Predicting non-native insect impact: focusing on the trees to see the forest

Non-native organisms have invaded novel ecosystems for centuries, yet we have only a limited understanding of why their impacts vary widely from minor to severe. Predicting the impact of non-established or newly detected species could help focus biosecurity measures on species with the highest potential to cause widespread damage. However, predictive models require an understanding of potential drivers of impact and the appropriate level at which these drivers should be evaluated. Here, we used non-native, specialist herbivorous insects of forest ecosystems to test which factors drive impact and if there were differences based on whether they used woody angiosperms or conifers as hosts. We identified convergent and divergent patterns between the two host types indicating fundamental similarities and differences in their interactions with non-native insects. Evolutionary divergence time between native and novel hosts was a significant driver of insect impact for both host types but was modulated by different factors in the two systems. Beetles in the subfamily Scolytinae posed the highest risk to woody angiosperms, and different host traits influenced impact of specialists on conifers and woody angiosperms. Tree wood density was a significant predictor of host impact for woody angiosperms with intermediate densities (0.5–0.6 mg/mm3) associated with highest risk, whereas risk of impact was highest for conifers that coupled shade tolerance with drought intolerance. These results underscore the importance of identifying the relevant levels of biological organization and ecological interactions needed to develop accurate risk models for species that may arrive in novel ecosystems

Northern Fennoscandia via the British Isles: evidence for a novel postglacial recolonization route by winter moth (Operophtera brumata)

The frequency and severity of outbreaks by pestiferous insects is increasing globally, likely as a result of human-mediated introductions of non-native organisms. However, it is not always apparent whether an outbreak is the result of a recent introduction of an evolutionarily naïve population, or of recent disturbance acting on an existing population that arrived previously during natural range expansion. Here we use approximate Bayesian computation to infer the colonization history of a pestiferous insect, the winter moth, Operophtera brumata L. (Lepidoptera: Geometridae), which has caused widespread defoliation in northern Fennoscandia. We generated genotypes using a suite of 24 microsatellite loci and find that populations of winter moth in northern Europe can be assigned to five genetically distinct clusters that correspond with 1) Iceland, 2) the British Isles, 3) Central Europe and southern Fennoscandia, 4) Eastern Europe, and 5) northern Fennoscandia. We find that the northern Fennoscandia winter moth cluster is most closely related to a population presently found in the British Isles, and that these populations likely diverged around 2,900 years ago. This result suggests that current outbreaks are not the result of a recent introduction, but rather that recent climate or habitat disturbance is acting on existing populations that may have arrived to northern Fennoscandia via pre-Roman traders from the British Isles, and/or by natural dispersal across the North Sea likely using the Orkney Islands of northern Scotland as a stepping-stone before dispersing up the Norwegian coast. © 2021. The authors, CC-BY 4.0 license.</p

PLCL1 rs7595412 variation is not associated with hip bone size variation in postmenopausal Danish women

<p>Abstract</p> <p>Background</p> <p>Bone size (BS) variation is under strong genetic control and plays an important role in determining bone strength and fracture risk. Recently, a genome-wide association study identified polymorphisms associated with hip BS variation in the <it>PLCL1 </it>(phospholipase c-like 1) locus. Carriers of the major A allele of the most significant polymorphism, rs7595412, have around 17% larger hip BS than non-carriers. We therefore hypothesized that this polymorphism may also influence postmenopausal complications.</p> <p>Methods</p> <p>The effects of rs7595412 on hip BS, bone mineral density (BMD), vertebral fractures, serum Crosslaps and osteocalcin levels were analyzed in 1,191 postmenopausal Danish women.</p> <p>Results</p> <p>This polymorphism had no influence on hip and spine BS as well as on femur and spine BMD. Women carrying at least one copy of the A allele had lower levels of serum osteocalcin as compared with those homozygous for the G allele (p = 0.03) whereas no effect on serum Crosslaps was detected. Furthermore, women homozygous for the A allele were more affected by vertebral fractures than those carrying at least one copy of the G allele (p = 0.04).</p> <p>Conclusions</p> <p>In postmenopausal women, our results suggest that the <it>PLCL1 </it>rs7595412 polymorphism has no obvious effect on hip BS or BMD but may be nominally associated with increased proportion of vertebral fracture and increased levels of osteocalcin.</p

Identification of PLCL1 Gene for Hip Bone Size Variation in Females in a Genome-Wide Association Study

Osteoporosis, the most prevalent metabolic bone disease among older people, increases risk for low trauma hip fractures (HF) that are associated with high morbidity and mortality. Hip bone size (BS) has been identified as one of the key measurable risk factors for HF. Although hip BS is highly genetically determined, genetic factors underlying the trait are still poorly defined. Here, we performed the first genome-wide association study (GWAS) of hip BS interrogating ∼380,000 SNPs on the Affymetrix platform in 1,000 homogeneous unrelated Caucasian subjects, including 501 females and 499 males. We identified a gene, PLCL1 (phospholipase c-like 1), that had four SNPs associated with hip BS at, or approaching, a genome-wide significance level in our female subjects; the most significant SNP, rs7595412, achieved a p value of 3.72×10−7. The gene's importance to hip BS was replicated using the Illumina genotyping platform in an independent UK cohort containing 1,216 Caucasian females. Two SNPs of the PLCL1 gene, rs892515 and rs9789480, surrounded by the four SNPs identified in our GWAS, achieved p values of 8.62×10−3 and 2.44×10−3, respectively, for association with hip BS. Imputation analyses on our GWAS and the UK samples further confirmed the replication signals; eight SNPs of the gene achieved combined imputed p values<10−5 in the two samples. The PLCL1 gene's relevance to HF was also observed in a Chinese sample containing 403 females, including 266 with HF and 177 control subjects. A SNP of the PLCL1 gene, rs3771362 that is only ∼0.6 kb apart from the most significant SNP detected in our GWAS (rs7595412), achieved a p value of 7.66×10−3 (odds ratio = 0.26) for association with HF. Additional biological support for the role of PLCL1 in BS comes from previous demonstrations that the PLCL1 protein inhibits IP3 (inositol 1,4,5-trisphosphate)-mediated calcium signaling, an important pathway regulating mechanical sensing of bone cells. Our findings suggest that PLCL1 is a novel gene associated with variation in hip BS, and provide new insights into the pathogenesis of HF

RNA-Seq Identifies SNP Markers for Growth Traits in Rainbow Trout

Fast growth is an important and highly desired trait, which affects the profitability of food animal production, with feed costs accounting for the largest proportion of production costs. Traditional phenotype-based selection is typically used to select for growth traits; however, genetic improvement is slow over generations. Single nucleotide polymorphisms (SNPs) explain 90% of the genetic differences between individuals; therefore, they are most suitable for genetic evaluation and strategies that employ molecular genetics for selective breeding. SNPs found within or near a coding sequence are of particular interest because they are more likely to alter the biological function of a protein. We aimed to use SNPs to identify markers and genes associated with genetic variation in growth. RNA-Seq whole-transcriptome analysis of pooled cDNA samples from a population of rainbow trout selected for improved growth versus unselected genetic cohorts (10 fish from 1 full-sib family each) identified SNP markers associated with growth-rate. The allelic imbalances (the ratio between the allele frequencies of the fast growing sample and that of the slow growing sample) were considered at scores >5.0 as an amplification and <0.2 as loss of heterozygosity. A subset of SNPs (n = 54) were validated and evaluated for association with growth traits in 778 individuals of a three-generation parent/offspring panel representing 40 families. Twenty-two SNP markers and one mitochondrial haplotype were significantly associated with growth traits. Polymorphism of 48 of the markers was confirmed in other commercially important aquaculture stocks. Many markers were clustered into genes of metabolic energy production pathways and are suitable candidates for genetic selection. The study demonstrates that RNA-Seq at low sequence coverage of divergent populations is a fast and effective means of identifying SNPs, with allelic imbalances between phenotypes. This technique is suitable for marker development in non-model species lacking complete and well-annotated genome reference sequences

Metacarpal trabecular bone varies with distinct hand-positions used in hominid locomotion

Trabecular bone remodels during life in response to loading and thus should, at least in part, reflect potential variation in the magnitude, frequency and direction of joint loading across different hominid species. Here we analyse the trabecular structure across all non-pollical metacarpal distal heads (Mc2-5) in extant great apes, expanding on previous volume of interest and whole-epiphysis analyses that have largely focussed on only the first or third metacarpal. Specifically, we employ both a univariate statistical mapping and a multivariate approach to test for both inter-ray and interspecific differences in relative trabecular bone volume fraction (RBV/TV) and degree of anisotropy (DA) in Mc2-5 subchondral trabecular bone. Results demonstrate that while DA values only separate Pongo from African apes (Pan troglodytes, Pan paniscus, Gorilla gorilla), RBV/TV distribution varies with the predicted loading of the metacarpophalangeal (McP) joints during locomotor behaviours in each species. Gorilla exhibits a relatively dorsal distribution of RBV/TV consistent with habitual hyper-extension of the McP joints during knuckle-walking, whereas Pongo has a palmar distribution consistent with flexed McP joints used to grasp arboreal substrates. Both Pan species possess a disto-dorsal distribution of RBV/TV, compatible with multiple hand postures associated with a more varied locomotor regime. Further inter-ray comparisons reveal RBV/TV patterns consistent with varied knuckle-walking postures in Pan species in contrast to higher RBV/TV values toward the midline of the hand in Mc2 and Mc5 of Gorilla, consistent with habitual palm-back knuckle-walking. These patterns of trabecular bone distribution and structure reflect different behavioural signals that could be useful for determining the behaviours of fossil hominins

Nitrate deposition in northern hardwood forests and the nitrogen metabolism of Acer saccharum marsh

It is generally assumed that plant assimilation constitutes the major sink for anthropogenic Nitrate NO 3 − deposited in temperate forests because plant growth is usually limited by nitrogen (N) availability. Nevertheless, plants are known to vary widely in their capacity for NO 3 − uptake and assimilation, and few studies have directly measured these parameters for overstory trees. Using a combination of field and greenhouse experiments, we studied the N nutrition of Acer saccharum Marsh. in four northern hardwood forests receiving experimental NO 3 − additions equivalent to 30 kg N ha −1 year −1 . We measured leaf and fine-root nitrate reductase activity (NRA) of overstory trees using an in vivo assay and used 15 N to determine the kinetic parameters of NO 3 − uptake by excised fine roots. In two greenhouse experiments, we measured leaf and root NRA in A. saccharum seedlings fertilized with 0–3.5 g NO 3 − −N m −2 and determined the kinetic parameters of NO 3 − and NH 4 + uptake in excised roots of seedlings. In both overstory trees and seedlings, rates of leaf and fine root NRA were substantially lower than previously reported rates for most woody plants and showed no response to NO 3 − fertilization (range = non-detectable to 33 nmol NO 2 − g −1 h −1 ). Maximal rates of NO 3 − uptake in overstory trees also were low, ranging from 0.2 to 1.0 μmol g −1 h −1 . In seedlings, the mean V max for NO 3 − uptake in fine roots (1 μmol g −1 h −1 ) was approximately 30 times lower than the V max for NH 4 + uptake (33 μmol g −1 h −1 ). Our results suggest that A. saccharum satisfies its N demand through rapid NH 4 + uptake and may have a limited capacity to serve as a direct sink for atmospheric additions of NO 3 − .Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/47695/1/442_2004_Article_BF00334659.pd