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1. Evolutionary constraint and innovation across hundreds of placental mammals

   https://doi.org/10.1126/science.abn3943  

   Christmas, Matthew J.; Kaplow, Irene M.; Genereux, Diane P.; Dong, Michael X.; Hughes, Graham M.; Li, Xue; Sullivan, Patrick F.; Hindle, Allyson G.; Andrews, Gregory; Armstrong, Joel C.; et al (April 2023, Science)

   INTRODUCTION A major challenge in genomics is discerning which bases among billions alter organismal phenotypes and affect health and disease risk. Evidence of past selective pressure on a base, whether highly conserved or fast evolving, is a marker of functional importance. Bases that are unchanged in all mammals may shape phenotypes that are essential for organismal health. Bases that are evolving quickly in some species, or changed only in species that share an adaptive trait, may shape phenotypes that support survival in specific niches. Identifying bases associated with exceptional capacity for cellular recovery, such as in species that hibernate, could inform therapeutic discovery. RATIONALE The power and resolution of evolutionary analyses scale with the number and diversity of species compared. By analyzing genomes for hundreds of placental mammals, we can detect which individual bases in the genome are exceptionally conserved (constrained) and likely to be functionally important in both coding and noncoding regions. By including species that represent all orders of placental mammals and aligning genomes using a method that does not require designating humans as the reference species, we explore unusual traits in other species. RESULTS Zoonomia’s mammalian comparative genomics resources are the most comprehensive and statistically well-powered produced to date, with a protein-coding alignment of 427 mammals and a whole-genome alignment of 240 placental mammals representing all orders. We estimate that at least 10.7% of the human genome is evolutionarily conserved relative to neutrally evolving repeats and identify about 101 million significantly constrained single bases (false discovery rate < 0.05). We cataloged 4552 ultraconserved elements at least 20 bases long that are identical in more than 98% of the 240 placental mammals. Many constrained bases have no known function, illustrating the potential for discovery using evolutionary measures. Eighty percent are outside protein-coding exons, and half have no functional annotations in the Encyclopedia of DNA Elements (ENCODE) resource. Constrained bases tend to vary less within human populations, which is consistent with purifying selection. Species threatened with extinction have few substitutions at constrained sites, possibly because severely deleterious alleles have been purged from their small populations. By pairing Zoonomia’s genomic resources with phenotype annotations, we find genomic elements associated with phenotypes that differ between species, including olfaction, hibernation, brain size, and vocal learning. We associate genomic traits, such as the number of olfactory receptor genes, with physical phenotypes, such as the number of olfactory turbinals. By comparing hibernators and nonhibernators, we implicate genes involved in mitochondrial disorders, protection against heat stress, and longevity in this physiologically intriguing phenotype. Using a machine learning–based approach that predicts tissue-specific cis - regulatory activity in hundreds of species using data from just a few, we associate changes in noncoding sequence with traits for which humans are exceptional: brain size and vocal learning. CONCLUSION Large-scale comparative genomics opens new opportunities to explore how genomes evolved as mammals adapted to a wide range of ecological niches and to discover what is shared across species and what is distinctively human. High-quality data for consistently defined phenotypes are necessary to realize this potential. Through partnerships with researchers in other fields, comparative genomics can address questions in human health and basic biology while guiding efforts to protect the biodiversity that is essential to these discoveries. Comparing genomes from 240 species to explore the evolution of placental mammals. Our new phylogeny (black lines) has alternating gray and white shading, which distinguishes mammalian orders (labeled around the perimeter). Rings around the phylogeny annotate species phenotypes. Seven species with diverse traits are illustrated, with black lines marking their branch in the phylogeny. Sequence conservation across species is described at the top left. IMAGE CREDIT: K. MORRILL 

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2. Spatial information from the odour environment in mammalian olfaction

   https://doi.org/10.1007/s00441-020-03395-3  

   Marin, Alina Cristina; Schaefer, Andreas T; Ackels, Tobias (January 2021, Cell and Tissue Research)

   null (Ed.)

   Abstract The sense of smell is an essential modality for many species, in particular nocturnal and crepuscular mammals, to gather information about their environment. Olfactory cues provide information over a large range of distances, allowing behaviours ranging from simple detection and recognition of objects, to tracking trails and navigating using odour plumes from afar. In this review, we discuss the features of the natural olfactory environment and provide a brief overview of how odour information can be sampled and might be represented and processed by the mammalian olfactory system. Finally, we discuss recent behavioural approaches that address how mammals extract spatial information from the environment in three different contexts: odour trail tracking, odour plume tracking and, more general, olfactory-guided navigation. Recent technological developments have seen the spatiotemporal aspect of mammalian olfaction gain significant attention, and we discuss both the promising aspects of rapidly developing paradigms and stimulus control technologies as well as their limitations. We conclude that, while still in its beginnings, research on the odour environment offers an entry point into understanding the mechanisms how mammals extract information about space. 

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3. The Role of the Stimulus in Olfactory Plasticity

   https://doi.org/10.3390/brainsci13111553  

   Coppola, David M.; Reisert, Johannes (November 2023, Brain Sciences)

   Cheetham, Claire E. (Ed.)

   Plasticity, the term we use to describe the ability of a nervous system to change with experience, is the evolutionary adaptation that freed animal behavior from the confines of genetic determinism. This capacity, which increases with brain complexity, is nowhere more evident than in vertebrates, especially mammals. Though the scientific study of brain plasticity dates back at least to the mid-19th century, the last several decades have seen unprecedented advances in the field afforded by new technologies. Olfaction is one system that has garnered particular attention in this realm because it is the only sensory modality with a lifelong supply of new neurons, from two niches no less! Here, we review some of the classical and contemporary literature dealing with the role of the stimulus or lack thereof in olfactory plasticity. We have restricted our comments to studies in mammals that have used dual tools of the field: stimulus deprivation and stimulus enrichment. The former manipulation has been implemented most frequently by unilateral naris occlusion and, thus, we have limited our comments to research using this technique. The work reviewed on deprivation provides substantial evidence of activity-dependent processes in both developing and adult mammals at multiple levels of the system from olfactory sensory neurons through to olfactory cortical areas. However, more recent evidence on the effects of deprivation also establishes several compensatory processes with mechanisms at every level of the system, whose function seems to be the restoration of information flow in the face of an impoverished signal. The results of sensory enrichment are more tentative, not least because of the actual manipulation: What odor or odors? At what concentrations? On what schedule? All of these have frequently not been sufficiently rationalized or characterized. Perhaps it is not surprising, then, that discrepant results are common in sensory enrichment studies. Despite this problem, evidence has accumulated that even passively encountered odors can “teach” olfactory cortical areas to better detect, discriminate, and more efficiently encode them for future encounters. We discuss these and other less-established roles for the stimulus in olfactory plasticity, culminating in our recommended “aspirations” for the field going forward. 

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4. Information about space from time: how mammals navigate the odour landscape

   https://doi.org/10.1515/nf-2022-0006  

   Ackels, Tobias (August 2022, Neuroforum)

   Abstract Sensory input across modalities is highly dynamic, continuously confronting the brain with the task of making sense of the external world. Olfaction is a key sense that many species depend on for survival, for example to locate food sources and mating partners or to avoid encountering predators. In the absence of visual cues, olfactory cues are especially useful, as they provide information over a large range of distances. Natural odours form temporally complex plumes that show rapid fluctuations in odour concentration carrying information about the location of an odour source. This review focuses on how primarily mammals use this spatial information from olfactory cues to navigate their environment. I highlight progress made on the physical description of dynamically fluctuating odours, behavioural paradigms to investigate odour-guided navigation and review initial findings on the underlying neural mechanisms that allow mammals to extract spatial information from the dynamic odour landscape. 

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5. Plant sex influences on riparian communities and ecosystems

   https://doi.org/10.1002/ece3.10308  

   Scheuerell, River P.; LeRoy, Carri J. (July 2023, Ecology and Evolution)

   Abstract Over the past several decades, we have increased our understanding of the influences of plant genetics on associated communities and ecosystem functions. These influences have been shown at both broad spatial scales and across many plant families, creating an active subdiscipline of ecology research focused on genes‐to‐ecosystems connections. One complex aspect of plant genetics is the distinction between males and females in dioecious plants. The genetic determinants of plant sex are poorly understood for most plants, but the influences of plant sex on morphological, physiological, and chemical plant traits are well‐studied. We argue that these plant traits, controlled by plant sex, may have wide‐reaching influences on both terrestrial and aquatic communities and ecosystem processes, particularly for riparian plants. Here we systematically review the influences of plant sex on plant traits, influences of plant traits on terrestrial community members, and how interactions between plant traits and terrestrial community members can influence terrestrial ecosystem functions in riparian forests. We then extend these influences into adjacent aquatic ecosystem functions and aquatic communities to explore how plant sex might influence linked terrestrial‐aquatic systems as well as the physical structure of riparian systems. This review highlights data gaps in empirical studies exploring the direct influences of plant sex on communities and ecosystems but draws inference from community and ecosystem genetics. Overall, this review highlights how variation by plant sex has implications for climate change adaptations in riparian habitats, the evolution and range shifts of riparian species and the methods used for conserving and restoring riparian systems. 

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