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Preserving reptiles for research

What are voucher specimens and why do we collect them? Voucher specimens are animals and/or their parts that are deposited in a research museum to document the occurrence of a taxon at a specific location in space and time (Pleijel et al., 2008; Reynolds and McDiarmid, 2012). For field biologists, vouchers are the repeatable element of a field study as they allow other biologists, now and in the future, to confirm the identity of species that were studied. The scientific importance of a voucher specimen or series of specimens is that other people are afforded the opportunity to examine the entire animal and confirm or correct identifications. A photographic record is somewhat useful for recording the occurrence of a species, but such records can be insufficient for reliable confirmation of specific identity. Even if a photo shows diagnostic characters of currently recognized taxa, it may not show characters that separate taxa that may be described in the future. Substantial cryptic biodiversity is being found in even relatively well-known herpetofaunas (Crawford et al., 2010), and specimens allow researchers to retroactively evaluate the true diversity in a study as understanding of taxonomy evolves. They enable biologists to study the systematic relationships of populations by quantifying variation in different traits. Specimens are also a source of biological data such as behaviour, ecology, epidemiology, and reproduction through examination of their anatomy, reproductive and digestive tracts, and parasites (Suarez and Tsutsui, 2004). Preserving reptiles as vouchers is not difficult, although doing it properly requires care, effort, and time. Poorly preserved vouchers can invalidate the results and conclusions of your study because of the inability to confirm the identity of your study animals. Good science requires repeatability of observations, and the absence of vouchers or poorly preserved ones prevents such confirmation. Due to space restrictions, we are unable to go into as much detail as we would like in this chapter. A number of publications give more details on some topics discussed in this chapter, such as Pisani (1973), Pisani and Villa (1974), Etheridge (1996), Karns (1986), McDiarmid (1994), Cortez et al. (2006), Foster (2012) (and subchapters therein), Reynolds and McDiarmid (2012), and Simmons (2015). Although some of these works focus on amphibians, they also apply to reptiles in many aspects.

Book chapter↗

High-precision 41K/39K measurements by MC-ICP-MS indicate terrestrial variability of δ41K

Potassium is a major component in continental crust, the fourth-most abundant cation in seawater, and a key element in biological processes. Until recently, difficulties with existing analytical techniques hindered our ability to identify natural isotopic variability of potassium isotopes in terrestrial materials. However, measurement precision has greatly improved and a range of K isotopic compositions has now been demonstrated in natural samples. In this study, we present a new technique for high-precision measurement of K isotopic ratios using high-resolution, cold plasma multi-collector mass spectrometry. We apply this technique to demonstrate natural variability in the ratio of 41 K to 39 K in a diverse group of geological and biological samples, including silicate and evaporite minerals, seawater, and plant and animal tissues. The total range in 41 K/ 39 K ratios is ca. 2.6‰, with a long-term external reproducibility of 0.17‰ (2, N=108). Seawater and seawater-derived evaporite minerals are systematically enriched in 41 K compared to silicate minerals by ca. 0.6‰, a result consistent with recent findings1, 2. Although our average bulk-silicate Earth value (-0.54‰) is indistinguishable from previously published values, we find systematic δ 41 K variability in some high-temperature sample suites, particularly those with evidence for the presence of fluids. The δ 41 K values of biological samples span a range of ca. 1.2‰ between terrestrial mammals, plants, and marine organisms. Implications of terrestrial K isotope variability for the atomic weight of K and K-based geochronology are discussed. Our results indicate that high-precision measurements of stable K isotopes, made using commercially available mass spectrometers, can provide unique insights into the chemistry of potassium in geological and biological systems.

Journal of Analytical Atomic Spectrometry↗

A metadata checklist and data formatting guidelines to make eDNA FAIR (Findable, Accessible, Interoperable and Reusable)

The success of environmental DNA (eDNA) approaches for species detection has revolutionized biodiversity monitoring and distribution mapping. Targeted eDNA amplification approaches, such as quantitative PCR, have improved our understanding of species distribution, and metabarcoding-based approaches have enabled biodiversity assessment at unprecedented scales and taxonomic resolution. eDNA datasets, however, are often scattered across repositories with inconsistent formats, varying access restrictions, and inadequate metadata; this limits their interoperation, reuse, and overall impact. Adopting FAIR (Findable, Accessible, Interoperable, and Reusable) data practices with eDNA data can transform the monitoring of biodiversity and individual species and support data-driven biodiversity management across broad scales. FAIR practices remain underdeveloped in the eDNA community, partly due to gaps in adapting existing vocabularies, such as Darwin Core (DwC) and Minimum Information about any (x) Sequence (MIxS), to eDNA-specific needs and workflows. To address these challenges, we propose a comprehensive FAIR eDNA (FAIRe) Metadata Checklist, which integrates existing data standards and introduces new terms tailored to eDNA workflows. Metadata are systematically linked to both raw data (e.g., metabarcoding sequences, Ct/Cq values of targeted qPCR assays) and derived biological observations (e.g., Amplicon Sequence Variant (ASV)/Operational Taxonomic Unit (OTU) tables, species presence/absence). Along with formatting guidelines, tools, templates, and example datasets, we introduce a standardized, ready-to-use approach for FAIR eDNA practices. Through broad collaboration, we seek to integrate these guidelines into established biodiversity and molecular data standards, promote journal data policies, and foster user-driven improvements and uptake of FAIR practices among eDNA data producers. In proposing this standardized approach and developing a long-term plan with key databases and data standard organizations, the goal is to enhance accessibility, maximize reuse, and elevate the scientific impact of these valuable biodiversity data resources.

Environmental DNA↗

Water resources data--Illinois, water year 2003

This annual Water-Data Report for Illinois contains current water year (Oct. 1, 2003, to Sept. 30, 2004) and historical data of discharge, stage, water quality and biology of streams; stage of lakes and reservoirs; levels and quality of ground water; and records of precipitation, air temperature, dew point, solar radiation, and wind speed. The current year's (2004) data provided in this report include (1) discharge for 177 surface-water gaging stations and for 10 crest-stage partial-record stations; (2) stage for 27 surface-water gaging stations; (3) stage for 8 reservoirs; (4) water-quality records for 7 surface-water stations; (5) sediment-discharge records for 16 surface-water stations; (6) water-level records for 14 ground-water wells; (7) precipitation records for 50 rain gages; (8) records of air temperature, dew point, solar radiation and wind speed for 1 meteorological station; and (9) biological records for 6 sample sites. Also included are miscellaneous data collected at various sites not in the systematic data-collection network. Data were collected and compiled as a part of the National Water Information System (NWIS) maintained by the U.S. Geological Survey in cooperation with Federal, State, and local agencies.

Water Data Report↗

Water Resources Data for Illinois - Water Year 2005 (Includes Historical Data)

This annual Water-Data Report for Illinois contains current water year (Oct. 1, 2004, to Sept. 30, 2005) and historical data of discharge, stage, water quality and biology of streams; stage of lakes and reservoirs; levels and quality of ground water; and records of precipitation, air temperature, dew point, solar radiation, and wind speed. The current year's (2005) data provided in this report include (1) discharge for 182 surface-water gaging stations and for 9 crest-stage partial-record stations; (2) stage for 33 surface-water gaging stations; (3) water-quality records for 10 surface-water stations; (4) sediment-discharge records for 14 surface-water stations; (5) water-level records for 98 ground-water wells; (6) water-quality records for 17 ground-water wells; (7) precipitation records for 48 rain gages; (8) records of air temperature, dew point, solar radiation and wind speed for 1 meteorological station; and (9) biological records for 6 sample sites. Also included are miscellaneous data collected at various sites not in the systematic data-collection network. Data were collected and compiled as a part of the National Water Information System (NWIS) maintained by the U.S. Geological Survey in cooperation with Federal, State, and local agencies.

Water Data Report↗

Critical uncertainties and research needs for the restoration and conservation of native lampreys in North America

We briefly reviewed the literature, queried selected researchers, and drew upon our own experience to describe some critical uncertainties and research needs for the conservation and restoration of native lampreys in North America. We parsed the uncertainties and research needs into five general categories: (1) population status; (2) systematics; (3) passage at dams, screens, and other structures; (4) species identification in the field; and (5) geneal biology and ecology. For each topic, we describe why the subject is important for lampreys, briefly smmarize our current state of knowledge, and discuss the key data or information gaps.

American Fisheries Society Symposium↗

Are all intertidal wetlands naturally created equal? Bottlenecks, thresholds and knowledge gaps to mangrove and saltmarsh ecosystems

Intertidal wetlands such as saltmarshes and mangroves provide numerous important ecological functions, though they are in rapid and global decline. To better conserve and restore these wetland ecosystems, we need an understanding of the fundamental natural bottlenecks and thresholds to their establishment and long-term ecological maintenance. Despite inhabiting similar intertidal positions, the biological traits of these systems differ markedly in structure, phenology, life history, phylogeny and dispersal, suggesting large differences in biophysical interactions. By providing the first systematic comparison between saltmarshes and mangroves, we unravel how the interplay between species-specific life-history traits, biophysical interactions and biogeomorphological feedback processes determine where, when and what wetland can establish, the thresholds to long-term ecosystem stability, and constraints to genetic connectivity between intertidal wetland populations at the landscape level. To understand these process interactions, research into the constraints to wetland development, and biological adaptations to overcome these critical bottlenecks and thresholds requires a truly interdisciplinary approach.

Biological Reviews↗

Stable isotopes of transition and post-transition metals as tracers in environmental studies

The transition and post-transition metals, which include the elements in Groups 3–12 of the Periodic Table, have a broad range of geological and biological roles as well as industrial applications and thus are widespread in the environment. Interdisciplinary research over the past decade has resulted in a broad understanding of the isotope systematics of this important group of elements and revealed largely unexpected variability in isotope composition for natural materials. Significant kinetic and equilibrium isotope fractionation has been observed for redox sensitive metals such as iron, chromium, copper, molybdenum and mercury, and for metals that are not redox sensitive in nature such as cadmium and zinc. In the environmental sciences, the isotopes are increasingly being used to understand important issues such as tracing of metal contaminant sources and fates, unraveling metal redox cycles, deciphering metal nutrient pathways and cycles, and developing isotope biosignatures that can indicate the role of biological activity in ancient and modern planetary systems.

Book↗

Ecosystem carbon stocks and sequestration potential of federal lands across the conterminous United States

Federal lands across the conterminous United States (CONUS) account for 23.5% of the CONUS terrestrial area but have received no systematic studies on their ecosystem carbon (C) dynamics and contribution to the national C budgets. The methodology for US Congress-mandated national biological C sequestration potential assessment was used to evaluate ecosystem C dynamics in CONUS federal lands at present and in the future under three Intergovernmental Panel on Climate Change Special Report on Emission Scenarios (IPCC SRES) A1B, A2, and B1. The total ecosystem C stock was estimated as 11,613 Tg C in 2005 and projected to be 13,965 Tg C in 2050, an average increase of 19.4% from the baseline. The projected annual C sequestration rate (in kilograms of carbon per hectare per year) from 2006 to 2050 would be sinks of 620 and 228 for forests and grasslands, respectively, and C sources of 13 for shrublands. The federal lands’ contribution to the national ecosystem C budget could decrease from 23.3% in 2005 to 20.8% in 2050. The C sequestration potential in the future depends not only on the footprint of individual ecosystems but also on each federal agency’s land use and management. The results presented here update our current knowledge about the baseline ecosystem C stock and sequestration potential of federal lands, which would be useful for federal agencies to decide management practices to achieve the national greenhouse gas (GHG) mitigation goal.

PNAS↗

Potential effects of structural controls and street sweeping on stormwater loads to the lower Charles River, Massachusetts

The water quality of the lower Charles River is periodically impaired by combined sewer overflows (CSOs) and non-CSO stormwater runoff. This study examined the potential non-CSO load reductions of suspended solids, fecal coliform bacteria, total phosphorus, and total lead that could reasonably be achieved by implementation of stormwater best management practices, including both structural controls and systematic street sweeping. Structural controls were grouped by major physical or chemical process; these included infiltration-filtration (physical separation), biofiltration-bioretention (biological mechanisms), or detention-retention (physical settling). For each of these categories, upper and lower quartiles, median, and average removal efficiencies were compiled from three national databases of structural control performance. Removal efficiencies obtained indicated a wide range of performance. Removal was generally greatest for infiltration-filtration controls and suspended solids, and least for biofiltration-bioretention controls and fecal coliform bacteria. Street sweeping has received renewed interest as a water-quality control practice because of reported improvements in sweeper technology and the recognition that opportunities for implementing structural controls are limited in highly urbanized areas. The Stormwater Management Model that was developed by the U.S. Geological Survey for the lower Charles River Watershed was modified to simulate the effects of street sweeping in a single-family land-use basin. Constituent buildup and washoff variable values were calibrated to observed annual and storm-event loads. Once calibrated, the street sweeping model was applied to various permutations of four sweeper efficiencies and six sweeping frequencies that ranged from every day to once every 30 days. Reduction of constituent loads to the lower Charles River by the combined hypothetical practices of structural controls and street sweeping was estimated for a range of removal efficiencies because of their inherent variability and uncertainty. This range of efficiencies, with upper and lower estimates, provides reasonable bounds on the load that could be removed by the practices examined. The upper estimated load reduction from combined street sweeping and structural controls, as a percentage of the total non-CSO load entering the lower Charles River downstream of Watertown Dam, was 44 percent for suspended solids, 34 percent for total lead, 14 percent for total phosphorus, and 17 percent for fecal coliform bacteria. The lower estimated load reduction from combined street sweeping and structural controls from non-CSO sources downstream of Watertown Dam, was 14 percent for suspended solids, 11 percent for total lead, 4.9 percent for total phosphorus, and 7.5 percent for fecal coliform bacteria. Load reductions by these combined management practices can be a small as 1.4 percent for total phosphorus to about 4 percent for the other constituents if the total load above Watertown Dam is added to the load from below the dam. Although the reductions in stormwater loads to the lower Charles River from the control practices examined appear to be minor, these practices would likely provide water-quality benefits to portions of the river during those times that they are most impaired-during and immediately after storms. It should also be recognized that only direct measurements of changes in stormwater loads before and after implementation of control practices can provide definitive evidence of the beneficial effects of these practices on water-quality conditions in the lower Charles River.

Massachusetts↗

The influence of coarse-scale environmental features on current and predicted future distributions of narrow-range endemic crayfish populations

1.A major limitation to effective management of narrow-range crayfish populations is the paucity of information on the spatial distribution of crayfish species and a general understanding of the interacting environmental variables that drive current and future potential distributional patterns. 2.Maximum Entropy Species Distribution Modeling Software (MaxEnt) was used to predict the current and future potential distributions of four endemic crayfish species in the Ouachita Mountains. Current distributions were modelled using climate, geology, soils, land use, landform and flow variables thought to be important to lotic crayfish. Potential changes in the distribution were forecast by using models trained on current conditions and projecting onto the landscape predicted under climate-change scenarios. 3.The modelled distribution of the four species closely resembled the perceived distribution of each species but also predicted populations in streams and catchments where they had not previously been collected. Soils, elevation and winter precipitation and temperature most strongly related to current distributions and represented 6587% of the predictive power of the models. Model accuracy was high for all models, and model predictions of new populations were verified through additional field sampling. 4.Current models created using two spatial resolutions (1 and 4.5km2) showed that fine-resolution data more accurately represented current distributions. For three of the four species, the 1-km2 resolution models resulted in more conservative predictions. However, the modelled distributional extent of Orconectes leptogonopodus was similar regardless of data resolution. Field validations indicated 1-km2 resolution models were more accurate than 4.5-km2 resolution models. 5.Future projected (4.5-km2 resolution models) model distributions indicated three of the four endemic species would have truncated ranges with low occurrence probabilities under the low-emission scenario, whereas two of four species would be severely restricted in range under moderatehigh emissions. Discrepancies in the two emission scenarios probably relate to the exclusion of behavioural adaptations from species-distribution models. 6.These model predictions illustrate possible impacts of climate change on narrow-range endemic crayfish populations. The predictions do not account for biotic interactions, migration, local habitat conditions or species adaptation. However, we identified the constraining landscape features acting on these populations that provide a framework for addressing habitat needs at a fine scale and developing targeted and systematic monitoring programmes.

Freshwater Biology↗

Ratcheting up rigor in wildlife management decision making

The wildlife management institution has been transforming to ensure relevance and positive conservation outcomes into the future. Continuous improvement of decision making is one aspect of this transformation, but many obstacles hinder systematic approaches to decision making. One can point to examples of formal decision science applications by state and federal agencies in the United States, but generally decision making is not as methodical as the biological, ecological, or social sciences that inform wildlife policy and management decisions. We describe our observations — based on first-hand experiences — with decision making in wildlife management, present reasons why making decisions is difficult, identify challenges faced by wildlife managers at various levels of governance, and address measures wildlife managers can employ to overcome these challenges. We acknowledge that no panacea, simple recipe or one-size-fits-all prescription exists for wildlife management decision making. Nevertheless, we hope the combination of (a) describing how a systematic framework for decision making can benefit stakeholders, managers and conservation outcomes and (b) providing specific suggestions for such a framework will encourage agencies to continue taking steps to improve decision making processes.

Wildlife Society Bulletin↗

Strategic Grassland Bird Conservation throughout the annual cycle: Linking policy alternatives, landowner decisions, and biological population outcomes

Grassland bird habitat has declined substantially in the United States. Remaining grasslands are increasingly fragmented, mostly privately owned, and vary greatly in terms of habitat quality and protection status. A coordinated strategic response for grassland bird conservation is difficult, largely due to the scope and complexity of the problem, further compounded by biological, sociological, and economic uncertainties. We describe the results from a collaborative Structured Decision Making (SDM) workshop focused on linking social and economic drivers of landscape change to grassland bird population outcomes. We identified and evaluated alternative strategies for grassland bird conservation using a series of rapid prototype models. We modeled change in grassland and agriculture cover in hypothetical landscapes resulting from different landowner decisions in response to alternative socio-economic conservation policy decisions. Resulting changes in land cover at all three stages of the annual cycle (breeding, wintering, and migration) were used to estimate changes in grassland bird populations. Our results suggest that successful grassland bird conservation may depend upon linkages with ecosystem services on working agricultural lands and grassland-based marketing campaigns to engage the public. With further development, spatial models that link landowner decisions with biological outcomes can be essential tools for making conservation policy decisions. A coordinated non-traditional partnership will likely be necessary to clearly understand and systematically respond to the many conservation challenges facing grassland birds.

PLoS ONE↗

Are we working towards global research priorities for management and conservation of sea turtles?

In 2010, an international group of 35 sea turtle researchers refined an initial list of more than 200 research questions into 20 metaquestions that were considered key for management and conservation of sea turtles. These were classified under 5 categories: reproductive biology, biogeography, population ecology, threats and conservation strategies. To obtain a picture of how research is being focused towards these key questions, we undertook a systematic review of the peer-reviewed literature (2014 and 2015) attributing papers to the original 20 questions. In total, we reviewed 605 articles in full and from these 355 (59%) were judged to substantively address the 20 key questions, with others focusing on basic science and monitoring. Progress to answering the 20 questions was not uniform, and there were biases regarding focal turtle species, geographic scope and publication outlet. Whilst it offers some meaningful indications as to effort, quantifying peer-reviewed literature output is obviously not the only, and possibly not the best, metric for understanding progress towards informing key conservation and management goals. Along with the literature review, an international group based on the original project consortium was assigned to critically summarise recent progress towards answering each of the 20 questions. We found that significant research is being expended towards global priorities for management and conservation of sea turtles. Although highly variable, there has been significant progress in all the key questions identified in 2010. Undertaking this critical review has highlighted that it may be timely to undertake one or more new prioritizing exercises. For this to have maximal benefit we make a range of recommendations for its execution. These include a far greater engagement with social sciences, widening the pool of contributors and focussing the questions, perhaps disaggregating ecology and conservation.

Endangered Species Research↗

Social and biological perspectives to investigate and address illegal shooting of raptors

Humans have shot raptors for centuries. However, in many countries these actions have been illegal since the mid-twentieth century. Despite this history, there is not a comprehensive understanding of the characteristics of this activity, its frequency, and why it occurs. We used literature review and principles drawn from ecology, sociology, and criminology to understand this problem. First, we review literature on raptor shooting globally to explore documented motivations for shooting and we describe the history of raptor shooting in the United States of America (USA). Then, to illustrate the contemporary frequency and geographic breadth of the shooting of raptors, we systematically compile records from scientific and media reports from across the USA. Finally, we outline a transdisciplinary framework to meet the challenge of understanding and managing illegal shooting of raptors. Our framework encompasses six best practices: (1) understand the biology of the problem, (2) build professional networks and partnerships, (3) leverage engagement and public support, (4) apply insights from study of human-wildlife interactions, (5) draw lessons from criminology, and (6) use implementation science to evaluate outcomes. We illustrate application of these best practices with a case study from an Illegal Shooting Working Group recently formed in Boise, Idaho, USA. There is growing recognition that illegal shooting of raptors is a pressing conservation challenge. Solving this challenge can be facilitated by inclusion of information from multiple fields of study; the approach we outline provides one potential mechanism to address this issue.

Global Ecology and Conservation↗

Geospatial characteristics of Florida's coastal and offshore environments: Distribution of important habitats for coastal and offshore biological resources and offshore sand resources

The Geospatial Characteristics GeoPDF of Florida's Coastal and Offshore Environments is a comprehensive collection of geospatial data describing the political boundaries and natural resources of Florida. This interactive map provides spatial information on bathymetry, sand resources, and locations of important habitats (for example, Essential Fish Habitats (EFH), nesting areas, strandings) for marine invertebrates, fish, reptiles, birds, and marine mammals. The map should be useful to coastal resource managers and others interested in marine habitats and submerged obstructions of Florida's coastal region. In particular, as oil and gas explorations continue to expand, the map can be used to explore information regarding sensitive areas and resources in the State of Florida. Users of this geospatial database will have access to synthesized information in a variety of scientific disciplines concerning Florida's coastal zone. This powerful tool provides a one-stop assembly of data that can be tailored to fit the needs of many natural resource managers. The map was originally developed to assist the Bureau of Ocean Energy Management, Regulation, and Enforcement (BOEMRE) and coastal resources managers with planning beach restoration projects. The BOEMRE uses a systematic approach in planning the development of submerged lands of the Continental Shelf seaward of Florida's territorial waters. Such development could affect the environment. BOEMRE is required to ascertain the existing physical, biological, and socioeconomic conditions of the submerged lands and estimate the impact of developing these lands. Data sources included the National Oceanic and Atmospheric Administration, BOEMRE, Florida Department of Environmental Protection, Florida Geographic Data Library, Florida Fish and Wildlife Conservation Commission, Florida Natural Areas Inventory, and the State of Florida, Bureau of Archeological Research. Federal Geographic Data Committee (FGDC) compliant metadata are provided as attached xml files for all geographic information system (GIS) layers.

Florida↗

Ca cycling and isotopic fluxes in forested ecosystems in Hawaii

Biogeochemical processes fractionate Ca isotopes in plants and soils along a 4 million year developmental sequence in the Hawaiian Islands. We observed that plants preferentially take up 40Ca relative to 44Ca, and that biological fractionation and changes in the relative contributions from volcanic and marine sources produce a significant increase in 44Ca in soil exchangeable pools. Our results imply moderate fluxes enriched in 44Ca from strongly nutrient-depleted old soils, in contrast with high 40Ca fluxes in young and little weathered environments. In addition, biological fractionation controls divergent geochemical pathways of Ca and Sr in the plant-soil system. While Ca depletes progressively with increasing soil age, Sr/Ca ratios increase systematically. Sr isotope ratios provide a valuable tracer for provenance studies of alkaline earth elements in forested ecosystems, but its usefulness is limited when deciphering biogeochemical processes involved in the terrestrial Ca cycle. Ca isotopes in combination with Sr/ Ca ratios reveal more complex processes involved in the biogeochemistry of Ca and Sr. Copyright 2005 by the American Geophysical Union.

Geophysical Research Letters↗

Bile salts as semiochemicals in fish

Bile salts are potent olfactory stimuli in fishes; however the biological functions driving such sensitivity remain poorly understood. We provide an integrative review of bile salts as semiochemicals in fish. First, we present characteristics of bile salt structure, metabolism, and function that are particularly relevant to chemical communication. Bile salts display a systematic pattern of structural variation across taxa, are efficiently synthesized, and are stable in the environment. Bile salts are released into the water via the intestine, urinary tract, or gills, and are highly water soluble. Second, we consider the potential role of bile salts as semiochemicals in the contexts of detecting nearby fish, foraging, assessing risk, migrating, and spawning. Lastly, we suggest future studies on bile salts as semiochemicals further characterize release into the environment, behavioral responses by receivers, and directly test the biological contexts underlying olfactory sensitivity.

Chemical Senses↗