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1. Large Comparative Analyses of Primate Body Site Microbiomes Indicate that the Oral Microbiome Is Unique among All Body Sites and Conserved among Nonhuman Primates

   https://doi.org/10.1128/spectrum.01643-21  

   Asangba, Abigail E. ; Mugisha, Lawrence ; Rukundo, Joshua ; Lewis, Rebecca J. ; Halajian, Ali ; Cortés-Ortiz, Liliana ; Junge, Randall E. ; Irwin, Mitchell T. ; Karlson, Johan ; Perkin, Andrew ; et al ( June 2022 , Microbiology Spectrum)

   Kormas, Konstantinos Aristomenis (Ed.)

   ABSTRACT The study of the mammalian microbiome serves as a critical tool for understanding host-microbial diversity and coevolution and the impact of bacterial communities on host health. While studies of specific microbial systems (e.g., in the human gut) have rapidly increased, large knowledge gaps remain, hindering our understanding of the determinants and levels of variation in microbiomes across multiple body sites and host species. Here, we compare microbiome community compositions from eight distinct body sites among 17 phylogenetically diverse species of nonhuman primates (NHPs), representing the largest comparative study of microbial diversity across primate host species and body sites. Analysis of 898 samples predominantly acquired in the wild demonstrated that oral microbiomes were unique in their clustering, with distinctive divergence from all other body site microbiomes. In contrast, all other body site microbiomes clustered principally by host species and differentiated by body site within host species. These results highlight two key findings: (i) the oral microbiome is unique compared to all other body site microbiomes and conserved among diverse nonhuman primates, despite their considerable dietary and phylogenetic differences, and (ii) assessments of the determinants of host-microbial diversity are relative to the level of the comparison (i.e., intra-/inter-body site, -host species, and -individual), emphasizing the need for broader comparative microbial analyses across diverse hosts to further elucidate host-microbial dynamics, evolutionary and biological patterns of variation, and implications for human-microbial coevolution. IMPORTANCE The microbiome is critical to host health and disease, but much remains unknown about the determinants, levels, and evolution of host-microbial diversity. The relationship between hosts and their associated microbes is complex. Most studies to date have focused on the gut microbiome; however, large gaps remain in our understanding of host-microbial diversity, coevolution, and levels of variation in microbiomes across multiple body sites and host species. To better understand the patterns of variation and evolutionary context of host-microbial communities, we conducted one of the largest comparative studies to date, which indicated that the oral microbiome was distinct from the microbiomes of all other body sites and convergent across host species, suggesting conserved niche specialization within the Primates order. We also show the importance of host species differences in shaping the microbiome within specific body sites. This large, comparative study contributes valuable information on key patterns of variation among hosts and body sites, with implications for understanding host-microbial dynamics and human-microbial coevolution. 

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2. Hibernation slows epigenetic ageing in yellow-bellied marmots

   https://doi.org/10.1038/s41559-022-01679-1  

   Pinho, Gabriela M. ; Martin, Julien G. A. ; Farrell, Colin ; Haghani, Amin ; Zoller, Joseph A. ; Zhang, Joshua ; Snir, Sagi ; Pellegrini, Matteo ; Wayne, Robert K. ; Blumstein, Daniel T. ; et al ( March 2022 , Nature Ecology & Evolution)

   Species that hibernate generally live longer than would be expected based solely on their body size. Hibernation is characterized by long periods of metabolic suppression (torpor) interspersed by short periods of increased metabolism (arousal). The torpor–arousal cycles occur multiple times during hibernation, and it has been suggested that processes controlling the transition between torpor and arousal states cause ageing suppression. Metabolic rate is also a known correlate of longevity; we thus proposed the ‘hibernation–ageing hypothesis’ whereby ageing is suspended during hibernation. We tested this hypothesis in a well-studied population of yellow-bellied marmots (Marmota flaviventer), which spend 7–8 months per year hibernating. We used two approaches to estimate epigenetic age: the epigenetic clock and the epigenetic pacemaker. Variation in epigenetic age of 149 samples collected throughout the life of 73 females was modelled using generalized additive mixed models (GAMM), where season (cyclic cubic spline) and chronological age (cubic spline) were fixed effects. As expected, the GAMM using epigenetic ages calculated from the epigenetic pacemaker was better able to detect nonlinear patterns in epigenetic ageing over time. We observed a logarithmic curve of epigenetic age with time, where the epigenetic age increased at a higher rate until females reached sexual maturity (two years old). With respect to circannual patterns, the epigenetic age increased during the active season and essentially stalled during the hibernation period. Taken together, our results are consistent with the hibernation–ageing hypothesis and may explain the enhanced longevity in hibernators.

    

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3. Neotropical stingless bees display a strong response in cold tolerance with changes in elevation

   Gonzalez, V.H. ; Oyen, K. ; Vitale, N. ; and Ospina, R. ( January 2022 , Conservation physiology)

   Tropical pollinators are expected to experience substantial effects due to climate change, but aspects of their thermal biology remain largely unknown. We investigated the thermal tolerance of stingless honey-making bees, the most ecologically, economically and culturally important group of tropical pollinators. We assessed changes in the lower (CTMin) and upper (CTMax) critical thermal limits of 17 species (12 genera) at two elevations (200 and 1500 m) in the Colombian Andes. In addition, we examined the influence of body size (intertegular distance, ITD), hairiness (thoracic hair length) and coloration (lightness value) on bees’ thermal tolerance. Because stingless beekeepers often relocate their colonies across the altitudinal gradient, as an initial attempt to explore potential social responses to climatic variability, we also tracked for several weeks brood temperature and humidity in nests of three species at both elevations. We found that CTMin decreased with elevation while CTMax was similar between elevations. CTMin and CTMax increased (low cold tolerance and high heat tolerance) with increasing ITD, hair length and lightness value, but these relationships were weak and explained at most 10% of the variance. Neither CTMin nor CTMax displayed significant phylogenetic signal. Brood nest temperature tracked ambient diel variations more closely in the low-elevation site, but it was constant and higher at the high-elevation site. In contrast, brood nest humidity was uniform throughout the day regardless of elevation. The stronger response in CTMin, and a similar CTMax between elevations, follows a pattern of variation documented across a wide range of taxa that is commonly known as the Brett’s heat-invariant hypothesis. Our results indicate differential thermal sensitivities and potential thermal adaptations to local climate, which support ongoing conservation policies to restrict the long-distance relocations of colonies. They also shed light on how malleable nest thermoregulation can be across elevations. 

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4. From telomere to telomere: The transcriptional and epigenetic state of human repeat elements

   https://doi.org/10.1126/science.abk3112  

   Hoyt, Savannah J. ; Storer, Jessica M. ; Hartley, Gabrielle A. ; Grady, Patrick G. ; Gershman, Ariel ; de Lima, Leonardo G. ; Limouse, Charles ; Halabian, Reza ; Wojenski, Luke ; Rodriguez, Matias ; et al ( April 2022 , Science)

   INTRODUCTION Transposable elements (TEs), repeat expansions, and repeat-mediated structural rearrangements play key roles in chromosome structure and species evolution, contribute to human genetic variation, and substantially influence human health through copy number variants, structural variants, insertions, deletions, and alterations to gene transcription and splicing. Despite their formative role in genome stability, repetitive regions have been relegated to gaps and collapsed regions in human genome reference GRCh38 owing to the technological limitations during its development. The lack of linear sequence in these regions, particularly in centromeres, resulted in the inability to fully explore the repeat content of the human genome in the context of both local and regional chromosomal environments. RATIONALE Long-read sequencing supported the complete, telomere-to-telomere (T2T) assembly of the pseudo-haploid human cell line CHM13. This resource affords a genome-scale assessment of all human repetitive sequences, including TEs and previously unknown repeats and satellites, both within and outside of gaps and collapsed regions. Additionally, a complete genome enables the opportunity to explore the epigenetic and transcriptional profiles of these elements that are fundamental to our understanding of chromosome structure, function, and evolution. Comparative analyses reveal modes of repeat divergence, evolution, and expansion or contraction with locus-level resolution. RESULTS We implemented a comprehensive repeat annotation workflow using previously known human repeats and de novo repeat modeling followed by manual curation, including assessing overlaps with gene annotations, segmental duplications, tandem repeats, and annotated repeats. Using this method, we developed an updated catalog of human repetitive sequences and refined previous repeat annotations. We discovered 43 previously unknown repeats and repeat variants and characterized 19 complex, composite repetitive structures, which often carry genes, across T2T-CHM13. Using precision nuclear run-on sequencing (PRO-seq) and CpG methylated sites generated from Oxford Nanopore Technologies long-read sequencing data, we assessed RNA polymerase engagement across retroelements genome-wide, revealing correlations between nascent transcription, sequence divergence, CpG density, and methylation. These analyses were extended to evaluate RNA polymerase occupancy for all repeats, including high-density satellite repeats that reside in previously inaccessible centromeric regions of all human chromosomes. Moreover, using both mapping-dependent and mapping-independent approaches across early developmental stages and a complete cell cycle time series, we found that engaged RNA polymerase across satellites is low; in contrast, TE transcription is abundant and serves as a boundary for changes in CpG methylation and centromere substructure. Together, these data reveal the dynamic relationship between transcriptionally active retroelement subclasses and DNA methylation, as well as potential mechanisms for the derivation and evolution of new repeat families and composite elements. Focusing on the emerging T2T-level assembly of the HG002 X chromosome, we reveal that a high level of repeat variation likely exists across the human population, including composite element copy numbers that affect gene copy number. Additionally, we highlight the impact of repeats on the structural diversity of the genome, revealing repeat expansions with extreme copy number differences between humans and primates while also providing high-confidence annotations of retroelement transduction events. CONCLUSION The comprehensive repeat annotations and updated repeat models described herein serve as a resource for expanding the compendium of human genome sequences and reveal the impact of specific repeats on the human genome. In developing this resource, we provide a methodological framework for assessing repeat variation within and between human genomes. The exhaustive assessment of the transcriptional landscape of repeats, at both the genome scale and locally, such as within centromeres, sets the stage for functional studies to disentangle the role transcription plays in the mechanisms essential for genome stability and chromosome segregation. Finally, our work demonstrates the need to increase efforts toward achieving T2T-level assemblies for nonhuman primates and other species to fully understand the complexity and impact of repeat-derived genomic innovations that define primate lineages, including humans. Telomere-to-telomere assembly of CHM13 supports repeat annotations and discoveries. The human reference T2T-CHM13 filled gaps and corrected collapsed regions (triangles) in GRCh38. Combining long read–based methylation calls, PRO-seq, and multilevel computational methods, we provide a compendium of human repeats, define retroelement expression and methylation profiles, and delineate locus-specific sites of nascent transcription genome-wide, including previously inaccessible centromeres. SINE, short interspersed element; SVA, SINE–variable number tandem repeat– Alu ; LINE, long interspersed element; LTR, long terminal repeat; TSS, transcription start site; pA, xxxxxxxxxxxxxxxx. 

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5. A Geometric Morphometric Examination of Hominoid Third Metacarpal Shape and Its Implications for Inferring the Precursor to Terrestrial Bipedalism

   https://doi.org/10.1002/ar.23985  

   Rein, Thomas R. ( November 2018 , The Anatomical Record)

   The third metacarpal has been a focus of study when examining questions surrounding early hominin locomotion since this bone is adapted to the diverse range of positional behaviors performed by extant hominoids. The shape of this bone is potentially under strong selective pressure related to the biomechanical demands of terrestrial knuckle‐walking, arboreal clambering, and brachiation performed by extant hominoids since the hand directly interacts with the substrate during the performance of these movements. The objective of the present study was to explore shape variation of the third metacarpal and examine how different parts of the bone discriminated between hominoid genera that perform these different locomotor behaviors. In addition to examining general interspecies variation, shape analysis was applied to testing the knuckle‐walking hypothesis for human evolution. Fourteen 3D landmark coordinates were collected on hominoid third metacarpals, and principal component analysis and Procrustes distances were used to examine metacarpal shape. Comparable measurements were collected on fossilized third metacarpals ofAustralopithecus afarensisas an early hominin test case for examining the knuckle‐walking hypothesis. Analyses that included landmarks collected on both ends of the bone distinguished humans from great apes and presented a strong functional signal related to suspensory locomotion among nonhuman hominoids, whereas the distal articular surface provided the strongest knuckle‐walking signal. The shapes ofAustralopithecus afarensismetacarpals examined in the current study did not provide evidence for a trajectory of shape change in early hominin evolution that started from a metacarpal adapted for terrestrial knuckle‐walking. Anat Rec, 302:983–998, 2019. © 2018 Wiley Periodicals, Inc.

    

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