Trends in functional composition of small mammal communities across millennial time scales

Collin S. VanBuren and Marta A. Jarzyna. Ecography 2022: e06096. doi: 10.1111/ecog.06096.

Rich fossil deposits of the late Quaternary help us understand responses of biodiversity to global change and thus predict the future of ecosystems. Studies from the late Quaternary, however, are often limited taxonomically, geographically (often one site), and by their use of largely taxon-based metrics that do not inform about ecosystem- level consequences of biodiversity change. Here, we compare change in functional composition of small mammal communities at El Mirón Cave (Spain) and Samwell Cave (California, USA) across the last 22 000 years, and examine their relationships with climate and vegetation. We find opposing temporal trends between the two locations. European small mammal communities occupied increasingly greater trait space, driven by increases in arboreal granivory and frugivory as ground-dwelling herbivory declined toward the late Holocene. North American communities occupied smaller trait space as ground-level foraging and insectivory increased and arboreal herbivory and mean body mass declined. Our results point to the importance of the interaction between climate change and vegetation shifts for explaining changes in small mammal functional diversity, through their synergistic impacts on individual traits. Specifically, increasing temperature across both continents likely led to increases in nocturnal activity and declines in assemblage mean body mass, while transition to mixed forest (El Mirón) or open woodland (Samwell) resulted in increasing structural complexity of vegetation that potentially supported more diverse community-level dietary characteristics. These results demonstrate the ability of a trait-based approach to identify how environmental variables correlate with changes in community functional composition through time and gain insight into the potential consequences of environmental change for ecosystem functioning.

Herbivory promotes more negative plant-soil feedbacks particularly for legumes and forbs

Scott Kelsey, Antonino Malacrinò, Matthew Marrero, Karen Snyder, Wed Alabyadh, James Bingman, Isabella Borrero, Chandu Chappidi, Danielle Darling, Vannessa Fulton, Kristian Harris, Christine Huynh, Xin Lin, Brianna Moore, Bryan Roach, Johannes Heinze, Alison Bennett. 2022. DOI: https://doi.org/10.21203/rs.3.rs-1608866/v1

Abstract

Purpose: Plant-soil feedbacks and herbivory impact plant growth. We conducted a meta-analysis to test for an interaction between plant-soil feedbacks and herbivory, including effects on the magnitude and direction of feedbacks and the biomass or growth of herbivores Methods: Our literature search identified 244 studies to address our first question about herbivore impacts on plant-soil feedbacks as well as 179 studies to address our second question about plant-soil impacts on herbivores. We developed a database, calculated plant-soil feedback values for each study, then calculated Hedge’s D values for 1) the difference in plant-soil feedback values with and without herbivory for plants, and 2) the difference between home and away soils for insects.
Results: We found an overall significant weak negative effect of herbivory on plant-soil feedbacks, and effects differed between plant functional type. In legumes herbivory changed the outcome of plant-soil feedbacks from positive to negative, in forbs it further decreased negative feedbacks, and grasses were unaffected. We also found soil preconditioned in the lab produced consistently negative feedbacks whereas there was no significant change for soil preconditioned in the field. By contrast, there was no significant overall effect of plant-soil feedbacks on herbivores. Conclusion: This first meta-analysis of the impact of herbivores on plant-soil feedbacks and vice versa identified an important potential role of plant functional type in determining the impact of conditioned soil on the magnitude and direction of feedbacks as well as some clear gaps that need to be addressed experimentally.

Population genomics for symbiotic anthozoans: can reduced representation approaches be used for taxa without reference genomes?

Benjamin M. Titus & Marymegan Daly. Heredity volume 128, pages 338–351 (2022). 

Abstract

Population genetic studies of symbiotic anthozoans have been historically challenging because their endosymbioses with dinoflagellates have impeded marker development. Genomic approaches like reduced representation sequencing alleviate marker development issues but produce anonymous loci, and without a reference genome, it is unknown which organism is contributing to the observed patterns. Alternative methods such as bait-capture sequencing targeting Ultra-Conserved Elements are now possible but costly. Thus, RADseq remains attractive, but how useful are these methods for symbiotic anthozoan taxa without a reference genome to separate anthozoan from algal sequences? We explore this through a case-study using a double-digest RADseq dataset for the sea anemone Bartholomea annulata. We assembled a holobiont dataset (3854 loci) for 101 individuals, then used a reference genome to create an aposymbiotic dataset (1402 loci). For both datasets, we investigated population structure and used coalescent simulations to estimate demography and population parameters. We demonstrate complete overlap in the spatial patterns of genetic diversity, demographic histories, and population parameter estimates for holobiont and aposymbiotic datasets. We hypothesize that the unique combination of anthozoan biology, diversity of the endosymbionts, and the manner in which assembly programs identify orthologous loci alleviates the need for reference genomes in some circumstances. We explore this hypothesis by assembling an additional 21 datasets using the assembly programs pyRAD and Stacks. We conclude that RADseq methods are more tractable for symbiotic anthozoans without reference genomes than previously realized.

Species Delimitation Using Molecular Data

Megan L. Smith, Bryan C. Carstens. 2022. Chapter in Species Problems and Beyond. CRC Press. DOI:10.1201/9780367855604-910.1201/9780367855604-9.

Diapause among the flesh flies (Diptera: Sarcophagidae)

David L. Denlinger. Eur. J. Entomol. 119: 170–182, 2022. doi: 10.14411/eje.2022.019

Abstract

The rich diversity of information focusing on pupal diapause in the sarcophagids makes this fly family among the best- understood diapause models. This review summarizes the occurrence of pupal diapause in flesh flies from broad geographic re- gions of the world, as well as the apparent absence of diapause in select regions. The environmental cues used for programming diapause are discussed, as well as the requirements for breaking diapause. This taxon has been used for experiments ranging from the ecological to the molecular and offers a comprehensive overview of the diapause phenotype. A wide range of diapause attributes define the diapause phenotype of flesh flies, offering insights into such features as clock mechanisms, signaling path- ways, maternal regulation, energy utilization, cell cycle regulation, metabolic depression, cyclic metabolic activity, cold tolerance, water balance, and other attributes, generating a diapause profile that offers an attractive comparison for diapause in other insect species as well as with other forms of animal dormancy.

Genetic characterization of potential venom resistance proteins in California ground squirrels (Otospermophilus beecheyi) using transcriptome analyses

Alexander Ochoa, H. Lisle Gibbs, Alyssa T. B. Hassinger, Matthew L. Holding. 2022.  Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 1–11. DOI: 10.1002/jez.b.23145

Abstract

Understanding the molecular basis of adaptations in coevolving species requires identifying the genes that underlie reciprocally selected phenotypes, such as those involved in venom in snakes and resistance to the venom in their prey. In this regard, California ground squirrels (CGS; Otospermophilus beecheyi) are eaten by northern Pacific rattlesnakes (Crotalus oreganus oreganus), but individual squirrels may still show substantial resistance to venom and survive bites. A recent study using proteomics identified venom interactive proteins (VIPs) in the blood serum of CGS. These VIPs represent possible resistance proteins, but the sequences of genes encoding them are unknown despite the value of such data to molecular studies of coevolution. To address this issue, we analyzed a de novo assembled transcriptome from CGS liver tissue—where many plasma proteins are synthesized—and other tissues from this species. We then examined VIP sequences in terms of three characteristics that identify them as possible resistance proteins: evidence for positive selection, high liver expression, and nonsynonymous variation across CGS populations. Based on these characteristics, we identified five VIPs (i.e., α‐2‐ macroglobulin, α‐1‐antitrypsin‐like protein GS55‐LT, apolipoprotein A‐II, hibernation‐associated plasma protein HP‐20, and hibernation‐associated plasma protein HP‐27) as the most likely candidates for resistance proteins among VIPs identified to date. Four of these proteins have been previously implicated in conferring resistance to the venom in mammals, validating our approach. When combined with the detailed information available for rattlesnake venom proteins, these results set the stage for future work focused on understanding coevolutionary interactions at the molecular level between these species.