t. altaica). Bayesian STRUCTURE analysis and parentage verification confirmed the verified subspecies ancestry (VSA) as the South China tiger in 74 individuals. Genetic introgression from other tigers was detected in 18 tigers, and subsequent exclusion of these and their offspring from the breeding program is recommended. Both STRUCTURE clustering and microsatellite-based phylogenetic analyses demonstrated a close genetic association of the VSA South China tigers to Indochinese tigers, an issue that could only be elucidated by analysis of historical South China tiger specimens with wild origin. Our results also indicated a moderate level of genetic diversity in the captive South China tiger population, suggesting a potential for genetic restoration.

Convergent and parallel amino acid substitutions in protein evolution, collectively referred to as molecular convergence here, have small probabilities under neutral evolution. For this reason, molecular convergence is commonly viewed as evidence for similar adaptations of different species. The surge in the number of reports of molecular convergence in the last decade raises the intriguing question of whether molecular convergence occurs substantially more frequently than expected under neutral evolution. We here address this question using all one-to-one orthologous proteins encoded by the genomes of 12 fruit fly species and those encoded by 17 mammals. We found that the expected amount of molecular convergence varies greatly depending on the specific neutral substitution model assumed at each amino acid site and that the observed amount of molecular convergence is explainable by neutral models incorporating site-specific information of acceptable amino acids. Interestingly, the total number of convergent and parallel substitutions between two lineages, relative to the neutral expectation, decreases with the genetic distance between the two lineages, regardless of the model used in computing the neutral expectation. We hypothesize that this trend results from differences in the amino acids acceptable at a given site among different clades of a phylogeny, due to prevalent epistasis, and provide simulation as well as empirical evidence for this hypothesis. Together, our study finds no genomic evidence for higher-than-neutral levels of molecular convergence, but suggests the presence of abundant epistasis that decreases the likelihood of molecular convergence between distantly related lineages.

We report on laser diode (LD) pumped passively Q-switched Yb,Gd:SrF2 lasers with high single-pulse energy for the first time, to the best of our knowledge. In addition, a stable Q-switched laser based on a Cr4+:Y3Al5O12 saturable absorber was demonstrated. The maximum output power of the Q-switched laser obtained was 495 mW, with a pulse width and a pulse repetition rate of 233 ns and 1.238 kHz, respectively. The corresponding single-pulse energy and the peak power were as high as 400 µJ and 1.714 kW. The laser was operated under a transverse electromagnetic mode, and the beam quality was near-diffraction-limited.

3 at.%Yb: Sr1-xGdxF2+x (x = 0,0.01,0.03,0.06,0.09) single crystals are grown by the temperature gradient technique (TGT), where the Gd3+ ions were used as a lattice structural modifier to form a disordered lattice site. The Yb: Sr1-xGdxF2+x crystals maintain cubic structure Fm3m. Specifically, the absorption cross section of 3 at.%Yb: Sr0.97Gd0.03F2.03 crystal was increased by more than 10% compared with that of 3 at.%Yb:SrF2. The emission cross section σem in 3 at.%Yb: Sr0.97Gd0.03F2.03 was 1.21 × 10−20 cm2 at a central wavelength of 976 nm with an enhancement of 11% as compared with that of 3 at.%Yb:SrF2. A direct continuous-wave diode pumped 3 at.%Yb: Sr0.97Gd0.03F2.03 laser could generate an output power of 3.8 W at 1052 nm with an optic-optic efficiency of 46.5% by using output coupler with a transmission T = 3%.

A (Yb0.05Nd0.003Sc0.947)2SiO5 (Yb3+,Nd3+:Sc2SiO5) single crystal grown by the Czochralski technique is designed to enhance the gain cross-section through the energy transfer between energy level 4F3/2 of Nd3+ ions and energy level 2F5/2 of Yb3+ ions. The cell parameters were calculated as a = 9.94 A, b = 6.29 A, c = 11.67 A, V = 710.67 A3 and β = 103.19 °. The absorption cross-section σ abs in Yb3+,Nd3+:Sc2SiO5 was 1.18 × 10−20 cm2 at 980 nm, which was an increase of 28.3% when compared with that in a Yb3+:Sc2SiO5 crystal. The emission cross-section σ em in Yb3+,Nd3+:Sc2SiO5 was 0.63 × 10−20 cm2 at 1063 nm, an enhancement of 18.9% when compared with that in Yb3+:Sc2SiO5. The minimum pump intensity parameter I min at 1063 nm was 0.39 kWcm−2, which is a 74.5% reduction compared with 1.53 kWcm−2 in the case of YAG. A direct continuous wave diode-pumped Yb3+,Nd3+:Sc2SiO5 laser could generate an output power of 6.14 W at 1057.88 nm with a slope efficiency of 56.7% by using an output coupler with transmission T = 10%.

Poaching and trans-boundary trafficking of tigers and body parts are threatening the world's last remaining wild tigers. Development of an efficient molecular genetic assay for tracing the origins of confiscated specimens will assist in law enforcement and wildlife forensics for this iconic flagship species. We developed a multiplex genotyping system “tigrisPlex” to simultaneously assess 22 short tandem repeat (STR, or microsatellite) loci and a gender-identifying SRY gene, all amplified in 4 reactions using as little as 1 ng of template DNA. With DNA samples used for between-run calibration, the system generates STR genotypes that are directly compatible with voucher tiger subspecies genetic profiles, hence making it possible to identify subspecies via bi-parentally inherited markers. We applied “tigrisPlex” to 12 confiscated specimens from Russia and identified 6 individuals (3 females and 3 males), each represented by duplicated samples and all designated as Amur tigers (Panthera tigris altaica) with high confidence. This STR multiplex system can serve as an effective and versatile approach for genetic profiling of both wild and captive tigers as well as confiscated tiger products, fulfilling various conservation needs for identifying the origins of tiger samples.

Toothed whales and two groups of bats independently acquired echolocation, the ability to locate and identify objects by reflected sound. Echolocation requires physiologically complex and coordinated vocal, auditory, and neural functions, but the molecular basis of the capacity for echolocation is not well understood. A recent study suggested that convergent amino acid substitutions widespread in the proteins of echolocators underlay the convergent origins of mammalian echolocation. Here, we show that genomic signatures of molecular convergence between echolocating lineages are generally no stronger than those between echolocating and comparable nonecholocating lineages. The same is true for the group of 29 hearing-related proteins claimed to be enriched with molecular convergence. Reexamining the previous selection test reveals several flaws and invalidates the asserted evidence for adaptive convergence. Together, these findings indicate that the reported genomic signatures of convergence largely reflect the background level of sequence convergence unrelated to the origins of echolocation.

Summary The white tiger, an elusive Bengal tiger ( Panthera tigris tigris ) variant with white fur and dark stripes, has fascinated humans for centuries ever since its discovery in the jungles of India [1]. Many white tigers in captivity are inbred in order to maintain this autosomal recessive trait [2–5] and consequently suffer some health problems, leading to the controversial speculation that the white tiger mutation is perhaps a genetic defect [6]. However, the genetic basis of this phenotype remains unknown. Here, we conducted genome-wide association mapping with restriction-site-associated DNA sequencing (RAD-seq) in a pedigree of 16 captive tigers segregating at the putative white locus, followed by whole-genome sequencing (WGS) of the three parents. Validation in 130 unrelated tigers identified the causative mutation to be an amino acid change (A477V) in the transporter protein SLC45A2. Three-dimensional homology modeling suggests that the substitution may partially block the transporter channel cavity and thus affect melanogenesis. We demonstrate the feasibility of combining RAD-seq and WGS to rapidly map exotic variants in nonmodel organisms. Our results identify the basis of the longstanding white tiger mystery as the same gene underlying color variation in human, horse, and chicken and highlight its significance as part of the species' natural polymorphism that is viable in the wild.