National Recording Scheme Research Articles

NBN Atlas: Making data work for nature

The National Biodiversity Network (NBN) Atlas is the United Kingdom's (UK) largest repository of publicly available biodiversity data, with more than 200 million records of almost 50,000 species. It is the largest Living Atlas installation and has been customised considerably to meet the needs of the UK biological recording community. The main customisation was the addition of support for Ordnance Survey grid references as the location of the occurrence, which was added to the core Atlas of Living Australia (ALA) code. UK-specific customisations include authorised access to the supplied location of sensitive records in downloads and an updated species search to better implement the UK Species Inventory, which is the taxonomic backbone of the NBN Atlas. The biggest source of records is from the professionals and volunteers working with the National Recording Schemes and Societies and environmental non-governmental organizations (eNGOs). We also receive a substantial number of records from government agencies, Local Environmental Record Centres, museums, and botanical gardens across the UK. Currently we don’t receive many records from universities or research organisations, however they are one of the biggest consumers of NBN Atlas records across all sectors. We will discuss the challenges of managing record collation from such a broad range of data providers to meet the data requirements of all users, and how we are upgrading the NBN Atlas to the latest version of the ALA platform, whilst maintaining the UK customisations in a separate code layer.

Target‐group backgrounds prove effective at correcting sampling bias in Maxent models

AbstractAimAccounting for sampling bias is the greatest challenge facing presence‐only and presence‐background species distribution models; no matter what type of model is chosen, using biased data will mask the true relationship between occurrences and environmental predictors. To address this issue, we review four established bias correction techniques, using empirical occurrences with known sampling effort, and virtual species with known distributions.InnovationOccurrence data come from a national recording scheme of hoverflies (Syrphidae) in Great Britain, spanning 1983–2002. Target‐group backgrounds, distance‐restricted backgrounds, travel time to cities and human population density were used to account for sampling bias in 58 species of hoverfly. Distributions generated by bias correction techniques were compared in geographical space to the distribution produced accounting for known sampling effort, using Schoener's distance, centroid shifts and range size changes. To validate our results, we performed the same comparisons using 50 randomly generated virtual species. We used sampling effort from the hoverfly recording scheme to structure our biased sampling regime, emulating complex real‐life sampling bias.Main conclusionsModels made without any correction typically produced distributions that mapped sampling effort rather than the underlying habitat suitability. Target‐group backgrounds performed the best at emulating sampling effort and unbiased virtual occurrences, but also showed signs of overcompensation in places. Other methods performed better than no‐correction, but often differences were difficult to visually detect. In line with previous studies, when sampling effort is unknown, target‐group backgrounds provide a useful tool for reducing the effect of sampling bias. Models should be visually inspected for biological realism to identify any areas of potential overcompensation. Given the disparity between corrected and un‐corrected models, sampling bias constitutes a major source of error in species distribution modelling, and more research is needed to confidently address the issue.

Annual estimates of occupancy for bryophytes, lichens and invertebrates in the UK, 1970\u20132015

Here, we determine annual estimates of occupancy and species trends for 5,293 UK bryophytes, lichens, and invertebrates, providing national scale information on UK biodiversity change for 31 taxonomic groups for the time period 1970 to 2015. The dataset was produced through the application of a Bayesian occupancy modelling framework to species occurrence records supplied by 29 national recording schemes or societies (n = 24,118,549 records). In the UK, annual measures of species status from fine scale data (e.g. 1 × 1 km) had previously been limited to a few taxa for which structured monitoring data are available, mainly birds, butterflies, bats and a subset of moth species. By using an occupancy modelling framework designed for use with relatively low recording intensity data, we have been able to estimate species trends and generate annual estimates of occupancy for taxa where annual trend estimates and status were previously limited or unknown at this scale. These data broaden our knowledge of UK biodiversity and can be used to investigate variation in and drivers of biodiversity change.

Mining Flickr: a method for expanding the known distribution of invasive species

It is important to map invasive species in order to demonstrate their rate of spread and current distribution. Most recording schemes rely on opportunistic sightings and awareness to collect and gather data. Mining data from online social media and other data sharing platforms has become more prevalent in recent years as increasing numbers of users share more information. In this study, sightings from the image sharing platform Flickr were compared with the records submitted to the national recording scheme Record Pool. This study was completed to determine whether or not there was a significant difference between these two as sources for sightings of fresh water turtles across the UK.

Phenological shifts in hoverflies (Diptera: Syrphidae): linking measurement and mechanism

An understanding of ecological and evolutionary responses to global environmental change requires both a robust measurement of the change that is occurring and a mechanistic framework for understanding the drivers of that change. Such a requirement provides a challenge because biological monitoring is often ad hoc, and mechanistic experiments are often performed under highly simplified conditions. This study integrates multiple datasets to evaluate our current knowledge of the measurement and mechanism of phenological shifts in a key pollinator taxon: the hoverflies (Diptera: Syrphidae). First, two large, complementary and independent monitoring datasets are used to test for trends in phenology: an ad hoc national recording scheme containing > 620 000 records, and standardised monitoring with consistent methods over 30 yr. Results show that ad hoc and standardised recording data give quantitatively the same value for phenological advance in hoverflies (ca 12 d°C–1 on average at the beginning of the flight period), supporting the value of biological recording for the measurement of global ecological change. While the end of the flight period appears static in ad hoc recording, the standardised dataset suggests a similar advance as in the beginning of the flight period. Second, an extensive traits dataset and a novel database of laboratory‐derived developmental data on Syrphidae (153 published studies) are used to test for mechanistic patterns in phenological shifts. The only species trait that influenced phenology was voltinism, where species with more generations per year exhibit stronger phenological advances. We demonstrate considerable variation in the laboratory‐derived sensitivity to temperature but this does not match field‐derived measures of phenology. The results demonstrate that, as for many taxa, we have a strong understanding of the patterns of global ecological change but that we currently lack a detailed mechanistic understanding of those processes despite extensive research into the fundamental biology of some taxonomic groups.

The Biological Records Centre: a pioneer of citizen science

People have been recording wildlife for centuries and the resulting datasets lead to important scientific research. The Biological Records Centre (BRC), established in 1964, is a national focus for terrestrial and freshwater species recording in the United Kingdom (UK). BRC works with the voluntary recording community (i.e. a mutualistic symbiosis) through support of national recording schemes (i.e. ‘citizen science’, but unlike most citizen science it is volunteer led) and adds value to the data through analysis and reporting. Biological recording represents a diverse range of activities, involving an estimated 70 000 people annually in the UK, from expert volunteers undertaking systematic monitoring to mass participation recording. It is an invaluable monitoring tool because the datasets are long term, have large geographic extent and are taxonomically diverse (85 taxonomic groups). It supports a diverse range of outputs, e.g. atlases showing national distributions (12 127 species from over 40 taxonomic groups) and quantified trends (1636 species). BRC pioneers the use of technology for data capture (online portals and smartphone apps) and verification (including automated verification) through customisable, inter-operable database systems to facilitate efficient data flow. We are confident that biological recording has a bright future with benefits for people, science, and nature.

Short communication: Genetic analysis for fertility traits of heifers and cows from smallholder dairy farms in a tropical environment

The objective of this study was to estimate genetic parameters for various fertility traits on Holstein upgraded dairy heifers and cows in a smallholder system under tropical conditions using data sets from the Thailand national recording scheme. The investigated traits were age at first service (AFS), age at first calving (AFC), days from calving to first service (DTFS), days between first and last service (DFLS), days open (DO), calving interval (CI), number of services per conception (NSPC), and conception at first service (FSC). The data consisted of 68,555, 34,401, and 54,004 records on heifers, primiparous, and multiparous cows, respectively, calving between 1996 and 2011. Gibbs sampling was employed to obtain (co)variance components using both univariate and bivariate analyses with linear and threshold animal models. Virgin heifers had better fertility performance than primiparous and multiparous cows. The reproductive performance in primiparous cows was inferior compared with multiparous cows. Cows with higher Holstein-Friesian blood showed lower reproductive efficiency. Estimated heritabilities for most of the fertility traits were 0.04 or less except for AFS (0.26) and AFC (0.25). The estimated genetic correlations among fertility traits within parity indicated that selection for cows with high conception rate could lead to shortened DO and CI, as well as DTFS. The FSC and NSPC could be used as the best indicators for heifer and cow fertility and could be complemented by other traits, which were genetically considered as different traits such as DTFS and DFLS in terms of a fertility index. This would enable efficient selection for better fertility. Genetic correlations for fertility traits in primiparous and multiparous cows were very high (>0.90), but those between heifers and cows were lower (0.03 to 0.83). The latter results indicated that fertility traits of heifers and cows should be considered as different traits.

Air pollution and its effects on lichens, bryophytes, and lichen-feeding Lepidoptera: review and evidence from biological records

Changing air quality has been one of the most important drivers of change for bryophytes and lichens in Britain and Ireland over the 20th Century, with acidic pollutants such as sulphur dioxide having large effects on the ranges and abundances of many species. At the same time, expert amateur and professional naturalists have put enormous efforts into recording the distributions of species within these groups. These efforts have provided much evidence for declines and recoveries within the bryophytes and lichens, with species distribution data being linked to airborne pollutants in many different ways. We provide a broad overview of some of the changes that have occurred in affected species, using biological records collected by national recording schemes to illustrate the various effects of air pollution; we also review the direct and indirect impacts of air pollutants on these groups. Environmental change affecting one group of species is also likely to cascade to other groups where trophic or other relationships exist between them. Using data from the volunteer-based National Moth Recording Scheme, we provide the first evidence for an indirect association between reductions in air pollution and increases in lichenivorous moths. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, ●●, ●●–●●.

Factors that influence the efficiency of beef and dairy cattle recording system in Kenya: A SWOT–AHP analysis

Animal recording in Kenya is characterised by erratic producer participation and high drop-out rates from the national recording scheme. This study evaluates factors influencing efficiency of beef and dairy cattle recording system. Factors influencing efficiency of animal identification and registration, pedigree and performance recording, and genetic evaluation and information utilisation were generated using qualitative and participatory methods. Pairwise comparison of factors was done by strengths, weaknesses, opportunities and threats-analytical hierarchical process analysis and priority scores to determine their relative importance to the system calculated using Eigenvalue method. For identification and registration, and evaluation and information utilisation, external factors had high priority scores. For pedigree and performance recording, threats and weaknesses had the highest priority scores. Strengths factors could not sustain the required efficiency of the system. Weaknesses of the system predisposed it to threats. Available opportunities could be explored as interventions to restore efficiency in the system. Defensive strategies such as reorienting the system to offer utility benefits to recording, forming symbiotic and binding collaboration between recording organisations and NARS, and development of institutions to support recording were feasible.

Amphibian Declines Are Not Uniquely High amongst the Vertebrates: Trend Determination and the British Perspective

Although amphibians have experienced major global declines and an increasing extinction rate, recent results indicate that they are not as uniquely disadvantaged as previously supposed. Acquisition of robust data is evidently crucial to the determination of both absolute and relative rates of biodiversity declines, and thus in prioritising conservation actions. In Britain there is arguably a longer history of recording, and attempting to conserve, a wide range of species groups than anywhere else in the world. This stems from the early activities of Victorian naturalists in the nineteenth century, the establishment of natural history societies and, since the mid-twentieth century, a range of national recording schemes and organisations actively involved in conservation. In this review we summarise comparative evidence for British amphibians and reptiles concerning historical abundance, population trends and their causes, and outline how they relate to the situation elsewhere in Europe (and possibly the World). We discuss possible reasons why the plight of ectothermic vertebrates (fish, amphibians and reptiles) seems generally worse than that of endotherms (birds and mammals), as well as research priorities and factors likely to impact amphibians and reptile conservation in future.

The Definition of British Water Beetle Species Pools (Coleoptera) and their Relationship to Altitude, Temperature, Precipitation and Land Cover Variables

Pooled water beetle species lists from 1826 British national grid 10-km squares were analysed using multivariate ordination and classification methods. The relationships of pool groups to the climate, altitude and land cover variables were assessed using constrained and partial ordinations. Ordination of the species pool data indicated a major trend between squares in the north-west of Scotland and those in southern England, illustrating differences in acid and basic water standing water. Secondary variation was from acid standing water to fast-flowing streams and rivers. Classification generated nine species pool groups. These showed a distinct north-west to south-east trend but there was no obvious coastal or brackish water effect on distribution. The climatic and land cover variables were all significantly related to each other, and to north-south variation in grid square location, but the constrained ordination results indicated that that the most important influence on water beetle species pool distribution was mean summer temperature. Although the amount of variation explained by the environmental variables was low, spatial variation in the environmental predictors was almost as important as the environmental variables themselves in determining species pool composition. Mean annual temperature was also strongly correlated with species pool distribution with two land cover variables slightly less important. Altitude and precipitation had the least influence. The water beetle national recording scheme database appears to be of sufficiently high quality for environmental investigations at the British scale. There is considerable potential for the synthesis of invertebrate species distribution, land cover and climate change predictions in the assessment of environmental change. The results, together with previous work on other invertebrate species, indicate that changing summer temperatures may have a considerable influence on the distribution British invertebrate species.

The effects of visual apparency on bias in butterfly recording and monitoring

A basic assumption in conservation is that comparable data are available for species to facilitate risk assessment of extinction. However, the capacity for carrying out cross-species comparisons for abundances and distributions among butterflies depends on the absence of bias in recording and monitoring or the existence of appropriate techniques for removing bias. Here, we investigate potential bias in cross-species comparisons for the apparency of butterfly adults (wing colour, size and behaviour) in three pivotal UK datasets: dates of discovery, Butterfly Monitoring Scheme (BMS) transect measures of abundance and Butterflies for the New Millennium (BNM) national recording scheme. Bias is found in all three datasets. Discovery date is affected by wing colour and size, BNM recording by adult behaviour and wing colour and BMS monitoring by adult behaviour. The nature and degree of bias differs between uncorrected cross-species comparisons and those with the application of phylogenetic contrasts. The findings urge caution in using these datasets for cross-species analysis without improvements and standardisation of recording and monitoring and the development of techniques to adjust for biases, in particular the use of suitable comparative techniques. The latter requires the construction of a molecular phylogeny for butterflies.

Genetic analysis of age at first service, return rate, litter size, and weaning-to-first service interval of gilts and sows1

The aim of this study was to estimate genetic parameters of seven traits related to sow reproductive performance. Data on all Norwegian Landrace pigs (NL) born in nucleus herds and raised in nucleus or multiplying herds from 1990 to 2000 were extracted from the Norwegian national recording scheme. Reproductive traits investigated were age at first service (AFS), return rate in gilts (RRg), age at first farrowing (AFF), live-born piglets in the first litter (NBA1), interval from weaning to first service after first litter (WTS1), return rate after first litter (RR1), live-born piglets in the second litter (NBA2), and interval from weaning to first service after second litter (WTS2). After editing, the data set comprised 12,583 to 56,042 records, depending on the trait. A mixed linear and a joint linear threshold animal model were used to estimate (co)variance components. A full Bayesian approach via Gibbs sampling was adopted. The statistical model used for analysis included contemporary groups of herd-year (-season), purebred or crossbred litter, single or double insemination, mating type, parity in which the animal was born, a regression on lactation length, and an additive genetic effect. Neither the estimated heritabilities nor the genetic correlations differed much between the two approaches, but there was a tendency for higher genetic correlations using the joint linear threshold model approach. Average heritabilities were as follows: AFS = 0.31; RRg = 0.03; RR1 = 0.02; NBA1 = 0.12; NBA2 = 0.14; WTS1 = 0.08; and WTS2 = 0.03. The highest genetic correlations were estimated between NBA1 and NBA2 (r(g) = 0.95), RR1 and WTS1 (r(g) = 0.93), and between WTS1 and WTS2 (r(g) = 0.78). The estimated genetic correlation between NBA and WTS were close to zero. Selection for increased NBA will slightly increase AFS and reduce the probability of a return. Selection for decreased AFS will have a favorable effect on WTS intervals; however, selection for decreased AFS seems to have an unfavorable effect on return rate both on gilts and sows. Conversely, selection for decreased WTS intervals will reduce the probability of a return. Potential selection candidates to include in a multivariate fertility index are AFS, NBA, and WTS1. Due to the low heritability and low, but favorable, genetic correlations to NBA and WTS, RR is not recommended as a selection candidate.

The relationship between British ground beetles (Coleoptera, Carabidae) and land cover

AbstractAims and methods Ground beetle and satellite‐derived land cover data from 1687 United Kingdom 10 km national grid squares were used to assess the relationship between species pool and cover data in Great Britain using fuzzy classification and constrained ordination.Results Ground beetle species pools classified into nine groups which were related to land cover variables using constrained ordination. There was a strong relationship between upland land cover and three ground beetle groups. Deciduous woodland, coastal and tilled land were associated with three other groups. Three further groups did not appear to be strongly associated with any particular cover, but differed in geographical position.Conclusion The distribution of species pools derived from the British national recording scheme at the 10 km scale was strongly related to satellite‐derived land cover data. There appears to be considerable potential for the use of a synthesis of land cover and ground beetle data in the monitoring of environmental change over a large, countrywide, area.

Genetic parameters for clinical mastitis in Holstein-Friesians in the United Kingdom: a Bayesian analysis

AbstractA Bayesian threshold-liability model with Markov chain Monte Carlo techniques was used to infer genetic parameters for clinical mastitis records collected on Holstein-Friesian cows by one of the United Kingdom’s national recording schemes. Four data sets were created to investigate the effect of data sampling methods on genetic parameter estimates for first and multi-lactation cows, separately. The data sets were: (1) cows with complete first lactations only (8671 cows); (2) all cows, with first lactations whether complete or incomplete (10 967 cows); (3) cows with complete multi-lactations (32 948 records); and (4) all cows with multiple lactations whether complete or incomplete (44 268 records). A Gaussian mixed linear model with sire effects was adopted for liability. Explanatory variables included in the model varied for each data set. Analyses were conducted using Gibbs sampling and estimates were on the liability scale. Posterior means of heritability for clinical mastitis were higher for first lactations (0·11 and 0·10 for data sets 1 and 2, respectively) than for multiple lactations (0·09 and 0·07, for data sets 3 and 4, respectively). For multiple lactations, estimates of permanent environmental variance were higher for complete than incomplete lactations. Repeatability was 0·21 and 0·17 for data sets 3 and 4, respectively. This suggests the existence of effects, other than additive genetic effects, on susceptibility to mastitis that are common to all lactations. In first or multi-lactation data sets, heritability was proportionately 0·10 to 0·19 lower for data sets with all records (in which case the models had days in milk as a covariate) than for data with only complete lactation records (models without days in milk as a covariate). This suggests an effect of data sampling on genetic parameter estimates. The regression of liability on days in milk differed from zero, indicating that the probability of mastitis is higher for longer lactations, as expected. Results also indicated that a regression on days in milk should be included in a model for genetic evaluation of sires for mastitis resistance based on records in progress.

Linear and threshold model genetic parameters for disease, fertility and milk production in dairy cattle

A combination of better management and genetic selection for good health and fertility would provide a more effective long term solution for economic loss due to diseases and poor fertility. This would also help to address public concerns about the use of medical treatment in milk production. A balance in the genetic improvement of health and fertility together with milk production could be achieved through their inclusion in national genetic selection indices, for which genetic parameters are needed. One of the main objectives of this study was to estimate genetic parameters for various disease and fertility traits in the UK dairy cattle population, using records from a national recording scheme run by Livestock Services UK Ltd. Genetic analysis of traits recorded as present or absent (binary traits; e.g. diseases) requires the use of non-linear threshold models, because linear models require normality assumptions (e.g., Gianola 1982). The other objective of this study was to estimate genetic parameters for binary disease and fertility traits based on threshold animal models and to compare results with those from linear animal models.

Association between protein feeding and reproductive efficiency in the dairy cow: specific emphasis on protein feeding in Finland

Associations between protein feeding and reproductive efficiency in the dairy cow are reviewed. Examination of published data indicated that reproductive responses assessed as days open, services per conception or conception rate following changes in protein feeding tend to be inconsistent. Discrepancies can arise due to between-study variations in experimental design, statistical analysis, sample population size, uterine health, cow age, parity, reproductive management or nutrient intake. Detri-mental effects on reproductive efficiency following periods of excessive protein feeding are often attributed to increases in tissue urea and ammonia oncentrations leading to impaired reproductive hysiology, modified endocrine function or exacerbated postpartum negative energy balance. Examination of data collected from Finnish dairy herds (n = 16 051) participating in the national milk recording scheme during 1993 indicated that milk production was maximised in herds fed diets containing 180 g crude protein/kg dry matter. In contrast, no consistent relationships were identified between increases in on-farm protein feeding necessary to secure higher milk production and herd reproductive efficiency assessed as calving interval, first service interval and number of inseminations per calving. Further examination of data derived from 5 437 herds within the National recording scheme indicated that on-farm reproductive efficiency was independent of large variations in the mean annual urea concentration of bulk tank milk. It is concluded that increases in the crude protein content of Finnish dairy cow rations from 150 to between 170 and 180 g/kg dry matter would allow improvements in milk production to be realised without leading to significant reductions in reproductive efficiency.;

Effect of environmental and social enrichment during lactation on the response of piglets to weaning

Weaning is a time at which many different stressors are imposed on the piglet and poor health and performance are significant commercial problems. It is therefore important to understand which factors influence a piglet's adaptation to weaning, and how this might be improved. UK national recording scheme data demonstrate consistently better post-weaning performance for piglets from outdoor breeding herds than for indoor-bred piglets. There are many differences between the outdoor and indoor situation, and these are being systematically investigated. One potential difference which might influence the response to weaning is the greater degree of environmental and social diversity typically experienced by outdoor piglets during lactation.Fifty-four sows and their litters were allocated according to farrowing date and parity to one of three enrichment treatments: treatments were (1) Control (C) in which litters remained in fully slatted farrowing pens with crates throughout lactation, (2) Socially enriched (SE) in which two adjacent litters were allowed to co-mingle from 12 days of age by removal of the dividing partition, and (3) Environmentally enriched (EE) in which piglets in similar housing were presented with a variety of small moveable objects and a rooting substrate.

Effect of environmental and social enrichment during lactation on the response of piglets to weaning

Weaning is a time at which many different stressors are imposed on the piglet and poor health and performance are significant commercial problems. It is therefore important to understand which factors influence a piglet's adaptation to weaning, and how this might be improved. UK national recording scheme data demonstrate consistently better post-weaning performance for piglets from outdoor breeding herds than for indoor-bred piglets. There are many differences between the outdoor and indoor situation, and these are being systematically investigated. One potential difference which might influence the response to weaning is the greater degree of environmental and social diversity typically experienced by outdoor piglets during lactation.Fifty-four sows and their litters were allocated according to farrowing date and parity to one of three enrichment treatments: treatments were (1) Control (C) in which litters remained in fully slatted farrowing pens with crates throughout lactation, (2) Socially enriched (SE) in which two adjacent litters were allowed to co-mingle from 12 days of age by removal of the dividing partition, and (3) Environmentally enriched (EE) in which piglets in similar housing were presented with a variety of small moveable objects and a rooting substrate.