Biology subjects

Malcom, J. W.

Publications and source records attributed to Malcom, J. W..

11 recordsLinked to original sources

bioRxiv2021

Targeting current species ranges and carbon stocks fails to conserve biodiversity in a changing climate: opportunities to support climate adaptation under 30x30

Protecting areas for climate adaptation will be essential to ensuring greater opportunity for species conservation well into the future. However, many proposals for protected areas expansion focus on our understanding of current spatial patterns, which may be ineffective surrogates for future needs. A science-driven call to address the biodiversity and climate crises by conserving at least 30% of lands and waters by 2030, 30x30, presents new opportunities to inform the siting of new protections globally and in the U.S. Here we identify climate refugia and corridors based on a weighted combination of currently available models; compare them to current biodiversity hotspots and carbon-rich areas to understand how 30x30 protections siting may be biased by data omission; and compare identified refugia and corridors to the Protected Areas Database to assess current levels of protection. Available data indicate that 20.5% and 27.5% of identified climate adaptation areas (refugia and/or corridor) coincides with current imperiled species hotspots and carbon-rich areas, respectively. With only 12.5% of climate refugia and corridors protected, a continued focus on current spatial patterns in species and carbon richness will not inherently conserve places critical for climate adaptation. However, there is ample opportunity for establishing future-minded protections: 52% of the contiguous U.S. falls into the top quartile of values for at least one class of climate refugia. Nearly 27% is already part of the protected areas network but managed for multiple uses that may limit their ability to contribute to the goals of 30x30. Additionally, nearly two-thirds of nationally identified refugia coincide with ecoregion-specific refugia suggesting representation of nearly all ecoregions in national efforts focused on conserving climate refugia. Based on these results, we recommend that land planners and managers make more explicit policy priorities and strategic decisions for future-minded protections and climate adaptation.

ecology↗

bioRxiv2021

Identifying key federal, state, and private lands strategies for achieving 30x30 in the US

Achieving ambitious conservation goals to conserve at least 30% of US lands and waters by 2030 ("30x30") will require a multi-scale baseline understanding of current protections, key decision makers, and policy tools for moving forward. To help conservationists and decision makers support the science-based call to address the biodiversity and climate crises, we analyze the current spatial patterns of imperiled species biodiversity and carbon stores in the U.S. relative to protected areas. Analyses demonstrate that 30x30 is numerically achievable nationally, but high spatial heterogeneity highlights the need for tailored approaches from a mix of authorities at federal, regional, and state scales. Critically, current land protections rarely overlap with areas essential for conserving imperiled species biodiversity and mitigating climate change. Nearly one-fifth of unprotected biodiversity hotspots and carbon-rich areas are also at risk of either land conversion or climate exposure by 2050. We discuss this baseline relative to key policy considerations for making practical, substantive progress toward the goal.

ecology↗

bioRxiv2021

Degradation of visible autumn icons and conservation opportunities: trends in deciduous forest loss in the contiguous US

Temperate deciduous forests are one of the most visible biomes on Earth because of their autumn aesthetics and because they harbor some of the most heavily populated regions. Their ability to attract visitors may increase opportunities for people to experience nature, which has been linked to greater conservation action. Identifying regions with high leaf-peeping opportunities and regions where color has been lost to landscape conversion may help to inform these connections. We use spatial overlay analyses to quantify temperate deciduous forest coverage, disturbance, and protections in each U.S. ecoregion. We evaluated recent (1984-2016) and predicted (2016-2050) disturbance under extreme future scenarios. Almost all ecoregions saw a decline in deciduous forest cover between 1985 and 2016. Some ecoregions with the greatest opportunities for leaf-peeping are also underrepresented in the protected areas network and vulnerable to additional losses. Under economic-growth forecasting scenarios, losses are predicted to continue. However, environmentally focused scenarios suggest there is still opportunity to reverse deciduous forest loss in some ecoregions. Differences in forest loss between predictions scenarios emphasize the importance of human approaches in securing environmental stability. Increasing public exposure to temperate forests may help ensure conservation of more natural areas and preserve the quantity and quality of autumn forest viewing. Key PointsO_LITemperate deciduous forests aesthetics attract visitors to experience nature, but degradation and loss can hinder connections. C_LIO_LIUS ecoregions with the greatest leaf-peeping opportunities are underrepresented in the protected areas and vulnerable to additional losses. C_LIO_LIDifferences in predictions scenarios emphasize the importance of conservation action, which may be linked to human connections with nature. C_LI

ecology↗

bioRxiv2020

Mountaintop Removal Mining Threatens the Survival and Recovery of Imperiled Species

Environmental laws need sound data to protect species and ecosystems. In 1996, a proliferation of mountaintop removal coal mines in a region home to over 50 federally protected species was approved under the Endangered Species Act. Although this type of mining can degrade terrestrial and aquatic habitats, the available data and tools limited the ability to analyze spatially extensive, aggregate effects of such a program. We used two large, public datasets to quantify the relationship between mountaintop removal coal mining and water quality measures important to the survival of imperiled species at a landscape scale across Kentucky, Tennessee, Virginia, and West Virginia. We combined an annual map of the extent of surface mines in this region from 1985 to 2015 generated from Landsat satellite imagery with public water quality data collected over the same time period from 4,260 monitoring stations within the same area. The water quality data show that chronic and acute thresholds for levels of aluminum, arsenic, cadmium, conductivity, copper, lead, manganese, mercury, pH, selenium, and zinc safe for aquatic life were exceeded thousands of times between 1985 and 2015 in streams that are important to the survival and recovery of species on the Endangered Species List. Linear mixed models showed that levels of manganese, sulfate, sulfur, total dissolved solids, total suspended solids, and zinc increased by 6.73E+01 to 6.87E+05 {micro}g/L and conductivity by 3.30E+06 {micro}S /cm for one percent increase in the mined proportion of the area draining into a monitoring station. The proportion of a drainage area that was mined also increased the likelihood that chronic thresholds for copper, lead, and zinc required to sustain aquatic life were exceeded. Finally, the proportion of a watershed that was mined was positively related to the likelihood that a waterway would be designated as impaired under the Clean Water Act. Together these results demonstrate that the extent of mountaintop removal mining, which can be derived from public satellite data, is predictive of water quality measures important to imperiled species - effects that must be considered under environmental law. These findings and the public data used in our analyses are pertinent to ongoing re-evaluations of the effects of current mine permitting regulations to the recovery and survival of federally protected species.

ecology↗

bioRxiv2020

Recovery units under the Endangered Species Act could be used more widely

Recovering species is one of the main goals of the Endangered Species Act (ESA). In the face of limited budgets, diverse tools are needed to find efficient solutions. Recovery units may be one such tool - designated portions of a species range that must be recovered individually before an entire species can be considered recovered. Recovery units allow for spatial flexibility in recovery goals and may be used in regulatory decisions such as section 7 consultation. Despite their availability, there is very little information on how recovery units have been developed and used. We mined available public data to determine the number and types of species for which recovery units have been designated; evaluated species and geographic characteristics associated with recovery unit designation; and examined how recovery units have been used in the implementation of the ESA, such as during consultation. We found 49 listed species have designated recovery units through 2017, and that these species had similar characteristics. Namely, they had relatively large ranges and were well-studied. We found taxonomic biases in recovery unit designation as well, with fish species being disproportionately likely to have recovery units and plants disproportionately less. Improvements in recovery priority numbers among species with recovery units indicate that the theoretical benefits of this tool may have translated to improved status. These data indicate that recovery units could be applied to more wide-ranging species to improve recovery under the ESA.

ecology↗

bioRxiv2020

Recovery plans need better science to support decisions that allow species to decline in abundance but be recovered

The U.S. Endangered Species Act (ESA) is widely considered the strongest biodiversity conservation law in the world. Part of its strength comes from the mandate to use the best available science to make decisions under the law, including whether to list a species, setting the criteria for when a species can be considered recovered, and determining when those criteria have been met and a species can be delisted. Both biological status and threat factors are considered at each stage of the listing and delisting process. In most cases, conservation science would suggest that species at risk enough to be listed under the Act should be more abundant and secure at delisting than they were at listing. Surprisingly, we identified 130 ESA-listed species that the U.S. Fish and Wildlife Service could consider recovered with fewer populations or individuals than existed at the time of listing. We ask whether their ESA recovery plans present scientific data, rationale, or evidence to support a decline in abundance as part of recovery. We find that almost no plan clearly explains why a decline is allowed. Fewer than half of the plans provide scientific support for a decline in the form of literature references or modeling results. We recommend that the U.S. Fish and Wildlife Service and the National Marine Fisheries Service create a decision support system to inform when species can decline in abundance and still recover, including guidance on (a) the need to explicitly address the declines and (b) the science used to support the decisions.

ecology↗

bioRxiv2019

Agency plans are inadequate to conserve US endangered species under climate change

Despite widespread evidence of climate change as a threat to biodiversity, it is unclear whether government policies and agencies are adequately addressing this threat to species1-4. We evaluate species sensitivity, a component of climate change vulnerability, and whether climate change is discussed as a threat in planning for climate-related management action in official documents from 1973-2018 for all 459 US animals listed as endangered under the Endangered Species Act. We find that 99.8% of species are sensitive to one or more of eight sensitivity factors, but agencies consider climate change as a threat to only 64% of species and plan management actions for only 18% of species. Agencies are more likely to plan actions for species sensitive to more factors, but such planning has declined since 2016. Results highlight the gap between climate change sensitivity and the attention from agencies charged with conserving endangered species.

ecology↗

bioRxiv2019

Automated Habitat Change Detection Methods using Satellite Data to Improve Conservation Law Implementation

A significant limitation in biodiversity conservation has been the effective implementation of laws and regulations that protect species habitats from degradation. Flexible, efficient, and effective monitoring and enforcement methods are needed to help conservation policies realize their full benefit. As remote sensing data become more numerous and accessible, they can be used to identify and quantify land cover changes and habitat loss. However, these data remain underused for systematic conservation monitoring in part because of a lack of simple tools. We adapted and developed two generalized methods that automatically detect land cover changes in a variety of habitat types using free and publicly available data and tools. We evaluated the performance of these algorithms in two ways. First, we tested the algorithms over 100 sites of known change in the United States, finding these approaches were effective (AUC > 0.90) at distinguishing between areas of land cover change and areas of no change. Second, we evaluated algorithm effectiveness by comparing results to manually identified areas of change in four case studies involving imperiled species habitat: oil and gas development in the range of the Greater Sage Grouse; sand mining operations in the range of the dunes sagebrush lizard; loss of Piping Plover coastal habitat in the wake of hurricane Michael (2018); and residential development in beach mouse habitat. The relative performance of each algorithm differed in each habitat type, but both provided effective means of detecting and delineating habitat loss. Our results show how these algorithms can be used to help close the implementation gap of monitoring and enforcement in biodiversity conservation and we provide a free online tool that can be used to run these analyses. Article impact statementMethods for automating the detection of habitat loss in satellite images that can be used to monitor and enforce conservation policy.

ecology↗

bioRxiv2019

30 years of satellite data show imperiled species are most vulnerable to habitat loss on private lands

To stem the ongoing loss of biodiversity, there is an urgent need to distinguish between effective and ineffective approaches for protecting species habitats. Using Google Earth Engine and 30 years of Landsat images, we quantify habitat change for 24 vertebrates on the U.S. Endangered Species List (ESA) and IUCN Red List across different categories of land ownership (e.g., federal, state, and private) that are subject to different conservation-focused legal restrictions. These estimates exclude changes due to agricultural conversion and burned areas. Imperiled species evaluated lost the least habitat (3.6%) on federal lands, while losses on private lands without conservation easements were more than twice as great (8.1%). Differences in annual percent loss before and after species were placed on the Endangered Species List, and between ESA and Red List species suggest that the ESA limited habitat loss and was most effective on federal lands. These results emphasize the importance of federal lands for protecting habitat for imperiled species and highlight the need to improve habitat protection on private lands for long-term conservation.

ecology↗

bioRxiv2018

Loci, genes, and gene networks associated with life history variation in a model ecological organism, Daphnia pulex (complex)

BackgroundIdentifying the molecular basis of heritable variation provides insight into the underlying mechanisms generating phenotypic variation and the evolutionary history of organismal traits. Life history trait variation is of central importance to ecological and evolutionary dynamics, and contemporary genomic tools permit studies of the basis of this variation in non-genetic model organisms. We used high density genotyping, RNA-Seq gene expression assays, and detailed phenotyping of fourteen ecologically important life history traits in a wild-caught panel of 32 Daphnia pulex clones to explore the molecular basis of trait variation in a model ecological species.\n\nResultsWe found extensive phenotypic and a range of heritable genetic variation (~0 < H2 < 0.44) in the panel, and accordingly identify 75-261 genes--organized in 3-6 coexpression modules--associated with genetic variation in each trait. The trait-related coexpression modules possess well-supported promoter motifs, and in conjunction with marker variation at trans- loci, suggest a relatively small number of important expression regulators. We further identify a candidate genetic network with SNPs in eight known transcriptional regulators, and dozens of differentially expressed genes, associated with life history variation. The gene-trait associations include numerous un-annotated genes, but also support several a priori hypotheses, including an ecdysone-induced protein and several Gene Ontology pathways.\n\nConclusionThe genetic and gene expression architecture of Daphnia life history traits is complex, and our results provide numerous candidate loci, genes, and coexpression modules to be tested as the molecular mechanisms that underlie Daphnia eco-evolutionary dynamics.

genomics↗

bioRxiv2018

The African Bullfrog (Pyxicephalus adspersus) genome unites the two ancestral ingredients formaking vertebrate sex chromosomes

Heteromorphic sex chromosomes have evolved repeatedly among vertebrate lineages despite largely deleterious reductions in gene dose. Understanding how this gene dose problem is overcome is hampered by the lack of genomic information at the base of tetrapods and comparisons across the evolutionary history of vertebrates. To address this problem, we produced a chromosome-level genome assembly for the African Bullfrog (Pyxicephalus adspersus)--an amphibian with heteromorphic ZW sex chromosomes--and discovered that the Bullfrog Z is surprisingly homologous to substantial portions of the human X. Using this new reference genome, we identified ancestral synteny among the sex chromosomes of major vertebrate lineages, showing that non-mammalian sex chromosomes are strongly associated with a single vertebrate ancestral chromosome, while mammals are associated with another that displays increased haploinsufficiency. The sex chromosomes of the African Bullfrog however, share genomic blocks with both humans and non-mammalian vertebrates, connecting the two ancestral chromosome sequences that repeatedly characterize vertebrate sex chromosomes. Our results highlight the consistency of sex-linked sequences despite sex determination system lability and reveal the repeated use of two major genomic sequence blocks during vertebrate sex chromosome evolution.

genomics↗