scispace - formally typeset
Search or ask a question

Showing papers in "Proceedings of The Royal Society B: Biological Sciences in 2022"


Journal ArticleDOI
TL;DR: In this article , the authors present a dataset of first flowering dates from 406 plant species in the UK between 1753 and 2019 CE, showing that the largest lifeform-specific shift of 32 days is found in herbs, which are generally characterized by fast turnover rates and high levels of genetic adaptation.
Abstract: Global temperatures are rising at an unprecedented rate, but environmental responses are often difficult to recognize and quantify. Long-term observations of plant phenology, the annually recurring sequence of plant developmental stages, can provide sensitive measures of climate change and important information for ecosystem services. Here, we present 419 354 recordings of the first flowering date from 406 plant species in the UK between 1753 and 2019 CE. Community-wide first flowering advanced by almost one month on average when comparing all observations before and after 1986 (p < 0.0001). The mean first flowering time is 6 days earlier in southern than northern sites, 5 days earlier under urban than rural settings, and 1 day earlier at lower than higher elevations. Compared to trees and shrubs, the largest lifeform-specific phenological shift of 32 days is found in herbs, which are generally characterized by fast turnover rates and potentially high levels of genetic adaptation. Correlated with January–April maximum temperatures at −0.81 from 1952–2019 (p < 0.0001), the observed trends (5.4 days per decade) and extremes (66 days between the earliest and latest annual mean) in the UK's first flowering dataset can affect the functioning and productivity of ecosystems and agriculture.

31 citations


Journal ArticleDOI
TL;DR: In this paper , a review of relevant research shows that for bees, this assumption is without empirical foundation and that there are only 19 studies that tested the effects of "inert" ingredients on bee health.
Abstract: Agrochemical formulations are composed of two broad groups of chemicals: active ingredients, which confer pest control action, and ‘inert’ ingredients, which facilitate the action of the active ingredient. Most research into the effects of agrochemicals focusses on the effects of active ingredients. This reflects the assumption that ‘inert’ ingredients are non-toxic. A review of relevant research shows that for bees, this assumption is without empirical foundation. After conducting a systematic literature search, we found just 19 studies that tested the effects of ‘inert’ ingredients on bee health. In these studies, ‘inert’ ingredients were found to cause mortality in bees through multiple exposure routes, act synergistically with other stressors and cause colony level effects. This lack of research is compounded by a lack of diversity in study organism used. We argue that ‘inert’ ingredients have distinct, and poorly understood, ecological persistency profiles and toxicities, making research into their individual effects necessary. We highlight the lack of mitigation in place to protect bees from ‘inert’ ingredients and argue that research efforts should be redistributed to address the knowledge gap identified here. If so-called ‘inert’ ingredients are, in fact, detrimental to bee health, their potential role in widespread bee declines needs urgent assessment.

29 citations


Journal ArticleDOI
TL;DR: In this paper , a large eDNA ocean survey (spanning 86 000 km2 to depths of 500 m) was conducted to understand the abundance and distribution of Pacific hake (Merluccius productus), the target of the largest finfish fishery along the west coast of the USA.
Abstract: All species inevitably leave genetic traces in their environments, and the resulting environmental DNA (eDNA) reflects the species present in a given habitat. It remains unclear whether eDNA signals can provide quantitative metrics of abundance on which human livelihoods or conservation successes depend. Here, we report the results of a large eDNA ocean survey (spanning 86 000 km2 to depths of 500 m) to understand the abundance and distribution of Pacific hake (Merluccius productus), the target of the largest finfish fishery along the west coast of the USA. We sampled eDNA in parallel with a traditional acoustic-trawl survey to assess the value of eDNA surveys at a scale relevant to fisheries management. Despite local differences, the two methods yield comparable information about the broad-scale spatial distribution and abundance. Furthermore, we find depth and spatial patterns of eDNA closely correspond to acoustic-trawl estimates for hake. We demonstrate the power and efficacy of eDNA sampling for estimating abundance and distribution and move the analysis eDNA data beyond sample-to-sample comparisons to management relevant scales. We posit that eDNA methods are capable of providing general quantitative applications that will prove especially valuable in data- or resource-limited contexts.

27 citations


Journal ArticleDOI
TL;DR: In this paper , the authors synthesize trait-based research globally (n = 865 studies) to examine the contexts in which traits may be used for global change prediction and identify over 2500 other morphological, physiological, behavioural and life-history traits known to mediate environmental filters of species' range and abundance as candidates for future predictive global change work.
Abstract: Trait-based approaches are increasingly recognized as a tool for understanding ecosystem re-assembly and function under intensifying global change. Here we synthesize trait-based research globally (n = 865 studies) to examine the contexts in which traits may be used for global change prediction. We find that exponential growth in the field over the last decade remains dominated by descriptive studies of terrestrial plant morphology, highlighting significant opportunities to expand trait-based thinking across systems and taxa. Very few studies (less than 3%) focus on predicting ecological effects of global change, mostly in the past 5 years and via singular traits that mediate abiotic limits on species distribution. Beyond organism size (the most examined trait), we identify over 2500 other morphological, physiological, behavioural and life-history traits known to mediate environmental filters of species' range and abundance as candidates for future predictive global change work. Though uncommon, spatially explicit process models—which mechanistically link traits to changes in organism distributions and abundance—are among the most promising frameworks for holistic global change prediction at scales relevant for conservation decision-making. Further progress towards trait-based forecasting requires addressing persistent barriers including (1) matching scales of multivariate trait and environment data to focal processes disrupted by global change, and (2) propagating variation in trait and environmental parameters throughout process model functions using simulation.

25 citations


Journal ArticleDOI
TL;DR: This article identified geographically restricted, diploid clones in a single location and a single widespread, high-heterozygosity, polyploid clone (2n = 40) in all other locations.
Abstract: Polyploidy has the potential to allow organisms to outcompete their diploid progenitor(s) and occupy new environments. Shark Bay, Western Australia, is a World Heritage Area dominated by temperate seagrass meadows including Poseidon's ribbon weed, Posidonia australis. This seagrass is at the northern extent of its natural geographic range and experiences extremes in temperature and salinity. Our genomic and cytogenetic assessments of 10 meadows identified geographically restricted, diploid clones (2n = 20) in a single location, and a single widespread, high-heterozygosity, polyploid clone (2n = 40) in all other locations. The polyploid clone spanned at least 180 km, making it the largest known example of a clone in any environment on earth. Whole-genome duplication through polyploidy, combined with clonality, may have provided the mechanism for P. australis to expand into new habitats and adapt to new environments that became increasingly stressful for its diploid progenitor(s). The new polyploid clone probably formed in shallow waters after the inundation of Shark Bay less than 8500 years ago and subsequently expanded via vegetative growth into newly submerged habitats.

20 citations


Journal ArticleDOI
TL;DR: In this article , the authors analyzed time-varying interaction networks that were reconstructed using 1197 species, DNA-based ecological time series taken from experimental rice plots and empirical dynamic modelling, and introduced the interaction capacity, namely, the sum of interaction strength that a single species gives and receives, as a potential driver of community diversity.
Abstract: How patterns in community diversity emerge is a long-standing question in ecology. Studies suggested that community diversity and interspecific interactions are interdependent. However, evidence from high-diversity ecological communities is lacking because of practical challenges in characterizing speciose communities and their interactions. Here, I analysed time-varying interaction networks that were reconstructed using 1197 species, DNA-based ecological time series taken from experimental rice plots and empirical dynamic modelling, and introduced ‘interaction capacity', namely, the sum of interaction strength that a single species gives and receives, as a potential driver of community diversity. As community diversity increases, the number of interactions increases exponentially but the mean interaction capacity of a community becomes saturated, weakening interspecific interactions. These patterns are modelled with simple mathematical equations, based on which I propose the ‘interaction capacity hypothesis': that interaction capacity and network connectance can be two fundamental properties that influence community diversity. Furthermore, I show that total DNA abundance and temperature influence interaction capacity and connectance nonlinearly, explaining a large proportion of diversity patterns observed in various systems. The interaction capacity hypothesis enables mechanistic explanations of community diversity. Therefore, analysing ecological community data from the viewpoint of interaction capacity would provide new insight into community diversity.

19 citations


Journal ArticleDOI
TL;DR: While empirical data point to widespread contributions of epigenetic mechanisms in generating phenotypic variation, there are still concerns as to whether epigenetic variation is instead ultimately controlled by genetic variation.
Abstract: Epigenetic mechanisms such as DNA methylation, histone modifications and non-coding RNAs are increasingly targeted in studies of natural populations. Here, I review some of the insights gained from this research, examine some of the methods currently in use and discuss some of the challenges that researchers working on natural populations are likely to face when probing epigenetic mechanisms. While studies supporting the involvement of epigenetic mechanisms in generating phenotypic variation in natural populations are amassing, many of these studies are currently correlative in nature. Thus, while empirical data point to widespread contributions of epigenetic mechanisms in generating phenotypic variation, there are still concerns as to whether epigenetic variation is instead ultimately controlled by genetic variation. Disentangling these two sources of variation will be a key to resolving the debate about the importance of epigenetic mechanisms, and studies on natural populations that partition the relative contribution of genetic and epigenetic factors to phenotypic variation can play an important role in this debate.

17 citations


Journal ArticleDOI
TL;DR: It is argued, from the understanding of male-killing mechanisms, that suppression will commonly involve evolution of the host sex determination pathways and that the host's response tomale-killing microbes thus represents an unrecognized driver of the diversity of arthropod sex determination.
Abstract: Arthropods host a range of sex-ratio-distorting selfish elements, including diverse maternally inherited endosymbionts that solely kill infected males. Male-killing heritable microbes are common, reach high frequency, but until recently have been poorly understood in terms of the host–microbe interaction. Additionally, while male killing should generate strong selection for host resistance, evidence of this has been scant. The interface of the microbe with host sex determination is integral to the understanding of how death is sex limited and how hosts can evolve evasion of male killing. We first review current knowledge of the mechanisms diverse endosymbionts use to induce male-specific death. We then examine recent evidence that these agents do produce intense selection for host nuclear suppressor elements. We argue, from our understanding of male-killing mechanisms, that suppression will commonly involve evolution of the host sex determination pathways and that the host's response to male-killing microbes thus represents an unrecognized driver of the diversity of arthropod sex determination. Further work is required to identify the genes and mechanisms responsible for male-killing suppression, which will both determine the components of sex determination (or other) systems associated with suppressor evolution, and allow insight into the mechanism of male killing itself.

17 citations


Journal ArticleDOI
TL;DR: In this article , the authors performed a self-report questionnaire and a systematic literature review to quantify how researchers interpreted conceptual and statistical definitions commonly used in animal personality research, and compared whether data obtained from the questionnaire matched with data from the literature review.
Abstract: Whether animal personality studies provide insights of broader evolutionary and ecological relevance to the field of behavioural ecology is frequently questioned. One of the sources of controversy is the vast, but often vague terminology present in the field. From a statistical perspective, animal personality is defined as among-individual variance in behaviour. However, numerous conceptual definitions of animal personality are available in the literature. Here, we performed (i) a self-report questionnaire and (ii) a systematic literature review to quantify how researchers interpreted conceptual and statistical definitions commonly used in animal personality research. We also compared whether data obtained from the questionnaire matched with data from the literature review. Among the 430 self-reported researchers that participated in our questionnaire, we observed discrepancies in key questions such as the conceptual definition of animal personality or the interpretation of repeatability. Furthermore, our literature review generally confirmed the global patterns revealed by the questionnaire. Overall, we identified common disagreements within the field of animal personality and discussed potential solutions. We advocate for adopting a terminology that avoids ambiguous interpretations and helps to make more explicit the widespread connotations implicit in the label ‘animal personality’.

15 citations


Journal ArticleDOI
TL;DR: It is concluded that the feeding apparatus and neck flexors of parrots have been co-opted to function biomechanically as a propulsive third limb during vertical climbing and it is hypothesized that this exaptation required substantive alterations to the neuromuscular system including enhanced force-generating capabilities of the neckflexors and modifications to locomotor central pattern generators.
Abstract: No vertebrate, living or extinct, is known to have possessed an odd number of limbs. Despite this ‘forbidden phenotype’, gaits that use odd numbers of limbs (e.g. tripedalism or pentapedalism) have evolved in both avian and mammalian lineages. Tripedal locomotion is commonly employed by parrots during climbing, who use their beaks as an additional support. However, it is unclear whether the beak functions simply as a stabilizing hook, or as a propulsive limb. Here, we present data on kinetics of tripedal climbing in six rosy-faced lovebirds (Agapornis roseicollis). Our findings demonstrate that parrots use cyclical tripedal gaits when climbing and the beak and hindlimbs generate comparable propulsive and tangential substrate reaction forces and power. Propulsive and tangential forces generated by the beak are of magnitudes equal to or greater than those forces generated by the forelimbs of humans and non-human primates during vertical climbing. We conclude that the feeding apparatus and neck flexors of parrots have been co-opted to function biomechanically as a propulsive third limb during vertical climbing. We hypothesize that this exaptation required substantive alterations to the neuromuscular system including enhanced force-generating capabilities of the neck flexors and modifications to locomotor central pattern generators.

14 citations


Journal ArticleDOI
TL;DR: This study reveals that CG10816 encodes not one but two prominent host defence peptides with different specificity against different pathogens, and demonstrates how natural polymorphisms found in Drosophila populations can affect host susceptibility.
Abstract: Antimicrobial peptides (AMPs) are key players in innate defence against infection in plants and animals. In Drosophila, many host defence peptides are produced downstream of the Toll and Imd NF-κB pathways. Use of single and compound AMP mutations in Drosophila has revealed that AMPs can additively or synergistically contribute to combat pathogens in vivo. However, these studies also revealed a high degree of specificity, wherein just one AMP can play a major role in combatting a specific pathogen. We recently uncovered a specific importance of the antibacterial peptide Drosocin for defence against Enterobacter cloacae. Here, we show that the Drosocin locus (CG10816) is more complex than previously described. In addition to its namesake peptide “Drosocin”, it encodes a second peptide generated from a precursor via furin cleavage. We name this peptide “Buletin”, and show that it corresponds to the uncharacterized “Immune-induced Molecule 7” previously identified by MALDI-TOF. The existence of a naturally occurring polymorphism (Thr52Ala) in the CG10816 precursor protein masked the identification of this peptide previously. Using mutations differently affecting the production of these two CG10816 gene products, we show that Drosocin, but not Buletin, contributes to the CG10816-mediated defence against E. cloacae. Strikingly, we observed that Buletin, but not Drosocin, contributes to the CG10816-mediated defence against Providencia burhodogranariea. Moreover, the Thr52Ala polymorphism in Buletin affects survival to P. burhodogranariea, wherein the Alanine allele confers better defence than the Threonine allele. However, we found no activity of Buletin against either P. burhodogranariea or E. coli in vitro. Collectively, our study reveals that CG10816 encodes not one but two prominent host defence peptides with different specificity against different pathogens. This finding emphasizes the complexity of the Drosophila humoral response consisting of multiple host defence peptides with specific activities, and demonstrates how natural polymorphisms found in Drosophila populations can affect host susceptibility.

Journal ArticleDOI
TL;DR: This study provides a new example of amhr2 as the SD gene in fish and sheds light on the convergent evolution of the duplication of AMH/AMHR2 pathway members underlying the evolution of sex determination in different fish lineages.
Abstract: Teleosts are important models to study sex chromosomes and sex-determining (SD) genes because they present a variety of sex determination systems. Here, we used Nanopore and Hi-C technologies to generate a high-contiguity chromosome-level genome assembly of a YY southern catfish (Silurus meridionalis). The assembly is 750.0 Mb long, with contig N50 of 15.96 Mb and scaffold N50 of 27.22 Mb. We also sequenced and assembled an XY male genome with a size of 727.2 Mb and contig N50 of 13.69 Mb. We identified a candidate SD gene through comparisons to our previous assembly of an XX individual. By resequencing male and female pools, we characterized a 2.38 Mb sex-determining region (SDR) on Chr24. Analysis of read coverage and comparison of the X and Y chromosome sequences showed a Y specific insertion (approx. 500 kb) in the SDR which contained a male-specific duplicate of amhr2 (named amhr2y). amhr2y and amhr2 shared high-nucleotide identity (81.0%) in the coding region but extremely low identity in the promotor and intron regions. The exclusive expression in the male gonadal primordium and loss-of-function inducing male to female sex reversal confirmed the role of amhr2y in male sex determination. Our study provides a new example of amhr2 as the SD gene in fish and sheds light on the convergent evolution of the duplication of AMH/AMHR2 pathway members underlying the evolution of sex determination in different fish lineages.

Journal ArticleDOI
TL;DR: The results suggest that selection for enhanced cognitive abilities in parrots have in turn promoted longer lifespans, and the Cognitive Buffer Hypothesis, which proposes that increased cognitive abilities enable longer life spans, is addressed.
Abstract: Previous studies have demonstrated a correlation between longevity and brain size in a variety of taxa. Little research has been devoted to understanding this link in parrots; yet parrots are well-known for both their exceptionally long lives and cognitive complexity. We employed a large-scale comparative analysis that investigated the influence of brain size and life history variables on longevity in parrots. Specifically, we addressed two hypotheses for evolutionary drivers of longevity: the Cognitive Buffer Hypothesis, which proposes that increased cognitive abilities enable longer life spans, and the Expensive Brain Hypothesis, which holds that increases in life span are caused by prolonged developmental time of, and increased parental investment in, large brained offspring. We estimated life expectancy from detailed zoo records for 133,818 individuals across 244 parrot species. Using a principled Bayesian approach that addresses data uncertainty and imputation of missing values, we found a consistent correlation between relative brain size and life expectancy in parrots. This correlation was best explained by a direct effect of relative brain size. Notably, we found no effects of developmental time, clutch size, or age at first reproduction. Our results suggest that selection for enhanced cognitive abilities in parrots have in turn promoted longer lifespans.

Journal ArticleDOI
TL;DR: In this article , the authors used DNA and RNA sequencing to reconstruct the lake virosphere in both its sediments and soils, as well as its range of eukaryotic hosts.
Abstract: The host spectrum of viruses is quite diverse, as they can sustainedly infect a few species to several phyla. When confronted with a new host, a virus may even infect it and transmit sustainably in this new host, a process called “viral spillover.” However, the risk of such events is difficult to quantify. As climate change is rapidly transforming environments, it is becoming critical to quantify the potential for spillovers. To address this issue, we resorted to a metagenomics approach and focused on two environments, soil and lake sediments from Lake Hazen, the largest High Arctic freshwater lake in the world. We used DNA and RNA sequencing to reconstruct the lake’s virosphere in both its sediments and soils, as well as its range of eukaryotic hosts. We then estimated the spillover risk by measuring the congruence between the viral and the eukaryotic host phylogenetic trees, and show that spillover risk is higher in lake sediments than in soil, and increases with runoff from glacier melt, a proxy for climate change. Should climate change also shift species range of potential viral vectors and reservoirs northwards, the High Arctic could become fertile ground for emerging pandemics.

Journal ArticleDOI
TL;DR: It is suggested that research data management training and culture within a PI's group are likely to be more important determinants of data archiving quality than other factors such as a journal's open data policy.
Abstract: Many leading journals in ecology and evolution now mandate open data upon publication. Yet, there is very little oversight to ensure the completeness and reusability of archived datasets, and we currently have a poor understanding of the factors associated with high-quality data sharing. We assessed 362 open datasets linked to first- or senior-authored papers published by 100 principal investigators (PIs) in the fields of ecology and evolution over a period of 7 years to identify predictors of data completeness and reusability (data archiving quality). Datasets scored low on these metrics: 56.4% were complete and 45.9% were reusable. Data reusability, but not completeness, was slightly higher for more recently archived datasets and PIs with less seniority. Journal open data policy, PI gender and PI corresponding author status were unrelated to data archiving quality. However, PI identity explained a large proportion of the variance in data completeness (27.8%) and reusability (22.0%), indicating consistent inter-individual differences in data sharing practices by PIs across time and contexts. Several PIs consistently shared data of either high or low archiving quality, but most PIs were inconsistent in how well they shared. One explanation for the high intra-individual variation we observed is that PIs often conduct research through students and postdoctoral researchers, who may be responsible for the data collection, curation and archiving. Levels of data literacy vary among trainees and PIs may not regularly perform quality control over archived files. Our findings suggest that research data management training and culture within a PI's group are likely to be more important determinants of data archiving quality than other factors such as a journal's open data policy. Greater incentives and training for individual researchers at all career stages could improve data sharing practices and enhance data transparency and reusability.

Journal ArticleDOI
TL;DR: In this article , the authors investigated the effects of human settlement density on the interspecific interaction of a carnivore guild comprising of tiger, leopard and dhole in Bhutan.
Abstract: In the face of a growing human footprint, understanding interactions among threatened large carnivores is fundamental to effectively mitigating anthropogenic threats and managing species. Using data from a large-scale camera trap survey, we investigated the effects of environmental and anthropogenic variables on the interspecific interaction of a carnivore guild comprising of tiger, leopard and dhole in Bhutan. We demonstrate the complex effects of human settlement density on large carnivore interactions. Specifically, we demonstrate that leopard–dhole co-occupancy probability was higher in areas with higher human settlement density. The opposite was true for tiger–leopard co-occupancy probability, but it was positively affected by large prey (gaur) abundance. These findings suggest that multi-carnivore communities across land-use gradients are spatially structured and mediated also by human presence and/or the availability of natural prey. Our findings show that space-use patterns are driven by a combination of the behavioural mechanism of each species and its interactions with competing species. The duality of the effect of settlement density on species interactions suggests that the benefits of exploiting anthropogenic environments are a trade-off between ecological opportunity (food subsidies or easy prey) and the risk of escalating conflict with humans.

Journal ArticleDOI
TL;DR: In this article , the authors explored how climate change and the mining of lithium for green technologies influence surface water availability, primary productivity and the abundance of three threatened and economically important flamingo species in the ‘Lithium Triangle’ of the Chilean Andes.
Abstract: The development of technologies to slow climate change has been identified as a global imperative. Nonetheless, such ‘green’ technologies can potentially have negative impacts on biodiversity. We explored how climate change and the mining of lithium for green technologies influence surface water availability, primary productivity and the abundance of three threatened and economically important flamingo species in the ‘Lithium Triangle’ of the Chilean Andes. We combined climate and primary productivity data with remotely sensed measures of surface water levels and a 30-year dataset on flamingo abundance using structural equation modelling. We found that, regionally, flamingo abundance fluctuated dramatically from year-to-year in response to variation in surface water levels and primary productivity but did not exhibit any temporal trends. Locally, in the Salar de Atacama—where lithium mining is focused—we found that mining was negatively correlated with the abundance of two of the three flamingo species. These results suggest continued increases in lithium mining and declines in surface water could soon have dramatic effects on flamingo abundance across their range. Efforts to slow the expansion of mining and the impacts of climate change are, therefore, urgently needed to benefit local biodiversity and the local human economy that depends on it.

Journal ArticleDOI
TL;DR: A consistent gender bias among species named after eminent scientists, with male scientists being immortalized disproportionately more frequently than female scientists, and the tendency for taxonomists to name new species after a family member or close friend has increased over the past 20 years.
Abstract: As our inventory of Earth's biodiversity progresses, the number of species given a Latin binomial name is also growing. While the coining of species names is bound by rules, the sources of inspiration used by taxonomists are an eclectic mix. We investigated naming trends for nearly 2900 new species of parasitic helminths described in the past two decades. Our analysis indicates that the likelihood of new species being given names that convey some information about them (name derived from morphology, host or locality of origin) or not (named after an eminent scientist, or for something else) depends on the higher taxonomic group to which the parasite or its host belongs. We also found a consistent gender bias among species named after eminent scientists, with male scientists being immortalized disproportionately more frequently than female scientists. Finally, we found that the tendency for taxonomists to name new species after a family member or close friend has increased over the past 20 years. We end by offering suggestions for future species naming, aimed at honouring the scientific community's diversity and avoiding etymological nepotism and cronyism, while still allowing for creativity in crafting new Latin species names.

Journal ArticleDOI
TL;DR: In this article , the authors show that a high incubation temperature induced a consistent and long-lasting increase in mitochondrial aerobic metabolism, which could potentially underlie among-individual variation in performance and health state.
Abstract: It is increasingly being postulated that among-individual variation in mitochondrial function underlies variation in individual performance (e.g. growth rate) and state of health. It has been suggested (but not adequately tested) that environmental conditions experienced before birth could programme postnatal mitochondrial function, with persistent effects potentially lasting into adulthood. We tested this hypothesis in an avian model by experimentally manipulating prenatal conditions (incubation temperature and stability) and then measuring mitochondrial aerobic metabolism in blood cells from the same individuals during the middle of the growth period and at adulthood. Mitochondrial aerobic metabolism changed markedly across life stages, and parts of these age-related changes were influenced by the prenatal temperature conditions. A high incubation temperature induced a consistent and long-lasting increase in mitochondrial aerobic metabolism. Postnatal mitochondrial aerobic metabolism was positively associated with oxidative damage on DNA but not telomere length. While we detected significant within-individual consistency in mitochondrial aerobic metabolism across life stages, the prenatal temperature regime only accounted for a relatively small proportion (less than 20%) of the consistent among-individual differences we observed. Our results demonstrate that prenatal conditions can programme consistent and long-lasting differences in mitochondrial function, which could potentially underlie among-individual variation in performance and health state.

Journal ArticleDOI
TL;DR: This work investigated the historical biogeography of Primates and their euarchontan relatives using a novel meta-analytical phylogeny of over 900 extant and extinct species spanning their entire evolutionary history, finding ancestral range estimates for young nodes were largely congruent with those derived from molecular phylogeny.
Abstract: A clade’s evolutionary history is shaped, in part, by geographical range expansion, sweepstakes dispersal and local extinction. A rigorous understanding of historical biogeography may therefore yield insights into macroevolutionary dynamics such as adaptive radiation. Modern historical biogeographic analyses typically fit statistical models to molecular phylogenies, but it remains unclear whether extant species provide sufficient signal or if well-sampled phylogenies of extinct and extant taxa are necessary to produce meaningful estimates of past ranges. We investigated the historical biogeography of Primates and their euarchontan relatives using a novel meta-analytical phylogeny of over 900 extant (n= 419) and extinct (n = 483) species spanning their entire evolutionary history. Ancestral range estimates for young nodes were largely congruent with those derived from molecular phylogeny. However, node age exerts a significant effect on ancestral range estimate congruence, and the probability of congruent inference dropped below 0.5 for nodes older than the late Eocene, corresponding to the origins of higher-level clades. Discordance was not observed in analyses of extinct taxa alone. Fossils are essential for robust ancestral range inference and biogeographic analyses of extant clades originating in the deep past should be viewed with scepticism without them.

Journal ArticleDOI
TL;DR: In this article , the authors study homing suppression gene drives in haplodiploids and find that a drive targeting a female fertility gene could still be successful, however, such drives are less powerful than in diploid and suffer more from functional resistance alleles.
Abstract: Gene drives have shown great promise for suppression of pest populations. These engineered alleles can function by a variety of mechanisms, but the most common is the CRISPR homing drive, which converts wild-type alleles to drive alleles in the germline of heterozygotes. Some potential target species are haplodiploid, in which males develop from unfertilized eggs and thus have only one copy of each chromosome. This prevents drive conversion, a substantial disadvantage compared to diploids where drive conversion can take place in both sexes. Here, we study homing suppression gene drives in haplodiploids and find that a drive targeting a female fertility gene could still be successful. However, such drives are less powerful than in diploids and suffer more from functional resistance alleles. They are substantially more vulnerable to high resistance allele formation in the embryo owing to maternally deposited Cas9 and guide RNA and also to somatic cleavage activity. Examining spatial models where organisms move over a continuous landscape, we find that haplodiploid suppression drives surprisingly perform nearly as well as in diploids, possibly owing to their ability to spread further before inducing strong suppression. Together, these results indicate that gene drive can potentially be used to effectively suppress haplodiploid populations.

Journal ArticleDOI
TL;DR: In this paper , the authors describe a 70-fold increase in annual nest numbers on the island of Sal (Cape Verde, North Atlantic) between 2008 and 2020 (from 506 to 35 507 nests), making this now one of the largest loggerhead nesting aggregations in the world.
Abstract: With some taxa, a reduction in the mean size of individuals may reflect over-harvesting and/or trophy hunting. However, we show that in sea turtles, a reduction in the mean size of breeding individuals may be part of the good news story of an expanding population. We describe a 70-fold increase in annual nest numbers on the island of Sal (Cape Verde, North Atlantic) between 2008 and 2020 (from 506 to 35 507 nests), making this now one of the largest loggerhead (Caretta caretta) nesting aggregations in the world. We use 20 128 measurements of the size of nesting turtles to show that their mean annual size has decreased by about 2.4 cm, from 83.2 to 80.8 cm. This decrease in the mean size of nesting turtles was not caused by the removal of larger turtles, for example by selective harvesting. Rather we develop a theoretical model to show than this decrease in mean size can be explained by an influx of first-time nesters, combined with a decrease in the size of those first-time nesters over time. A reduction in mean size of nesting turtles has been reported across the Atlantic, Pacific and Indian Oceans, and may be a common feature of population recoveries in sea turtles.

Journal ArticleDOI
TL;DR: In this paper , the authors reinterpreted a fossil from the Wheeler Formation of Utah as a new opabiniid, Utaurora comosa nov. gen. et sp.
Abstract: Once considered ‘weird wonders’ of the Cambrian, the emblematic Burgess Shale animals Anomalocaris and Opabinia are now recognized as lower stem-group euarthropods and have provided crucial data for constraining the polarity of key morphological characters in the group. Anomalocaris and its relatives (radiodonts) had worldwide distribution and survived until at least the Devonian. However, despite intense study, Opabinia remains the only formally described opabiniid to date. Here we reinterpret a fossil from the Wheeler Formation of Utah as a new opabiniid, Utaurora comosa nov. gen. et sp. By visualizing the sample of phylogenetic topologies in treespace, our results fortify support for the position of U. comosa beyond the nodal support traditionally applied. Our phylogenetic evidence expands opabiniids to multiple Cambrian stages. Our results underscore the power of treespace visualization for resolving imperfectly preserved fossils and expanding the known diversity and spatio-temporal ranges within the euarthropod lower stem group.

Journal ArticleDOI
TL;DR: Despite having no constraints on planning time, participants exhibited a robust bias towards the frequent target when movements were self-initiated quickly, the signature of a planning bias; notably, the peak near the rare target was shifted in the frequently practiced direction, the signatures of an execution bias.
Abstract: Repetition of specific movement biases subsequent actions towards the practiced movement, a phenomenon known as use-dependent learning (UDL). Recent experiments that impose strict constraints on planning time have revealed two sources of use-dependent biases, one arising from dynamic changes occurring during motor planning and another reflecting a stable shift in motor execution. Here, we used a distributional analysis to examine the contribution of these biases in reaching. To create the conditions for UDL, the target appeared at a designated ‘frequent’ location on most trials, and at one of six ‘rare’ locations on other trials. Strikingly, the heading angles were bimodally distributed, with peaks at both frequent and rare target locations. Despite having no constraints on planning time, participants exhibited a robust bias towards the frequent target when movements were self-initiated quickly, the signature of a planning bias; notably, the peak near the rare target was shifted in the frequently practiced direction, the signature of an execution bias. Furthermore, these execution biases were not only replicated in a delayed-response task but were also insensitive to reward. Taken together, these results extend our understanding of how volitional movements are influenced by recent experience.

Journal ArticleDOI
TL;DR: Why sour taste evolved, why it might have persisted as vertebrates made the transition to land and what factors might have favoured the preference for sour-tasting, acidic foods, particularly in hominins, such as humans are considered.
Abstract: The evolutionary history of sour taste has been little studied. Through a combination of literature review and trait mapping on the vertebrate phylogenetic tree, we consider the origin of sour taste, potential cases of the loss of sour taste, and those factors that might have favoured changes in the valence of sour taste—from aversive to appealing. We reconstruct sour taste as having evolved in ancient fish. By contrast to other tastes, sour taste does not appear to have been lost in any major vertebrate taxa. For most species, sour taste is aversive. Animals, including humans, that enjoy the sour taste triggered by acidic foods are exceptional. We conclude by considering why sour taste evolved, why it might have persisted as vertebrates made the transition to land and what factors might have favoured the preference for sour-tasting, acidic foods, particularly in hominins, such as humans.

Journal ArticleDOI
TL;DR: A crucial step in insect evolution is revealed and the importance of comprehensive studies even of putatively well-known systems is highlighted, as the shift from powerful chewing to precise cutting likely facilitated adaptations to parasitize hosts hidden in hard substrates, which pose challenges to the emerging wasps.
Abstract: One key event in insect evolution was the development of mandibles with two joints, which allowed powerful biting but restricted their movement to a single degree of freedom. These mandibles define the Dicondylia, which constitute over 99% of all extant insect species. It was common doctrine that the dicondylic articulation of chewing mandibles remained unaltered for more than 400 million years. We report highly modified mandibles overcoming the restrictions of a single degree of freedom and hypothesize their major role in insect diversification. These mandibles are defining features of parasitoid chalcid wasps, one of the most species-rich lineages of insects. The shift from powerful chewing to precise cutting likely facilitated adaptations to parasitize hosts hidden in hard substrates, which pose challenges to the emerging wasps. We reveal a crucial step in insect evolution and highlight the importance of comprehensive studies even of putatively well-known systems.

Journal ArticleDOI
TL;DR: Understanding of the relationship between coronaviruses and mammals, particularly bats, is augmented and taxonomically diverse data is provided for studies of how host proteins are bound by coronavirus and can inform surveillance, conservation and public health efforts.
Abstract: Pandemics originating from non-human animals highlight the need to understand how natural hosts have evolved in response to emerging human pathogens and which groups may be susceptible to infection and/or potential reservoirs to mitigate public health and conservation concerns. Multiple zoonotic coronaviruses, such as severe acute respiratory syndrome-associated coronavirus (SARS-CoV), SARS-CoV-2 and Middle Eastern respiratory syndrome-associated coronavirus (MERS-CoV), are hypothesized to have evolved in bats. We investigate angiotensin-converting enzyme 2 (ACE2), the host protein bound by SARS-CoV and SARS-CoV-2, and dipeptidyl-peptidase 4 (DPP4 or CD26), the host protein bound by MERS-CoV, in the largest bat datasets to date. Both the ACE2 and DPP4 genes are under strong selection pressure in bats, more so than in other mammals, and in residues that contact viruses. Additionally, mammalian groups vary in their similarity to humans in residues that contact SARS-CoV, SARS-CoV-2 and MERS-CoV, and increased similarity to humans in binding residues is broadly predictive of susceptibility to SARS-CoV-2. This work augments our understanding of the relationship between coronaviruses and mammals, particularly bats, provides taxonomically diverse data for studies of how host proteins are bound by coronaviruses and can inform surveillance, conservation and public health efforts.

Journal ArticleDOI
TL;DR: In this paper , the authors used environmental DNA metabarcoding to reconstruct well-known patterns of fish biodiversity on coral reefs and uncover hidden patterns on these highly diverse and threatened ecosystems.
Abstract: Increasing speed and magnitude of global change threaten the world's biodiversity and particularly coral reef fishes. A better understanding of large-scale patterns and processes on coral reefs is essential to prevent fish biodiversity decline but it requires new monitoring approaches. Here, we use environmental DNA metabarcoding to reconstruct well-known patterns of fish biodiversity on coral reefs and uncover hidden patterns on these highly diverse and threatened ecosystems. We analysed 226 environmental DNA (eDNA) seawater samples from 100 stations in five tropical regions (Caribbean, Central and Southwest Pacific, Coral Triangle and Western Indian Ocean) and compared those to 2047 underwater visual censuses from the Reef Life Survey in 1224 stations. Environmental DNA reveals a higher (16%) fish biodiversity, with 2650 taxa, and 25% more families than underwater visual surveys. By identifying more pelagic, reef-associated and crypto-benthic species, eDNA offers a fresh view on assembly rules across spatial scales. Nevertheless, the reef life survey identified more species than eDNA in 47 shared families, which can be due to incomplete sequence assignment, possibly combined with incomplete detection in the environment, for some species. Combining eDNA metabarcoding and extensive visual census offers novel insights on the spatial organization of the richest marine ecosystems.

Journal ArticleDOI
TL;DR: This article examined how females' early life adversity predicts sociality and temperament in wild olive baboons, and evaluated whether temperament mediates the relationship between early-life adversity and sociality.
Abstract: Social bonds enhance fitness in many group-living animals, generating interest in the processes that create individual variation in sociality. Previous work on female baboons shows that early life adversity and temperament both influence social connectedness in adulthood. Early life adversity might shape sociality by reducing ability to invest in social relationships or through effects on attractiveness as a social partner. We examine how females’ early life adversity predicts sociality and temperament in wild olive baboons, and evaluate whether temperament mediates the relationship between early life adversity and sociality. We use behavioural data on 31 females to quantify sociality. We measure interaction style as the tendency to produce grunts (signals of benign intent) in contexts in which the vocalization does not produce immediate benefits to the actor. Early life adversity was negatively correlated with overall sociality, but was a stronger predictor of social behaviours received than behaviours initiated. Females who experienced less early life adversity had more benign interaction styles and benign interaction styles were associated with receiving more social behaviours. Interaction style may partially mediate the association between early life adversity and sociality. These analyses add to our growing understanding of the processes connecting early life experiences to adult sociality.

Journal ArticleDOI
TL;DR: In this paper , the authors synthesized 187 effects from 78 experimental studies in a meta-analytic test of two questions; namely, whether predators, parasites and parasitoids express preferences for the sexual signals of prey, and whether sexual signals increase realized predation risk in the wild.
Abstract: Sexual signals are often central to reproduction, and their expression is thought to strike a balance between advertising to mates and avoiding detection by predatory eavesdroppers. Tests of the predicted predation costs have produced mixed results, however. Here we synthesized 187 effects from 78 experimental studies in a meta-analytic test of two questions; namely, whether predators, parasites and parasitoids express preferences for the sexual signals of prey, and whether sexual signals increase realized predation risk in the wild. We found that predators and parasitoids express strong and consistent preferences for signals in forced-choice contexts. We found a similarly strong overall increase in predation on sexual signallers in the wild, though here it was modality specific. Olfactory and acoustic signals increased the incidence of eavesdropping relative to visual signals, which experienced no greater risk than controls on average. Variation in outcome measures was universally high, suggesting that contexts in which sexual signalling may incur no cost, or even reduce the incidence of predation, are common. Our results reveal unexpected complexity in a central viability cost to sexual signalling, while also speaking to applied problems in invasion biology and pest management where signal exploitation holds promise for bio-inspired solutions.