PeerJ Preprints: Conservation Biologyhttps://peerj.com/preprints/index.atom?journal=peerj&subject=920Conservation Biology articles published in PeerJ PreprintsInbreeding depression in one of the last DFTD-free wild populations of Tasmanian devilshttps://peerj.com/preprints/279852019-09-262019-09-26Rebecca M GooleyCarolyn J HoggSamantha FoxDavid PembertonKatherine BelovCatherine E Grueber
Background. Vulnerable species experiencing inbreeding depression are prone to localised extinctions because of their reduced fitness. For Tasmanian devils, the rapid spread of devil facial tumour disease (DFTD) has led to population declines and fragmentation across the species’ range. Here we show that one of the few remaining DFTD-free populations of Tasmanian devils is experiencing inbreeding depression. Moreover, this population has experienced a significant reduction in reproductive success over recent years.
Methods. We used 32 microsatellite loci to examine changes in genetic diversity and inbreeding in the wild population at Woolnorth, alongside field data on breeding success from females to test for inbreeding depression.
Results. We found that maternal internal relatedness has a negative impact on litter sizes. The results of this study imply that this population has entered an extinction vortex and that to protect the population, genetic rescue may be required. This study provides conservation managers with useful information for managing wild devils and provides support for the “Wild Devil Recovery Program” which is currently augmenting small, isolated populations.
Background. Vulnerable species experiencing inbreeding depression are prone to localised extinctions because of their reduced fitness. For Tasmanian devils, the rapid spread of devil facial tumour disease (DFTD) has led to population declines and fragmentation across the species’ range. Here we show that one of the few remaining DFTD-free populations of Tasmanian devils is experiencing inbreeding depression. Moreover, this population has experienced a significant reduction in reproductive success over recent years.Methods. We used 32 microsatellite loci to examine changes in genetic diversity and inbreeding in the wild population at Woolnorth, alongside field data on breeding success from females to test for inbreeding depression.Results. Wefound that maternal internal relatedness has a negative impact on litter sizes. The results of this study imply that this population has entered an extinction vortex and that to protect the population, genetic rescue may be required. This study provides conservation managers with useful information for managing wild devils and provides support for the “Wild Devil Recovery Program” which is currently augmenting small, isolated populations.Inventory statistics meet big data: Complications for estimating numbers of specieshttps://peerj.com/preprints/279652019-09-172019-09-17Ali KhalighifarLaura JiménezClaudia Nuñez-PenichetBenedictus FreemanKate IngenloffDaniel Jiménez-GarcíaA. Townsend Peterson
Abstract
We point out complications inherent in biodiversity inventory metrics when applied to large-scale datasets. The number of samples in which a species is detected saturates, such that crucial numbers of detections of rare species approach zero. Any rare errors can then come to dominate species richness estimates, creating upward biases in estimates of species numbers. We document the problem via simulations of sampling from virtual biotas, illustrate its potential using a large empirical dataset (bird records from Cape May, New Jersey, USA), and outline the circumstances under which these problems may be expected to emerge.
AbstractWe point out complications inherent in biodiversity inventory metrics when applied to large-scale datasets. The number of samples in which a species is detected saturates, such that crucial numbers of detections of rare species approach zero. Any rare errors can then come to dominate species richness estimates, creating upward biases in estimates of species numbers. We document the problem via simulations of sampling from virtual biotas, illustrate its potential using a large empirical dataset (bird records from Cape May, New Jersey, USA), and outline the circumstances under which these problems may be expected to emerge.The social context for conservation: amphibians in human-shaped landscapeshttps://peerj.com/preprints/279182019-08-272019-08-27Tibor HartelBen C ScheeleLaurentiu RozylowiczAndra Horcea-MilcuDan Cogalniceanu
Many human-shaped landscapes support viable amphibian populations due to the habitats created and/or maintained as a consequence of human actions. The challenges and approaches required to achieve the persistence of amphibians in human-shaped landscapes are markedly different from approaches commonly applied in protected areas. Contrary to protected areas or natural landscapes where amphibian conservationists can have direct control over management, in human-shaped landscapes, management options are best approached through understanding local communities’ values and socio-economic aspirations. However, consideration of the social aspects of amphibian conservation are vastly under-represented in the amphibian conservation literature. We propose that amphibian conservationists should: (i) assess the controllability of their mitigation actions for achieving long-term sustainability, (ii) understand the values and attitudes of individual landowners towards amphibians and amphibian-friendly management (local scale) and land stewardship on which amphibian conservation initiatives can be built (landscape scale), and (iii) understand the social and economic drivers of land-use change operating at regional levels, which is crucial for building adaptive potential in conservation programs. Since targeted amphibian conservation initiatives are limited in many human-shaped landscapes, consideration of the socio-economic context conducive to amphibian persistence is crucial.
Many human-shaped landscapes support viable amphibian populations due to the habitats created and/or maintained as a consequence of human actions. The challenges and approaches required to achieve the persistence of amphibians in human-shaped landscapes are markedly different from approaches commonly applied in protected areas. Contrary to protected areas or natural landscapes where amphibian conservationists can have direct control over management, in human-shaped landscapes, management options are best approached through understanding local communities’ values and socio-economic aspirations. However, consideration of the social aspects of amphibian conservation are vastly under-represented in the amphibian conservation literature. We propose that amphibian conservationists should: (i) assess the controllability of their mitigation actions for achieving long-term sustainability, (ii) understand the values and attitudes of individual landowners towards amphibians and amphibian-friendly management (local scale) and land stewardship on which amphibian conservation initiatives can be built (landscape scale), and (iii) understand the social and economic drivers of land-use change operating at regional levels, which is crucial for building adaptive potential in conservation programs. Since targeted amphibian conservation initiatives are limited in many human-shaped landscapes, consideration of the socio-economic context conducive to amphibian persistence is crucial.Effect of coral reef restoration on demersal biodiversity in Okinawa, Japanhttps://peerj.com/preprints/279062019-08-182019-08-18Piera BiondiGiovanni D MasucciJames D Reimer
Global climate change is leading to damage and loss of coral reef ecosystems. On subtropical Okinawa Island in southwestern Japan, the prefectural government is working on coral reef restoration by outplanting coral colonies from family Acroporidae back to reefs after initially farming colonies inside protected nurseries. In this study we evaluated the ongoing restoration efforts by comparing outplanted locations with nearby control locations with no restoration activity. We examined 3 sites on the coast of Onna Village on the west coast of the island; each site included an outplanted and control location. We used 1) coral rubble sampling to evaluate and compare abundance and diversity of rubble cryptofauna; and 2) coral reef monitoring using photograph transects to track live coral coverage. Results showed that rubble shape had a positive correlation with the numbers of animals found within rubble themselves and may therefore constitute a reliable abundance predictor. Outplanted locations did not show differences with the controls in rubble cryptofauna abundance, but had significantly lower coral coverage. Differences between sites were significant, for both rubble cryptofauna and coral coverage.We recommend; 1) to evaluate outplanting colonies from more stress-resistant genera in place of Acropora, 2) to conduct regular surveys to monitor the situation closely, and 3) to establish conservation and sustainable practices that could aid restoration efforts, reducing coral mortality of both outplanted and native colonies.
Global climate change is leading to damage and loss of coral reef ecosystems. On subtropical Okinawa Island in southwestern Japan, the prefectural government is working on coral reef restoration by outplanting coral colonies from family Acroporidae back to reefs after initially farming colonies inside protected nurseries. In this study we evaluated the ongoing restoration efforts by comparing outplanted locations with nearby control locations with no restoration activity. We examined 3 sites on the coast of Onna Village on the west coast of the island; each site included an outplanted and control location. We used 1) coral rubble sampling to evaluate and compare abundance and diversity of rubble cryptofauna; and 2) coral reef monitoring using photograph transects to track live coral coverage. Results showed that rubble shape had a positive correlation with the numbers of animals found within rubble themselves and may therefore constitute a reliable abundance predictor. Outplanted locations did not show differences with the controls in rubble cryptofauna abundance, but had significantly lower coral coverage. Differences between sites were significant, for both rubble cryptofauna and coral coverage.We recommend; 1) to evaluate outplanting colonies from more stress-resistant genera in place of Acropora, 2) to conduct regular surveys to monitor the situation closely, and 3) to establish conservation and sustainable practices that could aid restoration efforts, reducing coral mortality of both outplanted and native colonies.A rapid spread of the Stony Coral Tissue Loss Disease outbreak in the Mexican Caribbeanhttps://peerj.com/preprints/278932019-08-122019-08-12Lorenzo Alvarez-FilipNuria Estrada-SaldívarEsmeralda Pérez-CervantesAna Molina-HernándezFrancisco J. Gonzalez-Barrios
Caribbean reef corals have experienced unprecedented declines from climate change, anthropogenic stressors and infectious diseases in recent decades. Since 2014 a highly lethal, new disease, called stony coral tissue loss disease (SCTLD), has impacted many species in Florida. During the summer of 2018 we noticed an anomalously high disease prevalence affecting different coral species in the northern portion of the Mexican Caribbean. We assessed the severity of this outbreak in 2018/2019 using the AGRRA coral protocol to survey 82 reef sites across the Mexican Caribbean. Then, using a subset of 14 sites we detailed information from before the outbreak (2016/2017) to explore the consequences of the disease on the condition and composition of coral communities. Our findings show that the disease outbreak has already spread across the entire region, affecting similar species (with similar disease patterns) to those previously described for Florida. However, we observed a great variability in prevalence and tissue mortality that was not attributable to any geographical gradient. Using long-term data, we determined that there is no evidence of such high coral disease prevalence anywhere in the region before 2018, which suggests that the entire Mexican Caribbean (~450 km) was afflicted by the disease within a few months. The analysis of sites that contained pre-outbreak information showed that this event considerably increased coral mortality and severely changed the structure of coral communities in the region. Given the high prevalence and lethality of this disease, and the high number of susceptible species, we encourage reef researchers, managers and stakeholders across the Western Atlantic to accord it the highest priority for the near future.
Caribbean reef corals have experienced unprecedented declines from climate change, anthropogenic stressors and infectious diseases in recent decades. Since 2014 a highly lethal, new disease, called stony coral tissue loss disease (SCTLD), has impacted many species in Florida. During the summer of 2018 we noticed an anomalously high disease prevalence affecting different coral species in the northern portion of the Mexican Caribbean. We assessed the severity of this outbreak in 2018/2019 using the AGRRA coral protocol to survey 82 reef sites across the Mexican Caribbean. Then, using a subset of 14 sites we detailed information from before the outbreak (2016/2017) to explore the consequences of the disease on the condition and composition of coral communities. Our findings show that the disease outbreak has already spread across the entire region, affecting similar species (with similar disease patterns) to those previously described for Florida. However, we observed a great variability in prevalence and tissue mortality that was not attributable to any geographical gradient. Using long-term data, we determined that there is no evidence of such high coral disease prevalence anywhere in the region before 2018, which suggests that the entire Mexican Caribbean (~450 km) was afflicted by the disease within a few months. The analysis of sites that contained pre-outbreak information showed that this event considerably increased coral mortality and severely changed the structure of coral communities in the region. Given the high prevalence and lethality of this disease, and the high number of susceptible species, we encourage reef researchers, managers and stakeholders across the Western Atlantic to accord it the highest priority for the near future.Below the canopy: global trends in forest vertebrate populations and their drivershttps://peerj.com/preprints/278822019-08-012019-08-01Elizabeth J. GreenLouise McRaeRobin FreemanMike B.J. HarfootSamantha L.L. HillWilliam Baldwin-CantelloWilliam D. Simonson
Global forest assessments use forest area as a proxy indicator of biodiversity status, which may mask below-canopy pressures driving forest biodiversity loss and ‘empty forest’ syndrome. The status of forest biodiversity is important not only for species conservation but also because species loss can have consequences for forest health and carbon storage. We aimed to develop a global indicator of forest specialist vertebrate populations to improve assessments of forest biodiversity status. For this purpose we used the Living Planet Index methodology, developing a weighted composite Forest Specialist Index for the period 1970-2014. We then investigated potential drivers of forest vertebrate population change, including tree cover change, to determine whether forest area is a good proxy for forest biodiversity. The effects of satellite-derived tree cover trends and other pressures on the average rate of change of forest vertebrate populations were analysed. We reviewed the literature to gain more context-specific information relating to drivers of forest specialist population change. On average, forest vertebrate populations declined by 53% between 1970 and 2014. We found little evidence of a consistent global effect of tree cover change on forest vertebrate populations but a significant negative effect of exploitation threat on forest specialists. However, time-series cross-correlation analyses showed some forest specialist populations are closely aligned to tree cover change. The literature review identified several drivers of population change that cannot be detected remotely and may cause populations to change independently of tree cover. Forest vertebrate populations have more than halved since the 1970s. In conclusion, we found that forest area is a poor proxy of forest biodiversity status. For forest biodiversity to recover, we must monitor and manage all threats to vertebrates, including those below the canopy.
Global forest assessments use forest area as a proxy indicator of biodiversity status, which may mask below-canopy pressures driving forest biodiversity loss and ‘empty forest’ syndrome. The status of forest biodiversity is important not only for species conservation but also because species loss can have consequences for forest health and carbon storage. We aimed to develop a global indicator of forest specialist vertebrate populations to improve assessments of forest biodiversity status. For this purpose we used the Living Planet Index methodology, developing a weighted composite Forest Specialist Index for the period 1970-2014. We then investigated potential drivers of forest vertebrate population change, including tree cover change, to determine whether forest area is a good proxy for forest biodiversity. The effects of satellite-derived tree cover trends and other pressures on the average rate of change of forest vertebrate populations were analysed. We reviewed the literature to gain more context-specific information relating to drivers of forest specialist population change. On average, forest vertebrate populations declined by 53% between 1970 and 2014. We found little evidence of a consistent global effect of tree cover change on forest vertebrate populations but a significant negative effect of exploitation threat on forest specialists. However, time-series cross-correlation analyses showed some forest specialist populations are closely aligned to tree cover change. The literature review identified several drivers of population change that cannot be detected remotely and may cause populations to change independently of tree cover. Forest vertebrate populations have more than halved since the 1970s. In conclusion, we found that forest area is a poor proxy of forest biodiversity status. For forest biodiversity to recover, we must monitor and manage all threats to vertebrates, including those below the canopy.Twisted tale of the tiger: the case of inappropriate data and deficient sciencehttps://peerj.com/preprints/273492019-07-312019-07-31Qamar QureshiRajesh GopalYadvendradev V Jhala
Publications in peer reviewed journals are often looked upon as tenets on which future scientific thought is built. Published information is not always flawless and errors in published research should be expediently reported, preferably by a peer review process. We review a recent publication by Gopalaswamy et al (doi:10.1111/2041-210X.12351) that challenges the use of “double sampling” in large scale animal surveys. Double sampling is often resorted to as an established economical and practical approach for large scale surveys since it calibrates abundance indices against absolute abundance, thereby potentially addressing the statistical shortfalls of indices. Empirical data used by Gopalaswamy et al. to test their theoretical model, relate to tiger sign and tiger abundance referred to as an Index Calibration experiment (IC-Karanth). These data on tiger abundance and signs should be paired in time and space to qualify as a calibration experiment for double sampling, but original data of IC-Karanth show lags of (up to) several years. Further, data points used in the paper do not match the original sources. We show that by use of inappropriate and incorrect data collected through a faulty experimental design, poor parameterization of their theoretical model, and selectively-picked estimates from literature on detection probability, the inferences of this paper are highly questionable. We highlight how the results of Gopalaswamy et al. were further distorted in popular media. If left unaddressed, Gopalaswamy et al. paper could have serious implications on statistical design of large-scale animal surveys by propagating unreliable inferences.
Publications in peer reviewed journals are often looked upon as tenets on which future scientific thought is built. Published information is not always flawless and errors in published research should be expediently reported, preferably by a peer review process. We review a recent publication by Gopalaswamy et al (doi:10.1111/2041-210X.12351) that challenges the use of “double sampling” in large scale animal surveys. Double sampling is often resorted to as an established economical and practical approach for large scale surveys since it calibrates abundance indices against absolute abundance, thereby potentially addressing the statistical shortfalls of indices. Empirical data used by Gopalaswamy et al. to test their theoretical model, relate to tiger sign and tiger abundance referred to as an Index Calibration experiment (IC-Karanth). These data on tiger abundance and signs should be paired in time and space to qualify as a calibration experiment for double sampling, but original data of IC-Karanth show lags of (up to) several years. Further, data points used in the paper do not match the original sources. We show that by use of inappropriate and incorrect data collected through a faulty experimental design, poor parameterization of their theoretical model, and selectively-picked estimates from literature on detection probability, the inferences of this paper are highly questionable. We highlight how the results of Gopalaswamy et al. were further distorted in popular media. If left unaddressed, Gopalaswamy et al. paper could have serious implications on statistical design of large-scale animal surveys by propagating unreliable inferences.Threatened plants species of Guinea-Conakry: A preliminary checklisthttps://peerj.com/preprints/34512019-07-172019-07-17Charlotte CouchSekou MagassoubaSaba RokniEmma WilliamsCatia CanteiroMartin Cheek
Guinea-Conakry has one of the highest plant diversities in Sub-Saharan West Africa and is part of the Upper Guinean Forest ecoregion and the Guinean Forests of West Africa biodiversity hotspot. Guinea is a major supplier of the world’s bauxite and has significant reserves of high grade iron ore, it also has small reserves of diamonds, gold and uranium. As a result large areas of open cast mining exist in the country and pressure on habitats and vegetation are increasing with the need to bring revenue into the country; this is in addition to unsustainable slash and burn agriculture and a growing population. An initial list of 482 species was compiled from Lisowski’s Flore (Angiospermes) de la République de Guinée, subsequent discussion and screening reduced the list to 253. This list has since increased, through new species and range extensions, to 270 which is presented here. It is estimated that c. 7-8% of the countries flora is threatened. Rediscoveries and new species are being made in Guinea, but they are often already threatened having been discovered as part of Environmental Impact Assessments (EIAs). A comprehensive red list of threatened species is much needed to support the country’s environmental policy as well as their international obligations. Data gathering for a Red Data Book for Guinea has been ongoing for several years and is due to be published in 2019.
Guinea-Conakry has one of the highest plant diversities in Sub-Saharan West Africa and is part of the Upper Guinean Forest ecoregion and the Guinean Forests of West Africa biodiversity hotspot. Guinea is a major supplier of the world’s bauxite and has significant reserves of high grade iron ore, it also has small reserves of diamonds, gold and uranium. As a result large areas of open cast mining exist in the country and pressure on habitats and vegetation are increasing with the need to bring revenue into the country; this is in addition to unsustainable slash and burn agriculture and a growing population. An initial list of 482 species was compiled from Lisowski’s Flore (Angiospermes) de la République de Guinée, subsequent discussion and screening reduced the list to 253. This list has since increased, through new species and range extensions, to 270 which is presented here. It is estimated that c. 7-8% of the countries flora is threatened. Rediscoveries and new species are being made in Guinea, but they are often already threatened having been discovered as part of Environmental Impact Assessments (EIAs). A comprehensive red list of threatened species is much needed to support the country’s environmental policy as well as their international obligations. Data gathering for a Red Data Book for Guinea has been ongoing for several years and is due to be published in 2019.Failure to respond to a coral disease outbreak: Potential costs and consequenceshttps://peerj.com/preprints/278602019-07-162019-07-16William F Precht
A coral disease with white plague-like signs was observed near Virginia Key, Florida, in September 2014. The disease outbreak directly followed a regional high temperature coral-bleaching event. Now called stony coral tissue loss disease (SCTLD), it has spread the length of the Florida Reef Tract from Key West to Martin County, a distance of about 450 km. Recently, the disease has also been observed at a number of sites throughout the Caribbean. The high prevalence of disease, the number of susceptible species, and the high mortality of corals affected suggests this outbreak is arguably one of the most lethal ever recorded. The initial response to this catastrophic disease by resource mangers with purview over the ecosystem was slow. There is generally a very short window of opportunity to intervene in disease amelioration or eradication in the marine environment. This slow response enabled the disease to spread unchecked. Why was the response to the loss of our coral reefs to a coral disease epidemic, such a massive failure? This includes our failure as scientists, regulators, resource managers, the local media, and policy makers alike. This review encapsulates the numerous reasons for our failures during the first few years of the outbreak. Specifically, I show how the Port Miami dredging project that was ongoing at the time of the initial outbreak created a distraction as local NGO's, regulatory agencies, and resource managers initially blamed the project for observed large-scale coral losses. However, detailed analysis of 650 tagged corals that were part of a repeated measures monitoring program required for permit compliance associated with the Port Miami dredge project reveal that both disease susceptibility and coral mortality are invariant with the results collected by a number of scientific teams throughout the region. Finally, when the agencies responded to the outbreak the effort it was too little and much too late to make a meaningful difference. Because of the languid management response to this outbreak, we are now sadly faced with a situation where much of our management efforts are focused on the rescue of genetic material from coral species now at risk of regional extinction.
A coral disease with white plague-like signs was observed near Virginia Key, Florida, in September 2014. The disease outbreak directly followed a regional high temperature coral-bleaching event. Now called stony coral tissue loss disease (SCTLD), it has spread the length of the Florida Reef Tract from Key West to Martin County, a distance of about 450 km. Recently, the disease has also been observed at a number of sites throughout the Caribbean. The high prevalence of disease, the number of susceptible species, and the high mortality of corals affected suggests this outbreak is arguably one of the most lethal ever recorded. The initial response to this catastrophic disease by resource mangers with purview over the ecosystem was slow. There is generally a very short window of opportunity to intervene in disease amelioration or eradication in the marine environment. This slow response enabled the disease to spread unchecked. Why was the response to the loss of our coral reefs to a coral disease epidemic, such a massive failure? This includes our failure as scientists, regulators, resource managers, the local media, and policy makers alike. This review encapsulates the numerous reasons for our failures during the first few years of the outbreak. Specifically, I show how the Port Miami dredging project that was ongoing at the time of the initial outbreak created a distraction as local NGO's, regulatory agencies, and resource managers initially blamed the project for observed large-scale coral losses. However, detailed analysis of 650 tagged corals that were part of a repeated measures monitoring program required for permit compliance associated with the Port Miami dredge project reveal that both disease susceptibility and coral mortality are invariant with the results collected by a number of scientific teams throughout the region. Finally, when the agencies responded to the outbreak the effort it was too little and much too late to make a meaningful difference. Because of the languid management response to this outbreak, we are now sadly faced with a situation where much of our management efforts are focused on the rescue of genetic material from coral species now at risk of regional extinction.Digitization and the future of natural history collectionshttps://peerj.com/preprints/278592019-07-152019-07-15Brandon HedrickMason HeberlingEmily MeinekeKathryn TurnerChristopher GrassaDaniel ParkJonathan KennedyJulia ClarkeJoseph CookDavid BlackburnScott EdwardsCharles Davis
Natural history collections (NHCs) are the foundation of historical baselines for assessing anthropogenic impacts on biodiversity. Along these lines, the online mobilization of specimens via digitization–the conversion of specimen data into accessible digital content–has greatly expanded the use of NHC collections across a diversity of disciplines. We broaden the current vision of digitization (Digitization 1.0)–whereby specimens are digitized within NHCs–to include new approaches that rely on digitized products rather than the physical specimen (Digitization 2.0). Digitization 2.0 builds upon the data, workflows, and infrastructure produced by Digitization 1.0 to create digital-only workflows that facilitate digitization, curation, and data linkages, thus returning value to physical specimens by creating new layers of annotation, empowering a global community, and developing automated approaches to advance biodiversity discovery and conservation. These efforts will transform large-scale biodiversity assessments to address fundamental questions including those pertaining to critical modern issues of global change.
Natural history collections (NHCs) are the foundation of historical baselines for assessing anthropogenic impacts on biodiversity. Along these lines, the online mobilization of specimens via digitization–the conversion of specimen data into accessible digital content–has greatly expanded the use of NHC collections across a diversity of disciplines. We broaden the current vision of digitization (Digitization 1.0)–whereby specimens are digitized within NHCs–to include new approaches that rely on digitized products rather than the physical specimen (Digitization 2.0). Digitization 2.0 builds upon the data, workflows, and infrastructure produced by Digitization 1.0 to create digital-only workflows that facilitate digitization, curation, and data linkages, thus returning value to physical specimens by creating new layers of annotation, empowering a global community, and developing automated approaches to advance biodiversity discovery and conservation. These efforts will transform large-scale biodiversity assessments to address fundamental questions including those pertaining to critical modern issues of global change.