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USGS2019

Functional divergence of thyrotropin beta-subunit paralogs gives new insights into salmon smoltification metamorphosis

Smoltification is a metamorphic event in salmon life history, which initiates downstream migration and pre-adapts juvenile salmon for seawater entry. While a number of reports concern thyroid hormones and smoltification, few and inconclusive studies have addressed the potential role of thyrotropin (TSH). TSH is composed of a α-subunit common to gonadotropins, and a β-subunit conferring hormone specificity. We report the presence and functional divergence of duplicated TSH β-subunit paralogs (tshβa and tshβb) in Atlantic salmon. Phylogeny and synteny analyses allowed us to infer that they originated from teleost-specific whole genome duplication. Expression profiles of both paralogs in the pituitary were measured by qPCR throughout smoltification in Atlantic salmon from the endangered Loire-Allier population raised at the Conservatoire National du Saumon Sauvage. This revealed a striking peak of tshβb expression in April, concomitant with downstream migration initiation, while tshβa expression remained relatively constant. In situ hybridization showed two distinct pituitary cell populations, tshβa cells in the anterior adenohypophysis, and tshβb cells near to the pituitary stalk, a location comparable to the pars tuberalis TSH cells involved in seasonal physiology and behaviour in birds and mammals. Functional divergence of tshβ paralogs in Atlantic salmon supports a specific role of tshβb in smoltification.

Scientific Reports↗

USGS2016

Skeletal variation and taxonomic boundaries among mainland and island populations of the common treeshrew (Mammalia: Scandentia: Tupaiidae)

Treeshrews (order Scandentia) include 23 currently recognized species of small-bodied mammals from South and Southeast Asia. The taxonomy of the common treeshrew, Tupaia glis , which inhabits the Malay Peninsula south of the Isthmus of Kra, as well as a variety of offshore islands, has an extremely complicated history resulting from its wide distribution and subtly variable pelage. In our ongoing investigation of species boundaries in Tupaia , we compared island and mainland populations of T. glis using multivariate analyses. Specifically, we compared the skull and hand morphology of 13 island populations, most of which have been recognized as separate species or subspecies, to that of the mainland population. Island populations generally average smaller body size than those on the mainland, but none of the island populations are sufficiently distinct from the mainland population to warrant species recognition. This has important conservation implications for this widespread and morphologically variable species. It also highlights the potential role that ecogeographic explanations can play in understanding intraspecific variation, a role that should be considered in taxonomic studies and investigated further in T. glis and other treeshrews.

Malay Peninsula↗

USGS2025

The American black bear (Ursus americanus) as an apex predator: Investigating the ecological role of the world’s most abundant large carnivore

Introduction American black bears ( Ursus americanus ) have been documented to have top-down effects, both consumptive (through predation) and nonconsumptive (through fear effects). However, their behavioural and dietary adaptability has led to uncertainty about the conditions under which these may occur. Objectives We aimed to (1) investigate when, where, and how often black bears influence lower trophic levels, and (2) critically assess the experimental design of such studies to determine trends and biases. Methods We conducted a systematic literature search and used linear mixed-effects models to assess the relationships among prey age class, the presence of other large carnivores, and the percentage of ungulate mortality due to black bears. We also summarised the measured effects of black bears on other carnivores and the results of any experimental studies. Results We found a strong negative relationship between puma presence and the percentage of ungulate mortality due to black bears, but only in areas with at least one other large carnivore (e.g., wolves). Among 16 studies of black bears' impacts on other carnivores, most documented negative behavioural effects. While only 5% of studies had strong experimental design, bear removal consistently increased juvenile ungulate survival. Discussion and Synthesis Our findings highlight black bears' strong top-down effects, resembling or exceeding those of other large carnivores. These effects were greatest when no other large carnivores were present, but as highly effective kleptoparasites, black bears can alter the feeding habits of other large carnivores. Thus, we argue that ‘apex’ is a conditional state, not a species-wide status.

Mammal Review↗

USGS2006

Association between perfluorinated compounds and pathological conditions in southern sea otters

Concentrations of four perfluorinated contaminants, including perfluorooctanesulfonate (PFOS) and perfluorooctanoic acid (PFOA), were measured in liver tissue from 80 adult female sea otters collected from the California coast during 1992a??2002. Concentrations of PFOS and PFOA were in the ranges of <1a??884 and <5a??147 ng/g, wet wt, respectively. Concentrations of PFOA in the livers of these sea otters were among the highest values reported for marine mammals to date. Liver tissue from 6 male sea otters also was analyzed and contained significantly higher concentrations of PFOS than did tissues from female otters. To examine the association between exposures and potential effects, concentrations of PFOS and PFOA were compared among the adult female otters that died from infectious diseases, noninfectious causes, and from apparent emaciation. Concentrations of both PFOA and PFOS were significantly higher in sea otters in the infectious disease category than in the noninfectious category. Concentrations of PFOS and PFOA were not significantly different between noninfectious and emaciated otters, suggesting that the poor nutritive (body) status of emaciated otters did not affect the concentrations of perfluorochemicals in livers. Concentrations of PFOA increased significantly from 1992 to 2002, whereas PFOS concentrations increased from 1992 to 1998 and then decreased after 2000. Significant association between infectious diseases and elevated concentrations of PFOS/PFOA in the livers of sea otters is a cause for concern and suggests the need for further studies.

California↗

USGS2016

Demography of an apex predator at the edge of its range: impacts of changing sea ice on polar bears in Hudson Bay

Changes in the abundance and distribution of wildlife populations are common consequences of historic and contemporary climate change. Some Arctic marine mammals, such as the polar bear ( Ursus maritimus ), may be particularly vulnerable to such changes due to the loss of Arctic sea ice. We evaluated the impacts of environmental variation on demographic rates for the Western Hudson Bay (WH), polar bear subpopulation from 1984 to 2011 using live-recapture and dead-recovery data in a Bayesian implementation of multistate capture–recapture models. We found that survival of female polar bears was related to the annual timing of sea ice break-up and formation. Using estimated vital rates (e.g., survival and reproduction) in matrix projection models, we calculated the growth rate of the WH subpopulation and projected population responses under different environmental scenarios while accounting for parametric uncertainty, temporal variation, and demographic stochasticity. Our analysis suggested a long-term decline in the number of bears from 1185 (95% Bayesian credible interval [BCI] = 993–1411) in 1987 to 806 (95% BCI = 653–984) in 2011. In the last 10 yr of the study, the number of bears appeared stable due to temporary stability in sea ice conditions (mean population growth rate for the period 2001–2010 = 1.02, 95% BCI = 0.98–1.06). Looking forward, we estimated long-term growth rates for the WH subpopulation of ~1.02 (95% BCI = 1.00–1.05) and 0.97 (95% BCI = 0.92–1.01) under hypothetical high and low sea ice conditions, respectively. Our findings support previous evidence for a demographic linkage between sea ice conditions and polar bear population dynamics. Furthermore, we present a robust framework for sensitivity analysis with respect to continued climate change (e.g., to inform scenario planning) and for evaluating the combined effects of climate change and management actions on the status of wildlife populations.

Hudson Bay↗

USGS2007

Understanding knowledge and perceptions of bats among residents of Fort Collins, Colorado

As regional urbanization increases in Colorado, so do interactions between humans and wildlife. Where previous habitat has been reduced due to urbanization and development, a few bat species that easily adapt to new environments now roost in homes and buildings (Kunz and Reynolds, 2003). Bats frequently serve as reservoirs of disease that have potential health consequences for humans and other mammals (Messenger and others, 2003). As bat use of buildings becomes more frequent, the incidences of bat/human contact and the risk of spreading disease also increase. In Colorado, rabies is most common in the big brown bat (Eptesicus fuscus) Pape and others, 1999), the most ubiquitous species of urban-dwelling bat in the United States (Barbour and Davis, 1969) and the most common species submitted for rabies testing in Colorado (Pape and others, 1999). An in-depth knowledge of the big brown bat - including its ecology, habitat and movements, and aspects of disease transmission - and of its interactions with humans is essential for making informed management decisions regarding this species. To balance the competing priorities of species preservation and public safety, natural resource managers and public health professionals must be able to accurately estimate citizens' knowledge, perceptions, and perceived risks regarding the bat species that use human dwellings and harbor diseases potentially dangerous to humans. A recently completed five-year ecological study (2001-2005) on bats inhabiting buildings in Fort Collins, Colo., has provided much information on the basic epidemiology of rabies and on the ecology of the local bat population (Davis, Rudd, and Bowen, 2007; Ellison and others, 2007; Neubaum, Douglas, and others, in press; Neubaum, O'Shea, and Wilson, 2006; Neubaum, Wilson, and O'Shea, 2007; O'Shea, Ellison, and Stanley, 2004; Pearce and O'Shea, 2007; Pearce and others, in press; Shankar and others, 2004; Shankar and others, 2005; Wimsatt and others 2005). Research investigating the human dimensions of bats and bat/rabies relationships, however, has been very limited (Gibbins and others, 2002; Liesener and others, 2006). Herein, we report the results of a study to evaluate perceptions and knowledge of bats and rabies among residents of Fort Collins, Colo. The study resulted from collaborations between U.S. Geological Survey (USGS) bat ecologists of the Trust Species and Habitats branch, and social scientists of the Policy Analysis and Science Assistance branch, both of the USGS Fort Collins Science Center (FORT).

Open-File Report↗

USGS2018

Protection from UV light is an evolutionarily conserved feature of the haematopoietic niche

Haematopoietic stem and progenitor cells (HSPCs) require a specific microenvironment, the haematopoietic niche, which regulates HSPC behaviour . The location of this niche varies across species, but the evolutionary pressures that drive HSPCs to different microenvironments remain unknown. The niche is located in the bone marrow in adult mammals, whereas it is found in other locations in non-mammalian vertebrates, for example, in the kidney marrow in teleost fish. Here we show that a melanocyte umbrella above the kidney marrow protects HSPCs against ultraviolet light in zebrafish. Because mutants that lack melanocytes have normal steady-state haematopoiesis under standard laboratory conditions, we hypothesized that melanocytes above the stem cell niche protect HSPCs against ultraviolet-light-induced DNA damage. Indeed, after ultraviolet-light irradiation, unpigmented larvae show higher levels of DNA damage in HSPCs, as indicated by staining of cyclobutane pyrimidine dimers and have reduced numbers of HSPCs, as shown by cmyb (also known as myb ) expression. The umbrella of melanocytes associated with the haematopoietic niche is highly evolutionarily conserved in aquatic animals, including the sea lamprey, a basal vertebrate. During the transition from an aquatic to a terrestrial environment, HSPCs relocated into the bone marrow, which is protected from ultraviolet light by the cortical bone around the marrow. Our studies reveal that melanocytes above the haematopoietic niche protect HSPCs from ultraviolet-light-induced DNA damage in aquatic vertebrates and suggest that during the transition to terrestrial life, ultraviolet light was an evolutionary pressure affecting the location of the haematopoietic niche.

Nature↗

USGS2010

Occupancy dynamics in a tropical bird community: Unexpectedly high forest use by birds classified as non‐forest species

1. Worldwide loss of biodiversity necessitates a clear understanding of the factors driving population declines as well as informed predictions about which species and populations are at greatest risk. The biggest threat to the long-term persistence of populations is the reduction and changes in configuration of their natural habitat. 2. Inconsistencies have been noted in the responses of populations to the combined effects of habitat loss and fragmentation. These have been widely attributed to the effects of the matrix habitats in which remnant focal habitats are typically embedded. 3. We quantified the potential effects of the inter-patch matrix by estimating occupancy and colonization of forest and surrounding non-forest matrix (NF). We estimated species-specific parameters using a dynamic, multi-species hierarchical model on a bird community in southwestern Costa Rica. 4. Overall, we found higher probabilities of occupancy and colonization of forest relative to the NF across bird species, including those previously categorized as open habitat generalists not needing forest to persist. Forest dependency was a poor predictor of occupancy dynamics in our study region, largely predicting occupancy and colonization of only non-forest habitats. 5. Our results indicate that the protection of remnant forest habitats is key for the long-term persistence of all members of the bird community in this fragmented landscape, including species typically associated with open, non-forest habitats. 6. Synthesis and applications. We identified 39 bird species of conservation concern defined by having high estimates of forest occupancy, and low estimates of occupancy and colonization of non-forest. These species survive in forest but are unlikely to venture out into open, non-forested habitats, therefore, they are vulnerable to the effects of habitat loss and fragmentation. Our hierarchical community-level model can be used to estimate species-specific occupancy dynamics for focal and inter-patch matrix habitats to identify which species within a community are likely to be impacted most by habitat loss and fragmentation. This model can be applied to other taxa (i.e. amphibians, mammals and insects) to estimate species and community occurrence dynamics in response to current environmental conditions and to make predictions in response to future changes in habitat configurations.

Journal of Applied Ecology↗

USGS2002

Availability of food resources, distribution of invasive species, and conservation of a Hawaiian bird along a gradient of elevation

Aim: We evaluated how an elevation gradient affects: (1) the availability of food required by a specialist seed-eater, Loxioides bailleui Oustalet (Drepanidinae), or pallia, and hence the distribution of this endangered Hawaiian bird, and (2) the distribution of alien threats to Loxioides populations, their primary foods, and their dry-forest habitat, and hence strategies for their conservation. Location: We worked throughout the subalpine forest that encircles Mauna Kea Volcano, Hawai'i Island, but we focused our studies mainly on the western slope between 2000 and 3000 m elevation, where the gradient of elevation was greatest and palila were most abundant. Methods: We determined phenology and productivity patterns of the endemic dry-forest tree species, Sophora chrysophylla (Salisb.) Seem. (Fabaceae), or ma??mane, which provides Loxioides with most of their food, and another common endemic tree, Myoporum sandwicense A. Gray (Myoporaceae), or naio, which provides some resources, along a 786-m elevation gradient at monthly intervals for 10 years (Sophora only). We also determined the availability each month of moth larvae (Lepidoptera) for that were important in the diet of nestling and adult palila. In addition, we documented the incidence of parasitism on moth larvae by several wasp (Hymenoptera) and fly (Diptera) species, and we determined the distribution of predatory wasps and ants (Hymenoptera), which potentially threaten insect prey of birds. Percentage cover of alien grass species that pose fire threats in palila habitat and other weeds were assessed during one survey. Small mammal abundance and distribution were determined by trapping during three (rodent) or five (carnivore) surveys. Results: Sophora flower and seed (pod) availability varied predictably along the elevation gradient, with about 4 months separating peaks in reproduction at high and low elevations. This, together with highly variable production of flowers and pods within elevation strata, resulted in Sophora resources being available to Loxioides throughout the year on the western slope of Mauna Kea. Sophora produced flowers and pods more seasonally where gradients of elevation were short; thus, resources were available less consistently. In contrast, Myoporum produced flowers and fruits with little variation with respect to season or elevation. The availability of important insect prey of Loxioides was also related to elevation, in part because threats to Lepidoptera larvae from parasitic wasps were generally less at higher elevations. Threats to insect prey from predatory ants was also less at higher elevations but the abundance of predatory wasps was not related to elevation. Several weeds that pose the most serious threats to Loxioides habitat were more abundant at mid and low elevations, and alien grass cover was somewhat greater at mid elevation, thereby increasing fire risks in the centre of Loxioides habitat. Predatory mammals, in particular Felis catus Linnaeus, were common throughout the subalpine forest of Mauna Kea. However, Rattus rattus Linnaeus was rare, especially at higher elevations, whereas Mus musculus Linnaeus was more abundant at lower elevations. Main conclusions: Loxioides are concentrated in habitat that is distributed along a substantial gradient of elevation at least in part because food is available throughout the year and threats to food resources are less concentrated. To recover Loxioides elsewhere in its former range, habitats must be restored and alien threats reduced along extensive elevation gradients. Conservation along environmental gradients will likely benefit other Hawaiian birds that track the availability of food across landscapes or that have been stranded in the higher portions of their original ranges because of the greater impacts of alien diseases, predators, food competitors, and habitat stressors at lower elevations.

Journal of Biogeography↗

USGS2018

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↗

USGS1999

Foods and foraging of prairie striped skunks during the avian nesting season

Food habits of prairie skunks are not well understood, yet such knowledge might provide insight into factors influencing nest depredation. We studied food habits of radiocollared adult striped skunks (Mephitis mephitis) during 1976-78 in North Dakota, where skunks are regarded as important predators of ground-nesting birds. Plant foods, primarily grain and sunflower seeds, occurred in a larger percentage of scats in spring (15 Apr 31 May) than summer (1 Jun 15 July, P=0.04), but overall, plant foods were a minor part of skunk diets. Animal foods, primarily birds (including eggs), small rodents, and insects occurred annually in a large percentage of scats of all skunks. These foods were acquired nearly exclusively in grasslands. Percentage of scats containing animal foods was similar, irrespective of sex, season, or year (P>0.45). In spring, vertebrates occurred in a smaller percentage of scats of females than males (P<0.01). Among females, vertebrates also occurred in a smaller percentage of scats in spring than summer (P<0.01). Among all skunks, birds occurred in a smaller percentage of scats in spring than in summer (P<0.01). Both birds (P<0.02) and mammals (P<0.01) occurred in a smaller proportion of scats when wetland conditions were poor. Percentage of scats containing insects, the primary invertebrate food of skunks, did not vary by sex, season, or year (P>0.15). Insects were mostly adult and larval Coleoptera, larval Lepidoptera, and adult and nymph Orthoptera.

Wildlife Society Bulletin↗

USGS2000

Establishment of warm season grasses with and without the use of compost soil amendments

Two compost materials (COMPRO and LEAFGRO) were evaluated as soil amendments to enhance wildlife habitats, while maintaining optimal floral and faunal biodiversity. Special emphasis was placed on the role of compost in the establishment and retention of native warm season grasses (Andropogon gerardi, Schizachyrium scoparium, and Sorghastrum nutans). This study was conducted at two sites that were degraded by previous military and farming operations. Sites were plowed twice in 1996 and then a one inch layer of COMPRO or LEAFGRO was applied with a modified manure spreader and disked into the soil to a depth of 3 inches. Vegetation sampling was conducted in 1996, 1997, 1998, and 1999. Initially the greatest vegetation cover occurred in plots treated with LEAFGRO. Plots treated with COMPRO had less vegetation cover than both types of controls plots (with and without warmseason grasses). The reduced plant growth in the plots treated with COMPRO may have been related to the much higher soil pH of these plots on both sites. In subsequent years, amounts of warm season grasses increased, however, in general there was more cover of warm season grasses in plots that did not receive compost than those that did receive compost. Sorghastrum nutans was more abundant on the sites than either of the other two species of warm season grasses. Invertebrate and mammal data collected for three years indicated that there was not more faunal activity in the plots treated with LEAFGRO or COMPRO compost soil amendments. Results indicate that compost amendments did not improve establishment of warm season grasses and the resultant faunal diversity or abundance.

Book chapter↗

USGS2019

Impact of prey occupancy and other ecological and anthropogenic factors on Tiger distribution in Thailand’s Western Forest Complex

Despite conservation efforts, large mammals such as tigers (Panthera tigris) and their main prey, gaur (Bos gaurus), banteng (Bos javanicus), and sambar (Rusa unicolor), are highly threatened and declining across their entire range. The only large viable source population of tigers in mainland Southeast Asia occurs in Thailand's Western Forest Complex (WEFCOM), an approximately 19,000 km 2 landscape of 17 contiguous protected areas. We used an occupancy modeling framework, which accounts for imperfect detection, to identify the factors that affect tiger distribution at the approximate scale of a female tiger's home range, 64 km 2 , and site use at a scale of 1-km 2 . At the larger scale, we estimated the proportion of sites at WEFCOM that were occupied by tigers; at the finer scale, we identified the key variables that influence site-use and developed a predictive distribution map. At both scales, we examined key anthropogenic and ecological factors that help explain tiger distribution and habitat use, including probabilities of gaur, banteng, and sambar occurrence from a companion study. Occupancy estimated at the 64-km 2 scale was primarily influenced by the combined presence of all three large prey species, and 37% or 5,858 km 2 of the landscape was predicted to be occupied by tigers. In contrast, site use estimated at the scale of 1 km 2 was most strongly influenced by the presence of sambar. By modeling occupancy while accounting for imperfect probability of detection, we established reliable benchmark data on the distribution of tigers in WEFCOM. This study also identified factors that limit tiger distributions; which managers can then target to expand tiger distribution and guide recovery elsewhere in Southeast Asia.

Ecology and Evolution↗

USGS1999

The diving physiology of bottlenose dolphins (Tursiops truncatus). III. Thermoregulation at depth

During diving, marine mammals initiate a series of cardiovascular changes that include bradycardia and decreased peripheral circulation. Because heat transfer from thermal windows located in peripheral sites of these mammals depends on blood flow, such adjustments may limit their thermoregulatory capabilities during submergence. Here, we demonstrate how the thermoregulatory responses of bottlenose dolphins ( Tursiops truncatus ) are coordinated with the diving response. Heart rate, skin temperature and heat transfer from the dorsal fin and flank were measured while dolphins rested on the water surface, stationed 5–50 m under water and floated at the surface immediately following a dive. The results showed that heat flow ranged from 42.9±7.3 to 126.2±23.1 W m −2 and varied with anatomical site and diving activity. Upon submergence, heat flow declined by 35 % from the dorsal fin and by 24 % from the flank. An immediate increase in heat flow to levels exceeding pre-dive values occurred at both sites upon resurfacing. Changes in heart rate during diving paralleled the thermoregulatory responses. Mean pre-dive heart rate (102.0±2.6 beats min −1 , N =26) decreased by 63.4 % during dives to 50 m and immediately returned to near resting levels upon resurfacing. These studies indicate that heat dissipation by dolphins is attenuated during diving. Rather than challenge the diving response, heat transfer is delayed until post-dive periods when the need for oxygen conservation is reduced.

Journal of Experimental Biology↗

USGS2012

Report on the reptiles of Upland Savai’i

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.

Report↗

USGS2002

An ecosystem report on the Panama Canal: Monitoring the status of the forest communities and the watershed

In 1996, the Smithsonian Tropical Research Institute and the Republic of Panama's Environmental Authority, with support from the United States Agency for International Development, undertook a comprehensive program to monitor the ecosystem of the Panama Canal watershed. The goals were to establish baseline indicators for the integrity of forest communities and rivers. Based on satellite image classification and ground surveys, the 2790 km2 watershed had 1570 km2 of forest in 1997, 1080 km2 of which was in national parks and nature monuments. Most of the 490 km2 of forest not currently in protected areas lies along the west bank of the Canal, and its management status after the year 2000 turnover of the Canal from the U.S. to Panama remains uncertain. In forest plots designed to monitor forest diversity and change, a total of 963 woody plant species were identified and mapped. We estimate there are a total of 850-1000 woody species in forests of the Canal corridor. Forests of the wetter upper reaches of the watershed are distinct in species composition from the Canal corridor, and have considerably higher diversity and many unknown species. These remote areas are extensively forested, poorly explored, and harbor an estimated 1400-2200 woody species. Vertebrate monitoring programs were also initiated, focusing on species threatened by hunting and forest fragmentation. Large mammals are heavily hunted in most forests of Canal corridor, and there was clear evidence that mammal density is greatly reduced in hunted areas and that this affects seed predation and dispersal. The human population of the watershed was 113 000 in 1990, and grew by nearly 4% per year from 1980 to 1990. Much of this growth was in a small region of the watershed on the outskirts of Panama City, but even rural areas, including villages near and within national parks, grew by 2% per year. There is no sewage treatment in the watershed, and many towns have no trash collection, thus streams near large towns are heavily polluted. Analyses of sediment loads in rivers throughout the watershed did not indicate that erosion has been increasing as a result of deforestation, rather, erosion seems to be driven largely by total rainfall and heavy rainfall events that cause landslides. Still, models suggest that large-scale deforestation would increase landslide frequency, and failure to detect increases in erosion could be due to the gradual deforestation rate and the short time period over which data are available. A study of runoff showed deforestation increased the amount of water from rainfall that passed directly into streams. As a result, dry season flow was reduced in a deforested catchment relative to a forested one. Currently, the Panama Canal watershed has extensive forest areas and streams relatively unaffected by humans. But impacts of hunting and pollution near towns are clear, and the burgeoning population will exacerbate these impacts in the next few decades. Changes in policies regarding forest protection and pollution control are necessary.

Environmental Monitoring and Assessment↗

USGS2013

Using hand proportions to test taxonomic boundaries within the Tupaia glis species complex (Scandentia, Tupaiidae)

Treeshrews (order Scandentia) comprise 2 families of squirrel-sized terrestrial, arboreal, and scansorial mammals distributed throughout much of tropical South and Southeast Asia. The last comprehensive taxonomic revision of treeshrews was published in 1913, and a well-supported phylogeny clarifying relationships among all currently recognized extant species within the order has only recently been published. Within the family Tupaiidae, 2 widely distributed species, the northern treeshrew, Tupaia belangeri (Wagner, 1841), and the common treeshrew, T. glis (Diard, 1820), represent a particularly vexing taxonomic complex. These 2 species are currently distinguished primarily based on their respective distributions north and south of the Isthmus of Kra on the Malay Peninsula and on their different mammae counts. This problematic species complex includes 54 published synonyms, many of which represent putative island endemics. The widespread T. glis and T. belangeri collectively comprise a monophyletic assemblage representing the sister lineage to a clade composed of the golden-bellied treeshrew, T. chrysogaster Miller, 1903 (Mentawai Islands), and the long-footed treeshrew, T. longipes (Thomas, 1893) (Borneo). As part of a morphological investigation of the T. glis – T. belangeri complex, we studied the proportions of hand bones, which have previously been shown to be useful in discriminating species of soricids (true shrews). We measured 38 variables from digital X-ray images of 148 museum study skins representing several subspecies of T. glis , T. belangeri , T. chrysogaster , and T. longipes and analyzed these data using principal components and cluster analyses. Manus proportions among these 4 species readily distinguish them, particularly in the cases of T. chrysogaster and T. longipes . We then tested the distinctiveness of several of the populations comprising T. glis and T. longipes . T. longipes longipes and T. l. salatana Lyon, 1913, are distinguishable from each other, and populations of T. "glis" from Bangka Island and Sumatra are distinct from those on the Malay Peninsula, supporting the recognition of T. salatana , T. discolor Lyon, 1906, and T. ferruginea Raffles, 1821 as distinct species in Indonesia. These relatively small, potentially vulnerable treeshrew populations occur in the Sundaland biodiversity hotspot and will require additional study to determine their appropriate conservation status.

Journal of Mammalogy↗

USGS2019

Standardized IMGT nomenclature of salmonidae IGH genes, the paradigm of Atlantic salmon and rainbow trout: From genomics to repertoires

In teleost fish as in mammals, humoral adaptive immunity is based on B lymphocytes expressing highly diverse immunoglobulins (IG). During B cell differentiation, IG loci are subjected to genomic rearrangements of V, D, and J genes, producing a unique antigen receptor expressed on the surface of each lymphocyte. During the course of an immune response to infections or immunizations, B cell clones specific of epitopes from the immunogen are expanded and activated, leading to production of specific antibodies. Among teleost fish, salmonids comprise key species for aquaculture. Rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar) are especially important from a commercial point of view and have emerged as critical models for fish immunology. The growing interest to capture accurate and comprehensive antibody responses against common pathogens and vaccines has resulted in recent efforts to sequence the IG repertoire in these species. In this context, a unified and standardized nomenclature of salmonid IG heavy chain (IGH) genes is urgently required, to improve accuracy of annotation of adaptive immune receptor repertoire dataset generated by high-throughput sequencing (AIRRseq) and facilitate comparisons between studies and species. Interestingly, the assembly of salmonids IGH genomic sequences is challenging due to the presence of two large size duplicated IGH loci and high numbers of IG genes and pseudogenes. We used data available for Atlantic salmon to establish an IMGT standardized nomenclature of IGH genes in this species and then applied the IMGT rules to the rainbow trout IGH loci to set up a nomenclature, which takes into account the specificities of Salmonid loci. This unique, consistent nomenclature for Salmonid IGH genes was then used to construct IMGT sequence reference directories allowing accurate annotation of AIRRseq data. The complex issues raised by the genetic diversity of salmon and trout strains are discussed in the context of IG repertoire annotation.

Frontiers in Immunology↗