Jacob W. Malcom

Habitat Associations of the San Bernardino Springsnail, Pyrgulopsis bernardina (Hydrobiidae)

ABSTRACT We studied a critically-endangered hydrobiid snail, Pyrgulopsis bernardina, in Snail Spring, Cochise County, Arizona. We determined the relationships between its abundance and a suite of habitat variables and document formerly-occupied sites. Using Akaikes Information Criterion for model selection and averaging, 14 models were defined a priori using eight habitat variables to explain its abundance. All biologically supported predictors, in the first order, provided the most parsimonious explanation of P. bernardina densities. Structural variables received stronger support than physicochemical variables. P. bernardina densities were positively associated with sand and cobble substrates, vegetation density, water velocity, and dissolved oxygen, as well as water temperatures of 14–22°C and pH values between 7.6 and 8.0. Snail densities were negatively associated with silt and organic substrates, deep water, and high conductance. The current and all former localities for P. bernardina are associated with a shallow aquifer that is distinct from an adjacent deep aquifer.

Data contradict common perceptions about a controversial provision of the US Endangered Species Act

Significance The US Endangered Species Act is the most comprehensive law any nation has enacted to protect imperiled species. Many of its protections come from section 7 of the Act, but how government regulators use this tool is poorly understood. Our analysis is the first to systematically evaluate how the US Fish and Wildlife Service has implemented section 7 over an extend timeframe and across all listed species. The results inform current efforts to improve the conservation effectiveness of section 7 and rebut certain claims about the regulatory burdens of complying with section 7. Separating myth and reality is essential for evaluating the effectiveness of laws. Section 7 of the US Endangered Species Act (Act) directs federal agencies to help conserve threatened and endangered species, including by consulting with the US Fish and Wildlife Service (FWS) or National Marine Fisheries Service on actions the agencies authorize, fund, or carry out. Consultations ensure that actions do not violate the Act’s prohibitions on “jeopardizing” listed species or “destroying or adversely modifying” these species’ critical habitat. Because these prohibitions are broad, many people consider section 7 the primary tool for protecting species under the Act, whereas others believe section 7 severely impedes economic development. This decades-old controversy is driven primarily by the lack of data on implementation: past analyses are either over 25 y old or taxonomically restricted. We analyze data on all 88,290 consultations recorded by FWS from January 2008 through April 2015. In contrast to conventional wisdom about section 7 implementation, no project was stopped or extensively altered as a result of FWS finding jeopardy or adverse modification during this period. We also show that median consultation duration is far lower than the maximum allowed by the Act, and several factors drive variation in consultation duration. The results discredit many of the claims about the onerous nature of section 7 but also raise questions as to how federal agencies could apply this tool more effectively to conserve species. We build on the results to identify ways to improve the effectiveness of consultations for imperiled species conservation and increase the efficiency of consultations.

A simple, sufficient, and consistent method to score the status of threats and demography of imperiled species

Managers of large, complex wildlife conservation programs need information on the conservation status of each of many species to help strategically allocate limited resources. Oversimplifying status data, however, runs the risk of missing information essential to strategic allocation. Conservation status consists of two components, the status of threats a species faces and the species’ demographic status. Neither component alone is sufficient to characterize conservation status. Here we present a simple key for scoring threat and demographic changes for species using detailed information provided in free-form textual descriptions of conservation status. This key is easy to use (simple), captures the two components of conservation status without the cost of more detailed measures (sufficient), and can be applied by different personnel to any taxon (consistent). To evaluate the key’s utility, we performed two analyses. First, we scored the threat and demographic status of 37 species recently recommended for reclassification under the Endangered Species Act (ESA) and 15 control species, then compared our scores to two metrics used for decision-making and reports to Congress. Second, we scored the threat and demographic status of all non-plant ESA-listed species from Florida (54 spp.), and evaluated scoring repeatability for a subset of those. While the metrics reported by the U.S. Fish and Wildlife Service (FWS) are often consistent with our scores in the first analysis, the results highlight two problems with the oversimplified metrics. First, we show that both metrics can mask underlying demographic declines or threat increases; for example, ∼40% of species not recommended for reclassification had changes in threats or demography. Second, we show that neither metric is consistent with either threats or demography alone, but conflates the two. The second analysis illustrates how the scoring key can be applied to a substantial set of species to understand overall patterns of ESA implementation. The scoring repeatability analysis shows promise, but indicates thorough training will be needed to ensure consistency. We propose that large conservation programs adopt our simple scoring system for threats and demography. By doing so, program administrators will have better information to monitor program effectiveness and guide their decisions.

Data indicate the importance of expert agencies in conservation policy.

Data on the implementation of laws and policies are essential to the evaluation and improvement of governance. For conservation laws like the U.S. Endangered Species Act (ESA), such data can inform actions that may determine the persistence or extinction of species. A central but controversial part of the ESA is section 7, which requires federal agencies to conserve threatened and endangered species. One way they do this is by consulting with expert agencies for the ESA, the U.S. Fish and Wildlife Service (FWS) and the National Marine Fisheries Service (NMFS), on actions they may undertake that impact listed species. Using data from all 24,893 consultations recorded by NMFS from 2000 through 2017, we show that federal agencies misestimated the effects of their actions on listed species in 21% of consultations, relative to the conclusions reached by NMFS. In 71% of these cases the federal agency underestimated the effects of their action. Those discrepancies were particularly important for the conservation of 14 species in 22 consultations, where the agency concluded that its action would not harm a species, while NMFS determined the action would jeopardize the species’ existence. Patterns of misestimation varied among federal agencies, and some of the agencies most frequently involved in consultation also frequently misestimated their effects. Jeopardy conclusions were very rare—about 0.3% of consultations—with a few project types more likely to lead to jeopardy. These data highlight the importance of consultation with the expert agencies and reveal opportunities to make the consultation process more effective. SIGNIFICANCE STATEMENT The US Endangered Species Act is the strongest environmental law any nation has enacted to conserve imperiled species. However, policy debates over how the Act should be implemented continue to this day. This study provides the first comprehensive evaluation of how the National Marine Fisheries Service (NMFS) implements one of the Act’s most important conservation programs – consultations under section 7. Our results reveal novel insights into the importance of NMFS role in ensuring federal actions do not jeopardize the existence of listed species. By using data to inform policy debate, we identify approaches to implementing section 7 that would undermine the conservation of imperiled species, and those that could improve the efficiency of the program without sacrificing these protections.

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

Background Identifying 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. Results We 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. Conclusion The 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.

Same law, different results: comparative analysis of Endangered Species Act consultations by two federal agencies

Evaluating how wildlife conservation laws are implemented is critical for safeguarding biodiversity. Two agencies, the U.S. Fish and Wildlife Service and National Marine Fisheries Service (FWS and NMFS; Services collectively), are responsible for implementing the U.S. Endangered Species Act (ESA), which requires federal protection for threatened and endangered species. FWS and NMFS’ comparable role for terrestrial and marine taxa, respectively, provides the opportunity to examine how implementation of the same law varies between agencies. We analyzed how the Services implement a core component of the ESA, section 7 consultations, by objectively assessing the contents of >120 consultations on sea turtle species against the requirements in the Services’ consultation handbook, supplemented with in-person interviews of Service biologists. Our results showed that NMFS consultations were 1.40 times as likely to have higher quality scores than FWS consultations. Consultations tiered from an FWS programmatic consultation inherited the higher quality scores of the programmatic consultation, indicating that programmatic consultations could increase the efficiency of the section 7 process. Both agencies commonly neglected to account for the effects of previous consultations and the potential for compounded effects on species. From these results, we recommend actions that can improve quality of consultations, such as a single database to track and integrate previously authorized harm in new analyses and the careful but more widespread use of programmatic consultations. Our study reveals several critical shortfalls in the current process of conducting ESA section 7 consultations that the Services could address to better safeguard North America’s most imperiled species.

Free Aerial Imagery as a Resource to Monitor Compliance with the Endangered Species Act

Compliance monitoring is an integral part of law and policy implementation. A lack of compliance monitoring for the Endangered Species Act (ESA), driven in part by resource limitations, may be undercutting efforts to recover threatened and endangered species. Here we evaluate the utility of freely available satellite and aerial imagery as a cost-efficient component of ESA compliance monitoring. Using data on actions authorized by the U.S. Fish and Wildlife Service (FWS) under section 7 of the ESA, we show that approximately 40% of actions can be found in remotely sensed imagery. Some types of actions, such as residential and commercial development, roadwork, and forestry, show substantially higher observability. Based on our results and the requirements of compliance monitoring, we recommend FWS standardize data collection requirements for consultations; record and publish terms and conditions of consultations; and encourage their staff to use technology such as remotely sensed data as a central part of their workflow for implementing the ESA.

Reply to Weiland et al.: The point is to bring data to inform policy, not to rely solely on anecdotes

We appreciate the response to our paper (1) from Weiland et al. (2). Rather than a point-by-point rebuttal, we focus our reply on three fundamental issues in their response.

Livestock Trampling and Lilaeopsis schaffneriana Var. Recurva (Brassicaceae)

Lilaeopsis schaffneriana var. recurva (Hill) Affolter, is a small aquatic to semi-aquatic plant restricted to mid-elevation cienega and riparian margins in southeastern Arizona and northwestern Sonora (Hendrickson and Minckley 1984). It was listed as Endangered in 1997 under the Endangered Species Act of 1973 (as amended) because of ‘‘degradation and destruction of habitat resulting from livestock overgrazing, water diversions, dredging, and groundwater pumping’’ (USFWS 1997). Trampling and overgrazing by livestock are commonly cited as threats to this species, however, we have found no documented cases or quantification of livestock effects. Herein, we document and quantify the effect of trampling by trespass livestock on Lilaeopsis schaffneriana var. recurva in Leslie Canyon National Wildlife Refuge, Cochise County, Arizona. During 2003, we established a pilot monitoring program for Lilaeopsis schaffneriana var. recurva, which occupied 12 distinct patches in Leslie Canyon National Wildlife Refuge. The protocol required taking multiple, cross-patch measurements of each patch and plotting the measurements on simplified drawings of the patches. The diagrams were then taken back to the lab, scaled polygons were drawn in TurboCAD (IMSI 2002), and from these polygons the area of each patch was estimated. The sum of the individual patch areas is the total area occupied. The trampling effect of trespass livestock was assessed in the same manner, where portions of patches destroyed by livestock were measured, described as polygons with area calculations, and summed across all trampled areas. All patch measurements were completed on 13 Jun 2003. Total area occupied by ten Lilaeopsis schaffneriana var. recurva patches along Leslie Creek was 27.11 m; individual patches averaged 2.71 m (SD 5 2.54). On 6 Jul 2004, a trespass bull entered Leslie Canyon National Wildlife Refuge and spent 4 d within the riparian area; it appeared that most of the individual’s time was spent away from the Lilaeopsis patches. During the time that the bull spent around the Lilaeopsis patches, 1.47 m (5.4% of the total area occupied) were lost to trampling. This event allowed us to quantify the effect of a single livestock individual on Lilaeopsis schaffneriana var. recurva, over a span of only 4 d. Even though resource use patterns by livestock could leave some patches unaffected, the damage caused by this single individual indicates that even a small number of livestock could eradicate most of the Leslie Creek Lilaeopsis population in several days to weeks. Therefore, based on the negative effect caused by this short-term event, our conclusion is that livestock should be excluded from areas occupied by Lilaeopsis schaffneriana var. recurva.