Robert C Lacy

Robert C Lacy
Species Conservation Toolkit Initiative

PhD

About

232
Publications
65,069
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12,789
Citations
Citations since 2016
63 Research Items
5011 Citations
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Publications

Publications (232)
Article
Genome resource banks (GRBs) have the potential to preserve the genetic diversity of a species over time, yet they are rarely utilized as effective components of conservation breeding programs. Advances have been made in reproductive biology, collection and storage techniques, and use of stored gametes for achieving successful reproduction, but the...
Presentation
Full-text available
Abstract: Assessing the population-level impact of human-caused mortality of wildlife typically relies upon deterministic methods. However, population declines are often accelerated by stochastic factors that are not accounted for in such conventional methods. Building upon the widely applied Potential Biological Removal (PBR) equation, we introduc...
Data
This is the supplementary material for our article "A stochastic model for estimating sustainable limits to wildlife mortality in a changing world" published in Conservation Biology (Manlik et al. 2022). This can be cited as: Manlik, O., Lacy, R. C., Sherwin, W. B., Finn, H., Loneragan, N. R., & Allen, S. J. (2022). A stochastic model for estimatin...
Article
An individual's ability to produce surviving descendants defines its evolutionary fitness, and loss of family lineages (i.e. having no surviving descendants or relatives) diminishes allelic diversity within closed populations. This high variance in individual reproductive success is difficult to detect and measure, so potential demographic impacts...
Article
Full-text available
Human-caused mortality of wildlife is a pervasive threat to biodiversity. Assessing the population-level impact of fisheries bycatch and other human-caused mortality of wildlife has typically relied upon deterministic methods. However, population declines are often accelerated by stochastic factors that are not accounted for in such conventional me...
Article
The long-distance, unpredictable movement patterns of nomadic species make them challenging to monitor and conserve. Critically endangered regent honeyeaters Anthochaera phrygia once roamed southeastern Australia in 'immense flocks' but now number fewer than 300 wild birds over a vast 300,000 km 2 range. Regent honeyeaters are a rare example where...
Article
Full-text available
Population models, such as those used for Population Viability Analysis (PVA), are valuable for projecting trends, assessing threats, guiding environmental resource management, and planning species conservation measures. However, rarely are the needed data on all aspects of the life history available for cetacean species, because they are long-live...
Article
Insurance populations can provide a short-term safeguard for at-risk species. The goal for all insurance populations should be to maintain a high welfare, genetically diverse, self-sustaining population that is available for eventual reintroduction of animals back into the wild when it is safe to do so. However, many insurance populations in zoos a...
Article
Full-text available
Decades after a ban on hunting, and despite focused management interventions, the endangered St. Lawrence Estuary (SLE) beluga (Delphinapterus leucas) population has failed to recover. We applied a population viability analysis to simulate the responses of the SLE beluga population across a wide range of variability and uncertainty under current an...
Article
Full-text available
Lacy, R. C., and D. R. Breininger. 2021. Population Viability Analysis (PVA) as a platform for predicting outcomes of management options for the Florida Scrub-Jay in Brevard County. NASA Scientific and Technical Information Report 20210022519 https://ntrs.nasa.gov/citations/20210022519.
Presentation
We are introducing a new population modelling approach for estimating sustainable limits to human-caused mortality. Our approach, termed ‘Maximum Sustainable Anthropogenic Mortality in Stochastic Environments’ (SAMSE), incorporates environmental and demographic stochasticity, including the dependency of offspring on their mothers.
Article
Full-text available
Like numerous species at risk, the resident killer whale populations of the Northeast Pacific are vulnerable to the cumulative effects of anthropogenic threats. A Pathways of Effects conceptual model summarised the current understanding of each threat (prey availability, acoustic and physical disturbance, and contaminants), threat interactions, and...
Article
Full-text available
Preventing declines in common species is key to sustaining the structure and function of marine ecosystems. Yet for many common marine mammals, including oceanic dolphins, statistical power to detect declines remains low due to patchy distribution and large variability in group sizes. In this study, population viability analyses (PVA) were used to...
Article
Full-text available
Small cetaceans face persistent threats from fisheries interactions, making effective mitigation a priority for conservation. In southwest Florida, interactions come primarily from small-scale recreational hook and line and trap/pot fisheries, with regional stranding network partners working with federal agency managers to assess and intervene as p...
Article
Full-text available
Recent years have seen the rapid development of tools and approaches to model the population consequences of disturbance in several marine mammal populations from high-amplitude, acute sound sources. Ocean noise from shipping and other maritime activities is now recognised as a chronic, habitat-level stressor. Advances are needed in several key are...
Article
Genetic rescue – ameliorating inbreeding depression and restoring genetic diversity of inbred populations through gene flow - is valuable in wildlife conservation. Empirically validated recommendations for genetic rescue supported by evolutionary genetics theory advise maximizing genetic diversity in target populations. Instead, recent papers based...
Article
Population viability analysis (PVA) utilizes simulation models to project the genetic and demographic trajectories of populations over time. One benefit to using PVA to assist in ex situ population planning is the ability to compare outcomes from multiple management scenarios. Reproductive viability analysis (RVA), used to identify biological and r...
Article
Full-text available
Maintaining a living plant collection is the most common method of ex situ conservation for plant species that cannot be seed banked i.e. “exceptional” species. Viability of living collections, and their value for future conservation efforts, can be limited without coordinated efforts to track and manage individuals across institutions. The zoologi...
Article
Full-text available
The great auk was once abundant and distributed across the North Atlantic. It is now extinct, having been heavily exploited for its eggs, meat, and feathers. We investigated the impact of human hunting on its demise by integrating genetic data, GPS-based ocean current data, and analyses of population viability. We sequenced complete mitochondrial g...
Chapter
The first step in conservation management is to delineate groups for separate versus combined management. However, there are many problems with species delineation, including diverse species definitions, lack of standardized protocols, and poor repeatability of delineations. Definitions that are too broad will lead to outbreeding depression if popu...
Chapter
Adverse genetic impacts on fragmented populations are expected to worsen under global climate change. Many populations and species may not be able to adapt in situ , or to move unassisted to suitable habitat. Management may reduce these threats by augmenting genetic diversity to improve the ability to adapt evolutionarily, by translocation, includi...
Chapter
Inbreeding is reduced and genetic diversity enhanced when a small isolated inbred population is crossed to another unrelated population. Crossing can have beneficial or harmful effects on fitness, but beneficial effects predominate, and the risks of harmful ones (outbreeding depression) can be predicted and avoided. For crosses with a low risk of o...
Chapter
Evidence of population structure and limited gene flow often leads to the questionable conclusion that populations should be managed as separate unit. A paradigm shift is needed where evidence of genetic differentiation among populations is followed by an assessment of whether populations are suffering genetic erosion, whether there are other popul...
Chapter
Genetic management of fragmented populations involves the application of evolutionary genetic theory and knowledge to alleviate problems due to inbreeding and loss of genetic diversity in small population fragments. Populations evolve through the effects of mutation, natural selection, chance (genetic drift), and gene flow. Large outbreeding sexual...
Chapter
Inbreeding reduces survival and reproduction (i.e. it causes inbreeding depression), and thereby increases extinction risk. Inbreeding depression is due to increased homozygosity for harmful alleles and at loci exhibiting heterozygote advantage. Inbreeding depression is nearly universal in sexually reproducing organisms that are diploid or have hig...
Chapter
Most species now have fragmented distributions, often with adverse genetic consequences. The genetic impacts of population fragmentation depend critically upon gene flow among fragments and their effective sizes. Fragmentation with cessation of gene flow is highly harmful in the long term, leading to greater inbreeding, increased loss of genetic di...
Chapter
Even without detailed genetic data, sound genetic management strategies for augmenting gene flow can be instituted by considering population genetics theory, and/or computer simulations. When detailed data are lacking, moving (translocating) some individuals into isolated inbred population fragments is better than moving none, as long as the risk o...
Article
Full-text available
Although population viability analysis (PVA) can be an important tool for strengthening endangered species recovery efforts, the extent to which such analyses remain embedded in the social process of recovery planning is often unrecognized. We analyzed two recovery plans for the Mexican wolf that were developed using similar data and methods but ar...
Technical Report
Full-text available
The Northern and Southern Resident Killer Whale populations (NRKW and SRKW) that inhabit the waters of the Canadian Pacific coast are listed as Threatened (NRKW) and Endangered (SRKW) under the Species at Risk Act (SARA). The SARA recovery plan developed for these populations identified the assessment of the cumulative effects of anthropogenic thre...
Article
Full-text available
Humans are responsible for a cataclysm of species extinction that will change the world as we see it, and will adversely affect human health and wellbeing. We need to understand at individual and societal levels why species conservation is important. Accepting the premise that species have value, we need to next consider the mechanisms underlying s...
Article
Population viability analysis (PVA) has been used for three decades to assess threats and evaluate conservation options for wildlife populations. What has been learned from PVA on in situ populations are valuable lessons also for assessing and managing viability and sustainability of ex situ populations. The dynamics of individual populations are u...
Research
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The purpose of this manual is to introduce the principles of epidemiological modeling of infectious disease in wildlife populations as modelled in the software OUTBREAK.
Article
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Breeding programs to conserve diversity are predicated on the assumption that genetic variation in adaptively important traits will be lost in parallel to the loss of variation at neutral loci. To test this assumption, we monitored quantitative traits across 18 generations of Peromyscus leucopus mice propagated with protocols that mirror breeding p...
Article
Full-text available
Conservation resources are limited, yet an increasing number of species are under threat. Assessing species for their conservation needs is, therefore, a vital first step in identifying and prioritizing species for both ex situ and in situ conservation actions. Using a transparent, logical and objective method, the Conservation Needs Assessment pro...
Article
Full-text available
1. Sensitivity analyses that assess the impact of changing vital rates on population growth have been widely used to guide conservation. If implemented with caution, they can provide guidance as to which management actions will optimize conservation outcomes. 2. In this review, we first focus on the commonly used proportional sensitivity and elast...
Article
Full-text available
Thousands of small populations are at increased risk of extinction because genetics and evolutionary biology are not well-integrated into conservation planning – a major lost opportunity for effective actions. We propose that if the risk of outbreeding depression is low, the default should be to evaluate restoration of gene flow to small inbred pop...
Article
Full-text available
Sex ratio allocation has important fitness consequences, and theory predicts that parents should adjust offspring sex ratio in cases where the fitness returns of producing male and female offspring varies. The ability of fathers to bias offspring sex ratios has traditionally been dismissed given the expectation of an equal proportion of X and Y-chr...
Article
Full-text available
Understanding cumulative effects of multiple threats is key to guiding effective management to conserve endangered species. The critically endangered, Southern Resident killer whale population of the northeastern Pacific Ocean provides a data-rich case to explore anthropogenic threats on population viability. Primary threats include: limitation of...
Data
Electronic Supplementary Material for malo et al 2017. "A father effect explains sex-ratio bias" by Malo, Martinez-Pastor, Garcia-Gonzalez, Garde, Ballou, Lacy 2017. Contents: S1. Materials and Methods S1.1. Set up of the original study population S1.2. Breeding protocols S1.3. Sampled Individuals S1.4. Spermatozoa collection S1.5. Sperm nuclei m...
Book
Full-text available
One of the greatest unmet issues in conservation biology is the genetic management of fragmented animal and plant populations. Many species across the planet have fragmented distributions with some small isolated populations that are potentially suffering from inbreeding, loss of genetic diversity, and elevated extinction risk. Fortunately, these e...
Article
Full-text available
Captive breeding programs are often initiated to prevent species extinction until reintroduction into the wild can occur. However, the evolution of captive populations via inbreeding, drift, and selection can impair fitness, compromising reintroduction programs. To better understand the evolutionary response of species bred in captivity, we used ne...
Data
Comparison of SNP estimated genomic diversity (multilocus heterozygosity) to pedigree estimates of genetic diversity (F). We used Spearman correlation coefficients (r) and p-values were estimated via 1000 permutations (all p <0.001). (DOCX)
Data
Final, quality filtered SNPs used in analyses. DNA samples were taken across 6 populations (random 1, random 2, mean kinship 1, mean kinship 2, docility 1, docility 2) and 4 generations (1, 6, 9, 19) and subsequently digested (using Pstl) and sequenced at Cornell according to [18]. The raw data were scored using Uneak pipeline within Tassel [20]. W...
Data
Number of nonneutral SNPs (i.e., those that are likely under selection). SNP counts are noted for each replicate protocol, at each generation and the number shared with all previous generations are noted in parentheses. The ‘Unique’ column indicates the number of unique SNPs within the row, whereas “Shared” indicates the number shared within the ro...
Data
Gene annotations for genotyping-by-sequencing identified SNPs. Pfam descriptions were collected from the protein family database, and gene ontology terms and codes for biological processes, molecular functions, and cellular components were identified using InterPro. (DOCX)
Article
Full-text available
The St. Lawrence Estuary (“SLE”) population of beluga (Delphinapterus leucas) was depleted by hunting. The population failed to increase in numbers at the rate one would expect after cessation of hunting. We conducted a population viability analysis (“PVA”) to quantify factors that most likely limit recovery of SLE beluga. The main threats consider...
Article
Full-text available
Globally, many wildlife species are declining and an increasing number are threatened by extinction or are extinct. Active management is generally required to mitigate these trends and population viability analysis (PVA) enables different scenarios to be evaluated and informs management decisions. Based on population parameters obtained from a thre...
Book
Full-text available
Predicting climate change impacts on biodiversity is a major scientific challenge, but doing so is important for assessing extinction risk, developing conservation action plans, providing guidance for laws and regulations, and identifying the mechanisms and patterns of impact to inform climate change adaptation. In the few decades since the threat...
Article
Full-text available
In summary, there are strikingly similar genetic management needs for plants and animals in ex situ conservation collections. To date, ex situ conservation programs in the botanic garden community have concentrated largely on banking of seeds and pollen, while the zoo community has focused largely on living collections of animals. We have much to l...
Article
Conservation of endangered species increasingly envisages complex strategies that integrate captive and wild management actions. Management decisions in this context must be made in the face of uncertainty, often with limited capacity to collect information. Adaptive management (AM) combines management and monitoring, with the aim of updating knowl...
Article
Animals with only partially known ancestry present a problem for population managers because it can be difficult to determine their relative genetic value to the population. So long as their ancestry is not completely unknown, population management software such as PMx can calculate a mean kinship for these animals, but that mean kinship is calcula...
Article
Full-text available
The effectiveness of invasive species control can be influenced by seasonal fluctuations in reproduction in response to environmental conditions. However, it is difficult to determine how demography and environmental conditions affect the efficacy of different control efforts from field trials alone. We incorporated an ontogenetic growth model into...
Article
Full-text available
It has been proposed that in slow-growing vertebrate populations survival generally has a greater influence on population growth than reproduction. Despite many studies cautioning against such generalizations for conservation, wildlife management for slow-growing populations still often focuses on perturbing survival without careful evaluation as t...
Data
Appendix S1 Study sites; includes Fig. S1 Appendix S2 Parameters other than reproductive and survival rates; includes Table S2 Appendix S3 Reproductive and survival rates; includes Fig. S3, Table S3 Appendix S4 Applicability of capture‐mark‐recapture methodology; includes Fig. S4 Appendix S5 Results of standard models: Fig. S5 Appendix S6 Elas...
Data
Appendix S2. Pedigree of the Texas blind cave salamander with group terminology for PMx.
Data
Appendix S1. Studbook of the Texas blind cave salamander.
Article
Full-text available
Invasive species pose a significant threat to native species persistence worldwide. Effective invasives management requires a detailed understanding of the mechanisms by which they impact native taxa, yet most quantitative models used to inform management do not address these complex interactions. Populations of the endangered Yellow-shouldered Bla...
Article
Stochastic simulation models requiring many input parameters are widely used to inform the management of ecological systems. The interpretation of complex models is aided by global sensitivity analysis, using simulations for distinct parameter sets sampled from multidimensional space. Ecologists typically analyze such output using an “emulator”; th...
Article
The goal of captive breeding programs is often to maintain genetic diversity until reintroductions can occur. However, due in part to changes that occur in captive populations, approximately one-third of reintroductions fail. We evaluated genetic changes in captive populations using microsatellites and mtDNA. We analyzed six populations of white-fo...
Article
Full-text available
Captive breeding programs are an important tool for the conservation of endangered species. These programs are commonly managed using pedigrees containing information about the history of each individual's family, such as breeding pairs and parentage. However, there are some species that are kept in groups where it is hard to distinguish between pa...
Article
Full-text available
1.Applied ecologists continually advocate further research, under the assumption that obtaining more information will lead to better decisions. Value of information (VoI) analysis can be used to quantify how additional information may improve management outcomes: despite its potential, this method is still underused in environmental decision-making...
Article
Telomerase reverse transcriptase (TERT) is the catalytic subunit of telomerase complex that regulates telomerase activity to maintain telomere length for all animals with linear chromosomes. As the Mus musculus (MM) laboratory mouse has very long telomeres compared to humans, a potential alternative animal model for telomere research is the Peromys...
Data
##Assembly-Data-START## Assembly Method :: SeqMan software v. 8.0.2(16).412 Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
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##Assembly-Data-START## Assembly Method :: SeqMan software v. 8.0.2(16).412 Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
Data
##Assembly-Data-START## Assembly Method :: SeqMan software v. 8.0.2(16).412 Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
Article
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Infectious diseases can exert a strong influence on the dynamics of host populations, but it remains unclear why such disease-mediated control only occurs under particular environmental conditions.We used 16 years of detailed field data on invasive European rabbits (Oryctolagus cuniculus) in Australia, linked to individual-based stochastic models a...