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1. What processes must we understand to forecast regional-scale population dynamics?

   https://doi.org/10.1098/rspb.2020.2219  

   Lasky, Jesse R.; Hooten, Mevin B.; Adler, Peter B. (December 2020, Proceedings of the Royal Society B: Biological Sciences)

   null (Ed.)

   An urgent challenge facing biologists is predicting the regional-scale population dynamics of species facing environmental change. Biologists suggest that we must move beyond predictions based on phenomenological models and instead base predictions on underlying processes. For example, population biologists, evolutionary biologists, community ecologists and ecophysiologists all argue that the respective processes they study are essential. Must our models include processes from all of these fields? We argue that answering this critical question is ultimately an empirical exercise requiring a substantial amount of data that have not been integrated for any system to date. To motivate and facilitate the necessary data collection and integration, we first review the potential importance of each mechanism for skilful prediction. We then develop a conceptual framework based on reaction norms, and propose a hierarchical Bayesian statistical framework to integrate processes affecting reaction norms at different scales. The ambitious research programme we advocate is rapidly becoming feasible due to novel collaborations, datasets and analytical tools. 

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2. Mitochondrial mutations in Caenorhabditis elegans show signatures of oxidative damage and an AT-bias

   https://doi.org/10.1093/genetics/iyab116  

   Waneka, Gus; Svendsen, Joshua M; Havird, Justin C; Sloan, Daniel B (August 2021, Genetics)

   Surtees, J A (Ed.)

   Abstract Rapid mutation rates are typical of mitochondrial genomes (mtDNAs) in animals, but it is not clear why. The difficulty of obtaining measurements of mtDNA mutation that are not biased by natural selection has stymied efforts to distinguish between competing hypotheses about the causes of high mtDNA mutation rates. Several studies which have measured mtDNA mutations in nematodes have yielded small datasets with conflicting conclusions about the relative abundance of different substitution classes (i.e., the mutation spectrum). We therefore leveraged Duplex Sequencing, a high-fidelity DNA sequencing technique, to characterize de novo mtDNA mutations in Caenorhabditis elegans. This approach detected nearly an order of magnitude more mtDNA mutations than documented in any previous nematode mutation study. Despite an existing extreme AT bias in the C. elegans mtDNA (75.6% AT), we found that a significant majority of mutations increase genomic AT content. Compared to some prior studies in nematodes and other animals, the mutation spectrum reported here contains an abundance of CG→AT transversions, supporting the hypothesis that oxidative damage may be a driver of mtDNA mutations in nematodes. Furthermore, we found an excess of G→T and C→T changes on the coding DNA strand relative to the template strand, consistent with increased exposure to oxidative damage. Analysis of the distribution of mutations across the mtDNA revealed significant variation among protein-coding genes and as well as among neighboring nucleotides. This high-resolution view of mitochondrial mutations in C. elegans highlights the value of this system for understanding relationships among oxidative damage, replication error, and mtDNA mutation. 

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3. Abscisic acid can augment, but is not essential for, autumnal leaf senescence

   https://doi.org/10.1093/jxb/erad089  

   Kane, Cade N.; McAdam, Scott A. M.; Lawson, ed., Tracy (March 2023, Journal of Experimental Botany)

   Abstract Senescence vividly marks the onset of the final stages of the life of a leaf, yet the triggers and drivers of this process are still not fully understood. The hormone abscisic acid (ABA) is an important regulator of leaf senescence in model herbs, but the function of this hormone has not been widely tested in deciduous trees. Here we investigate the importance of ABA as a driver of leaf senescence in winter deciduous trees. In four diverse species we tracked leaf gas exchange, water potential, chlorophyll content, and leaf ABA levels from the end of summer until leaves were abscised or died. We found that no change in ABA levels occurred at the onset of chlorophyll decline or throughout the duration of leaf senescence. To test whether ABA could enhance leaf senescence, we girdled branches to disrupt ABA export in the phloem. Girdling increased leaf ABA levels in two of the species, and this increase triggered an accelerated rate of chlorophyll decline in these species. We conclude that an increase in ABA level may augment leaf senescence in winter deciduous species but that it is not essential for this annual process. 

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4. Interrogating the Roles of Mutation–Selection Balance, Heterozygote Advantage, and Linked Selection in Maintaining Recessive Lethal Variation in Natural Populations

   https://doi.org/10.1146/annurev-animal-050422-092520  

   Marion, Sarah B.; Noor, Mohamed A.F. (February 2023, Annual Review of Animal Biosciences)

   For nearly a century, evolutionary biologists have observed chromosomes that cause lethality when made homozygous persisting at surprisingly high frequencies (>25%) in natural populations of many species. The evolutionary forces responsible for the maintenance of such detrimental mutations have been heavily debated—are some lethal mutations under balancing selection? We suggest that mutation–selection balance alone cannot explain lethal variation in nature and the possibility that other forces play a role. We review the potential that linked selection in particular may drive maintenance of lethal alleles through associative overdominance or linkage to beneficial mutations or by reducing effective population size. Over the past five decades, investigation into this mystery has tapered. During this time, key scientific advances have provided the ability to collect more accurate data and analyze them in new ways, making the underlying genetic bases and evolutionary forces of lethal alleles timely for study once more. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 11 is February 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates. 

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5. Reproductive success and offspring survival decline for female elephant seals past prime age

   https://doi.org/10.1111/1365-2656.14226  

   Payne, Allison_R; Czapanskiy, Max_F; Kilpatrick, A_Marm; Robinson, Patrick_W; Munro, Cara_M_O; Ong, Kelli; Bastidas, Adrien; Negrete, Alegra_O; Theders, Brecken; Stillwell, Bryn; et al (November 2024, Journal of Animal Ecology)

   Abstract Maternal age can influence reproductive success and offspring fitness, but the timing, magnitude and direction of those impacts are not well understood. Evolutionary theory predicts that selection on fertility senescence is stronger than maternal effect senescence, and therefore, the rate of maternal effect senescence will be faster than fertility senescence.We used a 36‐year study of northern elephant seals (Mirounga angustirostris) to investigate reproductive senescence. Our dataset included 103,746 sightings of 1203 known‐age female northern elephant seals.We hypothesized that fertility (maternal reproductive success), offspring survival and recruitment into the breeding population, and male offspring production would decline with advanced maternal age. Furthermore, we hypothesized that older females would shorten their moulting haul out to allow for more time spent foraging.We found evidence for both fertility and maternal effect senescence, but no evidence for senescence impacting offspring recruitment or sex ratio. Breeding probability declined from 96.4% (95% CI: 94.8%–97.5%) at 11 years old to 89.7% (81.9%–94.3%) at 19 years old, and the probability of offspring survival declined from 30.3% (23.6%–38.0%) at 11 years old to 9.1% (3.2%–22.9%) at 19 years old.The rates of decline for fertility and maternal effect senescence were not different from each other. However, maternal effect senescence had a substantially greater impact on the number of offspring surviving to age 1 compared to fertility senescence. Compared to a hypothetical non‐senescent population, maternal effect senescence resulted in 5.3% fewer surviving pups, whereas fertility senescence resulted in only 0.3% fewer pups produced per year. These results are consistent with evolutionary theory predicting weaker selection on maternal effect than fertility senescence. Maternal effect senescence may therefore be more influential on population dynamics than fertility senescence in some systems. 

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