Temporal correlations among demographic parameters are ubiquitous but highly variable across species

Temporal correlations among demographic parameters can strongly influence population dynamics. Our empirical knowledge, however, is very limited regarding the direction and the magnitude of these correlations and how they vary among demographic parameters and species’ life histories. Here, we use long-term demographic data from 15 bird and mammal species with contrasting pace of life to quantify correlation patterns among five key demographic parameters: juvenile and adult survival, reproductive probability, reproductive success and productivity. Correlations among demographic parameters were ubiquitous, more frequently positive than negative, but strongly differed across species. Correlations did not markedly change along the slow-fast continuum of life histories, suggesting that they were more strongly driven by ecological than evolutionary factors. As positive temporal demographic correlations decrease the mean of the long-run population growth rate, the common practice of ignoring temporal correlations in population models could lead to the underestimation of extinction risks in most species

Inferring transient dynamics of human populations from matrix non-normality

This is the final version of the article. Available from Springer Verlag via the DOI in this record.In our increasingly unstable and unpredictable world, population dynamics rarely settle uniformly to long-term behaviour. However, projecting period-by-period through the preceding fluctuations is more data-intensive and analytically involved than evaluating at equilibrium. To efficiently model populations and best inform policy, we require pragmatic suggestions as to when it is necessary to incorporate short-term transient dynamics and their effect on eventual projected population size. To estimate this need for matrix population modelling, we adopt a linear algebraic quantity known as non-normality. Matrix non-normality is distinct from normality in the Gaussian sense, and indicates the amplificatory potential of the population projection matrix given a particular population vector. In this paper, we compare and contrast three well-regarded metrics of non-normality, which were calculated for over 1000 age-structured human population projection matrices from 42 European countries in the period 1960 to 2014. Non-normality increased over time, mirroring the indices of transient dynamics that peaked around the millennium. By standardising the matrices to focus on transient dynamics and not changes in the asymptotic growth rate, we show that the damping ratio is an uninformative predictor of whether a population is prone to transient booms or busts in its size. These analyses suggest that population ecology approaches to inferring transient dynamics have too often relied on suboptimal analytical tools focussed on an initial population vector rather than the capacity of the life cycle to amplify or dampen transient fluctuations. Finally, we introduce the engineering technique of pseudospectra analysis to population ecology, which, like matrix non-normality, provides a more complete description of the transient fluctuations than the damping ratio. Pseudospectra analysis could further support non-normality assessment to enable a greater understanding of when we might expect transient phases to impact eventual population dynamics.This work was funded by Wellcome Trust New Investigator 103780 to TE, who is also funded by NERC Fellowship NE/J018163/1. JB gratefully acknowledges the ESRC Centre for Population Change ES/K007394/1

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Demographic consequences and conservation implications of intermittent breeding in the common eider and black-browed albatross

Modelling of populations and their components is central to theoretical and applied ecology, but the required demographic information is often unavailable or incomplete across the life cycle. Inferences drawn from models missing important life stages and/or population segments may be limited or flawed, with implications for conservation applications. The detailed data required for comprehensive models may be easiest to collect or access for abundant species, which are themselves often declining. This thesis contributes to population management for one such species (the common eider, Somateria mollissima) through data collation and population modelling. Chapter 2 presents a curated demographic database for this species, which should help to increase data re-use and act as a reference for the less-studied sea ducks. In Chapter 3, quantitative synthesis of this dataset presents global mean values for use in modelling, and uncovers a mismatch in study effort relative to influence on population dynamics. Breeding propensity (the probability of an adult individual attempting to breed in a given year) is proportionally understudied, and Chapter 4 identifies that the return to breeding after a period of non-breeding is a key life-stage transition which should be considered in future data collection and conservation interventions. In Chapter 5, a detailed individual-based dataset available for another long-lived marine bird (the black-browed albatross, Thalassarche melanophris) facilitates disaggregation of demographic parameter means, variances and covariances across different previous breeding states, revealing distinct ‘demographic profiles’ as an important source of heterogeneity within the population. Thus for both species, novel model formulations incorporate breeding propensity, a known knowledge gap in the demography and conservation of marine birds, to draw out its broader significance for our understanding of population dynamics and reproductive ecology

Conservation implications of a mismatch between data availability and demographic impact

Cost-effective use of limited conservation resources requires understanding which data most contribute to alleviating biodiversity declines. Interventions might reasonably prioritise life-cycle transitions with the greatest influence on population dynamics, yet some contributing vital rates are particularly challenging to document. This risks managers making decisions without sufficient empirical coverage of the spatiotemporal variation experienced by the species. Here, we aimed to explore whether the number of studies contributing estimates for a given life-stage transition aligns with that transition's demographic impact on population growth rate, λ. We parameterised a matrix population model using meta-analysis of vital rates for the common eider (Somateria mollissima), an increasingly threatened yet comparatively data-rich species of seaduck, for which some life stages are particularly problematic to study. Female common eiders exhibit intermittent breeding, with some established breeders skipping one or more years between breeding attempts. Our meta-analysis yielded a breeding propensity of 0.72, which we incorporated into our model with a discrete and reversible ‘nonbreeder’ stage (to which surviving adults transition with a probability of 0.28). The transitions between breeding and nonbreeding states had twice the influence on λ than fertility (summed matrix-element elasticities of 24% and 11%, respectively), whereas almost 15 times as many studies document components of fertility than breeding propensity (n = 103 and n = 7, respectively). The implications of such mismatches are complex because the motivations for feasible on-the-ground conservation actions may be different from what is needed to reduce uncertainty in population projections. Our workflow could form an early part of the toolkit informing future investment of finite resources, to avoid repeated disconnects between data needs and availability thwarting evidence-led conservation

Inferring transient dynamics of human populations from non-normality metrics

In our increasingly unstable and unpredictable world, population dynamics rarely settle uniformly to long-term behaviour. However, projecting period-by-period through the preceding fluctuations is more data-intensive and analytically involved than evaluating at equilibrium. To efficiently model populations and best inform policy, we require pragmatic suggestions as to when it is necessary to incorporate short-term transient dynamics and their effect on eventual projected population size. To estimate this need for matrix population modelling, we adopt a linear algebraic quantity known as non-normality. Matrix non-normality is distinct from normality in the Gaussian sense, and indicates the amplificatory potential of the population projection matrix given a particular population vector. In this paper, we compare and contrast three well-regarded metrics of non-normality, which were calculated for over 1000 age-structured human population projection matrices from 42 European countries in the period 1960 to 2014. Non-normality increased over time, mirroring the indices of transient dynamics that peaked around the millennium. By standardising the matrices to focus on transient dynamics and not changes in the asymptotic growth rate, we show that the damping ratio is an uninformative predictor of whether a population is prone to transient booms or busts in its size. These analyses suggest that population ecology approaches to inferring transient dynamics have too often relied on suboptimal analytical tools focussed on an initial population vector rather than the capacity of the life cycle to amplify or dampen transient fluctuations. Finally, we introduce the engineering technique of pseudospectra analysis to population ecology, which, like matrix non-normality, provides a more complete description of the transient fluctuations than the damping ratio. Pseudospectra analysis could further support non-normality assessment to enable a greater understanding of when we might expect transient phases to impact eventual population dynamics.<br/

Vital rate estimates for the common eider Somateria mollissima, a data-rich exemplar of the seaduck tribe

This database collates vital rate estimates for the common eider (Somateria mollissima), providing a complete demographic parameterization for this slow life‐history species. Monitored across its circumpolar range, the common eider represents a data‐rich exemplar species for the less‐studied seaducks, many of which are under threat.The database contains estimates of the following vital rates: first- year survival; second- year survival; adult annual survival; first breeding (both age‐specific recruitment probability, and breeding propensity across potential recruitment ages); breeding propensity of established female breeders; clutch size; hatching success; and fledging success. These estimates are drawn from 134 studies, across the scientific and grey literature, including three previously inaccessible datasets on clutch size that were contributed in response to a call for data through the IUCN Species Survival Commission's Duck Specialist Group.Although clutch size has been much studied, the contributed datasets have enhanced coverage of studies reported in non‐English languages, which were otherwise only represented when cited in English‐language publications. Breeding propensity has been little studied, perhaps because adult females are often assumed to attempt breeding every year; we obtained a mean breeding propensity of 0.72. Our synthesis highlights the following gaps in data availability: juvenile and male survival; population change; and studies from Russia (at least accessible in English).The database is intended to serve population modellers and scientists involved in the policy and practice of seaduck conservation and management

Vital rate estimates for the common eider Somateria mollissima, a data-rich exemplar of the seaduck tribe

This database contains estimates of the following vital rates (as required to parameterise matrix population models), for the common eider (Somateria mollissima): 1st year survival (measured either from hatching, or from fledging, to 1 year old); 2nd year survival; adult annual survival; first breeding (both age-specific recruitment probability, and breeding propensity across potential recruitment ages); breeding propensity of established female breeders; clutch size; hatching success; and fledging success. These estimates are drawn from 134 studies, across the scientific and grey literature &ndash; including three previously inaccessible datasets on clutch size that were contributed in response to a call for data through the IUCN Species Survival Commission&rsquo;s Duck Specialist Group (IDs 127, A and B). This is a relational database, linking estimates and associated metadata to the relevant study (or unique unpublished combination thereof) by a unique ID number in the &#39;MASTER&#39; sheet. For further information, refer to the associated publication, and/or explanatory notes on the column headings of each sheet (.xlsx version only, but provided in the dataset README .txt file).,We surveyed published academic and grey literature via keyword searches (e.g. &ldquo;Somateria mollissima&rdquo; &ldquo;clutch size&rdquo;) through Google Scholar, &lsquo;citation snowballing&rsquo; (pursuing reference trails; see e.g. Greenhalgh &amp;amp; Peacock, 2005), and cross-referencing authors&rsquo; personal databases. Additionally, a call for data was posted on the IUCN Species Survival Commission&rsquo;s Duck Specialist Group website (www.ducksg.org/2018/10/seaducks/the-not-so-common-eider-can-you-help/), circulated through the corresponding mailing list, and advertised by ANH on Twitter in January 2019 and at conferences (the British Ecological Society&rsquo;s &lsquo;Quantitative Ecology&rsquo; meeting in July 2019; the European Ornithologists&rsquo; Union Conference in August 2019; and the Ecological Society of America&rsquo;s annual meeting in August 2020) thereafter. The call for data elicited three previously inaccessible datasets, of which one was recorded in Icelandic and another in Russian, broadening language coverage since non-English language reports were otherwise only covered by citations in English-language publications. Accessible vital rate estimates, and associated metadata, were collated in a relational database in Microsoft Excel, linked by a unique ID number associated with each study (or unique unpublished combinations thereof). A list of data sources used in the study are provided in the Data sources section of the associated publication. We focussed on the vital rates required to parameterise matrix population models (MPMs), which are used widely by population ecologists and conservation biologists to project population dynamics over time. We therefore included the following vital rates: 1st year survival (measured either from hatching, or from fledging, to 1 year old), 2nd year survival, adult survival, breeding propensities for 2- to 5-year-olds (both probability of having recruited at a given age, and breeding propensity at a given age), adult female breeding propensity, clutch size, hatching success and fledging success (alternatively included in 1st year survival where measured from hatching). We define: (i) hatching success as the proportion of all laid eggs that hatch (if probability of successful nesting &ndash; i.e. of at least one egg hatching &ndash; was provided, we used it to calculate hatching success where feasible), and (ii) fledging success as the proportion of hatchlings that fledge. Where provided by the authors, we recorded the following metadata at the study level: location (country and geographic coordinates); subspecies; and population trend (classified as increasing, decreasing, stable, or variable). Further, for each estimate we recorded: sample size; variance measures (as provided and/or calculable from reported information); start and end years; and any covariates (freeform). We did not formally screen studies, preferring instead to provide as complete a reference database as possible. We facilitate filtering with the following assignations: verification status (whether the source was seen in the original or cited by another verified source); precision (some estimates were simply the midpoints of observed ranges); and independence (which is not met when multiple estimates are provided by the same study, or when separate studies are based on the same datasets). Greenhalgh, T., &amp;amp; Peacock, R. (2005). Effectiveness and efficiency of search methods in systematic reviews of complex evidence: Audit of primary sources. British Medical Journal, 331(7524), 1064&ndash;1065. https://doi.org/10.1136/bmj.38636.593461.68,The database is available in full as an xlsx spreadsheet (including header comments providing further information), or as a series of csv files for each sheet (comments not included, although they are provided in the dataset README .txt file). The &lsquo;master&rsquo; sheet provides study-level information, with each study being assigned a unique identifier: numeric 1-127 for published studies, upper case A-B for unpublished contributed datasets (ID 127/Ragnarsd&oacute;ttir et al., 2021 was contributed through the call for data but is published online, as an Icelandic-language publication not accessible through English-language searches), and lower case aa-ee for combinations of datasets reported in published studies (such as the combination: &ldquo;Nyegaard, 2004 [thesis]; H.G. Gilchrist unpubl. data&rdquo; reported in Gilliland et al., 2009, Table 1). Estimates and associated metadata for each vital rate are then recorded in separate sheets, with the ID column relating back to the studies in the &lsquo;master&rsquo; sheet. Vital rate sheets include columns to replace imprecise overall study-level population growth rate, geographical coordinates, and subspecies entries where appropriate; for example, if the study provided vital rate data for each of several locations. Further information specific to each column can be found in comment boxes associated with the headers (.xlsx file only), and both studies and estimates are further annotated in &lsquo;Comments&rsquo; columns where relevant. A text file with an English translation by AP of the summary from ID 127/Ragnarsd&oacute;ttir et al., 2021 is also provided (see Nicol-Harper_202110_VitalRates_RagnarsdottirTranslation.txt). The two forms of breeding propensities for 2- to 5-year-olds correspond to two of the recruitment quantities discussed in Pradel &amp;amp; Lebreton (1999): the probability of having recruited at a given age, which sums to 1 across all possible ages of recruitment, is equivalent to their &alpha;i (specifically, the second version described on p. S80); breeding propensities at age i (2 &le; i &le; 5) correspond to their ai. Vital rates referring to subadults are assumed to refer to both sexes, whereas adult survival may refer to either sex or both (specified in the database), while adult breeding propensity has thus far only been estimated for females. Pradel, R., &amp;amp; Lebreton, J.-D. (1999). Comparison of different approaches to the study of local recruitment of breeders. Bird Study, 46(sup1), S74&ndash;S81. https://doi.org/10.1080/00063659909477234 Ragnarsd&oacute;ttir, S. B., Thorstensen, S., &amp;amp; Met&uacute;salemsson, S. (2021). Fuglal&iacute;f &iacute; &oacute;sh&oacute;lmum Eyjafjar&eth;ar&aacute;r: k&ouml;nnun 2020 me&eth; samanbur&eth;i vi&eth; fyrri &aacute;r. [The birdlife of the delta area of river Eyjafja&eth;ar&aacute;, N-Iceland: The results of a survey in year 2020 in comparison to former years.] N&aacute;tt&uacute;rufr&aelig;&eth;istofnun &Iacute;slands N&Iacute;21001. 62 pp. (In Icelandic). Available at: https://utgafa.ni.is/skyrslur/2021/NI-21001.pdf accessed 5th October 2021. Gilliland, S. G., Grant Gilchrist, H., Rockwell, R. F., Robertson, G. J., Savard, J.-P. L., Merkel, F., &amp;amp; Mosbech, A. (2009). Evaluating the Sustainability of Harvest Among Northern Common Eiders Somateria mollissima borealis in Greenland and Canada. Wildlife Biology, 15(1), 24&ndash;36. https://doi.org/10.2981/07-005</span