Incidental take and endangered species demography

The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file.Title from title screen of research.pdf file (viewed on June 9, 2009)Vita.Thesis (Ph. D.) University of Missouri-Columbia 2008.Incidental take is the permitted killing, harming, harassing or destroying habitat of an endangered species under endangered species law. Legislation assumes that endangered or threatened populations can somehow compensate for the potentially negative effects of incidental take. However if the species in question does not have the assumed capacity to compensate it is possible for incidental take to dramatically lower abundance and lead to decreasing population trends for a protected species. With this research I explored the concept of incidental take from an ecological and demographic stand point to evaluate the basis and application of the policy. I reviewed literature on incidental take, compensatory mortality, and harvest theory to elucidate the conditions under which incidental take might be sustainable from a demographic perspective. I also developed and used a predictive population model for Piping Plovers in the Great Plains to evaluate the potential effects of currently permitted take of eggs and chicks in the Missouri River on plover population viability. Lastly I examined the use of science and specifically quantitative population models in incidental take permitting decisions by reviewing biological opinions for Piping Plovers from throughout their range. Biological opinions are the official documents prepared and released by the US Fish and Wildlife Service detailing the ecology and biology of an incidental take action and determining whether and under what conditions incidental take can proceed.Includes bibliographical reference

Estimating survival of precocial chicks during the prefledging period using a catch-curve analysis and count-based age-class data

ABSTRACT: Estimating reproductive success for birds with pre-cocial young can be difficult because chicks leave nests soon after hatching and individuals or broods can be difficult to track. Researchers often turn to estimating survival during the pre-fledging period and, though effective, mark-recapture based approaches are not always feasible due to cost, time, and animal welfare concerns. Using a threatened population of Piping Plovers (Charadrius melodus) that breeds along the Missouri River, we present an approach for estimating chick survival during the pre-fledging period using long-term (1993–2005), count-based, age-class data. We used a modified catch-curve analysis, and data collected during three 5-day sampling periods near the middle of the breeding season. The approach has several ecological and statistical assumptions and our analyses were designed to minimize the probability of violating those assumptions. For example, limiting the sampling periods to only 5 days gave reasonable assurance that population size was stable during the sampling period. Annual daily survival estimates ranged from 0.825 (SD = 0.03) to 0.931 (0.02) depending on year and sampling period, with these estimates assuming constant survival during the pre-fledging period and no change in the age structure of the population. The average probability of survival to fledging ranged from 0.126 to 0.188. Our results are similar to other published estimates for this species in similar habitats. This method of estimating chick survival may be useful for a variety of pre-cocial bird species when mark-recapture methods are not feasible and only count-based age class data are available. RESUMEN. La estimaci´on de la supervivencia de polluelos precociales durante el periodo pre-volant´on usando un an´alisis de curva de captura y datos con clases de edades basados en conteos Estimar el ´exito reproductivo de aves con polluelos precociales puede ser dif´ıcil debido a que los polluelos dejan el nido poco despu´es de eclosionar y los individuos o nidadas pueden ser dif´ıciles de seguir. Los investigadores a menudo estiman la supervivencia durante el periodo pre-volant´on y aunque son efectivos, los m´etodos de marcaje y recaptura no son siempre factibles por razones del costo, tiempo y bienestar del animal. Usando una poblaci´on amenazada de Charadrius melodus que se reproduce sobre el R´ıo Missouri, presentamos un m´etodo para estimar la supervivencia de polluelos durante el periodo pre-volant´on usando datos de largo plazo (1993–2005) con clases de edades, basados en conteos. Utilizamos un an´alisis de curva de captura modificada y datos colectados durante tres periodos de muestreo de cinco d´ıas cada uno, cerca del medio de la ´epoca reproductiva. Este m´etodo tiene algunos supuestos ecol´ogicos y estad´ısticos y nuestros an´alisis fueron dise˜nados para minimizar la probabilidad de violar dichos supuestos. Por ejemplo, limitando los periodos de muestreo a solo cinco d´ıas dio el resultado razonable de que el tama˜no de la poblaci´on fue estable durante el periodo de muestreo. Las estimaciones de la supervivencia diaria anual variaron entre 0.825 (DE = 0.03) y 0.931 (0.02), dependiendo del a˜no y periodo de muestreo. Estas estimaciones dependieron de la suposici´on de una supervivencia constante durante el periodo pre-volant´on y de ning´un cambio en la estructura de la edad de la poblaci´on. El promedio de la probabilidad de supervivencia en la etapa pre-volant´on vari´o desde 0.126 hasta 0.188. Nuestros resultados son similares a otras estimaciones publicadas para esta especie en h´abitats similares. Este m´etodo de estimar la supervivencia de los polluelos podr´ıa ser ´util para una variedad de especies de aves precociales cuando los m´etodos de marcaje y recaptura no son factibles y cuando solo est´an disponibles datos con clases de edades basados en conteos

Establishing endangered species recovery criteria using predictive simulation modeling

Listing a species under the Endangered Species Act (ESA) and developing a recovery plan requires U.S. Fish and Wildlife Service to establish specific and measurable criteria for delisting. Generally, species are listed because they face (or are perceived to face) elevated risk of extinction due to issues such as habitat loss, invasive species, or other factors. Recovery plans identify recovery criteria that reduce extinction risk to an acceptable level. It logically follows that the recovery criteria, the defined conditions for removing a species from ESA protections, need to be closely related to extinction risk. Extinction probability is a population parameter estimated with a model that uses current demographic information to project the population into the future over a number of replicates, calculating the proportion of replicated populations that go extinct. We simulated extinction probabilities of piping plovers in the Great Plains and estimated the relationship between extinction probability and various demographic parameters. We tested the fit of regression models linking initial abundance, productivity, or population growth rate to extinction risk, and then, using the regression parameter estimates, determined the conditions required to reduce extinction probability to some pre-defined acceptable threshold. Binomial regression models with mean population growth rate and the natural log of initial abundance were the best predictors of extinction probability 50 years into the future. For example, based on our regression models, an initial abundance of approximately 2400 females with an expected mean population growth rate of 1.0 will limit extinction risk for piping plovers in the Great Plains to less than 0.048. Our method provides a straightforward way of developing specific and measurable recovery criteria linked directly to the core issue of extinction risk

Linking Monitoring and Data Analysis to Predictions and Decisions for the Range-wide Eastern Black Rail Status Assessment

The US Fish and Wildlife Service (USFWS) has initiated a re-envisioned approach for providing decision makers with the best available science and synthesis of that information, called the Species Status Assessment (SSA), for endangered species decision making. The SSA report is a descriptive document that provides decision makers with an assessment of the current and pre - dicted future status of a species. These analyses support all manner of decisions under the US Endangered Species Act, such as listing, reclassification, and recovery planning. Novel scientific analysis and predictive modeling in SSAs could be an important part of rooting conservation decisions in current data and cutting edge analytical and modeling techniques. Here, we describe a novel analysis of available data to assess the current condition of eastern black rail Laterallus jamai censis jamai cen sis across its range in a dynamic occupancy analysis. We used the results of the ana lysis to develop a site occupancy projection model where the model parameters (initial occupancy, site persistence, colo nization) were linked to environmental covariates, such as land management and land cover change (sea-level rise, development, etc.). We used the projection model to predict future status under multiple sea-level rise and habitat management scenarios. Occupancy probability and site colonization were low in all analysis units, and site persistence was also low, suggesting low resiliency and redundancy currently. Extinction probability was high for all analysis units in all simulated scenarios except one with significant effort to preserve existing habitat, suggesting low future re siliency and redundancy. With the results of these data analyses and predictive models, the USFWS concluded that protections of the Endangered Species Act were warranted for this subspecies

Extinction risk and conservation options for Maui Parrotbill, an endangered Hawaiian honeycreeper

Extinction rates for island birds around the world have been historically high. For forest passerines, the Hawaiian archipelago has suffered some of the highest extinction rates and reintroduction is a conservation tool that can be used to prevent the extinction of some of the remaining endangered species. Population viability analyses can be used to assess risks to vulnerable populations and evaluate the relative benefits of conservation strategies. Here we present a population viability analysis to assess the long-term viability for Maui parrotbill(s) (Kiwikiu) Pseudonestor xanthophrys, a federally endangered passerine on the Hawaiian island of Maui. Contrary to indications from population monitoring, our results indicate Maui parrotbills may be unlikely to persist beyond 25 years. Our modeling suggests female mortality as a primary factor driving this decline. To evaluate and compare management options involving captive rearing and translocation strategies we made a female-only stage-structured, meta-population simulation model. Due to the low reproductive potential of Maui parrotbills in captivity, the number of individuals (~ 20% of the global population) needed to source a reintroduction solely from captive reared birds is unrealistic. A reintroduction strategy that incorporates a minimal contribution from captivity and instead translocates mostly wild individuals was found to be the most feasible management option. Habitat is being restored on leeward east Maui, which may provide more favorable climate and habitat conditions and promote increased reproductive output. Our model provides managers with benchmarks for fecundity and survival needed to ensure reintroduction success, and highlights the importance of establishing a new population in potentially favorable habitat to ensure long-term persistence

The coronary microvascular angina cardiovascular magnetic resonance imaging trial: rationale and design

Background: Coronary microvascular dysfunction may cause myocardial ischemia with no obstructive coronary artery disease (INOCA). If functional testing is not performed INOCA may pass undetected. Stress perfusion cardiovascular MRI (CMR) quantifies myocardial blood flow (MBF) but the clinical utility of stress CMR in the management of patients with suspected angina with no obstructive coronary arteries (ANOCA) is uncertain. Objectives: First, to undertake a diagnostic study using stress CMR in patients with ANOCA following invasive coronary angiography and, second, in a nested, double-blind, randomized, controlled trial to assess the effect of disclosure on the final diagnosis and health status in the longer term. Design: All-comers referred for clinically indicated coronary angiography for the investigation of suspected coronary artery disease will be screened in three regional centers in the United Kingdom. Following invasive coronary angiography, patients with ANOCA who provide informed consent will undergo noninvasive endotyping using stress CMR within 3 months of the angiogram. Diagnostic study: Stress perfusion CMR imaging to assess the prevalence of coronary microvascular dysfunction and clinically significant incidental findings in patients with ANOCA. The primary outcome is the between-group difference in the reclassification rate of the initial diagnosis based on invasive angiography versus the final diagnosis after CMR imaging. Randomized, controlled trial: Participants will be randomized to inclusion (intervention group) or exclusion (control group) of myocardial blood flow to inform the final diagnosis. The primary outcome of the clinical trial is the mean within-subject change in the Seattle Angina Questionnaire summary score (SAQSS) at 6 months. Secondary outcome assessments include the EUROQOL EQ-5D-5L questionnaire, the Brief Illness Perception Questionnaire (Brief-IPQ), the Treatment Satisfaction Questionnaire (TSQM-9), the Patient Health Questionnaire-4 (PHQ-4), the Duke Activity Status Index (DASI), the International Physical Activity Questionnaire- Short Form (IPAQ-SF), the Montreal Cognitive Assessment (MOCA) and the 8-item Productivity Cost Questionnaire (iPCQ). Health and economic outcomes will be assessed using electronic healthcare records. Value: To clarify if routine stress perfusion CMR imaging reclassifies the final diagnosis in patients with ANOCA and whether this strategy improves symptoms, health-related quality of life and health economic outcomes. Clinicaltrials.gov: NCT0480581

Genomic attributes of airway commensal bacteria and mucosa

Microbial communities at the airway mucosal barrier are conserved and highly ordered, in likelihood reflecting co-evolution with human host factors. Freed of selection to digest nutrients, the airway microbiome underpins cognate management of mucosal immunity and pathogen resistance. We show here the initial results of systematic culture and whole-genome sequencing of the thoracic airway bacteria, identifying 52 novel species amongst 126 organisms that constitute 75% of commensals typically present in heathy individuals. Clinically relevant genes encode antimicrobial synthesis, adhesion and biofilm formation, immune modulation, iron utilisation, nitrous oxide (NO) metabolism and sphingolipid signalling. Using whole-genome content we identify dysbiotic features that may influence asthma and chronic obstructive pulmonary disease. We match isolate gene content to transcripts and metabolites expressed late in airway epithelial differentiation, identifying pathways to sustain host interactions with microbiota. Our results provide a systematic basis for decrypting interactions between commensals, pathogens, and mucosa in lung diseases of global significance

Incorporating parametric uncertainty into population viability analysis models

Uncertainty in parameter estimates from sampling variation or expert judgment can introduce substantial uncertainty into ecological predictions based on those estimates. However, in standard population viability analyses, one of the most widely used tools for managing plant, fish and wildlife populations, parametric uncertainty is often ignored in or discarded from model projections. We present a method for explicitly incorporating this source of uncertainty into population models to fully account for risk in management and decision contexts. Our method involves a two-step simulation process where parametric uncertainty is incorporated into the replication loop of the model and temporal variance is incorporated into the loop for time steps in the model. Using the piping plover, a federally threatened shorebird in the USA and Canada, as an example, we compare abundance projections and extinction probabilities from simulations that exclude and include parametric uncertainty. Although final abundance was very low for all sets of simulations, estimated extinction risk was much greater for the simulation that incorporated parametric uncertainty in the replication loop. Decisions about species conservation (e.g., listing, delisting, and jeopardy) might differ greatly depending on the treatment of parametric uncertainty in population models

EFFECTS OF HUMAN RECREATION ON THE INCUBATION BEHAVIOR OF AMERICAN OYSTERCATCHERS

Volume: 118Start Page: 485End Page: 49