Biology subjects

Kilian, A.

Publications and source records attributed to Kilian, A..

6 recordsLinked to original sources

bioRxiv2025

An investigation of social learning of tool-use in bottlenose dolphins (Tursiops truncatus) using a ball-up / ball-down task

Whether and how dolphins can engage in spontaneous, untrained social learning to solve novel tool problems via action- or result- (or other) social learning remains debated. In the present study we tested the spontaneous social learning abilities of six dolphins (all not trained to copy) on two tool-using tasks (what we call the ball-up / ball-down task) - using a dolphin demonstrator and a human demonstrator. Regardless of task type and demonstrator type none of the tested dolphins reproduced the demonstrated tool solutions. We experienced several issues regarding our test apparatus, and so these negative results may be due to apparatus failures. However, these findings may also fully or partially indicate that untrained dolphins are not generalized, spontaneous social learners across information types, especially regarding the acquisition of tool solutions in puzzle tasks. More studies are required to precisely determine the capacity for spontaneous tool solution copying in dolphins.

animal behavior and cognition↗

bioRxiv2025

Diagnosability to inform species delimitation for the genus Emydura (Testudines: Chelidae) from northern Australia

Understanding the evolutionary history of diversifying lineages and the delineation of species remain major challenges for evolutionary biology. Here we use single nucleotide polymorphisms (SNPs) and sequence fragment presence-absence (SilicoDArT) data to combine phylogenetics and population genetics to assess species boundaries with a focus on diagnosability. We challenge current and proposed taxonomies in a genus of Australian freshwater turtles (Chelidae: Emydura) from northern Australia and southern New Guinea. In a six-step process, we combine phylogeny with the concept of diagnosability based on fixed allelic differences to select diagnosable lineages as candidate species. Four taxa are supported as diagnosable lineages, two of which we elevate to species status. The nuclear and mitochondrial phylogenies differed in important respects, which we attribute to recent or contemporary lateral transfer of mitochondria during hybridization events, deeper historical hybridization or possibly incomplete lineage sorting of the mitochondrial genome. Taxonomic decisions in cases of allopatry require subjective judgement. Our six-step strategy and the necessary (but not sufficient) criterion of diagnosability adds an additional level of objectivity before that subjectivity is applied, and so reduces the risk of taxonomic inflation that can accompany lineage approaches to species delimitation. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=124 SRC="FIGDIR/small/664252v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@1b89bc8org.highwire.dtl.DTLVardef@fb892dorg.highwire.dtl.DTLVardef@1eb09a8org.highwire.dtl.DTLVardef@1c7300c_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

bioRxiv2025

A pan-generic marker panel for apples to enable genetic research and breeding across Malus species

AbstractWild Malus species harbor untapped genetic diversity to advance apple breeding, particularly for disease resistance and stress tolerance. However, existing marker panels, developed mainly using Malus domestica accessions, introduce ascertainment bias and limit detecting rare variants in wild species. We developed and validated a medium-density and cost-effective pan-generic 3K apple DArTag panel optimized to capture genome-wide variation across the Malus genus. The panel was constructed using conserved, syntenic, and collinear genomic blocks identified within the core genome of 13 Malus accessions for cross-species transferability. The panel was validated across three bi-parental mapping populations totaling 593 progeny. Across these populations, 2,461-3,234 SNP markers were polymorphic and 1,482-2,620 were informative. Each population contained over 900 multiallelic micro-haplotype loci, with several hundred loci exhibiting three or four distinct haplotypes. Markers were uniformly distributed across all 17 chromosomes, each containing between 60- 230 informative SNPs. The panel was further evaluated on 174 diverse germplasm accessions from 20 Malus species. It exhibited strong cross-species transferability, exceptionally low rates of missing data (<0.5%), and clear genetic differentiation between wild and domesticated accessions. Genome-wide association studies (GWAS) identified a major locus on chromosome 4 significantly linked to fruit length, weight, and width in addition to trait-specific associations on chromosomes 1, 6, 9, and 11. The cost-effectiveness of genotyping per sample (<$15), combined with these results, underscore the panels broad utility for quantitative trait locus (QTL) mapping in bi- parental and diverse populations, marker-assisted selection in the breeding programs, and genetic diversity analysis across the Malus genus.

genetics↗

bioRxiv2025

Refining the resistance-to-damage (RD) score to predict operational Insecticide-Treated Net lifespan and identify paths to innovation

BackgroundInsecticide Treated Nets (ITNs) vary greatly in their physical characteristics yet the relationship with field durability remains poorly understood. To address this, we refined the existing resistance-to-damage (RD) metric for greater predictive power in estimating operational lifespan and to identify key avenues of innovation. MethodsThe original resistance-to-damage (oRD) score was calculated by comparing four physical attributes; snag strength, bursting strength, hole enlargement resistance and abrasion resistance; against aspirational values previously determined to provide resistance to routine damage. Here, the weighting of each is improved to provide a better prediction of field life, resulting in a weighted resistance-to-damage (wRD) score. Durability data from 37 field sites (across 14 countries) involving 10,000 campaign ITNs was used to quantify the relationship between physical characteristics and field life. Bivariable linear regression models were used to assess the correlation between RD scores and ITN survival time. A Cox regression survival analysis was applied to examine the impact of the RD score on physical survival, adjusting for net care and environment variables (Risk Index), evaluating the risk of ITN failure from the time they were first hung. ResultsThe bivariate analysis, not adjusting for differences between sites, shows that the wRD was a better predictor for net lifespan than oRD (wRD r2= 0.07 oRD r2= 0.01). In the multivariate analysis, adjusting for risk index, the wRD model was able to explain more than 70% of variability in net survival (wRD r2 = 0.74). Consequently, when comparing nets with different wRD scores in the same site, a 10-point increase in wRD score was associated with a 3.9-month gain in median survival (p=0.016). Increasing wRD from 35 to 70, the range of current products, increases median field life by 13.65 months (95% CI: 3.03-24.16). An ITN product with an wRD score of 68 is associated with a median lifespan of 2.7 years. The increase in predictive power of the wRD score came primarily from increasing the weighting of the hole enlargement resistance variable, which is a strong differentiator between ITN products. In contrast, abrasion-resistance was a negligible contributor to predictive power. DiscussionThe wRD score more accurately predicts ITN survival in the field than the oRD score. These findings highlight that resistance to hole enlargement is the primary differentiating factor in predicting field life, with some products performing far better than others. Snag and bursting strength remain essential characteristics yet are similarly low compared to aspirational values across available ITN products. All ITNs WHO prequalified in 2020 perform poorly on snag strength, indicating this as a core bottleneck in achieving longer operational ITN lifespan. Consequently, resistance to snagging and hole enlargement should be keys targets for future innovation to enhance the physical durability of ITNs.

ecology↗

bioRxiv2024

Targeted genotyping-by-sequencing of potato and software for imputation

Mid-density targeted genotyping-by-sequencing (GBS) combines trait-specific markers with thousands of genomic markers at an attractive price for linkage mapping and genomic selection. A 2.5K targeted GBS assay for potato was developed using the DArTagTM technology and later expanded to 4K targets. Genomic markers were selected from the potato InfiniumTM SNP array to maximize genome coverage and polymorphism rates. The DArTag and SNP array platforms produced equivalent dendrograms in a test set of 298 tetraploid samples, and 83% of the common markers showed good quantitative agreement, with RMSE (root-mean-squared-error) less than 0.5. DArTag is suited for genomic selection candidates in the clonal evaluation trial, coupled with imputation to a higher density platform for the training population. Using the software polyBreedR, an R package for the manipulation and analysis of polyploid marker data, the RMSE for imputation by linkage analysis was 0.15 in a small half-diallel population (N=85), which was significantly lower than the RMSE of 0.42 with the Random Forest method. Regarding high-value traits, the DArTag markers for resistance to potato virus Y, golden cyst nematode, and potato wart appeared to track their targets successfully, as did multi-allelic markers for maturity and tuber shape. In summary, the potato DArTag assay is a transformative and publicly available technology for potato breeding and genetics. Core IdeasO_LIA mid-density, targeted genotyping-by-sequencing (GBS) assay was developed for potato. C_LIO_LIThe GBS assay includes markers for resistance to potato virus Y, golden cyst nematode, and potato wart. C_LIO_LIThe GBS assay includes multi-allelic markers for potato maturity and tuber shape. C_LIO_LIThe polyBreedR software has functions for manipulating and imputing polyploid marker data in Variant Call Format. C_LIO_LILinkage Analysis was more accurate than the Random Forest method when imputing from 2K to 10K markers. C_LI

genomics↗

bioRxiv2016

Mitochondrial-nuclear interactions maintain a deep mitochondrial split in the face of nuclear gene flow

Metabolic processes in eukaryotic cells depend on interactions between mitochondrial and nuclear gene products (mitonuclear interactions). These interactions could play a direct role in population divergence. We studied the evolution of mitonuclear interactions in a widespread passerine that experienced population divergence followed by bi-directional mitochondrial introgression into different nuclear backgrounds. Using >60,000 SNPs, we quantified patterns of nuclear genetic differentiation between populations that occupy different climates and harbour deeply divergent mitolineages despite ongoing nuclear gene flow. Analyses were performed independently for two sampling transects intersecting mitochondrial divergence in different nuclear backgrounds. In both transects, low genome-wide nuclear differentiation was accompanied by strong differentiation at a ~15.4 Mb region of chromosome 1A. This region is enriched for genes performing mitochondrial functions. Molecular signatures of selective sweeps in this region alongside those in the mitochondrial genome suggest a history of adaptive mitonuclear co-introgression. The chromosome 1A region has elevated linkage disequilibrium, suggesting that selection on genomic architecture may favour low recombination among nuclear-encoded genes with mitochondrial functions. In this system, mitonuclear interactions appear to maintain the geographic separation of two mitolineages in the face of nuclear gene flow, supporting mitonuclear co-evolution as an important vehicle for climatic adaptation and population divergence.

evolutionary biology↗