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1. Regional Occupancy Is Negatively Related to Richness Across Time and Space

   https://doi.org/10.1111/geb.70009  

   Shipley, B_R; Saupe, E_E (February 2025, Global Ecology and Biogeography)

   ABSTRACT AimBiological diversity is shaped by processes occurring at different spatial and temporal scales. However, the direct influence of the spatial and temporal scale on patterns of occupancy is still understudied. Today, occupancy is often negatively correlated with species richness, but it is unknown whether this relationship is scale dependent and consistent through time. Here, we use datasets of contemporary and paleontological communities to explore the occupancy‐richness relationship across space and time, examining how scale influences this relationship. LocationVarying spatial extents with global coverage. TimeVaries from 7 mya to 2021 CE. Taxaforaminifera, mammals, birds, fish, and plants. MethodsWe gathered datasets spanning different spatial, temporal, and taxonomic extents. We binned each dataset into distinct time periods and spatially subsampled them into regional pools of varying sizes. We calculated regional occupancy and richness for each pool, measuring the strength of the relationship between the two. Using linear mixed models, we related the occupancy‐richness relationship to the size of the regional pools, overall species richness, and climatic changes through time. ResultsWe observed nearly ubiquitous negative occupancy‐richness relationships across taxa, spatial scale, and time. The size of the regional pools and time bins had no consistent effects on the strength of the relationship, but the strength of the negative relationship varied substantially among taxa, with foraminifera and North American pollen showing weaker relationships than mammals and birds. Changes in this relationship through time were not driven by climatic perturbations but by the species richness observed across all regional pools. ConclusionsPatterns of regional richness and occupancy are consistently negatively related and independent of spatial and temporal scale and of direct climatic changes. However, differences in the ecology of species (e.g., dispersal ability) and changes in biodiversity and community composition through time may cause fluctuations in the strength of the occupancy‐richness relationship. 

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2. Mammalian body size is determined by interactions between climate, urbanization, and ecological traits

   https://doi.org/10.1038/s42003-021-02505-3  

   Hantak, Maggie M.; McLean, Bryan S.; Li, Daijiang; Guralnick, Robert P. (December 2021, Communications Biology)

   Abstract Anthropogenically-driven climate warming is a hypothesized driver of animal body size reductions. Less understood are effects of other human-caused disturbances on body size, such as urbanization. We compiled 140,499 body size records of over 100 North American mammals to test how climate and human population density, a proxy for urbanization, and their interactions with species traits, impact body size. We tested three hypotheses of body size variation across urbanization gradients: urban heat island effects, habitat fragmentation, and resource availability. Our results demonstrate that both urbanization and temperature influence mammalian body size variation, most often leading to larger individuals, thus supporting the resource availability hypothesis. In addition, life history and other ecological factors play a critical role in mediating the effects of climate and urbanization on body size. Larger mammals and species that utilize thermal buffering are more sensitive to warmer temperatures, while flexibility in activity time appears to be advantageous in urbanized areas. This work highlights the value of using digitized, natural history data to track how human disturbance drives morphological variation. 

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3. Functional diversity of small-mammal postcrania is linked to both substrate preference and body size

   https://doi.org/10.1093/cz/zoaa057  

   Weaver, Lucas N; Grossnickle, David M (September 2020, Current Zoology)

   Muñoz, Martha (Ed.)

   Abstract Selective pressures favor morphologies that are adapted to distinct ecologies, resulting in trait partitioning among ecomorphotypes. However, the effects of these selective pressures vary across taxa, especially because morphology is also influenced by factors such as phylogeny, body size, and functional trade-offs. In this study, we examine how these factors impact functional diversification in mammals. It has been proposed that trait partitioning among mammalian ecomorphotypes is less pronounced at small body sizes due to biomechanical, energetic, and environmental factors that favor a “generalist” body plan, whereas larger taxa exhibit more substantial functional adaptations. We title this the Divergence Hypothesis (DH) because it predicts greater morphological divergence among ecomorphotypes at larger body sizes. We test DH by using phylogenetic comparative methods to examine the postcranial skeletons of 129 species of taxonomically diverse, small-to-medium-sized (<15 kg) mammals, which we categorize as either “tree-dwellers” or “ground-dwellers.” In some analyses, the morphologies of ground-dwellers and tree-dwellers suggest greater between-group differentiation at larger sizes, providing some evidence for DH. However, this trend is neither particularly strong nor supported by all analyses. Instead, a more pronounced pattern emerges that is distinct from the predictions of DH: within-group phenotypic disparity increases with body size in both ground-dwellers and tree-dwellers, driven by morphological outliers among “medium”-sized mammals. Thus, evolutionary increases in body size are more closely linked to increases in within-locomotor-group disparity than to increases in between-group disparity. We discuss biomechanical and ecological factors that may drive these evolutionary patterns, and we emphasize the significant evolutionary influences of ecology and body size on phenotypic diversity. 

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4. Functional Studies with Primary Cells Provide a System for Genome-to-Phenome Investigations in Marine Mammals

   https://doi.org/10.1093/icb/icaa065  

   Lam, Emily K; Allen, Kaitlin N; Torres-Velarde, Julia María; Vázquez-Medina, José Pablo (June 2020, Integrative and Comparative Biology)

   Synopsis Marine mammals exhibit some of the most dramatic physiological adaptations in their clade and offer unparalleled insights into the mechanisms driving convergent evolution on relatively short time scales. Some of these adaptations, such as extreme tolerance to hypoxia and prolonged food deprivation, are uncommon among most terrestrial mammals and challenge established metabolic principles of supply and demand balance. Non-targeted omics studies are starting to uncover the genetic foundations of such adaptations, but tools for testing functional significance in these animals are currently lacking. Cellular modeling with primary cells represents a powerful approach for elucidating the molecular etiology of physiological adaptation, a critical step in accelerating genome-to-phenome studies in organisms in which transgenesis is impossible (e.g., large-bodied, long-lived, fully aquatic, federally protected species). Gene perturbation studies in primary cells can directly evaluate whether specific mutations, gene loss, or duplication confer functional advantages such as hypoxia or stress tolerance in marine mammals. Here, we summarize how genetic and pharmacological manipulation approaches in primary cells have advanced mechanistic investigations in other non-traditional mammalian species, and highlight the need for such investigations in marine mammals. We also provide key considerations for isolating, culturing, and conducting experiments with marine mammal cells under conditions that mimic in vivo states. We propose that primary cell culture is a critical tool for conducting functional mechanistic studies (e.g., gene knockdown, over-expression, or editing) that can provide the missing link between genome- and organismal-level understanding of physiological adaptations in marine mammals. 

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5. Variable Gene Copy Number in Cancer-Related Pathways Is Associated With Cancer Prevalence Across Mammals

   https://doi.org/10.1093/molbev/msaf056  

   Matthews, Sophie; Nikoonejad_Fard, Vahid; Tollis, Marc; Seoighe, Cathal (March 2025, Molecular Biology and Evolution)

   Yeager, Meredith (Ed.)

   Abstract Cancer is a disease of multicellularity, observed across the tree of life. In principle, animals with larger body sizes and longer lifespans should be at increased risk of developing cancer. However, there is no strong relationship between these traits and cancer across mammals. Previous studies have proposed that increased copy number of cancer-related genes may enhance the robustness of cancer suppression pathways in long-lived mammals, but these studies have not extended beyond known cancer-related genes. In this study, we conducted a phylogenetic generalized least squares analysis to test for associations between copy number of all protein-coding genes and longevity, body size, and cancer prevalence across 94 species of mammals. In addition to investigating the copy number of individual genes, we tested sets of related genes for a relationship between the aggregated gene copy number of the set and these traits. We did not find strong evidence to support the hypothesis that adaptive changes in gene copy number contribute to the lack of correlation between cancer prevalence and body size or lifespan. However, we found several biological processes where aggregate copy number was associated with malignancy rate. The strongest association was for the gene set relating to transforming growth factor beta, a cytokine that plays a role in cancer progression. Overall, this study provides a comprehensive evaluation of the role of gene copy number in adaptation to body size and lifespan and sheds light on the contribution of gene copy number to variation in cancer prevalence across mammals. 

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