Accounting for the nested nature of genetic variation across levels of organization improves our understanding of biodiversity and community ecology

Recent work has demonstrated that the presence or abundance of specific genotypes, populations, species and phylogenetic clades may influence community and ecosystem properties such as resilience or productivity. Many ecological studies, however, use simple linear models to test for such relationships, including species identity as the predictor variable and some measured trait or function as the response variable without accounting for the nestedness of genetic variation across levels of organization. This omission may lead to incorrect inference about which source of variation influences community and ecosystem properties. Here, we explicitly compare this common approach to alternative ways of modeling variation in trait data, using simulated trait data and empirical results of common‐garden trials using multiple levels of genetic variation within Eucalyptus, Populus and Picea. We show that: 1) when nested variation is ignored, an incorrect conclusion of species effect is drawn in up to 20% of cases; 2) overestimation of the species effect increases – up to 60% in some scenarios – as the nested term explains more of the variation; and 3) the sample sizes needed to overcome these potential problems associated with aggregating nested hierarchical variation may be impractically large. In common‐garden trials, incorporating nested models increased explanatory power twofold for mammal browsing rate in Eucalyptus, threefold for leaf area in Populus, and tenfold for branch number in Picea. Thoroughly measuring intraspecific variation and characterizing hierarchical genetic variation beyond the species level has implications for developing more robust theory in community ecology, managing invaded natural systems, and improving inference in biodiversity–ecosystem functioning research. Synthesis Until recently, ecologists acknowledged the ubiquity of within‐species trait variation, but paid scant attention to how much it affects communities and ecosystems. Here, the authors used simulated trait data and common‐garden studies to demonstrate that we ignore intraspecific trait variation at our peril. In both simulated and experimental systems, in many cases ignoring intraspecific variation led to incorrect statistical inferences and inflated the effect size of species identity. This study shows that ecologists must characterize hierarchically nested genetic and phenotypic variation to fully understand the links between individual traits, community structure and ecosystem functioning.     

Odontocete occurrence in relation to changes in oceanography at a remote equatorial Pacific seamount

Seamounts are considered hot spots of biodiversity and can aggregate pelagic predators and their prey. Passive acoustic monitoring was conducted over 3 mo in 2012 to document the occurrence of odontocetes near a seamount chain in the central equatorial Pacific in relation to oceanographic changes over time. Beaked whale echolocation signals were most frequently encountered. The main beaked whale signal was an unknown type, BW38, which resembled signals produced by Blainville's beaked whales. It had high occurrence during high sea surface temperature and low sea surface salinity. Cuvier's beaked whales were the second most detected. They had an opposite pattern and were encountered more often when sea surface temperature was low and net primary productivity was high. Risso's dolphins and short‐finned pilot whales had high acoustic densities, and echolocated predominantly at night. Risso's dolphins occurred more often during low sea surface height deviation. False killer whales were less frequently detected and mostly occurred during the day. Sperm whale detections were fewer than expected and associated with high chlorophyll a. Short duration Kogiidae encounters occurred on average every third day. These types of long‐term site studies are an informative tool to comparatively assess species composition, relative abundance, and relationship to oceanographic changes.     

Structural Insight into Layer Gliding and Lattice Distortion in Layered Manganese Oxide Electrodes for Potassium‐Ion Batteries

Potassium‐ion batteries (PIBs) are an emerging, affordable, and environmentally friendly alternative to lithium‐ion batteries, with their further development driven by the need for suitably performing electrode materials capable of reversibly accommodating the relatively large K⁺. Layer‐structured manganese oxides are attractive as electrodes for PIBs, but suffer from structural instability and sluggish kinetics of K⁺ insertion/extraction, leading to poor rate capability. Herein, cobalt is successfully introduced at the manganese site in the K_xMnO₂ layered oxide electrode material and it is shown that with only 5% Co, the reversible capacity increases by 30% at 22 mA g^‐1 and by 92% at 440 mA g^‐1. In operando synchrotron X‐ray diffraction reveals that Co suppresses Jahn–Teller distortion, leading to more isotropic migration pathways for K⁺ in the interlayer, thus enhancing the ionic diffusion and consequently, rate capability. The detailed analysis reveals that additional phase transitions and larger volume change occur in the Co‐doped material as a result of layer gliding, with these associated with faster capacity decay, despite the overall capacity remaining higher than the pristine material, even after 500 cycles. These results assert the importance of understanding the detailed structural evolution that underpins performance that will inform the strategic design of electrode materials for high‐performance PIBs.     

Senescence‐associated tissue microenvironment promotes colon cancer formation through the secretory factor GDF15

The risk of colorectal cancer (CRC) varies between people, and the cellular mechanisms mediating the differences in risk are largely unknown. Senescence has been implicated as a causative cellular mechanism for many diseases, including cancer, and may affect the risk for CRC. Senescent fibroblasts that accumulate in tissues secondary to aging and oxidative stress have been shown to promote cancer formation via a senescence‐associated secretory phenotype (SASP). In this study, we assessed the role of senescence and the SASP in CRC formation. Using primary human colon tissue, we found an accumulation of senescent fibroblasts in normal tissues from individuals with advanced adenomas or carcinomas in comparison with individuals with no polyps or CRC. In in vitro and ex vivo model systems, we induced senescence using oxidative stress in colon fibroblasts and demonstrated that the senescent fibroblasts secrete GDF15 as an essential SASP factor that promotes cell proliferation, migration, and invasion in colon adenoma and CRC cell lines as well as primary colon organoids via the MAPK and PI3K signaling pathways. In addition, we observed increased mRNA expression of GDF15 in primary normal colon tissue from people at increased risk for CRC in comparison with average risk individuals. These findings implicate the importance of a senescence‐associated tissue microenvironment and the secretory factor GDF15 in promoting CRC formation.     

Hybridization between two parapatric ranid frog species in the northern Sierra Nevada,California, USA

Contact zones between species provide a unique opportunity to test whether taxa can hybridize or not. Cross‐breeding or hybridization between closely related taxa can promote gene flow (introgression) between species, adaptation, or even speciation. Though hybridization events may be short‐lived and difficult to detect in the field, genetic data can provide information about the level of introgression between closely related taxa. Hybridization can promote introgression between species, which may be an important evolutionary mechanism for either homogenization (reversing initial divergence between species) or reproductive isolation (potentially leading to speciation). Here, we used thousands of genetic markers from nuclear DNA to detect hybridization between two parapatric frog species (Rana boylii and Rana sierrae) in the Sierra Nevada of California. Based on principal components analysis, admixture, and analysis of heterozygosity at species diagnostic SNPs, we detected two F1 hybrid individuals in the Feather River basin, as well as a weak signal of introgression and gene flow between the frog species compared with frog populations from two other adjacent watersheds. This study provides the first documentation of hybridization and introgression between these two species, which are of conservation concern.     

A global review and meta-analysis of applications of the freshwater Fish Invasiveness Screening Kit

Reviews in Fish Biology and Fisheries - The freshwater Fish Invasiveness Screening Kit (FISK) has been applied in 35 risk assessment areas in 45 countries across the six inhabited continents (11...     

Selection for genetics‐based architecture traits in a native cottonwood negatively affects invasive tamarisk in a restoration field trial

Climate change and competition from invasive species remain two important challenges in restoration. We examined the hypothesis that non‐native tamarisk (Tamarix spp.) reestablishment after aboveground removal is affected by genetics‐based architecture of native Fremont cottonwood (Populus fremontii) used in restoration. As cottonwood architecture (height, canopy width, number of stems, and trunk diameter) is, in part, determined by genetics, we predicted that trees from different provenances would exhibit different architecture, and mean annual maximum temperature transfer distance from the provenances would interact with the architecture to affect tamarisk. In a common garden in Chevelon, AZ, U.S.A. (elevation 1,496 m), with cottonwoods from provenances spanning its elevation distribution, we measured the performance of both cottonwoods and tamarisk. Several key findings emerged. On average, cottonwoods from higher elevations were (1) two times taller and wider, covered approximately 3.5 times more basal area, and were less shrubby in appearance, by exhibiting four times fewer number of stems than cottonwoods from lower elevations; (2) had 50% fewer tamarisk growing underneath, which were two times shorter and covered 6.5 times less basal area than tamarisk growing underneath cottonwoods of smaller stature; and (3) the number of cottonwood stems did not affect tamarisk growth, possibly because the negative relationship between cottonwood stems and basal area. In combination, these findings argue that cottonwood architecture is affected by local conditions that interact with genetics‐based architecture. These interactions can negatively affect the growth of reinvading tamarisk and enhance restoration success. Our study emphasizes the importance of incorporating genetic and environmental interactions of plants used in restoration.