A guide to constructing and understanding synonymies for mammalian species
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No abstract available.
No abstract available.
The purpose of this chapter is to provide an overview of the ecotoxicology of major classes of environmental contaminants, with respect to sources, environmental chemistry, most likely routes of exposure, potential bioaccumulation and biomagification, mechanisms of toxicity, and effects on potentially vulnerable species of mammalian wildlife. Major contaminants reviewed were selected on the basis of their use patterns, availability and potential toxicity to wild mammals. These included pesticides used in agroecosystems (organochlorines, organophosphorus and carbamate compounds, anticoagulants, herbicides and fungicides), various organic pollutants (chlorobenzenes, chlorophenols, polychlorinated biphenyls, dibenzodioxins and dibenzofurans, and polycyclic aromatic hydrocarbons), heavy metals (lead, mercury, and cadmium), agricultural drainwater mixtures, leachates and radionuclides. Many of the above aspects of ecotoxicology and contaminants will be expanded upon in subsequent chapters of this book as they relate to distinct mammalian species and potential risk.
The reptile team conducted a 21 kilometre transect from the coast east of Asau to the uplands ending near Mauga Silisili at over 1720 m elevation. This transect covered the main habitats on Savai’i and allowed the team to determine where various reptile species and invasive species occurred across this elevational gradient. No previous reptile research had taken place on Savai’i above the elevation of A’opo Village. Limited sampling was also done around the Forestry Station in Asau. The team detected 11 species of lizards during these surveys, which is the majority of species known from Samoa. Noticeably absent was the Pacific black skink (Emoia nigra), which is a dominant element of the Samoan lizard fauna. Also no individuals of the Pacific boa (Candoia bibroni) were detected despite the concentrated effort spent looking for them. One boa was detected by the avifauna team at their Site 1, by the TV tower on a log in a marsh. The invasive house gecko (Hemidactylus frenatus) was also not detected along the main transect, but was the most abundant gecko on buildings in Asau. No reptiles were found above 1320 m elevation and most species were found significantly below there. Snakeeyed skinks (Cryptoblepharus poecilopleurus) were detected on Savai’i for the first time at Asau Getaway Resort then above the sawmill on the way to A’opo. Since western Savai’i is so poorly known for reptiles, this is the first time many of these species were recorded from this part of the island. Surveys for invasive species detected mammalian species (cats, rats, and pigs) and invertebrate species (Yellow Crazy ants and Big-headed ants). The mammals were found at various sites along the transect, including high elevations. The ants were found at lower elevations along the transect, but the Yellow Crazy ants appear to be irrupting currently on Savai’i and were swamping our traps from sea level to 500 m elevation. The low elevation lizard occurrences from sea level to 500 m appeared impaired by the invasive ants. Although habitat looked good in many places along the transect, certain species were rare or absent when the invasive ants were present, e.g. the Samoan skink (Emoia samoensis) which only occurred at elevations higher than the ants, whereas elsewhere in its range it occurs down to sea level. Currently the uplands over 500 m are free of invasive ants. We know from Hawai’i that invasive ants occur to over 2,000 m elevation and are ecologically very destructive to native flora and fauna. There is an immediate need to try to stop this upward ant invasion to protect this at-risk ecosystem, and to study the intact system now prior to an invasion.
Douglass Creek basin lies west of the Continental Divide in the northern part of the Rocky Mountain physiographic province. Numerous minor environmental differences exist between the Douglass Creek area and the Pipestone Springs and Canyon Ferry areas east of the Divide. In the 19th century, however, the three areas had identical mammalian species representation, although not equally dense populations. Fossils of an early Oligocene biota have been collected from the Douglass Creek basin . Presence of all but one of the Douglass Creek mammalian species in the Pipestone Springs-Canyon Ferry early Oligocene fauna suggests that the three ancient ecosystems resembled each other in much the same way as the 19th century systems. The early Oligocene deposits and biota of the Douglass Creek basin indicate a moist, temperate climate with seasonal variations. Sediment size and distribution suggest that the cross-valley relief was no greater than it is now. The fish and invertebrate faunas show that a shallow, hard-water lake existed in the area. The flora included a lowland, lake-border association and an upland coniferous forest. Although the ancient Douglass Creek biota doubtless included many species not represented in the fossil collections, most of the mammalian species are probably represented in the combined Douglass Creek , Pipestone Springs, and Canyon Ferry fossil assemblages. If so, the number of mammalian species was about the same as in the 19th century ecosystem.
Sequence-based species identification relies on the extent and integrity of sequence data available in online databases such as GenBank. When identifying species from a sample of unknown origin, partial DNA sequences obtained from the sample are aligned against existing sequences in databases. When the sequence from the matching species is not present in the database, high-scoring alignments with closely related sequences might produce unreliable results on species identity. For species identification in mammals, the cytochrome b (cyt b ) gene has been identified to be highly informative; thus, large amounts of reference sequence data from the cyt b gene are much needed. To enhance availability of cyt b gene sequence data on a large number of mammalian species in GenBank and other such publicly accessible online databases, we identified a primer pair for complete cyt b gene sequencing in mammals. Using this primer pair, we successfully PCR amplified and sequenced the complete cyt b gene from 40 of 44 mammalian species representing 10 orders of mammals. We submitted 40 complete, correctly annotated, cyt b protein coding sequences to GenBank. To our knowledge, this is the first single primer pair to amplify the complete cyt b gene in a broad range of mammalian species. This primer pair can be used for the addition of new cyt b gene sequences and to enhance data available on species represented in GenBank. The availability of novel and complete gene sequences as high-quality reference data can improve the reliability of sequence-based species identification.
Commercial tree plantations of fast-growing species have become increasingly important in Southeast Asia to meet global demand for wood and wood fiber products. There is a growing need to understand more about their value for wildlife and how they can be managed for biodiversity. We evaluated the effects of landscape attributes on mammal communities in a timber concession consisting of 83 % secondary forest and 17 % tree plantations in northern Sabah, Malaysia. Using camera traps, we compared mammalian species assemblages of secondary forest and commercial tree plantation stands and identified habitat predictors associated with total mammal species detections and species richness in the landscape mosaic. We used 87 camera stations deployed for 23 days across two major land-use types: 62 sites in secondary forest (previously logged natural forest) and 25 sites in tree plantations. We evaluated variation in species richness in these two major land-use categories and assessed the effects of natural and anthropogenic predictors on variation in total mammal detections and species richness. We detected at least 23 large and medium-sized mammal species over 2035 trap nights. Fourteen of those species were classified as threatened or near-threatened by the International Union for the Conservation of Nature. Rarefaction did not reveal differences in mammal species richness or diversity between camera sites placed in tree plantations and secondary forests, likely because most camera sites in tree plantations were close to secondary forest and comprised < 30 % of all sites. However, generalized linear models indicated lower mammal diversity as proportions of tree plantation and proximity to human settlements increased. Total mammal records, including those of threatened mammals, increased with greater proportions of secondary forest. Retention of larger tracts of secondary forest around plantation areas appears to be important to maintain mammalian species richness and contributes to the conservation value of commercial timber plantations. These findings may assist in the management of mammals of conservation concern and implementation of adaptive management plans to enhance biodiversity conservation in commercial plantations.
The introduction of HPAI H5N1 clade 2.3.4.4b viruses to North America in late 2021 resulted in avian influenza outbreaks in poultry, mortality events in many wild bird species, and spillover into many mammalian species. Reassortment events with North American low pathogenic virus were identified as early as February 2022 and over 100 genotypes have been characterized. Such diversity increases the complexity and time required for monitoring virus evolution. Here, we performed ordination and clustering analyses on sequence data from H5N1 viruses identified in North America between January 2020 to December 2023 to visualize virus genotypic diversity in poultry and wildlife populations. Our results reveal that ordination and cluster-based approaches can complement traditional phylogenetic analyses specifically for the preliminary assignment of H5N1 viruses to genotypic groups or to identify novel genotypes. Our study expands current knowledge on genotype diversity of H5N1 viruses in North America and describes a rapid approach for early virus genotype assignment.
Mountain pine beetle ( Dendroctonus ponderosae ) (MPB) outbreaks are increasingly prevalent in western North America, causing considerable ecological change in pine ( Pinus spp.) forests with important implications for wildlife. We reviewed studies examining wildlife responses to MPB outbreaks and postoutbreak salvage logging to inform forest management and guide future research. Our review included 16 studies describing MPB outbreak relationships with 89 bird species and 6 studies describing relationships with 11 mammalian species, but no studies of reptiles or amphibians. We included studies that compared wildlife response metrics temporally (before versus after the outbreak) and spatially (across sites that varied in severity of outbreak) in relation to beetle outbreaks. Outbreaks ranged in size from 20,600 to ≥10 7 ha and studies occurred 1‐30 years after the peak MPB outbreak, but most studies were conducted over the short-term (i.e., ≤6 years after the peak of MPB-induced tree mortality). Birds were the only taxa studied frequently; however, high variability existed among those studies to allow many inferences, although some patterns were evident. Avian studies concluded that cavity-nesting species responded more favorably to beetle-killed forests than species with open-cup nests, and species nesting in the shrub layer favored outbreak forests compared with ground and open-cup canopy nesters that generally showed mixed relationships. Bark-drilling species as a group clearly demonstrated a positive short-term association with MPB epidemics compared with that of other foraging assemblages. Cavity-nesting birds that do not consume bark beetles (i.e., secondary cavity-nesting species and nonbark-drilling woodpeckers) also exhibited some positive responses to MPB outbreaks, although not as pronounced or consistent as those of bark-drilling woodpeckers. Mammalian responses to MPB outbreaks were mixed. Studies consistently reported negative effects of MPB outbreaks on red squirrels ( Tamiasciurus hudsonicus ). However, there is evidence that red squirrels can persist after an outbreak under some conditions, e.g., when nonhost tree species are present. For small mammal species associated with forest understories, responses may be most pronounced during the postepidemic period (>6 years after the peak of beetle-induced tree mortality) when snags fall to produce coarse woody debris. Postoutbreak salvage logging studies ( n = 6) reported results that lacked consensus. Postoutbreak salvage logging may have an impact on fewer wildlife species than postfire salvage logging, probably because only host-specific tree species are removed after beetle outbreaks.
Exploring trends in species richness and the distribution of individual species over time as well as the factors affecting these trends informs conservation priorities in protecting species and ecosystems as a whole. We used data from 41 park-wide line transect surveys in 2009 and 2014 and multi-season occupancy models with multi-species data to explore trends in species richness and distribution of individual species and factors affecting these trends in Nyungwe National Park (NNP), Rwanda. Mammalian species richness and the distributional range of 5 of the 7 species increased between 2009 and 2014 in NNP. The probability of colonization of a species into a new area in 2014, where it was not present in 2009, was highest in sites with a lower probability of poaching activity, close to tourist trails, and at lower elevations. The probability of colonization with no poaching activity was about 50% but dropped to about 10% with a 100% chance of poaching activity. Duiker species had the largest increase in distribution during the study, while there was a decrease in the distribution of the eastern chimpanzee and blue monkey. Our results suggest that increased patrols should be implemented in areas of the park with low species richness and areas with a low probability of occurrence for species of conservation concern to combat poaching activity and thus increase the probability of a species moving into a new area. Our use of a single multi-season model for multiple species explicitly accounts for imperfect detection and species-specific identities, while allowing for inferences to be made about rarely detected species by sharing covariates with common species. These results can be used to improve conservation planning in NNP for species management and ranger patrol protocols and our modelling framework is broadly applicable to any protected area with presence/absence species field data.
An international group of 32 scientists has critically reviewed the scientific literature on exposure and effects of environmental contaminants in wild mammals. Although the absolute number of toxicological studies in domesticated and wild mammals eclipses that for birds, a detailed examination of scientific publications and databases reveal that information for 'wild' birds is actually greater than that for 'wild' mammals. Of the various taxa of mammals, ecotoxicological data is most noticeably lacking for marsupials and monotremes. In contrast, rodents (comprising 43% of all mammal species) have been studied extensively, despite evidence of their tolerance to some organochlorine compounds, rodenticides, and even radionuclides. Mammalian species at greatest risk of exposure include those that consume a high percentage of their body weight on a daily basis (e.g., shrews, moles and bats). Aquatic mammals tend to bioaccumulate tremendous burdens of lipophilic contaminants, although storage in their fat depots may actually limit toxicity. Carnivores appear to be more sensitive to adverse effects of environmental contaminants than herbivores. Remarkably few of the thousands of compounds manufactured worldwide have been toxicologically evaluated in wild mammals, and concentrations of even fewer have been monitored in tissues. Overarching research needs include: development of new exposure/effects models and better methods for estimation of species sensitivities; generation of comparative data on contaminant bioavailability, sublethal responses and detoxication mechanisms; enhanced understanding of pesticide, industrial contaminant and metal interactions; identification of endocrine disruptive contaminants and their overall ecological significance; and finally, estimating the relative contribution of environmental contamination as a factor affecting wild mammal populations.
Vicuñas ( Vicugna vicugna ) and guanacos ( Lama guanicoe ) are the two species of wild South American camelids whose distributions range from Peru to northern Argentina and southern Peru to southern Argentina, respectively. Listed as critically endangered in the 1960s due to poaching, vicuña numbers had been gradually recovering; however, new concerns about population stability have arisen with recent observations of sarcoptic mange outbreaks in this species. Sarcoptic mange is an infectious skin disease caused by the microscopic burrowing mite, Sarcoptes scabiei , which infects nearly 150 mammalian species globally, including guanaco and vicuña. Wild camelid populations across Argentina, Bolivia, Chile, and Peru have been affected by sarcoptic mange, with the most severe outbreaks resulting in localized extirpation. Population declines have conservation and economic implications, as many local communities harvest vicuña and guanaco fiber for profit. We review the current literature on sarcoptic mange in wild camelids from Argentina, Bolivia, Chile, and Peru to establish a current state of knowledge on spatial prevalence, management, and therapeutics, and identify existing knowledge gaps. Critical next steps include 1) implementation of effective management strategies that limit the transmission of sarcoptic mange, 2) standardization of data collected during community capture (i.e., chaccu) events, 3) assessing the potential role of community captures in mite transmission, and 4) evaluation of treatment options and best practices for implementation. Further, there is a need for capacity building to improve disease diagnostics and surveillance in wild camelids. A multisectoral collaboration between governmental authorities, communities, academic institutions, and national and international organizations focusing on wild South American camelid conservation could contribute to building actions aimed at preventing future outbreaks and mitigating the current burden of sarcoptic mange disease.
The phenomenon of 'acid rain' is not new; it was recognized in the mid-1800s in industrialized Europe. In the 1960s a synthesis of information about acidification began in Europe, along with predictions of ecological effects. In the U.S. studies of acidification began in the 1920s. By the late 1970s research efforts in the U.S. and Canada were better coordinated and in 1980 a 10-year research program was undertaken through the National Acid Precipitation Assessment Plan (NAPAP) to determine the causes and consequences of acidic depositions. Much of the bedrock in the northeastern U.S. and Canada contains total alkalinity of <200 ?eq 1-1, thus, it lacks acid-neutralizing capacity. In the U.S. about 5% of the land area and in Canada about 43 % of the land area is sensitive to acidic depositions. Further, these areas receive >20 kg/ha/yr of wet sulphate depositions and are vulnerable to acidifying processes. Acidic depositions contribute directly to acidifying processes of soil and soil water. Soils must have sufficient acid-neutralizing capacity or acidity of soil will increase. Natural soil-forming processes that lead to acidification can be accelerated by acidic depositions. Long-term effects of acidification are predicted, which will reduce soil productivity mainly through reduced availability of nutrients and mobilization of toxic metals. Severe effects may lead to major alteration of soil chemistry, soil biota, and even loss of vegetation. Several species of earthworms and several other taxa of soil-inhabiting invertebrates, which are important food of many vertebrate wildlife species, are affected by low pH in soil. Loss of canopy in declining sugar maples results in loss of insects fed on by certain neotropical migrant bird species. No definitive studies categorically link atmospheric acidic depositions with direct or indirect effects on wild mammals. Researchers have concentrated on vegetative and aquatic effects. Circumstantial evidence suggests that effects are probable for certain species of aquatic-dependent mammals (water shrew, mink, and otter) and that these species are at risk from the loss of foods or contamination of these foods by metals, especially methylmercury. Continued acidification of terrestrial habitats, to the extent that earthworm populations are broadly reduced, might expose some fossorial mammalian species to risk because of decline in their major prey species. Acidic deposition affects primarily aquatic habitats of avian species by disrupting food webs (ecological effects) and increasing amounts of available heavy metals (mercury, aluminum, cadmium) in prey of avian species (toxicological effects). The ecological effects of acidifying wetlands are to reduce acid-intolerant prey (invertebrates) and to change prey quality from high-calcium bearing prey to low-calcium bearing prey. The toxicological effects are to increase contamination by heavy metals, especially methylated mercury, in foods of breeding waterbirds. The combination of these 2 types of effects results in potentially lower survival of adults and reduced production, growth, or survival of young of many bird species. Effects of acidification on herpteofauna and their habitats are mainly reproductive failure of susceptible species and reduced or metal-contaminated foods for both amphibians and reptiles.
C3a, C4a, and C5a anaphylatoxins generated during complement activation play a key role in inflammation. C5a is the most potent of the three anaphylatoxins in eliciting biological responses. The effects of C5a are mediated by its binding to C5a receptor (C5aR, CD88). To date, C5aR has only been identified and cloned in mammalian species, and its evolutionary history remains ill-defined. To gain insights into the evolution, conserved structural domains, and functions of C5aR, we have cloned and characterized a C5aR in rainbow trout, a teleost fish. The isolated cDNA encoded a 350-aa protein that showed the highest sequence similarity to C5aR from other species. Genomic analysis revealed the presence of one continuous exon encoding the entire open reading frame. Northern blot analysis showed significant expression of the trout C5a receptor (TC5aR) message in PBLs and kidney. Flow cytometric analysis showed that two Abs generated against two different areas of the extracellular N-terminal region of TC5aR positively stained the same leukocyte populations from PBLs. B lymphocytes and granulocytes comprised the majority of cells recognized by the anti-TC5aR. More importantly, these Abs inhibited chemotaxis of PBLs toward a chemoattractant fraction purified from complement-activated trout serum. Our data suggest that the split between C5aR and C3aR from a common ancestral molecule occurred before the emergence of teleost fish. Moreover, we demonstrate that the overall structure of C5aR as well as its role in chemotaxis have remained conserved for >300 million years.
The richness and composition of a small mammal community inhabiting semiarid California oak woodland may be changing in response to climate change, but we know little about the causes or consequence of these changes. We applied a capture-mark-recapture model to 17 years (1997–2013) of live trapping data to estimate species-specific abundances. The big-eared woodrat was the most frequently captured species in the area, contributing 58% of total captures. All small mammal populations exhibited seasonal fluctuations, whereas those of the California mouse, brush mouse, and pinyon mouse declined during the study period. We also applied a multispecies dynamic occupancy model to our small mammal detection history data to estimate species richness, occupancy ( ), detection (p), local extinction ( ), and colonization ( ) probabilities, and to discern factors affecting these parameters. We found that decreased from 0.369 ± 0.088 in 1997 to 0.248 ± 0.054 in 2013; was lower during the dry season (May–September) than the wet season (October–April) and was positively influenced by total seasonal rainfall (slope parameter, = 0.859 ± 0.371; 95% CI = 0.132–1.587). Mean mammalian species richness decreased from 11.943 ± 0.461 in 1997 to 7.185 ± 0.425 in 2013. With highly variable climatic patterns expected in the future, especially increased frequency and intensity of droughts, it is important to monitor small mammal communities inhabiting threatened California oak woodlands.
More than 60% of emerging infectious diseases of humans have a wildlife origin, and when these diseases spread through human populations to new geographical areas, there is a considerable risk of spillback from humans to wildlife species. Spillback events can have severe consequences for wildlife populations, where the disease may cause morbidity and mortality, and human populations, where the establishment in wildlife may lead to prolonged transmission or new exposures in humans. Mitigating these consequences requires identifying the key risk factors that lead to human–wildlife transmission events and implementing risk-reducing actions, a challenge given that cross-species transmission events are rare and often data deficient. To identify potential species and locations that are most likely to lead to these rare events, we developed a spatially explicit, rapid risk assessment framework that incorporates three components of the spillback process: wildlife susceptibility, wildlife exposure, and pathogen introduction pressure. To demonstrate the broad applicability of our framework, we conducted a rapid risk assessment on two recent emerging zoonotic pathogens in humans, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and mpox, to determine the relative spillback risk to wild mammalian species in the continental United States. The rapid risk assessment identified both species and locations with higher than expected spillback risk, providing managers and researchers with valuable information to prioritize surveillance and risk-mitigation actions. Our framework represents a rapid and flexible approach to assess the risks of spillback to wildlife populations during rapidly evolving zoonotic disease outbreaks.
Reproductive output can vary widely among mammalian species. There are many drivers that affect reproductive output including evolutionary, environmental, population, social, and individual traits. Although several factors, including human-caused mortality, can affect reproductive output, we generally have a poor understanding of how such factors interact to affect reproduction, particularly in cooperative breeders. Gray wolves ( Canis lupus ) in Idaho, USA, are exposed to annual hunting and trapping. Thus, they are an ideal species to answer questions about how turnover within groups affects reproduction in cooperative breeders. I hypothesized that the reproductive output of wolves would be affected by individual, social, and environmental factors. Contrary to my prediction, mid-summer litter size was positively associated with wolf harvest density, suggesting a compensatory response to harvest in cooperatively breeding gray wolves. Such compensation is only partial, however, and does not fully account for all the individuals lost from harvest. At the very highest harvest densities observed, mean litter size increased nearly 28%. In contrast, mid-summer litter size was negatively associated with multiple breeding in groups, suggesting resource limitation and competition within groups. I show that characteristics associated with harvest and breeding strategies predict variations in litter size in a cooperative breeder.
The conversion of natural lands to developed uses may pose the single greatest human threat to global terrestrial biodiversity. Continued human growth and development over the next century will further exacerbate these effects of habitat loss and fragmentation. Natural resource managers are tasked with managing wildlife as a public trust, yet often have little say in land use decisions. Generally speaking, decision makers could benefit from an understanding of what different regulations mean in terms of wildlife distribution. In a previous paper ( Bettigole et al., 2013 ), we surveyed town residents throughout Vermont to measure how respondents feel about a range of development levels within their town boundaries. We estimated the “social carrying capacity for development” – or SK d – for 251 towns in Vermont. SK d provides an estimate of the level of developed land cover classes that town residents deem “acceptable” within their town boundaries. In this paper, we design a framework for linking the town-specific SK d estimates with the wildlife distribution patterns for three wide-ranging mammalian species: American black bear ( Ursus americanus ), fisher ( Martes pennanti ), and bobcat ( Lynx rufus ). We simulated landscape conditions at SK d for each town in Vermont, and then used existing occupancy models for the three target species to spatially map and compare occupancy rates in the baseline year 2000 with occupancy rates at SK d . With nearly 90% of Vermont towns willing to increase developed landcover classes within town boundaries compared to baseline levels, significant state-wide changes in occupancy rates were predicted for all three focal species. Average occupancy rates declined by −15.9% and −3.1% for black bear and bobcats, respectively. Average occupancy rates for fisher increased by 9.0%. This study provides a method for linking development standards within a town with wildlife occurrence. Across towns, the methodology spatially identifies areas that may be at risk of future development, as well as identifying areas where wildlife distribution patterns may face future change as a result of increased human population growth and development.