The effect of sampling density and study area size on landscape genetics inferences for the Mississippi slimy salamander (Plethodon mississippi)

In landscape genetics, it is largely unknown how choices regarding sampling density and study area size impact inferences upon which habitat features impede vs. facilitate gene flow. While it is recommended that sampling locations be spaced no further apart than the average individual''s dispersal distance, for low‐mobility species, this could lead to a challenging number of sampling locations, or an unrepresentative study area. We assessed the effects of sampling density and study area size on landscape genetic inferences for a dispersal‐limited amphibian, Plethodon mississippi, via analysis of nested datasets. Microsatellite‐based genetic distances among individuals were divided into three datasets representing sparse sampling across a large study area, dense sampling across a small study area, or sparse sampling across the same small study area. These datasets were a proxy for gene flow (i.e., the response variable) in maximum‐likelihood population effects models that assessed the nature and strength of their relationship with each of five land‐use classes (i.e., potential predictor variables). Comparisons of outcomes were based on the rank order of effect, sign of effect (i.e., gene flow resistance vs. facilitation), spatial scale of effect, and functional relationship with gene flow. The best‐fit model for each dataset had the same sign of effect for hardwood forests, manmade structures, and pine forests, indicating the impacts of these land‐use classes on dispersal and gene flow in P. mississippi are robust to sampling scheme. Contrasting sampling densities led to a different inferred functional relationship between agricultural areas and gene flow. Study area size appeared to influence the scale of effect of manmade structures and the sign of effect of pine forests. Our findings provided evidence for an influence of sampling density, study area size, and sampling effort upon inferences. Accordingly, we recommend iterative subsampling of empirical datasets and continued investigation into the sensitivities of landscape genetic analyses using simulations.     

Do mallard ducks feature in the diet of stoats in an agricultural landscape?

ABSTRACT

Research on stoat diet composition in New Zealand has primarily focussed on consumption of indigenous fauna in largely unmodified landscapes. This study used stomach content and stable isotope (δ¹³C and δ¹⁵N) analysis to assess stoat diet in a highly modified agricultural landscape in Southland, New Zealand, focussing on stoat predation of the mallard duck. Stoats were captured in Lochiel, Southland during August–November 2016 and 2017. Stomach content analysis of 26 captured stoats revealed limited stoat predation of mallards (n?=?1) and mallard eggs (n?=?1). Using liver tissue, stable isotope mixing models suggested that bird eggs on average met between 73 and 85% of stoat metabolic requirements throughout the mallard breeding period. Furthermore, mixing model outputs suggested that bird eggs made up a substantial proportion (77–84%) of stoat assimilated diet early in the mallard breeding period, when mallard eggs are readily available. In contrast, isotope mixing models suggested that mallard ducks/ducklings did not make a large overall contribution to stoat diets (< 3%). This study shows that stoats are an egg predator in the Southland agricultural landscape and mallard eggs may contribute to stoat assimilated diet early in the mallard breeding season before alternative prey items become available.     

Increasing the accuracy of genomic prediction in pure‐bred Limousin beef cattle by including cross‐bred Limousin data and accounting for an F94L variant in MSTN

Explicitly fitting effects for major genes or QTL that account for a large percentage of variation in a whole genomic prediction model may increase prediction accuracy. This study compared approaches to account for a major effect of an F94L variant in the MSTN gene within the genomic prediction using bovine whole‐genomic SNP markers. Among the beef cattle breeds, Limousin have been known to have an F94L variant that is not present in Angus. The reference population in this study consisted of 3060 beef cattle including pure‐bred Limousin (PL), cross‐bred Limousin with Angus (LF) and pure‐bred Angus, genotyped using a BovineSNP50 BeadChip and directly for the MSTN‐F94L variant. We compared prediction accuracies in PL animals using the three datasets from only the PL population, admixed PL and LF (AL) or multibreed analysis using all of the PL, LF and Angus (MB) population according to four‐fold cross‐validation after K‐means clustering. The MSTN‐F94L variant was the most strongly associated with five traits (birth weight, calving ease direct, milk, weaning weight and yield grade) among the 13 measured traits in PL and AL populations. Fitting the MSTN‐F94L variant as a random effect, the genomic prediction accuracies for birth weight increased by 2.7% in PL, by 2.2% in AL and by 3.2% in MB. Prediction accuracies for five traits increased in the MB analysis. Fitting MSTN‐F94L as a fixed effect in PL, AL and MB analyses resulted in increased prediction accuracy in PL for eight traits. Prediction accuracies can be improved by including a causal variant in genomic evaluation compared with simply using whole‐genome SNP markers. Fitting the causal variant as a fixed effect along with markers fitted as random effects resulted in greater prediction accuracies for most traits. Causal variants should be genotyped along with SNP markers.     

Transformation of leukotriene A4 to lipoxins by rat kidney mesangial cell

Incubation of rat mesangial cells with leukotriene A4 in the presence of calcium ionophore A23187 led to a substrate dependent formation of lipoxin and its isomers. The major metabolite coeluted with authentic lipoxin A4 (LXA4) and lipoxin B4 (LXB4) in RP-HPLC system, and possessed a characteristic U.V. spectrum and C-value which were identical to authentic standards. GC/MS analysis on LXA4 further demonstrates that the mesangial cell derived LXA4 was identical to that reported by Serhan et al. (1) as LXA4 [5(S), 6,(R), 15(S)-trihydroxy7,9,13-trans-11-cis-eicosatetraenoic acid]. The formation of LXA4 was linear with substrate (LTA4) concentration. No similar products occurred in boiled controls. Incubation of mesangial cell with 15-HPETE failed to produce any lipoxin-like material. The absence of LX-like substance following incubation of 15-HPETE with mesangial cells suggested that 5-lipoxygenase activity is not expressed in mesangial cells under these conditions. The generation of LXA4 from LTA4 in mesangial cells suggested that there is an active 15- or 12- lipoxygenase activity in the kidney. The production of LX may play an important role in the regulation of renal function and the response to inflammatory stimuli.     

Covalent Attachment of Peptides to Cytochrome C for Automated Sequence Determination

Because small peptides are lost into the organic solvents used, it is virtually impossible to obtain the complete amino acid sequence of a small peptide using only an automated peptide sequencer of the spinning cup type. To overcome this problem we have extended peptides at the carboxy terminus by attachment to equine cytochrome c by a water soluble carbodiimide, relying on the acetylated N-terminus of the cytochrome to minimize its direct contribution to recovery of PTH-amino acids. The Model Peptide H-Leu-Trp-Met-Arg-Phe-Ala-OH was used for most experiments. After reac-tion of³H-peptide with cytochrome c, about one-third of the tritium counts migrated with cytochrome c during gel filtration. After attachment, the amino acid sequence of the hexapeptide was readily determined with a single cleavage Quadrol program in a Beckman 890B sequencer, whereas only the N-terminal residue was recovered without attachment. The repetitive yield after attachment was 95–96%, with 21–27% overlap and an initial yield of 18-20%. Sequence data with other peptides illustrate applications and present limitations of our approach.     

Differential inhibition of globin chain synthesis by tosyl-L-lysyl chloromethyl ketone

Tosyl-L-lysyl chloromethyl ketone (TLCK), added to an incubation of rabbit reticulocytes, inhibits the synthesis of α globin chain more than that of β chain. TLCK has been previously shown to inhibit initiation of translation in a variety of cells. Thus this drug could be used to test for such a differential effect at the level of peptide initiation on the various mRNAs in these cells.