Robert C Lacy

Species Conservation Toolkit Initiative

Population dynamics and viability are driven by interactions among habitat and species biology. The Florida scrub-jay (Aphelocoma coerulescens) is a declining and Federally Threatened bird species that requires mid-succession habitat of partly open soil surface with mid-height vegetation. This habitat is created and sustained in a dynamic state of...

The focus of this selection of papers is the linkage of habitat and population dynamics for the purpose of conservation. We thus provide a general framework for making conservation decisions, emphasizing how knowledge of habitat–population linkages fits into this framework. We begin by describing structured decision-making (SDM) as a general approa...

The success of reintroductions using captive-bred populations of wild species is potentially impacted by adaptations to non-natural captive environments. Little research has been done into how physiological traits change from wild to captive populations. We do not yet understand how glucocorticoid secretion patterns, a critical aspect of the stress...

Summarizes the result of the second PHVA Worksop on Humboldt Penguin in LIma, Peru, in October 2019

This presentation was delivered at the North American Congress for Conservation Biology (2024) and is based on our publication in Conservation Biology: Manlik O, Lacy RC, Sherwin WB, Finn H, Loneragan NR, Allen SJ. (2022). A stochastic model for estimating sustainable limits to wildlife mortality in a changing world. Conservation Biology. e13897. d...

Wildlife species and populations are being driven toward extinction by a combination of historic and emerging stressors (e.g., overexploitation, habitat loss, contaminants, climate change), suggesting that we are in the midst of the planet’s sixth mass extinction. The invisible loss of biodiversity before species have been identified and described...

Molecular tools are increasingly applied for assessing and monitoring biodiversity and informing conservation action. While recent developments in genetic and genomic methods provide greater sensitivity in analysis and the capacity to address new questions, they are not equally available to all practitioners: There is considerable bias across insti...

The application of molecular tools to population management can improve the long-term genetic viability of ex situ populations. In this study, we aimed to understand the implications of integrating empirical kinships into the genetic management of an ex situ population of the endangered waterfowl, Baer’s pochard (Aythya baeri), in North America. Si...

Tis study modeled the efect of an EBOV outbreak on the endangered mountain gorilla population of the Virunga Massif, which spans protected areas in Rwanda, Uganda, and the Democratic Republic of Congo. We used the simulation model to ask the following questions: How fast will EBOV spread through the population? Will it move through the entire po...

Genetic diversity among and within populations of all species is necessary for people and nature to survive and thrive in a changing world. Over the past three years, commitments for conserving genetic diversity have become more ambitious and specific under the Convention on Biological Diversity’s (CBD) draft post-2020 global biodiversity framework...

Genetic diversity among and within populations of all species is necessary for people and the planet to survive in a changing world. Over the past three years, the conservation of genetic diversity has received increased ambition and specificity in commitments under the draft Convention on Biological Diversity's (CBD) post 2020 Global Biodiversity...

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...

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...

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...

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...

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...

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...

Humboldt penguin (Spheniscus humboldti) Population and Habitat Viability Assessment Workshop Final Report

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...

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...

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...

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.

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.

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...

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...

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...

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...

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...

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...

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. Using a pe...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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.

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...

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...

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...

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...

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...

The biological diversity of the planet is being rapidly depleted due to the direct and indirect consequences of human activity. As the size of animal and plant populations decrease and fragmentation increases, loss of genetic diversity reduces their ability to adapt to changes in the environment, with inbreeding and reduced fitness inevitable conse...

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...

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...

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...

The biological diversity of the planet is being rapidly depleted due to the direct and indirect consequences of human activity. As the size of animal and plant populations decrease and fragmentation increases, loss of genetic diversity reduces their ability to adapt to changes in the environment, with inbreeding and reduced fitness inevitable conse...

The biological diversity of the planet is being rapidly depleted due to the direct and indirect consequences of human activity. As the size of animal and plant populations decrease and fragmentation increases, loss of genetic diversity reduces their ability to adapt to changes in the environment, with inbreeding and reduced fitness inevitable conse...

The biological diversity of the planet is being rapidly depleted due to the direct and indirect consequences of human activity. As the size of animal and plant populations decrease and fragmentation increases, loss of genetic diversity reduces their ability to adapt to changes in the environment, with inbreeding and reduced fitness inevitable conse...

The biological diversity of the planet is being rapidly depleted due to the direct and indirect consequences of human activity. As the size of animal and plant populations decrease and fragmentation increases, loss of genetic diversity reduces their ability to adapt to changes in the environment, with inbreeding and reduced fitness inevitable conse...

The biological diversity of the planet is being rapidly depleted due to the direct and indirect consequences of human activity. As the size of animal and plant populations decrease and fragmentation increases, loss of genetic diversity reduces their ability to adapt to changes in the environment, with inbreeding and reduced fitness inevitable conse...

The biological diversity of the planet is being rapidly depleted due to the direct and indirect consequences of human activity. As the size of animal and plant populations decrease and fragmentation increases, loss of genetic diversity reduces their ability to adapt to changes in the environment, with inbreeding and reduced fitness inevitable conse...

The biological diversity of the planet is being rapidly depleted due to the direct and indirect consequences of human activity. As the size of animal and plant populations decrease and fragmentation increases, loss of genetic diversity reduces their ability to adapt to changes in the environment, with inbreeding and reduced fitness inevitable conse...

The biological diversity of the planet is being rapidly depleted due to the direct and indirect consequences of human activity. As the size of animal and plant populations decrease and fragmentation increases, loss of genetic diversity reduces their ability to adapt to changes in the environment, with inbreeding and reduced fitness inevitable conse...

The biological diversity of the planet is being rapidly depleted due to the direct and indirect consequences of human activity. As the size of animal and plant populations decrease and fragmentation increases, loss of genetic diversity reduces their ability to adapt to changes in the environment, with inbreeding and reduced fitness inevitable conse...

The biological diversity of the planet is being rapidly depleted due to the direct and indirect consequences of human activity. As the size of animal and plant populations decrease and fragmentation increases, loss of genetic diversity reduces their ability to adapt to changes in the environment, with inbreeding and reduced fitness inevitable conse...

The biological diversity of the planet is being rapidly depleted due to the direct and indirect consequences of human activity. As the size of animal and plant populations decrease and fragmentation increases, loss of genetic diversity reduces their ability to adapt to changes in the environment, with inbreeding and reduced fitness inevitable conse...

The biological diversity of the planet is being rapidly depleted due to the direct and indirect consequences of human activity. As the size of animal and plant populations decrease and fragmentation increases, loss of genetic diversity reduces their ability to adapt to changes in the environment, with inbreeding and reduced fitness inevitable conse...

The biological diversity of the planet is being rapidly depleted due to the direct and indirect consequences of human activity. As the size of animal and plant populations decrease and fragmentation increases, loss of genetic diversity reduces their ability to adapt to changes in the environment, with inbreeding and reduced fitness inevitable conse...

The biological diversity of the planet is being rapidly depleted due to the direct and indirect consequences of human activity. As the size of animal and plant populations decrease and fragmentation increases, loss of genetic diversity reduces their ability to adapt to changes in the environment, with inbreeding and reduced fitness inevitable conse...

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...

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)

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...

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...

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)

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...

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...