Teaching transposon classification as a means to crowd source the curation of repeat annotation - a tardigrade perspective.

BACKGROUND: The advancement of sequencing technologies results in the rapid release of hundreds of new genome assemblies a year providing unprecedented resources for the study of genome evolution. Within this context, the significance of in-depth analyses of repetitive elements, transposable elements (TEs) in particular, is increasingly recognized in understanding genome evolution. Despite the plethora of available bioinformatic tools for identifying and annotating TEs, the phylogenetic distance of the target species from a curated and classified database of repetitive element sequences constrains any automated annotation effort. Moreover, manual curation of raw repeat libraries is deemed essential due to the frequent incompleteness of automatically generated consensus sequences. RESULTS: Here, we present an example of a crowd-sourcing effort aimed at curating and annotating TE libraries of two non-model species built around a collaborative, peer-reviewed teaching process. Manual curation and classification are time-consuming processes that offer limited short-term academic rewards and are typically confined to a few research groups where methods are taught through hands-on experience. Crowd-sourcing efforts could therefore offer a significant opportunity to bridge the gap between learning the methods of curation effectively and empowering the scientific community with high-quality, reusable repeat libraries. CONCLUSIONS: The collaborative manual curation of TEs from two tardigrade species, for which there were no TE libraries available, resulted in the successful characterization of hundreds of new and diverse TEs in a reasonable time frame. Our crowd-sourcing setting can be used as a teaching reference guide for similar projects: A hidden treasure awaits discovery within non-model organisms.

Songbird germline-restricted chromosome as a potential arena of genetic conflicts.

Genetic conflicts can arise between components of the genome with different inheritance strategies. The germline-restricted chromosome (GRC) of songbirds shows unusual mitotic and meiotic transmission compared with the rest of the genome. It is excluded from somatic cells and maintained only in the germline. It is usually present in one copy in the male germline and eliminated during spermatogenesis, while in the female germline, it usually occurs in two copies and behaves as a regular chromosome. Here, we review what is known about the GRC's evolutionary history, genetic content, and expression and discuss how it may be involved in different types of genetic conflicts. Finally, we interrogate the potential role of the GRC in songbird germline development, highlighting several unsolved mysteries.

Micro Germline-Restricted Chromosome in Blue Tits: Evidence for Meiotic Functions.

The germline-restricted chromosome (GRC) is likely present in all songbird species but differs widely in size and gene content. This extra chromosome has been described as either a microchromosome with only limited basic gene content or a macrochromosome with enriched gene functions related to female gonad and embryo development. Here, we assembled, annotated, and characterized the first micro-GRC in the blue tit (Cyanistes caeruleus) using high-fidelity long-read sequencing data. Although some genes on the blue tit GRC show signals of pseudogenization, others potentially have important functions, either currently or in the past. We highlight the GRC gene paralog BMP15, which is among the highest expressed GRC genes both in blue tits and in zebra finches (Taeniopygia guttata) and is known to play a role in oocyte and follicular maturation in other vertebrates. The GRC genes of the blue tit are further enriched for functions related to the synaptonemal complex. We found a similar functional enrichment when analyzing published data on GRC genes from two nightingale species (Luscinia spp.). We hypothesize that these genes play a role in maintaining standard maternal inheritance or in recombining maternal and paternal GRCs during potential episodes of biparental inheritance.

Weak antagonistic fitness effects can maintain an inversion polymorphism.

The study of chromosomal inversion polymorphisms has received much recent attention, particularly in cases where inversions have drastic effects on phenotypes and fitness (e.g. lethality of homozygotes). Less attention has been paid to the question of the maintenance of inversion polymorphisms that show only weak effects. Here, we study the maintenance of such an inversion polymorphism that links 250 genes on chromosome Tgu11 in the zebra finch (Taeniopygia guttata). Based on data from over 6000 captive birds, we estimated the effects of this inversion on a wide range of fitness-related traits. We found that, compared with the ancestral allele A, the inverted allele D had small additive beneficial effects on male siring success and on female fecundity. These fitness-enhancing effects may explain the initial spread of the derived D allele (allele frequency 53%). However, individuals that were homozygous for D had a slightly lower survival rate, which may explain why the D allele has not spread to fixation. We used individual-based simulations to examine how an inversion polymorphism with such antagonistic fitness effects behaves over time. Our results indicate that polymorphisms become stabilized at an intermediate allele frequency if the inversion links an additively beneficial allele of small effect size to a recessive weakly deleterious mutation, overall resulting in weak net heterosis. Importantly, this conclusion remains valid over a wide range of selection coefficients against the homozygous DD (up to lethality), suggesting that the conditions needed to maintain the polymorphism may frequently be met. However, the simulations also suggest that in our zebra finch populations, the estimated recessive deleterious effect of the D allele (on survival in captivity) is not quite large enough to prevent fixation of the D allele in the long run. Estimates of fitness effects from free-living populations are needed to validate these results.

Spatial and temporal resource partitioning in a mixed-species colony of avian echolocators.

Resource partitioning may facilitate the coexistence of sympatric species with similar ecological requirements. Here, we study a colony of unusual echolocating birds called swiftlets, which nest underground on an island off the coast of Singapore. The colony comprises two congeneric swiftlet species, black-nest swiftlets (Aerodramus maximus) and edible-nest swiftlets (A. fuciphagus), nesting at high densities and in close proximity. Bioacoustic recordings and monitoring of nesting biology at the site across multiple seasons revealed significant differences in echolocation calls as well as survival rates between the species, with the larger black-nest swiftlet nesting at locations with the highest fledging rates. We also observe an additional off-season breeding peak by the smaller species, the edible-nest swiftlet. Unexpectedly, off-season egg-hatching rates were significantly higher compared with the rates during the shared breeding season (mean difference = 14%). Our study on the breeding biology of these echolocating cave-dwelling birds provides an example of spatial and temporal strategies that animals employ to partition resources within a confined habitat.

Unveiling Local Electronic Structure of Lanthanide-Doped Cs2 NaInCl6 Double Perovskites for Realizing Efficient Near-Infrared Luminescence.

Lanthanide ion (Ln3+ )-doped halide double perovskites (DPs) have evoked tremendous interest due to their unique optical properties. However, Ln3+ ions in these DPs still suffer from weak emissions due to their parity-forbidden 4f-4f electronic transitions. Herein, the local electronic structure of Ln3+ -doped Cs2 NaInCl6 DPs is unveiled. Benefiting from the localized electrons of [YbCl6 ]3- octahedron in Cs2 NaInCl6 DPs, an efficient strategy of Cl- -Yb3+ charge transfer sensitization is proposed to obtain intense near-infrared (NIR) luminescence of Ln3+ . NIR photoluminescence (PL) quantum yield (QY) up to 39.4% of Yb3+ in Cs2 NaInCl6 is achieved, which is more than three orders of magnitude higher than that (0.1%) in the well-established Cs2 AgInCl6 via conventional self-trapped excitons sensitization. Density functional theory calculation and Bader charge analysis indicate that the [YbCl6 ]3- octahedron is strongly localized in Cs2 NaInCl6 :Yb3+ , which facilitates the Cl- -Yb3+ charge transfer process. The Cl- -Yb3+ charge transfer sensitization mechanism in Cs2 NaInCl6 :Yb3+ is further verified by temperature-dependent steady-state and transient PL spectra. Furthermore, efficient NIR emission of Er3+ with the NIR PLQY of 7.9% via the Cl- -Yb3+ charge transfer sensitization is realized. These findings provide fundamental insights into the optical manipulation of Ln3+ -doped halide DPs, thus laying a foundation for the future design of efficient NIR-emitting DPs.

Boosting Near-Infrared Luminescence of Lanthanide in Cs2 AgBiCl6 Double Perovskites via Breakdown of the Local Site Symmetry.

Currently, lanthanide (Ln3+ )-doped near-infrared (NIR)-emitting double perovskites (DPs) suffer from low photoluminescence quantum yield (PLQY). Herein, we develop a new class of NIR-emitting DPs based on Ln3+ -doped Cs2 (Na/Ag)BiCl6 . Benefiting from the Na+ -induced breakdown of local site symmetry in the Cs2 AgBiCl6 DPs, effective NIR emissions of Ln3+ are realized through Bi3+ sensitization. Specifically, 7.3-fold and 362.9-fold enhanced NIR emissions of Yb3+ and Er3+ are achieved in Cs2 Ag0.2 Na0.8 BiCl6 DPs relative to those in Na-free Cs2 AgBiCl6 counterparts, respectively. The optimal absolute NIR PLQYs for Yb3+ and Er3+ in Cs2 Ag0.2 Na0.8 BiCl6 DPs are determined to be 19.0 % and 4.3 %, respectively. Raman spectroscopy and first-principles density functional theory calculations verify the sublattice distortion in Cs2 (Na/Ag)BiCl6 DPs via Na+ doping. These findings provide fundamental insights into the design of efficient NIR-emitting Ln3+ -doped DPs for versatile optoelectronic applications.

Mendelian nightmares: the germline-restricted chromosome of songbirds.

Germline-restricted chromosomes (GRCs) are accessory chromosomes that occur only in germ cells. They are eliminated from somatic cells through programmed DNA elimination during embryo development. GRCs have been observed in several unrelated animal taxa and show peculiar modes of non-Mendelian inheritance and within-individual elimination. Recent cytogenetic and phylogenomic evidence suggests that a GRC is present across the species-rich songbirds, but absent in non-passerine birds, implying that over half of all 10,500 bird species have extensive germline/soma genome differences. Here, we review recent insights gained from genomic, transcriptomic, and cytogenetic approaches with regard to the genetic content, phylogenetic distribution, and inheritance of the songbird GRC. While many questions remain unsolved in terms of GRC inheritance, elimination, and function, we discuss plausible scenarios and future directions for understanding this widespread form of programmed DNA elimination.

Machine learning reveals cryptic dialects that explain mate choice in a songbird.

Culturally transmitted communication signals - such as human language or bird song - can change over time through cultural drift, and the resulting dialects may consequently enhance the separation of populations. However, the emergence of song dialects has been considered unlikely when songs are highly individual-specific, as in the zebra finch (Taeniopygia guttata). Here we show that machine learning can nevertheless distinguish the songs from multiple captive zebra finch populations with remarkable precision, and that 'cryptic song dialects' predict strong assortative mating in this species. We examine mating patterns across three consecutive generations using captive populations that have evolved in isolation for about 100 generations. We cross-fostered eggs within and between these populations and used an automated barcode tracking system to quantify social interactions. We find that females preferentially pair with males whose song resembles that of the females' adolescent peers. Our study shows evidence that in zebra finches, a model species for song learning, individuals are sensitive to differences in song that have hitherto remained unnoticed by researchers.

Occasional paternal inheritance of the germline-restricted chromosome in songbirds.

Songbirds have one special accessory chromosome, the so-called germline-restricted chromosome (GRC), which is only present in germline cells and absent from all somatic tissues. Earlier work on the zebra finch (Taeniopygia guttata castanotis) showed that the GRC is inherited only through the female line-like the mitochondria-and is eliminated from the sperm during spermatogenesis. Here, we show that the GRC has the potential to be paternally inherited. Confocal microscopy using GRC-specific fluorescent in situ hybridization probes indicated that a considerable fraction of sperm heads (1 to 19%) in zebra finch ejaculates still contained the GRC. In line with these cytogenetic data, sequencing of ejaculates revealed that individual males from two families differed strongly and consistently in the number of GRCs in their ejaculates. Examining a captive-bred male hybrid of the two zebra finch subspecies (T. g. guttata and T. g. castanotis) revealed that the mitochondria originated from a castanotis mother, whereas the GRC came from a guttata father. Moreover, analyzing GRC haplotypes across nine castanotis matrilines, estimated to have diverged for up to 250,000 y, showed surprisingly little variability among GRCs. This suggests that a single GRC haplotype has spread relatively recently across all examined matrilines. A few diagnostic GRC mutations that arose since this inferred spreading suggest that the GRC has continued to jump across matriline boundaries. Our findings raise the possibility that certain GRC haplotypes could selfishly spread through the population via occasional paternal transmission, thereby outcompeting other GRC haplotypes that were limited to strict maternal inheritance, even if this was partly detrimental to organismal fitness.

Enhancing Dye-Triplet-Sensitized Upconversion Emission Through the Heavy-Atom Effect in CsLu2 F7 :Yb/Er Nanoprobes.

Lanthanide (Ln3+ )-doped upconversion (UC) nanoprobes, which have drawn extensive attention for various bioapplications, usually suffer from small absorption cross-sections and weak luminescence intensity of Ln3+ ions. Herein, we report the controlled synthesis of a new class of Ln3+ -doped UC nanoprobes based on CsLu2 F7 :Yb/Er nanocrystals (NCs), which can effectively increase the intersystem crossing (ISC) efficiency from singlet excited state to triplet excited state of IR808 up to 99.3 % through the heavy atom effect. By virtue of the efficient triplet sensitization of IR808, the optimal UC luminescence (UCL) intensity of IR808-modified CsLu2 F7 :Yb/Er NCs is enhanced by 1309 times upon excitation at 808 nm. Benefiting from the intense dye-triplet-sensitized UCL, the nanoprobes are demonstrated for sensitive assay of extracellular and intracellular hypochlorite with an 808-nm/980-nm dual excited ratiometric strategy.

DW-FBCSP: EEG emotion recognition algorithm based on scale distance weighted optimization.

Emotion calibration is measured by the valence and arousal scales and the ideal center is used to directly divide valence arousal into high scores and low scores. This division method has a big classification and labeling defect, and the influence of emotion stimulation material on the subjects cannot be accurately measured. To address this problem, this paper proposes an EEG emotion recognition algorithm (DW-FBCSP: Distance Weighted Filter Bank Common Spatial Pattern) based on scale distance weighted optimization to optimize the classification according to the distance of the scores from ideal center. This method is a natural extension of CSP that optimize the user's EEG signal projection matrix. Then, the LDA classifier is used to recognize emotions using the features set which fused the selected features and the features extracted by the projection matrix. The results show that the mean correct rate of the valence and arousal achieves 81.14% and 84.45% using the DEAP dataset. The results demonstrate that our proposed method outperforms better than some other results published in recent years.

A test for meiotic drive in hybrids between Australian and Timor zebra finches.

Meiotic drivers have been proposed as a potent evolutionary force underlying genetic and phenotypic variation, genome structure, and also speciation. Due to their strong selective advantage, they are expected to rapidly spread through a population despite potentially detrimental effects on organismal fitness. Once fixed, autosomal drivers are cryptic within populations and only become visible in between-population crosses lacking the driver or corresponding suppressor. However, the assumed ubiquity of meiotic drivers has rarely been assessed in crosses between populations or species. Here we test for meiotic drive in hybrid embryos and offspring of Timor and Australian zebra finches-subspecies that have evolved in isolation for about two million years-using 38,541 informative transmissions of 56 markers linked to either centromeres or distal chromosome ends. We did not find evidence for meiotic driver loci on specific chromosomes. However, we observed a weak overall transmission bias toward Timor alleles at centromeres in females (transmission probability of Australian alleles of 47%, nominal p = 6 × 10-5). While this is in line with the centromere drive theory, it goes against the expectation that the subspecies with the larger effective population size (i.e., the Australian zebra finch) should have evolved the more potent meiotic drivers. We thus caution against interpreting our finding as definite evidence for centromeric drive. Yet, weak centromeric meiotic drivers may be more common than generally anticipated and we encourage further studies that are designed to detect also small effect meiotic drivers.

Offspring performance is well buffered against stress experienced by ancestors.

Evolution should render individuals resistant to stress and particularly to stress experienced by ancestors. However, many studies report negative effects of stress experienced by one generation on the performance of subsequent generations. To assess the strength of such transgenerational effects we propose a strategy aimed at overcoming the problem of type I errors when testing multiple proxies of stress in multiple ancestors against multiple offspring performance traits, and we apply it to a large observational dataset on captive zebra finches (Taeniopygia guttata). We combine clear one-tailed hypotheses with steps of validation, meta-analytic summary of mean effect sizes, and independent confirmatory testing. We find that drastic differences in early growth conditions (nestling body mass 8 days after hatching varied sevenfold between 1.7 and 12.4 g) had only moderate direct effects on adult morphology (95% confidence interval [CI]: r = 0.19-0.27) and small direct effects on adult fitness traits (r = 0.02-0.12). In contrast, we found no indirect effects of parental or grandparental condition (r = -0.017 to 0.002; meta-analytic summary of 138 effect sizes), and mixed evidence for small benefits of matching environments between parents and offspring, as the latter was not robust to confirmatory testing in independent datasets. This study shows that evolution has led to a remarkable robustness of zebra finches against undernourishment. Our study suggests that transgenerational effects are absent in this species, because CIs exclude all biologically relevant effect sizes.

Interference competition pressure predicts the number of avian predators that shifted their timing of activity.

Being active at different times facilitates the coexistence of functionally similar species. Hence, time partitioning might be induced by competition. However, the relative importance of direct interference and indirect exploitation competition on time partitioning remains unclear. The aim of this study was to investigate the relative importance of these two forms of competition on the occurrence of time-shifting among avian predator species. As a measure of interference competition pressure, we used the species richness of day-active avian predator species or of night-active avian predator species (i.e. species of Accipitriformes, Falconiformes and Strigiformes) in a particular geographical area (assemblage). As an estimate of exploitation competition pressure, we used the total species richness of avian predators in each assemblage. Estimates of the intensity of interference competition robustly predicted the number of Accipitriformes species that became crepuscular and the number of Strigiformes species that became day-active or strictly crepuscular. Interference competition pressure may depend on body size and on the total duration of the typical active period (day or night length). Our results support-to some extent-that smaller species are more likely to become time-shifters. Day length did not have an effect on the number of time-shifter species in the Accipitriformes. Among the large Strigiformes, more time-shifter species occur in areas where nights are shorter (i.e. where less of the typical time resource is available). However, in the small Strigiformes, we found the opposite, counterintuitive effect: more time-shifters where nights are longer. Exploitation competition may have had an additional positive effect on the number of time-shifters, but only in Accipitriformes, and the effect was not as robust. Our results thus support the interference competition hypothesis, suggesting that animals may have shifted their time of activity, despite phylogenetic constraints on the ability to do so, to reduce the costs of direct interactions. Our findings also highlight the influence of body size as a surrogate of competitive ability during encounters on time partitioning, at least among avian predators.

A sex-chromosome inversion causes strong overdominance for sperm traits that affect siring success.

Male reproductive success depends on the competitive ability of sperm to fertilize the ova, which should lead to strong selection on sperm characteristics. This raises the question of how heritable variation in sperm traits is maintained. Here we show that in zebra finches (Taeniopygia guttata) nearly half of the variance in sperm morphology is explained by an inversion on the Z chromosome with a 40% allele frequency in the wild. The sperm of males that are heterozygous for the inversion had the longest midpieces and the highest velocity. Furthermore, such males achieved the highest fertility and the highest siring success, both within-pair and extra-pair. Males homozygous for the derived allele show detrimental sperm characteristics and the lowest siring success. Our results suggest heterozygote advantage as the mechanism that maintains the inversion polymorphism and hence variance in sperm design and in fitness.