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opencc-zeroMay 2022View details →

Use of cenotes and the cave environment by mammals on the Yucatán Peninsula, Mexico

Mammals are important sources of nutrients to cave ecosystems, and in some circumstances, caves may be an essential resource for mammals. Few studies, however, have focused on the use of caves by terrestrial mammals. We used camera traps at 17 cenotes on the Yucatán Peninsula to determine patterns of use by mammals. Eighteen non-volant mammal taxa were identified using cenotes, the most commonly occurring being lowland paca (Agouti paca), opossums (Didelphis spp.), white-nosed coati (Nasua narica), gray fox (Urocyon cinereoargenteus), tayra, (Eira barbara) and gray four-eyed opossum (Philander opossum); collectively these taxa accounted for 76% of all mammal records. We also recorded several felids using cenotes, including jaguar (Panthera onca) and puma (Puma concolor). Activity patterns at cenotes usually matched normal activity schedules but some species were nocturnal in the forest but diurnal at cenotes. Mammals mostly accessed cenotes to drink, but a range of activities were recorded including foraging, nesting, mating, resting and bathing.

opencc-zeroJun 2022View details →

Use of road underpasses by mammals and a monitor lizard in eastern Australia and consideration of the prey-trap hypothesis

Road networks continue to expand globally with predictable effects on ecological systems. Research into the effectiveness of road underpasses and overpasses for wildlife has been concentrated in North America and Europe. In Australia, most studies of underpasses have been of relatively short duration and without reference sites to give context to the measured rates of use. We studied 5–7 road underpasses at two locations in eastern Australia over 2–3 years, comparing camera trap detections of animals in underpasses with those at nearby forest sites. Three species of large macropod (wallabies and kangaroos) were frequently detected in the underpasses, with some underpasses traversed 1–4 times per week, and in many cases exceeded detections in the forest. The lace monitor (Varanus various) was detected in all underpasses, often once per week during spring and summer, and infrequently in the forest. At each location a different small macropod species, including one regionally threatened, showed a higher probability of detection in one underpass compared to several of the forest sites. The vulnerable koala (Phascolartos cinereus) was detected infrequently in underpasses and in the adjoining forest. The short-beaked echidna (Tachyglossus aculeatus) had a high probability of detection in a single underpass. The 'prey-trap hypothesis' postulates that predators will exhibit increased activity at underpasses as a consequence of prey being funnelled. We found the red fox (Vulpes vulpes) had high activity in some underpasses. However, its activity coincided less than expected with the activity of the mammals most at risk to it. Our results provide no consistent support for the 'prey-trap hypothesis'. Instead, our study confirms the generic value of underpasses for a range of medium-large mammals as well as one large reptile. Habitat adjoining underpasses exerts a strong influence on their use and requires greater consideration to maximise underpass use.

opencc-zeroJul 2022View details →

Data from: Integrating 3D models with morphometric measurements to improve volumetric estimates in marine mammals

1. Studies of body condition are key to understanding the health, bioenergetics, and ecological roles of marine mammals. Due to challenges in studying marine mammals at sea, body condition is often approximated using metrics representing the size of the dorsal surface visible from aerial imagery, but quantifying variability in body volume would enable a more holistic understanding of bioenergetics. Further, the number and location of measurements needed to accurately quantify body condition has received little attention. Three-dimensional (3D) models provide a promising tool for representing morphology and providing holistic estimates of marine mammal body condition when combined with field-based morphometric measurements. 2. We use humpback whales (Megaptera novaeangliae) to demonstrate the utility of 3D models for estimating body condition in marine mammals. We integrate morphometric measurements taken from Unoccupied Aerial Vehicles (UAVs) with scalable 3D models to generate estimates of humpback whale body volume. We assess which and how many morphometric measurements are required to accurately estimate body volume and compare the error between volume estimates derived from 3D models and previously developed models representing volume as a series of ellipses. Using UAV measurements, we assess the contribution of each morphometric measurement to volumetric estimates, and quantify the error produced by all combinations and numbers of morphometric measurements (131,072 combinations). 3. Error in volume estimates from 3D models generated with as few as five width measurements was <5% compared to the full models and was lower than the error produced when using five width measurements with the elliptical approach. We suggest that by conserving the external morphology of marine mammals, 3D models allow body volume and body condition to be estimated accurately with few measurements. 4. We provide code and guidelines for creating 3D models using the open-source software Blender and for assessing which measurements are needed to accurately capture the morphology of cetaceans. The 3D modeling approach we present will facilitate studies of intra- and interannual changes in body volume in marine mammals, which is vital to providing a more holistic understanding of bioenergetics and to assessing responses to environmental change and anthropogenic stressors.

opencc-by-4.0Aug 2022View details →

Mammal mitogenomics from invertebrate-derived DNA (iDNA)

Mitogenomic capture of Non-human Primates from invertebrate derived DNA using hybridisation capture.  Files are in fastq format and sequenced with illumina Mi-Seq using the Mi-Seq Reagent Kit v3 (2 x 250bp; illumina) .

opencc-zeroDec 2021View details →

Elevational range of mammals, birds, and amphibians in the Himalayas

The lowest and highest elevations known for each species are used to delineate its elevational limits. We assume that species potentially exist between their elevational limits. For species that have a single elevational distribution record (resulting in an elevational range of zero) as well as those with elevational ranges less than 200 m, we adjusted their elevation ranges to 200 m. We verified all data for accuracy by experts within the region and any dubious outlying records were removed. Elevational limits were given for 1,488 species, including 314 mammals, 1027 birds, and 147 amphibians in the Himalayas.

opencc-zeroSep 2022View details →

Population genomics of a predatory mammal reveals patterns of decline and impacts of exposure to toxic toads

Mammal declines across northern Australia are one of the major biodiversity loss events occurring globally. There has been no regional assessment of the implications of these species declines for genomic diversity. To address this, we conducted a species-wide assessment of genomic diversity in the northern quoll (Dasyurus hallucatus), an Endangered marsupial carnivore. We used next-generation sequencing methods to genotype 10,191 SNPs in 352 individuals from across a 3220 km length of the continent, investigating patterns of population genomic structure and diversity, and identifying loci showing signals of putative selection. We found strong heterogeneity in the distribution of genomic diversity across the continent, characterised by (1) biogeographic barriers driving hierarchical population structure through long-term isolation, and (2) severe reductions in diversity resulting from population declines, exacerbated by the spread of introduced toxic cane toads (Rhinella marina). These results warn of a large ongoing loss of genomic diversity and associated adaptive capacity as mammals decline across northern Australia. Encouragingly, populations of the northern quoll established on toad-free islands by translocations appear to have maintained most of the initial genomic diversity after 16 years. By mapping patterns of genomic diversity within and among populations, and investigating these patterns in the context of population declines, we can provide conservation managers with data critical to informed decision-making. This includes the identification of populations that are candidates for genetic management, the importance of remnant island and insurance/translocated populations for the conservation of genetic diversity, and the characterisation of putative evolutionarily significant units.

Figure 6 in High richness of non-volant mammals in a seasonal forest fragment in southeastern Brazil

Figure 6. Cluster analysis of medium and large mammal communities' similarity between 19 Atlantic Forest remnants in São Paulo, southeastern Brazil (including a single remnant in Paraná, Brazil). AGPE = Água do Peão; AGUA = Aguapeí State Park; AMBO = Amadeu Botelho Private Nature Reserve; CBSP = Carlos Botelho State Park; COSM = Matão de Cosmópolis; ESAL = Estrela da Alcídia Água Sumida; ISP = Intervales State Park; LUNO = Lua Nova; MATU = Maturi; MDSP = Morro do Diabo State Park; MGFR = Morro Grande Forest Reserve; PBES = Ponte Branca (Black Lion Tamarin Ecological Station); SBNP = Serra da Bocaina National Park; SEIR = Seis R; SMES = Santa Maria Água Sumida (Black Lion Tamarin Ecological Station); SMA = Santa Maria Forest; STMO = Santa Mônica; TUES = Tucano (Black Lion Tamarin Ecological Station).

Figure 5 in High richness of non-volant mammals in a seasonal forest fragment in southeastern Brazil

Figure 5. Carnivora, Artiodactlya, and Perissodactyla recorded in Santa Maria fragment. (A) Puma concolor; (B) Leopardus pardalis; (C) Panthera onca; (D) Cerdocyon thous; (E) Chrysocyon brachyurus; (F) Mazama rufa; (G) Dicotyles tajacu; (H) Tapirus terrestris.

Figure 7 in High richness of non-volant mammals in a seasonal forest fragment in southeastern Brazil

Figure 7. Scatterplot of non-volant mammal species richness according to fragment area in 14 Atlantic Forest fragments of Pontal do Paranapanema, São Paulo, Southeastern Brazil. The study site, Santa Maria is represented by a blue triangle. AGPE = Água do Peão; ARIZ = Fazenda Arizona; ASES = Água Sumida (Black Lion Tamarin Ecological Station); ESAL = Estrela da Alcídia; LUNO = Lua Nova; MATU = Maturi; MDSP = Morro do Diabo State Park; NOPO = Nova Pontal; PBES = Ponte Branca (Black Lion Tamarin Ecological Station); SASE = São Sebastião; SEIR = Seis R; STMO = Santa Mônica; TUES = Tucano (Black Lion Tamarin Ecological Station).

Figure 1 in High richness of non-volant mammals in a seasonal forest fragment in southeastern Brazil

Figure 1. Santa Maria forest fragment and its location in Pontal do Paranapanema, São Paulo, southeastern Brazil. Note the small creek (Ribeirão Água Sumida) that passes on its southern edges and the SPV-035 road along its northeastern edge. Green are native forest remnants and blue are the rivers and creeks.

Figure 4 in High richness of non-volant mammals in a seasonal forest fragment in southeastern Brazil

Figure 4. Didelphidae, Xenarthra, Primates and Rodentia recorded in Santa Maria fragment. (A) Marmosa paraguayana; (B) Didelphis albiventris; (C) Gracilinanus microtarsus; (D) Euphractus sexcinctus; (E) Dasypus novemcinctus (preyed); (F) Tamandua tetradactyla; (G) Sapajus nigritus; (H) Leontopithecus chrysopygus; (I) Dasyprocta azarae; J) Oecomys cleberi.

Figure 3 in High richness of non-volant mammals in a seasonal forest fragment in southeastern Brazil

Figure 3. Locations of the 18 medium and large mammal inventories (green dots) that were compared to the mammal community of Santa Maria forest fragment (red square). Atlantic Forest remnants (sensu Ribeiro et al., 2009), are in light gray. AGPE = Água do Peão (Ditt et al., 1999); AGUA = Aguapeí State Park (Faria & Pires, 2010); AMBO = Amadeu Botelho Private Nature Reserve (Reale et al., 2014); CBSP = Carlos Botelho State Park (Brocardo et al., 2012); COSM = Matão de Cosmópolis (Magioli et al., 2014); ESAL = Estrela da Alcídia Água Sumida (Ditt et al., 1999); ISP = Intervales State Park (de Vivo & Gregorin, 2001); LUNO = Lua Nova (Ditt et al., 1999); MATU = Maturi (Ditt et al., 1999); MDSP = Morro do Diabo State Park (Faria & Pires, 2006); MGFR = Morro Grande Forest Reserve (Negrão & Valladares-Pádua, 2006); PBES = Ponte Branca (Black Lion Tamarin Ecological Station) (Valladares-Pádua, 2007); SBNP = Serra da Bocaina National Park (Delciellos et al., 2012); SEIR = Seis R (Ditt et al., 1999); SMES = Santa Maria Água Sumida (Black Lion Tamarin Ecological Station) (Valladares-Pádua, 2007); SMA = Santa Maria Forest (this study); STMO = Santa Mônica (Ditt et al., 1999); TUES = Tucano (Black Lion Tamarin Ecological Station) (Valladares-Pádua, 2007).

opencc-zeroOct 2022View details →

Interpreting the mammal deposits of Cloggs Cave (SE Australia), GunaiKurnai Aboriginal Country, through community-led partnership research

Palaeontological animal bone deposits are rarely investigated through research partnerships where the local First Nations communities have a defining hand in both the research questions asked and the research processes. Here we report research undertaken through such a partnership approach at the iconic archaeological site of Cloggs Cave (GunaiKurnai Country, East Gippsland), in the southern foothills of SE Australia's Great Dividing Range. A new excavation was combined with detailed chronometric dating, high-resolution 3D mapping, and geomorphological studies. This allowed for the interpretation of a sequence of stratigraphic layers spanning from a lowermost excavated mixed layer dated to between 25,640–48,470 cal BP, to a dense set of uppermost, ash layers dated to between 1460–3360 cal BP. This long and well-dated chronostratigraphic sequence enabled temporal trends in the abundant small mammal remains to be examined. The fossil assemblage consists of at least 31 taxa of mammals which change in proportions through time. Despite clear evidence that the Old Ancestors repeatedly carried vegetation into the cave to fuel cool fires (no visible vegetation grows in Cloggs Cave), we observed little to no evidence of cooking fires or calcined bone, suggesting that people had little involvement with the accumulation of the faunal remains. Small mammal bones were most likely deposited in the cave by large disc-faced owls, Tyto novaehollandae (Masked Owl) or Tyto tenebricosa (Sooty Owl). Despite being well-dated and largely undisturbed, the Cloggs Cave assemblage does not appear to track known Late Quaternary environmental change. Instead, the complex geomorphology of the area fostered a vegetation mosaic that supported mammals with divergent habitat preferences. The faunal deposit suggests a local ancestral landscape characterised by a resilient mosaic of habitats that persisted over thousands of years, signaling that the Old Ancestors burned landscape fires to encourage and manage patches of different vegetation types and ages within and through periods of climate change.

opencc-zeroOct 2022View details →

Does artificial feeding impact neonate growth rates in a large free-ranging mammal?

Variation and disparity in resource access between individuals in an animal population require attention within human-dominated landscapes where artificial selection processes may be at work. Independent, recreational human-wildlife feeding interactions constitute an increasingly prevalent yet understudied food resource for birds and mammals living in our cities, but only a limited number of risk-taking individuals may access it. Using urban fallow deer as our model species, we hypothesised that if these interactions result in positive effects for the engaging individual, e.g. increased milk quality and yield, then this would result in the increased growth rates of their offspring. Alternatively, if these individuals were prioritising investing time in engagement with humans, resulting in decreased maternal care, then this would result in slower growth rates in offspring. We found that the offspring of those females that regularly interacted with humans displayed significantly faster growth rates than the risk-avoider counterparts. This advantage for fearless mothers in terms of boosted neonatal growth rates could be mirrored in birds accessing garden feeders, seagulls or pigeons utilizing urban resources, or seals approaching city harbours. Here, we add a new piece to the complex puzzle of how humans are manipulating wildlife living within human-dominated landscapes.

opencc-zeroOct 2022View details →

Two notorious nodes: A critical examination of relaxed molecular clock age estimates of the bilaterian animals and placental mammals

The popularity of relaxed clock Bayesian inference of clade origin timings has generated several recent publications with focal results considerably older than the fossils of the clades in question. Here we critically examine two such clades: the animals (with focus on the bilaterians); and the mammals (with focus on the placentals). Each example displays a set of characteristic pathologies which, although much commented on, are rarely corrected for. We conclude that in neither case does the molecular clock analysis provide any evidence for an origin of the clade deeper than what is suggested by the fossil record. In addition, both these clades have other features (including, in the case of the placental mammals, proximity to a large mass extinction) that allow us to generate precise expectations of the timings of their origins. Thus, in these instances the fossil record can provide a powerful test of molecular clock methodology, and why it goes astray; and we have every reason to think these problems are general.

opencc-zeroApr 2024View details →

Supplementary material: Mammal diversity responses to anthropic, environmental, and seasonal changes within Caatinga seasonal dry forest landscapes

Caatinga's conservation and biodiversity are threatened due to the intensification of anthropic activities and climate change. The mammals have different responses to seasonal and anthropic changes, however particularly in Caatinga, these effects are still poorly understood. We assessed the influence of anthropic (distance from urban areas and wind farms), environmental (distance from water), and seasonal (Normalized Difference Vegetation Index – NDVI and land surface temperature - LST) variables on the number of records and richness of medium and large-sized mammals in Brazilian Caatinga. We used camera traps in 2016/2017 and 2018/2019, estimated the variation (cv) of NDVI and LST, and generated Euclidean distance maps to anthropic and environmental variables at 250, 500, and 1000 m spatial scales. We performed Generalized Linear Models, used the Akaike information criterion, and calculated model averaging to assess the strength and direction of effect and the uncertainties of the winner models, respectively. The distance from wind farms and maximum LST had a noticeable effect on the number of records and total richness. The distance from wind farms had a negative effect on the records of Dicotyles tajacu and a positive effect on the records of Leopardus pardalis and richness. The maximum LST had a negative effect on the records of Leopardus pardalis and a positive effect on the records of Puma concolor and Cerdocyon thous. Our results emphasize that an unsustainable expansion of wind farms is likely to compromise mammal diversity. We found an opposite pattern for some species regarding LST. However, it is important to highlight that the conservation of vegetation areas on the top of mountains and springs, and the installation of artificial water sources are important strategies to mitigate the impacts of high temperatures on mammals' biodiversity in Caatinga.

Ecosystem-wide responses to fire and large mammal herbivores in an African savanna

Fire and large mammal herbivores (LMH) are the principal top-down forces maintaining savanna structure. Nonetheless, experiments designed to investigate interactions between fire and LMH are rare in savannas, and relationships between environmental variation and biodiversity in the context of fire and LMH are poorly understood. This study addresses these gaps by manipulating the presence of LMH and early and late dry season fires in a tropical African savanna. In addition, this work simultaneously explores environmental variables including soil and foliar quality, vegetation cover, and nearby water sources to more holistically describe factors affecting savanna functioning and biodiversity. After one year of experimental treatments, changes in vegetation were already apparent. Shrub abundance and richness and grass richness were higher in the absence of LMH, while grass biomass increased three-fold in burned plots as compared to unburned plots. Foliar nutrients tended to increase in open plots, while phenolics decreased. Amphibian abundance decreased with early burns and was higher with LMH. In contrast, small mammal abundance and richness increased without LMH and with time since fire. Richness and foraging of LMH were highest after late burns. These results demonstrate ecosystem-wide effects of LMH, illustrating the importance of considering multiple taxa when designing fire management programs. For example, burning negatively affected amphibians and small mammals and changed vegetation at the same time it increased LMH foraging. In the long-term, this experiment will shed light on interacting effects of fire and LMH on savanna biodiversity and function.

Data from: Vrba was right: Historical climatic fragmentation, and not current climate, explains mammal biogeography

Climate plays a crucial role in shaping species distribution and evolution over time. Dr. Elisabeth Vrba's Resource-Use hypothesis posited that zones at the extremes of temperature and precipitation conditions should host a greater number of climate specialist species than other zones because of higher historical fragmentation. Here, we tested this hypothesis by examining climate-induced fragmentation over the past 5 million years. Our findings revealed that, as stated by Vrba, the number of climate specialist species increases with historical regional climate fragmentation, whereas climate generalist species richness decreases. This relationship is approximately 40% stronger than the correlation between current climate and species richness for climate specialist species and 77% stronger for generalist species. These evidences suggest that the effect of climate historical fragmentation is more significant than that of current climate conditions in explaining mammal biogeography. These results provide empirical support for the role of historical climate fragmentation and physiography in shaping the distribution and evolution of life on Earth.

Data for: Planning for a future of changes: prioritizing areas for conservation of small mammals in the Caatinga, Brazil

Human land use and climate change are two of the main threats affecting biodiversity, especially in arid/semiarid regions. The most effective way to protect the species in these ecosystems against these threats is through the delimitation of Protected Areas (PAs). However, such PAs need to be targeted cost-efficiently and consider future climate change. We identify priority areas to preserve small mammal species in the Caatinga in the present and in the future of climate change. We also evaluate how well these priority areas are protected by current PAs and identify ways forward to improve their protection. We use ecological niche models and Zonation spatial prioritisation software to identify the top 30% priority areas to preserve small mammal species under current climate and land use scenarios, besides considering optimistic and pessimistic scenarios of future climate change. We also evaluate how much these priority areas are covered by current PAs, identify ways to further improve their protection using hierarchical mask analysis, and evaluate species mean distribution coverage. The consequences of climate change will not hugely impact the distribution of priority areas for species conservation in the Caatinga. Around 13% of the identified priority areas overlap with current PAs, and planning the expansion of PAs considering integral protection areas increases the coverage of priority areas to more than 18% and captures more than 72% of species-suitable areas. Our prioritisations take into account climate change and provide low risk if conducted as a "no-regrets" conservation action. These priority areas are poorly supported by the Brazilian PA system, and need of further protection. One cost-effective option could be to upgrade some Sustainable Use PAs into more restrictive ones. Securing these priority areas helps preserve the long-term ecosystem functioning and to prevent biodiversity loss in a changing world.

The counteracting effects of human-driven speciation and extinction on mammal species richness and phylogenetic diversity

Human activities are causing massive increases in extinction rates, but may also lead to drastic increases in speciation rates – for example following the human-mediated spread of species to otherwise unreachable landmasses. The long-term net anthropogenic effects on biodiversity, therefore, remain uncertain. The aim of this paper is to assess the combined anthropogenic effects of extinctions and speciations on biodiversity over geological time scales. We estimate known anthropogenic and predicted future extinctions based on Red List categories from the International Union for Conservation of Nature. We infer potential anthropogenic speciations assuming that all introductions to isolated landmasses will over time evolve into distinct species. We then estimate changes in regional and global species richness and phylogenetic diversity due to these extinctions and speciations. We show that if all species introduced into new landmasses develop into new species, the number of anthropogenic speciation and extinctions eventually become similar. However, even after accounting for an anthropogenic increase in speciation, our estimates suggest recovery times for phylogenetic diversity of several million years. Our results highlight that while humans are causing drastic biodiversity losses, human-driven speciation could eventually counterbalance these losses in species numbers, while phylogenetic diversity at least within our simulation scenarios would remain permanently reduced. This conclusion, however, requires our pressures on biodiversity to cease soon and requires us to consider geological timescales rather than changes over this century.