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Figure 9. Ultra high resolution X in Cranial anatomy of Paleocene and Eocene Labidolemur kayi (Mammalia: Apatotheria), and the relationships of the Apatemyidae to other mammals
Figure 9. Ultra high resolution X-ray computed tomography (uhrCT) slices of USNM 530208, and enlarged view of the left auditory region. See caption for Figure 8. In all images the white arrow indicates a fragment of bone, identified as a piece of the basisphenoid, which has been displaced rostrally along the basisphenoid process. In all four uhrCT images the portion of the basisphenoid medial to the fragment in question is clearly damaged. This can be seen in its irregular outline, and in the lack of symmetry with the less damaged right side. Panel (D) also shows some fragments of bone ventrally, which underscore the damage that has occurred in this region. The enlarged view of the left auditory region has been tipped medially so that the medial wall of the tympanic cavity is visible. Note the step fractures along the fragment of basisphenoid, indicated with the black arrow, indicating damage and probably displacement.
Figure 1 in Cranial anatomy of Paleocene and Eocene Labidolemur kayi (Mammalia: Apatotheria), and the relationships of the Apatemyidae to other mammals
Figure 1. Photographs of Labidolemur kayi, USNM 530221. Skull in (A) dorsal, (B) left, (C) right, and (D) right view tilted ventrally. As this skull is part of a semiarticulated skeleton, it is not possible to take a photograph from a strictly ventral perspective. Scale bar: 5 mm.
Determining the efficacy of camera traps, live capture traps, and detection dogs for locating cryptic small mammal species
<p>Metal box (e.g., Elliott, Sherman) traps and remote cameras are two of the most commonly employed methods presently used to survey terrestrial mammals. However, their relative efficacy at accurately detecting cryptic small mammals has not been adequately assessed. The present study therefore compared the effectiveness of metal box (Elliott) traps and vertically oriented, close range, white flash camera traps in detecting small mammals occurring in the Scenic Rim of eastern Australia. We also conducted a preliminary survey to determine effectiveness of a conservation detection dog (CDD) for identifying presence of a threatened carnivorous marsupial, <i>Antechinus arktos,</i> in present-day and historical locations, using camera traps to corroborate detections. 200 Elliott traps and 20 white flash camera traps were set for four deployments per method, across a site where the target small mammals, including <i>A. arktos</i>, are known to occur. Camera traps produced higher detection probabilities than Elliott traps for all four species. Thus, vertically mounted white flash cameras were preferable for detecting the presence of cryptic small mammals in our survey. The CDD, which had been trained to detect <i>A. arktos</i> scat, indicated in total 31 times when deployed in the field survey area, with subsequent camera trap deployments specifically corroborating <i>A. arktos</i> presence at 100% (3) indication locations. Importantly, the dog indicated twice within Border Ranges National Park, where historical (1980s-1990s) specimen-based records indicate the species was present, but extensive Elliott and camera trapping over the last 5-10 years have resulted in zero <i>A. arktos</i> captures. Camera traps subsequently corroborated <i>A. arktos</i> presence at these sites. This demonstrates that detection dogs can be a highly effective means of locating threatened, cryptic species, especially when traditional methods are unable to detect low-density mammal populations.</p>
Global camera trap synthesis highlights the importance of protected areas in maintaining mammal diversity
<p>The establishment of protected areas (PAs) is a central strategy for global biodiversity conservation. While the role of PAs in protecting habitat has been highlighted, their effectiveness at protecting mammal communities remains unclear. We analyzed a global dataset from over 8,671 camera traps in 23 countries on four continents that detected 321 medium- to large-bodied mammal species. We found a strong positive correlation between mammal taxonomic diversity and the proportion of a surveyed area covered by PAs at a global scale (b = 0.39, 95% CI = 0.19, 0.60) and in Indomalaya (b = 0.69, 95% CI = 0.19,1.2), as well as between functional diversity and PA coverage in the Nearctic (b = 0.47, 95% CI = 0.09, 0.85), after controlling for human disturbances and environmental variation. Functional diversity was only weakly (and insignificantly) correlated with PA coverage at the global scale (b =0.22, 95% CI = -0.02, 0.46), pointing to a need to better understand the functional response of mammal communities to protection. Our study provides important evidence of the global effectiveness of PAs in conserving terrestrial mammals and emphasizes the critical role of area-based conservation in a post-2020 biodiversity framework.</p>
Western Antarctic marine mammal and seabird distance sampling data
<p>These datasets are:</p> <p>1) Raw (MS Access) IFAW Logger2010 tables (<a href="http://www.marineconservationresearch.co.uk/downloads/logger-2000-rainbowclick-software-downloads/">http://www.marineconservationresearch.co.uk/downloads/logger-2000-rainbowclick-software-downloads/</a>) and</p> <p>2) .RData objects preprocessed by the R package LoggeR (<a href="https://github.com/embiuw/LoggeR">https://github.com/embiuw/LoggeR</a>), for distance sampling of marine mammals and seabirds from two ships of opportunity along the Western Antarctic Peninsula, Drake Passage and Scotia Sea during the 2019 - 2020 austral summer. The ships were the MS Fram and MS Midnatsol of the Hurtigruten fleet, with data collected from the start of December 2019 until late January 2020. </p>
Mammal-mediated seed dispersal in Vanilla: its rewards and clues to the evolution of fleshy fruits in orchids
<p>Data on frequency of visits by Vanilla bahiana dispersers and data on acid scarification of seeds.</p>
Data from: Scat DNA provides important data for effective monitoring of mammal and bird biodiversity
<p>Fauna has long been neglected in the monitoring of ecological restoration, despite the key role they play in ecosystem function. Vertebrate surveys can be time consuming and costly, often requiring multiple methodologies and taxonomic expertise, making comprehensive monitoring cost prohibitive. Here we evaluate a new method of assessing mammal and bird diversity through the genetic identification of scat collections. Using DNA metabarcoding of scat collections from three bioregions we generated bird and mammalian assemblage data and distinguished between sites with different restoration histories. However, scat detectability was affected by environmental conditions (e.g. rainfall and soil), suggesting that our approach is most applicable at certain times of year or in arid (or semi-arid) environments with rocky soils, where conditions are favourable for scat preservation. Taken together these data provide a pathway to: plan, monitor and establish best-practice when restoring landscapes and add to the growing body of literature on the value of DNA metabarcoding in biomonitoring applications.</p>
Figure 3. A in The evolution of anteriorly directed molar occlusion in mammals
Figure 3. A, reconstructions of muscle orientation that highlight the posited shift to anteriorly directed resultant force vectors in cladotherians. Although early cladotherians did not possess anterior occlusal movement, they did have increased transverse movement that might have been generated by anteriorly oriented muscles (see main text; Grossnickle, 2017). For simplicity, the temporalis is not included in the reconstructions, but it is expected to remain posteriorly oriented in all synapsids (Turnbull, 1970; DeMar & Barghusen, 1972; Lautenschlager et al., 2017). B, the evolution of a posterior angular process and detached middle ear (DME) in cladotherians, but note that the DME evolved independently in multituberculates (not illustrated here) and that there is uncertainty about the evolutionary timing of the DME in the lineage leading to therians (Urban et al., 2017; Luo & Manley, 2020; Mao et al., 2020). For the jaw representing eutriconodontans and spalacotherioids, the middle ear elements are displaced medially from the jaw, but the ossified Meckel's cartilage (MC; yellow) maintains an ear–jaw connection. Skull and jaw reconstructions are based on images in papers by Allin (1975), Sues (1986), Kermack et al. (1981), Krause (1982), Fish (1983), Krebs (1991), Rougier et al. (2003), Kielan-Jaworowska et al. (2004), Hu et al. (2005), Paéz Arango (2008), Wible et al. (2009), Lautenschlager et al. (2017), Bhullar et al. (2019) and Panciroli et al. (2021).
Figure 1 in The evolution of anteriorly directed molar occlusion in mammals
Figure 1. Jaw movement during molar occlusion in a didelphid opossum. The straight red arrows represent movement during the two phases of occlusion (Schwermann, 2014), and the dashed line is the outline of the upper molar. In both the occlusal view (left box) and posterior view (right box), the arrows follow the path of homologous cusps (the protoconids). The 'compass rose' illustrates the occlusal movement in occlusal view, with the lengths of the arrows reflecting the inclination angles of the phase; the shorter arrow represents a steeper, dorsomedial movement, and the longer arrow represents a shallower medial movement (von Koenigswald et al., 2013). We categorize this taxon (Monodelphis) as having an 'anterior component' because at least one of the phases includes anterior movement. Inserting on the jaw are three muscles that contract simultaneously in many therians to create medial movement via yaw (curved red arrow): working-side superficial masseter (SM), working-side medial pterygoid (MP) and balancing-side temporalis (T). The silhouette is by Sarah Werning (license CC BY 3.0, unaltered image).
Figure 2 in The evolution of anteriorly directed molar occlusion in mammals
Figure 2. Jaw directional movement during postcanine occlusion in synapsids, highlighting the evolutionary origin of anteriorly directed occlusion at or near the therian node. Lineage colours correspond to the 'compass rose' directions (see main text; Supporting Information, Table S1), with 'transverse-shearing' represented by black-and-grey dashed lines. For the didelphid, docodontan and ungulate jaws, the left hemimandible is the working side. Ancestral reconstructions of occlusal direction are based, in part, on ancestral molar morphologies. For instance, early therian lineages possess a tribosphenic molar morphology, which generally includes some degree of anterior occlusal movement (Fig. 1; Crompton & Hiiemae, 1970; Kallen & Gans, 1972; Kay & Hiiemae, 1974a; Schwermann, 2014). Lineages along the phylogenetic backbone of the non-mammalian cynodont portion of the phylogeny are likely to have possessed triconodont dentitions, with occlusion that is primarily orthal or 'transverse-shearing' (Crompton, 1972; Bonaparte et al., 2005; Jäger et al., 2019). For additional information and sources, see the Supporting Information (Table S1). The phylogeny and fossil ages are from Rougier et al. (2012), Huttenlocker et al. (2018), Jones et al. (2019), Upham et al. (2019), King & Beck (2020) and the Paleobiology Database (paleobiodb.org). The multituberculate silhouette is based on artwork by Misaki Ouchida. Additional silhouettes are from phylopic.org and attributed to Sarah Werning (licence CC BY 3.0, unaltered image; didelphid), Rebecca Groom (CC BY-SA 3.0; rodent), Dfoidl (CC BY-SA 3.0; ungulate) and FunkMonk Michael B. H. (CC BY-SA 3.0; docodontan).
Counting the bodies: estimating the numbers and spatial variation of Australian reptiles, birds and mammals killed by two invasive mesopredators
<p>Aim: Introduced predators negatively impact biodiversity globally, with insular fauna often most severely affected. Here, we assess spatial variation in the number of terrestrial vertebrates (excluding amphibians) killed by two mammalian mesopredators introduced to Australia, the red fox (Vulpes vulpes) and feral cat (Felis catus). We aim to identify prey groups that suffer especially high rates of predation, and regions where losses to foxes and/or cats are most substantial. Location: Australia Methods: We draw information on the spatial variation in tallies of reptiles, birds and mammals killed by cats in Australia from published studies. We derive tallies for fox predation by (i) modelling continental-scale spatial variation in fox density, (ii) modelling spatial variation in the frequency of occurrence of prey groups in fox diet, (iii) analysing the number of prey individuals within dietary samples, and (iv) discounting animals taken as carrion. We derive point estimates of the numbers of individuals killed annually by foxes and by cats, and map spatial variation in these tallies. Results: Foxes kill more reptiles, birds and mammals (peaking at 1,071 km-2 yr-1) than cats (55 km-2 yr-1) across most of the unmodified temperate and forested areas of mainland Australia, reflecting the generally higher density of foxes than cats in these environments. However, across most of the continent – mainly the arid central and tropical northern regions (and on most Australian islands) – cats kill more animals than foxes. We estimate that foxes and cats together kill 697 million reptiles annually in Australia, 510 million birds and 1435 million mammals. Main conclusions: This continental-scale analysis demonstrates that predation by two introduced species takes a substantial and ongoing toll on Australian reptiles, birds and mammals. Continuing population declines and potential extinctions of some of these species threatens to further compound Australia's poor contemporary conservation record.</p>
Histological and life history data for small-bodied mammals from: Multituberculate mammals show evidence of a life history strategy similar to that of placentals, not marsupials
<p>The remarkable evolutionary success of placental mammals has been partly attributed to their reproductive strategy of prolonged gestation and birthing of relatively precocial, quickly weaned neonates. Although this strategy was conventionally considered derived relative to that of marsupials with highly altricial neonates and long lactation periods, mounting evidence has challenged this view. Until now, the fossil record has been relatively silent on this debate, but here we find that proportions of different bone tissue microstructures in the femoral cortices of small extant marsupials and placentals correlate with length of lactation period, allowing us to apply this histological correlate of reproductive strategies to Late Cretaceous and Paleocene members of Multituberculata, an extinct mammalian clade that is phylogenetically stemward of Theria. Multituberculate bone histology closely resembles that of placentals, suggesting that they had similar life history strategies. That a stem-therian clade exhibits evidence of placental-like life histories supports the hypothesis that intense maternal-fetal contact characteristic of placentals is ancestral for therians. Alternatively, multituberculates and placentals may have independently evolved prolonged gestation and abbreviated lactation periods. Our results challenge the hypothesis that the rise of placental mammals was driven by unique life history innovations, and shed new light on early mammalian diversification.</p>
Figure 4 in A new rhinoceros clade from the Pleistocene of Asia sheds light on mammal dispersals to the Philippines
Figure 4. Ancestral biogeographical ranges of Rhinocerotinae, as calculated using BioGeoBEARS package in R (Matzke, 2013; Massana et al., 2015) and mapped on the phylogeny retrieved in Figure 3. Spatial ranges of all terminal taxa included in the phylogenetic and biogeographical analyses were split into eight domains, likely to coalesce: Americas (R), Afro-Arabia (A), Europe + Mediterranean (E), Central Asia (C), South and South-East Asia (M), Indonesia (S), Taiwan (T), Philippines (P).
Figure 3 in A new rhinoceros clade from the Pleistocene of Asia sheds light on mammal dispersals to the Philippines
Figure 3. Dental and postcranial features characterizing the new genus Nesorhinus in the phylogenetic framework as depicted in Figure 2. Red circles denote synapomorphies of Nesorhinus, whilst green and blue circles correspond to diagnostic characters (autapomorphies) of N. philippinensis and of N. hayasakai, respectively. Nesorhinus philippinensis: A, left upper dental series (D1–M1) in occlusal view (II-2014-J1-294, 095, 409, 427); B, left m2–3 in occlusal view (II-2014-J1-405); C, right p3–m1 in labial view (II-2014-J1-451); D, left scapula in lateral view (II-2014-J1-291). Nesorhinus hayasakai: E, left upper dental series (D1–M3) in occlusal view (DGNTU-FV11b; modified from Hayasaka, 1942); F, right m3 in occlusolabial view (HTR-55); G, left m3 in labial view (HTR-91); H, left fragmentary scapula (HTR-1). Completeness of the skeleton of N. philippinensis found at Kalinga (I): preserved elements appear in dark green. Tentative silhouettes of N philippinensis (J) and N. hayasakai (K) are drawn at a same scale, with a shoulder height of 1.26 m for N. philippinensis. See Supporting Information for further details on body size. Scale bar, 5 cm (A–C, E–G) and 10 cm (D, H).
Figure 2 in A new rhinoceros clade from the Pleistocene of Asia sheds light on mammal dispersals to the Philippines
Figure 2. Phylogenetic tree of the Rhinocerotidae, built from 278 unweighted craniomandibular, dental and postcranial characters scored in 30 ceratomorph species, and replaced in their stratigraphical context. Tapirus terrestris (Linnaeus, 1758), Hyrachyus eximius Leidy, 1871, Trigonias osborni and Ronzotherium filholi were used as outgroups. Most-parsimonious tree (length: 1315 steps; CI = 0.2821; RI = 0.4858). Node ages were obtained using the approach of Brusatte et al. (2008), as implemented in the paleotree package (Bapst, 2012) in R 4.0.3 (R Core Team, 2020), with the first splitting event set to 60 Mya. Red star and green diamond indicate the earliest occurrences of Dicerorhinus sensu stricto (13 Mya; Heissig, 1972; Antoine et al., 2013) and Teleoceratina (25 Mya; see Supporting Information, Table S2). Aceini, Aceratheriini; DRc, Dicerorhinus–Rhinoceros clade; Dti, Diceroti; Elinae, Elasmotheriinae; Rti, Rhinoceroti; Telina, Teleoceratina. Recent species names are underlined.
Establishment of a fecal DNA quantification technique for rare and cryptic diet constituents in small mammals - raw data
<p class="MsoNormal"><span>DNA-based approaches have highly improved the applicability of dietary studies aimed at investigating ecological processes. These studies have provided direct insights into, otherwise difficult to measure, interactions between species and trophic levels, food web structure and ecosystem functioning. However, despite these advances, DNA-based methods have been struggling to accurately quantify the whole breadth of diet constituents because of methodological biases, such as amplification bias and digestive processes. This study is, to our knowledge, the first diet study that used droplet digital PCR to quantify diet constituents. We manipulated the diet of wild caught wood mice (<em>Apodemus sylvaticus</em>) by feeding them with a known amount of small vegetable seeds (onion and carrot) and quantified the DNA traces of these diet constituents in fecal samples. The sensitivity of the technique combined with the control on the experimental design allowed mitigation of methodological bias. We were able to accurately determine DNA concentrations of small vegetable seeds in the diet of wood mice. Quantification of target DNA demonstrated significant differences in DNA content when one vs. five seeds were consumed. <a name="_Hlk96526385"></a>These differences remained significant when the age, sex, and other diet constituents of the mice were altered. Different DNA markers, targeting different parts of the chloroplast, influenced onion DNA detectability. However, all onion and carrot markers showed higher DNA content for higher seed numbers. Overall, the sensitive DNA based approach developed in this study allows for minimally-invasive quantification of small diet constituents in feces, which would otherwise be undetectable with traditional methods.</span></p>
Mammals adjust diel activity across gradients of urbanization
<p>Time is a fundamental component of ecological processes. How animal behavior changes over time has been explored through well-known ecological theories like niche partitioning and predator-prey dynamics. Yet, changes in animal behavior within the shorter 24-hour light-dark cycle have largely gone unstudied. Understanding if an animal can adjust their temporal activity to mitigate or adapt to environmental change has become a recent topic of discussion and is important for effective wildlife management and conservation. While spatial habitat is a fundamental consideration in wildlife management and conservation, temporal habitat is often ignored. We formulated a temporal resource selection model to quantify the diel behavior of eight mammal species across ten U.S. cities. We found high variability in diel activity patterns within and among species and species-specific correlations between diel activity and human population density, impervious land cover, available greenspace, vegetation cover, and mean daily temperature. We also found that some species may modulate temporal behaviors to manage both natural and anthropogenic risks. Our results highlight the complexity with which temporal activity patterns interact with local environmental characteristics, and suggest that urban mammals may use time along the 24-hour cycle to reduce risk, adapt, and therefore persist in human-dominated ecosystems.</p>
Figure 5 in Diegoaelurus, a new machaeroidine (Oxyaenidae) from the Santiago Formation (late Uintan) of southern California and the relationships of Machaeroidinae, the oldest group of sabertooth mammals
Figure 5 Radiograph of the left dentary of Diegoaelurus vanvalkenburghae sp. nov. (SDSNH 38343). Note the absence of alveoli in the expected position of p4 (arrow) indicating that the tooth was either pathologically absent or that loss occurred well antemortem. Scale bar is 1 cm. Full-size DOI: 10.7717/peerj.13032/fig-5
Figure 6 in Diegoaelurus, a new machaeroidine (Oxyaenidae) from the Santiago Formation (late Uintan) of southern California and the relationships of Machaeroidinae, the oldest group of sabertooth mammals
Figure 6 Phylogeny of Machaeroidinae. Single most parsimonious tree (L: 30; CI: 0.83; RI: 0.61) depicting the interrelationships of Machaeroidinae. Numbers below nodes within the ingroup indicate Bremer support. Full-size DOI: 10.7717/peerj.13032/fig-6
Figure 3 in Diegoaelurus, a new machaeroidine (Oxyaenidae) from the Santiago Formation (late Uintan) of southern California and the relationships of Machaeroidinae, the oldest group of sabertooth mammals
Figure 3 Anterior view of the holotype of Diegoaelurus vanvalkenburghae sp. nov. (SDSNH 38343) showing the lateral flaring of the mandibular flange. Image is taken from a 3D model of the holotype. Scale bar is 10 mm. Full-size DOI: 10.7717/peerj.13032/fig-3
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.