Global analysis reveals complex demographic responses of mammals to climate change

Approximately 25 % of mammals are threatened globally with extinction, a risk that is amplified under climate change1. Persistence under climate change is determined by the combined effects of climatic factors on multiple demographic rates (survival, development, reproduction), and hence, on population dynamics2. Thus, to quantify which species and places on Earth are most vulnerable to climate-driven extinction, a global understanding of how demographic rates respond to climate is needed3. We synthesise information on such responses in terrestrial mammals, where extensive demographic data are available4. Given the importance of assessing the full spectrum of responses, we focus on studies that quantitatively link climate to multiple demographic rates. We identify 106 such studies, corresponding to 86 mammal species. We reveal a strong mismatch between the locations of demographic studies and the regions and taxa currently recognised as most vulnerable to climate change5,6. Moreover, we show that the effects of climate change on mammals will operate via complex demographic mechanisms: a vast majority of mammal populations display projected increases in some demographic rates but declines in others. Assessments of population viability under climate change therefore need to account for multiple demographic responses. We advocate to prioritise coordinated actions to assess mammal demography holistically for effective conservation worldwide

Herbaceous perennial plants with short generation time have stronger responses to climate anomalies than those with longer generation time

There is an urgent need to synthesize the state of our knowledge on plant responses to climate. The availability of open-access data provide opportunities to examine quantitative generalizations regarding which biomes and species are most responsive to climate drivers. Here, we synthesize time series of structured population models from 162 populations of 62 plants, mostly herbaceous species from temperate biomes, to link plant population growth rates (λ) to precipitation and temperature drivers. We expect: (1) more pronounced demographic responses to precipitation than temperature, especially in arid biomes; and (2) a higher climate sensitivity in short-lived rather than long-lived species. We find that precipitation anomalies have a nearly three-fold larger effect on λ than temperature. Species with shorter generation time have much stronger absolute responses to climate anomalies. We conclude that key species-level traits can predict plant population responses to climate, and discuss the relevance of this generalization for conservation planning

A standard protocol to report discrete stage‐structured demographic information

Stage-based demographic methods, such as matrix population models (MPMs), are powerful tools used to address a broad range of fundamental questions in ecology, evolutionary biology and conservation science. Accordingly, MPMs now exist for over 3000 species worldwide. These data are being digitised as an ongoing process and periodically released into two large open-access online repositories: the COMPADRE Plant Matrix Database and the COMADRE Animal Matrix Database. During the last decade, data archiving and curation of COMPADRE and COMADRE, and subsequent comparative research, have revealed pronounced variation in how MPMs are parameterized and reported. Here, we summarise current issues related to the parameterisation and reporting of MPMs that arise most frequently and outline how they affect MPM construction, analysis, and interpretation. To quantify variation in how MPMs are reported, we present results from a survey identifying key aspects of MPMs that are frequently unreported in manuscripts. We then screen COMPADRE and COMADRE to quantify how often key pieces of information are omitted from manuscripts using MPMs. Over 80% of surveyed researchers (n = 60) state a clear benefit to adopting more standardised methodologies for reporting MPMs. Furthermore, over 85% of the 300 MPMs assessed from COMPADRE and COMADRE omitted one or more elements that are key to their accurate interpretation. Based on these insights, we identify fundamental issues that can arise from MPM construction and communication and provide suggestions to improve clarity, reproducibility and future research utilising MPMs and their required metadata. To fortify reproducibility and empower researchers to take full advantage of their demographic data, we introduce a standardised protocol to present MPMs in publications. This standard is linked to www.compadre-db.org, so that authors wishing to archive their MPMs can do so prior to submission of publications, following examples from other open-access repositories such as DRYAD, Figshare and Zenodo. Combining and standardising MPMs parameterized from populations around the globe and across the tree of life opens up powerful research opportunities in evolutionary biology, ecology and conservation research. However, this potential can only be fully realised by adopting standardised methods to ensure reproducibility

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism

Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2,3,4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease

Oxidative stress and the evolution of sex differences in life span and ageing in the decorated cricket, gryllodes sigillatus

The Free Radical Theory of Ageing (FRTA) predicts that oxidative stress, induced when levels of reactive oxygen species exceed the capacity of antioxidant defenses, causes ageing. Recently, it has also been argued that oxidative damage may mediate important life-history trade-offs. Here, we use inbred lines of the decorated cricket, Gryllodes sigillatus, to estimate the genetic (co)variance between age-dependent reproductive effort, life span, ageing, oxidative damage, and total antioxidant capacity within and between the sexes. The FRTA predicts that oxidative damage should accumulate with age and negatively correlate with life span. We find that protein oxidation is greater in the shorter lived sex (females) and negatively genetically correlated with life span in both sexes. However, oxidative damage did not accumulate with age in either sex. Previously we have shown antagonistic pleiotropy between the genes for early-life reproductive effort and ageing rate in both sexes, although this was stronger in females. In females, we find that elevated fecundity early in life is associated with greater protein oxidation later in life, which is in turn positively correlated with the rate of ageing. Our results provide mixed support for the FRTA but suggest that oxidative stress may mediate sex-specific life-history strategies in G. sigillatus

Selection on female reproductive schedules in the marula fly, Ceratitis cosyra (Diptera : Tephritidae) affects dietary optima for female reproductive traits but not lifespan

Introduction: A changing environment can select on life-history traits and trade-offs in a myriad of ways. For example, global warming may shift phenology and thus the availability of host-plants. This may alter selection on survival and fertility schedules in herbivorous insects. If selection on life-histories changes, this may in turn select for altered nutrient intake, because the blend of nutrients organisms consume helps determine the expression of life-history traits. However, we lack empirical work testing whether shifts in the timing of oviposition alter nutrient intake and life-history strategies. Methods: We tested in the marula fruit fly, Ceratitis cosyra, how upward-selection on the age of female oviposition, in comparison with laboratory adapted control flies, affects the sex-specific relationship between protein and carbohydrate intake and life-history traits including lifespan, female lifetime egg production and daily egg production. We then determined the macronutrient ratio consumed when flies from each selection line and sex were allowed to self-regulate their intake. Results: Lifespan, lifetime egg production and daily egg production were optimised at similar protein to carbohydrate (P:C) ratios in flies from both selection lines. Likewise, females and males of both lines actively defended similar nutrient intake ratios (control =1:3.6 P:C; upward-selected = 1:3.2 P:C). Discussion: Our results are comparable to those in non-selected C. cosyra, where the optima for each trait and the self-selected protein to carbohydrate ratio observed were nearly identical. The nutrient blend that needs to be ingested for optimal expression of a given trait appeared to be well conserved across laboratory adapted and experimentally selected populations. These results suggest that in C. cosyra, nutritional requirements do not respond to a temporal change in oviposition substrate availability