Biology subjects

Espeland, M.

Publications and source records attributed to Espeland, M..

5 recordsLinked to original sources

bioRxiv2022

Diversification is correlated with temperature in white and sulfur butterflies

Temperature is thought to be a key variable explaining global patterns of species richness. However, to investigate this relationship carefully, it is necessary to study clades with broad geographic ranges that are comprised of species inhabiting diverse biomes with well- characterized species ranges. In the present study, we investigate the link between temperature and diversification in the butterfly family Pieridae (sulfurs and whites) by combining Next Generation sequences and published molecular data with fine-grained distribution information. After building the most comprehensive phylogeny of the group, with almost 600 species and all higher taxa (subfamilies, tribes and subtribes), we found strong support for the following relationships within the family: Dismorphiinae + (Coliadinae + (Pseudopontiinae + Pierinae)). With a curated distribution dataset of over 800,000 occurrences, we conducted multiple comparative phylogenetic analyses that provided strong evidence that species in environments with more stable daily temperatures or with cooler maximum temperatures in the warm seasons have higher diversification rates. We also found a positive correlation between speciation and extinction with paleotemperature: as global temperature decreased through geological time, so did diversification rates. Although many studies demonstrate higher diversity in the tropics, we have been able to identify specific climate variables associated with changes in diversification, while also inferring the most robust and well sampled phylogenomic framework for Pieridae to date.

evolutionary biology↗

bioRxiv2022

Genetic, clinical underpinnings of subtle early brain change along Alzheimer's dimensions

Alzheimers disease (AD) is associated with heterogeneous atrophy patterns. We employed a semi-supervised clustering technique known as Surreal-GAN, through which we identified two dominant dimensions of brain atrophy in symptomatic mild cognitive impairment (MCI) and AD patients: the "diffuse-AD" (R1) dimension shows widespread brain atrophy, and the "MTL-AD" (R2) dimension displays focal medial temporal lobe (MTL) atrophy. Critically, only R2 was associated with widely known sporadic AD genetic risk factors (e.g., APOE {varepsilon}4) in MCI and AD patients at baseline. We then independently detected the presence of the two dimensions in the early stages by deploying the trained model in the general population and two cognitively unimpaired cohorts of asymptomatic participants. In the general population, genome-wide association studies found 77 genes unrelated to APOE differentially associated with R1 and R2. Functional analyses revealed that these genes were overrepresented in differentially expressed gene sets in organs beyond the brain (R1 and R2), including the heart (R1) and the pituitary gland, muscle, and kidney (R2). These genes were enriched in biological pathways implicated in dendritic cells (R2), macrophage functions (R1), and cancer (R1 and R2). Several of them were "druggable genes" for cancer (R1), inflammation (R1), cardiovascular diseases (R1), and diseases of the nervous system (R2). The longitudinal progression showed that APOE {varepsilon}4, amyloid, and tau were associated with R2 at early asymptomatic stages, but this longitudinal association occurs only at late symptomatic stages in R1. Our findings deepen our understanding of the multifaceted pathogenesis of AD beyond the brain. In early asymptomatic stages, the two dimensions are associated with diverse pathological mechanisms, including cardiovascular diseases, inflammation, and hormonal dysfunction - driven by genes different from APOE - which may collectively contribute to the early pathogenesis of AD.

bioengineering↗

bioRxiv2022

Delimiting Continuity: Comparison of Target Enrichment and ddRAD for Delineating Admixing Parapatric Melitaea Butterflies

Parapatrically distributed taxa pose a challenge for species delimitation due to the presence of gene flow and inherent arbitrariness of exactly defining the species boundaries in such systems. We tackled the problem of species delimitation in a parapatric species pair of Melitaea butterflies using two popular genomic methods - double digest restriction-site associated DNA sequencing (ddRAD) and target enrichment. The former is mainly applied at shallow phylogenetic scales and the latter at both deep and shallow scales. Although both of these methods have been adequately utilised for species delimitation purposes, there are only a handful of studies that have compared these two genomic approaches in the same study system. We applied phylogenetic, population genetic and species delimitation methods and compared the results obtained from the two approaches. Using a recently developed target enrichment probe kit, we were able to capture 1,743 loci with a low amount of missing data and compared these with already available ddRAD data from a previous study on the same set of specimens. We recovered consistent phylogenetic relationships across the datasets, both demonstrating the presence of a genetically distinct Balkan lineage and paraphyly of Melitaea athalia with respect to Melitaea celadussa. The same relationships were also found in a species tree analysis of the target enrichment dataset using ASTRAL. Population genetic STRUCTURE analyses supported the presence of two species when using ddRAD data, but three species when using target enrichment, while the Bayes factor delimitation analysis found both two and three species scenarios equally decisive in both datasets. From the geographic distribution of genomic admixture, we confirm the patterns observed by a previous study that used ddRAD data. As the results obtained from both methods were largely congruent, we discuss some practical considerations and benefits of target enrichment over RAD sequencing. We conclude that the choice of method of genomic data collection does not influence the results of phylogenetic analyses at alpha taxonomic level, given a sufficient number of loci. Finally, we recommend a solution for delineating species in parapatric scenarios by proposing that parapatric taxa be consistently classified as subspecies or complete species, but not both, to promote taxonomic stability.

evolutionary biology↗

bioRxiv2021

Association between Cognitive Function and Large Optic Nerve Cupping, Accounting for Cup-Disc-Ratio Genetic Risk Score

PurposeTo investigate if accounting for a cup-to-disc ratio (CDR) genetic risk score (GRS) modified the association between large CDR and cognitive function among women. DesignThis was a retrospective study using data from the Womens Health Initiative. MethodsPatients with glaucoma or ocular hypertension were excluded. Large CDR was defined as [≥] 0.6 in either eye. Cognitive function was measured by the Modified Mini-Mental State Examination (3MSE). We used the combined effects from 13 single nucleotide polymorphisms (SNPs) to formulate the GRS for CDR. We used logistic regression to investigate associations between weighted GRS and large CDR, then a linear regression to assess the association between weighted GRS and 3MSE scores, and between weighted GRS, CDR, and 3MSE scores, adjusted for demographic and clinical characteristics. ResultsFinal analyses included 1,196 White women with mean age of 69.60 {+/-} 3.62 years and 7.27% with large CDR. Mean GRS in women with and without large CDR was 1.51 {+/-} 0.31 vs. 1.41 {+/-} 0.36, respectively (p = 0.004). The odds of large CDR for a one unit increase in GRS was 2.30 (95% CI: (1.22, 4.36), p = 0.011). Adding the CDR GRS in the model with CDR and 3MSE, women with large CDR still had statistically significantly lower 3MSE scores than those without large CDR, yielding a predicted mean difference in 3MSE scores of 0.84 (p = 0.007). ConclusionsIndependent of the CDR GRS, women with large CDR had a lower cognitive function.

genetics↗

bioRxiv2021

Standardized nuclear markers advance metazoan taxonomy

Species are the fundamental units of life and their recognition is essential for science and society. DNA barcoding, the use of a single and often mitochondrial gene, has been increasingly employed as a universal approach for the identification of animal species. However, this approach faces several challenges. Here, we demonstrate with empirical data from a number of metazoan animal lineages that multiple nuclear-encoded markers, so called universal single-copy orthologs (USCOs) performs much better than the single barcode gene to discriminate closely related species. Overcoming the general shortcomings of mitochondrial DNA barcodes, USCOs also accurately assign samples to higher taxonomic levels. These loci thus provide a powerful and unifying framework for species delimitation which considerably improves the DNA-based inference of animal species.

molecular biology↗