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1. Genetic variation in aneuploidy prevalence and tolerance across Saccharomyces cerevisiae lineages

   https://doi.org/10.1093/genetics/iyab015  

   Scopel, Eduardo F; Hose, James; Bensasson, Douda; Gasch, Audrey P (April 2021, Genetics)

   Hahn, M (Ed.)

   Abstract Individuals carrying an aberrant number of chromosomes can vary widely in their expression of aneuploidy phenotypes. A major unanswered question is the degree to which an individual’s genetic makeup influences its tolerance of karyotypic imbalance. Here we investigated within-species variation in aneuploidy prevalence and tolerance, using Saccharomyces cerevisiae as a model for eukaryotic biology. We analyzed genotypic and phenotypic variation recently published for over 1,000 S. cerevisiae strains spanning dozens of genetically defined clades and ecological associations. Our results show that the prevalence of chromosome gain and loss varies by clade and can be better explained by differences in genetic background than ecology. The relationships between lineages with high aneuploidy frequencies suggest that increased aneuploidy prevalence emerged multiple times in S. cerevisiae evolution. Separate from aneuploidy prevalence, analyzing growth phenotypes revealed that some genetic backgrounds—such as the European Wine lineage—show fitness costs in aneuploids compared to euploids, whereas other clades with high aneuploidy frequencies show little evidence of major deleterious effects. Our analysis confirms that chromosome gain can produce phenotypic benefits, which could influence evolutionary trajectories. These results have important implications for understanding genetic variation in aneuploidy prevalence in health, disease, and evolution. 

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2. Contrasting responses of functional diversity to major losses in taxonomic diversity

   Edie, S.M.; Jablonski, D.; Valentine, J. W. (January 2018, Proceedings of the National Academy of Sciences of the United States of America)

   Taxonomic diversity of benthic marine invertebrate shelf species declines at present by nearly an order of magnitude from the tropics to the poles in each hemisphere along the latitudinal diversity gradient (LDG), most steeply along the western Pacific where shallow-sea diversity is at its tropical maximum. In the Bivalvia, a model system for macroevolution and macroecology, this taxonomic trend is accompanied by a decline in the number of functional groups and an increase in the evenness of taxa distributed among those groups, with maximum functional evenness (FE) in polar waters of both hemispheres. In contrast, analyses of this model system across the two era-defining events of the Phanerozoic, the Permian–Triassic and Cretaceous–Paleogene mass extinctions, show only minor declines in functional richness despite high extinction intensities, resulting in a rise in FE owing to the persistence of functional groups. We hypothesize that the spatial decline of taxonomic diversity and increase in FE along the present-day LDG primarily reflect diversity-dependent factors, whereas retention of almost all functional groups through the two mass extinctions suggests the operation of diversity-independent factors. Comparative analyses of different aspects of biodiversity thus reveal strongly contrasting biological consequences of similarly severe declines in taxonomic diversity and can help predict the consequences for functional diversity among different drivers of past, present, and future biodiversity loss. 

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3. Multiple dimensions of dietary diversity in large mammalian herbivores

   https://doi.org/10.1111/1365-2656.13206  

   Kartzinel, Tyler R.; Pringle, Robert M.; Eizaguirre, ed., Christophe (April 2020, Journal of Animal Ecology)

   Abstract Theory predicts that trophic specialization (i.e. low dietary diversity) should make consumer populations sensitive to environmental disturbances. Yet diagnosing specialization is complicated both by the difficulty of precisely quantifying diet composition and by definitional ambiguity: what makes a diet ‘diverse’?We sought to characterize the relationship between taxonomic dietary diversity (TDD) and phylogenetic dietary diversity (PDD) in a species‐rich community of large mammalian herbivores in a semi‐arid East African savanna. We hypothesized that TDD and PDD would be positively correlated within and among species, because taxonomically diverse diets are likely to include plants from many lineages.By using DNA metabarcoding to analyse 1,281 faecal samples collected across multiple seasons, we compiled high‐resolution diet profiles for 25 sympatric large‐herbivore species. For each of these populations, we calculated TDD and PDD with reference to a DNA reference library for local plants.Contrary to our hypothesis, measures of TDD and PDD were either uncorrelated or negatively correlated with each other. Thus, these metrics reflect distinct dimensions of dietary specialization both within and among species. In general, grazers and ruminants exhibited greater TDD, but lower PDD, than did browsers and non‐ruminants. We found significant seasonal variation in TDD and/or PDD for all but four species (Grevy's zebra, buffalo, elephant, Grant's gazelle); however, the relationship between TDD and PDD was consistent across seasons for all but one of the 12 best‐sampled species (plains zebra).Our results show that taxonomic generalists can be phylogenetic specialists, and vice versa. These two dimensions of dietary diversity suggest contrasting implications for efforts to predict how consumers will respond to climate change and other environmental perturbations. For example, populations with low TDD may be sensitive to phylogenetically ‘random’ losses of food species, whereas populations with low PDD may be comparatively more sensitive to environmental changes that disadvantage entire plant lineages—and populations with low dietary diversity in both taxonomic and phylogenetic dimensions may be most vulnerable of all. 

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4. Making remote sense of biodiversity: What grassland characteristics make spectral diversity a good proxy for taxonomic diversity?

   https://doi.org/10.1111/geb.13759  

   Van Cleemput, Elisa; Adler, Peter; Suding, Katharine Nash (October 2023, Global Ecology and Biogeography)

   Abstract AimThe spectral variability hypothesis (SVH) predicts that spectral diversity, defined as the variability of radiation reflected from vegetation, increases with biodiversity. While confirmation of this hypothesis would pave the path for use of remote sensing to monitor biodiversity, support in herbaceous ecosystems is mixed. Methodological aspects related to scale have been the predominant explanation for the mixed support, yet biological characteristics that vary among herbaceous systems may also affect the strength of the relationship. Therefore, we examined the influence of three biological characteristics on the relationship between spectral and taxonomic diversity: vegetation density, spatial species turnover and invasion by non‐native species. We aimed to understand when and why spectral diversity may serve as an indicator of taxonomic diversity and be useful for monitoring. LocationContinental U.S.A. Time PeriodPeak greenness in 2017. Major Taxa StudiedGrassland and herbaceous ecosystems. MethodsFor nine herbaceous sites in the National Ecological Observatory Network, we calculated taxonomic diversity from field surveys of 20 m × 20 m plots and derived spectral diversity for those same plots from airborne hyperspectral imagery with a spatial resolution of 1 m. The strength of the taxonomic diversity–spectral diversity relationship at each site was subsequently assessed against measurements of vegetation density, spatial species turnover and invasion. ResultsWe found a significant relationship between taxonomic and spectral diversity at some, but not all, sites. Spectral diversity was more strongly related to taxonomic diversity in sites with high species turnover and low invasion, but vegetation density had no effect on the relationship. Main ConclusionsUsing spectral diversity as a proxy for taxonomic diversity in grasslands is possible in some circumstances but should not just be assumed based on the SVH. It is important to understand the biological characteristics of a community prior to considering spectral diversity to monitor taxonomic diversity. 

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5. Diversity and disease: The effects of coral diversity on prevalence and impacts of stony coral tissue loss disease in Saint Thomas, U.S. Virgin Islands

   https://doi.org/10.3389/fmars.2021.682688  

   Costa, S. V.; Hibberts, S. J.; Olive, D. A.; Budd, K. A.; Long, A. E.; Meiling, S. S.; Miller, M. B.; Vaughn, K. M.; Carrion, C. I.; Cohen, M. B.; et al (June 2021, Frontiers in marine science)

   Stony coral tissue loss disease (SCTLD) was first observed in St. Thomas, U.S. Virgin Islands (USVI) in January 2019. This disease affects at least 20 scleractinian coral species; however, it is not well understood how reef diversity affects its spread or its impacts on reef ecosystems. With a large number of susceptible species, SCTLD may not follow the diversity-disease hypothesis, which proposes that high species diversity is negatively correlated with disease prevalence. Instead, SCTLD may have a higher prevalence and a greater impact on reefs with higher coral diversity. To test this, in 2020 we resampled 54 sites around St. Thomas previously surveyed in 2017 or 2019 by the National Oceanic and Atmospheric Administration National Coral Reef Monitoring Program. These sites represented a variety of species diversity values [categorized into poor (<12 spp. rich.) and rich (12 spp. rich.)] in multiple disease zones (Endemic: disease present  9 months; Epidemic: disease present 2–6 months; Control and Emergent: disease present no disease/<2 months). We hypothesized that, contrary to the diversity-disease hypothesis, sites with high species diversity (as measured by species richness or Simpson’s index) would have higher disease prevalence within the epidemic zone, and that high species diversity sites would have a greater impact from disease within the endemic zone. Results indicated a significant positive relationship between disease prevalence and diversity in the epidemic zone, and a similar trend in the endemic zones. Additionally, a negative relationship was seen between pre-outbreak diversity and loss of diversity and coral cover within the endemic zone. This supports the hypothesis that higher diversity predicts greater disease impact and suggests that SCTLD does not follow the diversity-disease hypothesis. Within the epidemic zone, the species with the highest SCTLD prevalence were Dendrogyra cylindrus, Colpophyllia natans, and Meandrina meandrites, while in the endemic zone, Diploria labyrinthiformis, Pseudodiploria strigosa, Montastraea cavernosa, and Siderastrea siderea had the highest SCTLD prevalence. Understanding the relationship between species diversity and SCTLD will help managers predict the most vulnerable reefs, which should be prioritized within the USVI and greater Caribbean region. 

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