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opencc-by-4.0Oct 2022View details →

Small mammal classification model

Classification model for small mammals and images used for training, validating and testing the model. The script used for training and further information are available on https://github.com/hannaboe/camera_trap_workflow.

opencc-by-4.0Apr 2023View details →

Figure 1 in Notes on Mammals Collected on the 1885 Geographical Society of Australasia's Expedition to New Guinea

Figure 1. Strickland River, Papua New Guinea: (A) satellite image from Google Earth; (B) extracts from map of the Strickland River, New Guinea, survey by SS Bonito Expedition (available in State Library of NSW: Z/M2 921.46/1885/1) showing location of Fly/Strickland junction, Observatory Bend, and Fossil Camp; and (C) Google Earth image and map superimposed.

opencc-by-4.0Apr 2023View details →

Figure 2 in Notes on Mammals Collected on the 1885 Geographical Society of Australasia's Expedition to New Guinea

Figure 2. Tags associated with Australian Museum specimens collected on the Expedition. (A) earliest tag associated with M.26666, Melomys rufescens (Alston, 1877), found unregistered in the Collection in 1992; (B, C) presumed taxidermist's tag attached in 1912, in handwriting characteristic of similar tags attached to all specimens attributed to the Expedition (M.2375, Rattus lutreolus).

opencc-by-4.0Dec 2022View details →

A genomic timescale for placental mammal evolution: Datasets

Datasets used in Foley N.M., Mason, V.C., Harris A.J., Bredemeyer K.R., Damas J., Lewin H.A., Eizirik E., Gatesy J., Zoonomia Consortium, Springer M.S., and W.J. Murphy (2022) A genomic timescale for placental mammal evolution. Science. x:x-x This repository includes - Alignments for whole genome analyses - Alignments for sliding windows analyses across chromosome 1, chromosome 21, chromosome 22 and the X chromosome - Sliding window alignments used to estimate divergence times - Preliminary topologies derived from the low recombining region on the X chromosome - Machine readable (.csv) versions of tables presented in the paper - Per chromosome fasta files referenced to the human genome exported from the HAL alignment as described in the paper. ~~~~~~~~~~~~~~ v1.1 added nexus topologies for datasets listed in Table S2

opencc-zeroMay 2023View details →

Data from: Early Cenozoic increases in mammal diversity cannot be explained solely by expansion into larger body sizes

A prominent hypothesis in the diversification of placental mammals after the Cretaceous/Paleogene (K/Pg) boundary suggests that the extinction of non-avian dinosaurs resulted in the ecological release of mammals, which were previously constrained to small body sizes and limited species richness. This "dinosaur incumbency hypothesis" may therefore explain increases in mammalian diversity via expansion into larger body sizes, that were previously occupied by dinosaurs, but does not directly predict increases in other body size classes. To evaluate this, we estimate sampling-standardised diversity patterns of terrestrial North American fossil mammals within body size classes, through the Cretaceous and Paleogene. We find strong evidence for post-extinction diversity increases in all size classes. Increases in the diversity of small-bodied species (less than 100 g, the common body size class of Cretaceous mammals, and much smaller than the smallest non-avialan dinosaurs [~400 g]) were similar to those of larger species. We propose that small-bodied mammals had access to greater energetic resources or were able to partition resources more finely after the K/Pg mass extinction. This likely resulted from a combination of widespread niche clearing due to the K/Pg mass extinctions, alongside a suite of biotic and abiotic changes that occurred during the Late Cretaceous and across the K/Pg boundary, such as shifting floral composition, and novel key innovations among eutherian mammals.

opencc-zeroJun 2023View details →

Area, isolation, and climate explain the diversity of mammals on island worldwide

Identifying the determinants of insular biodiversity at large scales remains a question in biogeography. We conducted a global test of island biogeography theory by evaluating the importance of island physical, environmental, and historical characteristics on mammal species richness and endemism. We quantified the effects of island characteristics while accommodating variation among biogeographic realms by fitting generalized linear and mixed models. Analyzes were also performed separately for bats and non-volant mammals. Diversity patterns were most consistently influenced by the physical characteristics of the islands. Area positively affected mammal diversity, in particular the number of non-volant endemics. Island isolation, both current and past, was associated with lower richness but greater endemism. Flight capacity modified the relative importance of past versus current isolation, with bats responding more strongly to current and non-volant mammals to past isolation. Environmental effects on biodiversity were more variable, with a tendency for greater effects on endemism than on richness. Unexpectedly, climate change velocity was positively associated with endemism. In line with island biogeography theory, we found that area and isolation were among the strongest drivers of overall mammalian biodiversity. Moreover, our results support the growing evidence on the importance of past conditions on current patterns, particularly on non-volant species.

opencc-zeroDec 2022View details →

Behavioral responses of terrestrial mammals to COVID-19 lockdowns

COVID-19 lockdowns in early 2020 reduced human mobility, providing an opportunity to disentangle its effects on animals from those of landscape modifications. Using GPS data, we compared movements and road avoidance of 2300 terrestrial mammals (43 species) during the lockdowns to the same period in 2019. Individual responses were variable, with no change in average movements or road avoidance behavior, likely due to variable lockdown conditions. However, under strict lockdowns, 10-day 95th percentile displacements increased by 73%, suggesting increased landscape permeability. Animals' 1-hour 95th percentile displacements declined by 12%, and animals were 36% closer to roads in areas of high human footprint, indicating reduced avoidance during lockdowns. Overall, lockdowns rapidly altered some spatial behaviors, highlighting variable but substantial impacts of human mobility on wildlife worldwide.

opencc-zeroJun 2023View details →

Diet and the evolution of ADH7 across seven orders of mammals

Dietary variation within and across species drives the eco-evolutionary responsiveness of genes necessary to metabolize nutrients and other components. Recent evidence from humans and other mammals suggests that sugar-rich diets of floral nectar and ripe fruit have favored mutations in, and functional preservation of, the ADH7 gene, which encodes the ADH class 4 enzyme responsible for metabolizing ethanol. Here we interrogate a large, comparative dataset of ADH7 gene sequence variation, including the amino acid residue located at key site 294 that regulates the affinity of ADH7 for ethanol. Our analyses span 171 mammal species, including 59 newly sequenced. We report extensive variation, especially among frugivorous and nectarivorous bats, with potential for functional impact, and widespread variation in the retention and probable pseudogenization of ADH7. However, we find little statistical evidence of a broad impact of diet on putative ADH7 function or tuning at site 294 across mammals, suggesting that the evolution of ADH7 is shaped by complex factors. Our study reports extensive new diversity in a gene of longstanding ecological interest, offers new sources of variation to be explored in functional assays in future studies, and advances our understanding of the processes of molecular evolution.

opencc-zeroJun 2023View details →

Ecological marginalization is widespread and increases extinction risk in mammals

Human land-use results in widespread range change across taxa. Anthropogenic pressures can result in species' realized niches expanding, shifting, or contracting. Marginalization occurs when contraction constrains species to the geographic or ecological extremes of their historic niche. Using 4,785 terrestrial mammal species, we show that range contraction results in niche space and habitat diversity loss. Additionally, ecological marginalization is a common consequence of range contraction caused by human land use change. Remnant populations become located in the climatic and topographic extremes of their historic niche that are more likely to be at the periphery of their historic niche at greater distances from historic niche centroids. This ecological marginalization is associated with poor performance and increased extinction risk independent of geographic range loss. Range loss and marginalization may create a "double whammy" in vulnerable groups, such as large-bodied species and species with small geographical range size. Our results reveal a hitherto unrecognized conservation threat that is vital to incorporate into conservation assessment and management.

FIG. 54 in Cranial And Postcranial Morphology Of The Insectivoran-Grade Mammals Hsiangolestes And Naranius (Mammalia, Eutheria) With Analyses Of Their Phylogenetic Relationships

FIG. 54. Drawing of anterior part of skull of?Didymoconidae: A. dorsal, B. ventral, and C. left lateral views (based on IVPP V7441).

FIG. 51 in Cranial And Postcranial Morphology Of The Insectivoran-Grade Mammals Hsiangolestes And Naranius (Mammalia, Eutheria) With Analyses Of Their Phylogenetic Relationships

FIG. 51. Drawing of temporal region of skull of Naranius hengdongensis, sp. n. (based on IVPP V 5353).

FIG. 47 in Cranial And Postcranial Morphology Of The Insectivoran-Grade Mammals Hsiangolestes And Naranius (Mammalia, Eutheria) With Analyses Of Their Phylogenetic Relationships

FIG. 47. Skull and lower jaw of Naranius hengdongensis, sp. n., IVPP V5352: A. right lateral, B. left lateral, C. dorsal, and D. right dorsal-lateral views.

FIG. 44 in Cranial And Postcranial Morphology Of The Insectivoran-Grade Mammals Hsiangolestes And Naranius (Mammalia, Eutheria) With Analyses Of Their Phylogenetic Relationships

FIG. 44. Anterior part of skull of Naranius hengdongensis, sp. n., IVPP V7440: A. right lateral, B. left lateral, and C. dorsal views.

FIG. 38. Hsiangolestes youngi, IVPP V5797 in Cranial And Postcranial Morphology Of The Insectivoran-Grade Mammals Hsiangolestes And Naranius (Mammalia, Eutheria) With Analyses Of Their Phylogenetic Relationships

FIG. 38. Hsiangolestes youngi, IVPP V5797, skull and postcranial bones: A. ventral and B. dorsal views of skull, showing preservation before preparation.

FIG. 53 in Cranial And Postcranial Morphology Of The Insectivoran-Grade Mammals Hsiangolestes And Naranius (Mammalia, Eutheria) With Analyses Of Their Phylogenetic Relationships

FIG. 53. Anterior part of skull of?Didymoconidae, IVPP V7441: A. ventral, B. dorsal, and C. left lateral views.

FIG. 46 in Cranial And Postcranial Morphology Of The Insectivoran-Grade Mammals Hsiangolestes And Naranius (Mammalia, Eutheria) With Analyses Of Their Phylogenetic Relationships

FIG. 46. Lower jaws of Naranius hengdongensis, sp. n., IVPP V7439: A. stereophotograph of left lower jaw in occlusal view; B. lingual view of left lower jaw; C. labial view of left lower jaw; D. stereophotograph of right lower jaw in occlusal view; E. lingual view of right lower jaw; F. labial view of right lower jaw.

FIG. 50 in Cranial And Postcranial Morphology Of The Insectivoran-Grade Mammals Hsiangolestes And Naranius (Mammalia, Eutheria) With Analyses Of Their Phylogenetic Relationships

FIG. 50. Skull of Naranius hengdongensis, sp. n., IVPP V7439: A. right lateral and B. left lateral views.

FIG. 39. Hsiangolestes youngi, IVPP V5797 in Cranial And Postcranial Morphology Of The Insectivoran-Grade Mammals Hsiangolestes And Naranius (Mammalia, Eutheria) With Analyses Of Their Phylogenetic Relationships

FIG. 39. Hsiangolestes youngi, IVPP V5797: A. left femur; B. right pelvic girdle; C. rib; D. right tibia.

FIG. 34. Hsiangolestes youngi, IVPP V7454 in Cranial And Postcranial Morphology Of The Insectivoran-Grade Mammals Hsiangolestes And Naranius (Mammalia, Eutheria) With Analyses Of Their Phylogenetic Relationships

FIG. 34. Hsiangolestes youngi, IVPP V7454, stereophotograph of right ear region in A. turning lateral side to ventral and B. ventral views.

FIG. 48 in Cranial And Postcranial Morphology Of The Insectivoran-Grade Mammals Hsiangolestes And Naranius (Mammalia, Eutheria) With Analyses Of Their Phylogenetic Relationships

FIG. 48. Skull and lower jaw of Naranius hengdongensis, sp. n., IVPP V5353: A. ventral, B. dorsal, C. left lateral, and D. right lateral views.