Biology subjects

Gossmann, T. I.

Publications and source records attributed to Gossmann, T. I..

11 recordsLinked to original sources

bioRxiv2025

SwarmGenomics: A Unified Pipeline for Individual-Based Whole-Genome Analyses

Advances in sequencing technologies have made whole-genome data widely accessible, enabling research in population genetics, evolutionary biology, and conservation. However, analyzing whole-genome sequencing (WGS) data remains challenging, often requiring multiple specialized tools and substantial bioinformatics expertise. We present SwarmGenomics, a modular, user-friendly command-line pipeline for reference-based genome assembly and individual-based genetic analyses. The pipeline integrates seven modules: heterozygosity estimation, runs of homozygosity detection, Pairwise Sequentially Markovian Coalescent (PSMC) analysis, unmapped reads classification, repeat analysis, mitochondrial genome assembly, and nuclear mitochondrial DNA segment (NUMT) identification. Each module can be run independently or as part of a complete workflow. We demonstrate the pipelines utility with a case study on the giant panda (Ailuropoda melanoleuca), revealing insights into genetic diversity, inbreeding history, historical population size changes, transposable element activity, and microbial contamination. SwarmGenomics lowers the entry barrier for genomic analysis of diploid, non-model species, serving both as a research and teaching tool. The pipeline and documentation are available at https://github.com/AureKylmanen/Swarmgenomics.

genomics↗

bioRxiv2025

Dietary restriction is evolutionary conserved on the phenotypic and mechanistic level

The anti-ageing response of Dietary Restriction (DR) is thought to be an ancient mechanistic response, reasoning from its phenotypic conservation in a wide range of organisms. However, DR is implemented using different diets and methods across species, and evidence for conservation at the mechanistic level remains limited. Here we tested the longevity and fecundity response to DR across eight different species of Drosophila using the same diets in a reaction norm framework. We confirm that DR is phenotypically conserved across Drosophila. Next, we used comparative transcriptomics across six species and found strongly concordant differential expression in response to DR (rs > 0.28, < 0.72, P < 0.0001). We studied the evolutionary history of the top concordantly differentially expressed orthologous genes and identified that the large majority of these genes are "young" genes and are Diptera specific. Our results indicate that large parts of the DR response are likely to be taxonomic specific, suggesting that the genetic basis of DR is not widely conserved. To validate this hypothesis we tested whether the 15 most conserved genes that change in transcription in response to DR using conditional in vivo RNAi. Surprisingly, we found that 12 out of 15 genes tested had a lifespan phenotype, with 9 extending lifespan. Five of these genes are related to cysteine metabolism implicating it in the mechanisms of DR, further suggesting physiological compensation to DR is ubiquitous and providing a possible biomedical target. Our findings suggest that while large parts of the DR response are taxonomically specific, some core mechanisms are conserved across divergent species. The comparative approaches we used here hold promise to identify shared mechanisms relevant to our own species and therefore ultimately anti-ageing interventions.

evolutionary biology↗

bioRxiv2024

DNA barcoding of passerine birds at an ornithological crossroad reveals significant East-West genetic lineage divergence

Exploring genetic diversity is essential for precise species delimitation, especially within taxonomically complex groups like passerine birds. Traditional morphological methods often fail to resolve species boundaries; however, DNA barcoding, particularly through the mitochondrial cytochrome c oxidase subunit I (COI) gene, provides a powerful alternative method for accurate species identification. This study establishes a comprehensive DNA barcode library for Iranian passerine birds, analyzing 537 COI sequences from 94 species across 23 families and 53 genera. We observed a pronounced barcode gap, with average intraspecific divergence at 0.4% and interspecific divergence at 18.6%. Notable intraspecific variation emerged in the Persian nuthatch (Sitta tephronota) and the Lesser whitethroat (Curruca curruca), while the goldfinch (Carduelis carduelis) showed limited genetic differentiation despite marked morphological distinctions. Phylogenetic analysis revealed significant east-west genetic splits in C. curruca and S. tephronota, reflecting geographic and zoogeographic boundaries of Iran. These findings demonstrate the effectiveness of DNA barcoding in elucidating biogeographic patterns, emphasizing the key role of Iran as an ornithological crossroads for avian biodiversity. Moreover, our results suggest that much of the genetic variation in the COI gene arises from synonymous mutations, highlighting the role of purifying selection in shaping mtDNA diversity across species.

zoology↗

bioRxiv2024

A comprehensive representation of selection at loci with multiple alleles that allows complex forms of genotypic fitness

Genetic diversity is central to evolutionary change, with both natural selection and random genetic drift depending on variation within a population. An individual in a diploid population carries two alleles per locus, yet the population as a whole can harbour many alleles, giving rise to a rich spectrum of homozygous and heterozygous genotypes. Such multiallelic variation is common at biologically and medically important loci such as the major histocompatibility complex, the ABO blood group system, and genes underlying monogenic diseases. However, much of population genetic theory and data analysis has focussed on biallelic loci. Here, we introduce a matrix representation of the genotypic selection acting at a multiallelic locus. This exploits the common mathematical structure underlying selection and drift, and separates the effects of genetic diversity and fitness. The representation accommodates diverse selection regimes, including additive, multiplicative, frequency-dependent, and temporally varying selection, as well as heterozygote advantage. We show how, under specific assumptions, genotype-specific fitness-effects can be estimated from allele frequency trajectories over microevolutionary timescales. Applying this estimation procedure to time-series data from experimental yeast evolution illustrates how multiallelic fitness interactions, including heterozygote advantage, may be characterised from haplotype frequency data. More broadly, this work provides a practical foundation for analysing evolutionary dynamics at multiallelic loci in experimental and natural populations.

evolutionary biology↗

bioRxiv2024

Identification of 5mC within heterogenous tissue using de-novo somatic mutations

Tissues represent a fundamental evolutionary interface at the junction of genotype and phenotype. Indeed, gene regulation often occurs at the tissue level and manifests itself through tissue-specific epigenetic modifications. Studies investigating tissue epigenetics are limited by access to pure tissues. Tissues not only differ epigenetically, they are also subject to genetic differentiation through somatic mutations. As somatic mutations follow predictable patterns of inheritance, the application of population genomic approaches to inter- and intra-tissue variation could allow for the efficient detection of epigenetic modifications, even when tissue samples are convoluted. Here, we present an approach that uses de-novo somatic mutations to deconvolute 5mC methylation patterns through analysis of shifts in tissue-specific allele frequencies. We use simulations and bisulfite sequencing data to show that somatic mutations are common and detectable in next-generation sequencing data. We then use changes in mutation frequencies to accurately derive the proportional tissue of origin along a gradient of in silico subsamples of mixed-tissue bisulfite reads. We confirm that mixed tissues bias estimates of methylation levels and prevent detection of methylation differences at high levels of mixture. Our derived estimates of tissue contamination allow for unbiased and accurate deconvolution of mixed-tissue methylations in CpG and non-CpG context. We are ultimately able to recover 15-30% of differentially-methylated sites, and approximately 40-90% of differentially-methylated CpG islands and gene bodies in any cytosine context at contamination levels up to 90%. Our findings highlight the utility of population genomic approaches across scales, and expand the accessibility of epigenetics studies within evolutionary biology.

genomics↗

bioRxiv2024

The Role of Metabolism in Shaping Enzyme Structures Over 400 Million Years of Evolution

The functions of cells and proteins depend on their biochemical microenvironment. To understand how biochemical constraints shaped protein structural evolution, we coupled the extensive genetic and metabolic data from the Saccharomycotina subphylum with the capability of AlphaFold2 to systematically predict protein structures from sequence. Determining how 11,269 enzyme structures catalysing 361 different metabolic reactions evolved over 400 million years alongside their molecular functions, we report that metabolism has shaped the structural evolution of enzymes at different levels: the organisms overall metabolism; the topological organisation of the metabolic network; and each enzymes molecular properties. For example, structural evolution depends on each enzymes reaction mechanism, on the variability rather than the amount of metabolic flux, and on biosynthetic cost. Evolutionary cost-optimization is stronger on highly abundant enzymes and acts differently on different structural domains, with the exception of small-molecule binding sites, which are prioritised over other structural domains and lack cost-optimisation. Finally, while enzyme surfaces are less constrained, surface residues can also be exposed to positive selection for the co-evolution of protein-protein interaction sites. Accessing AlphaFolds power to predict protein structures systematically and across species barriers, facilitating the integration of protein structures with functional genomics, we were thus able to map biological constraints which shape protein structural evolution at scale and over long timelines.

systems biology↗

bioRxiv2022

High nucleotide diversity accompanies differential DNA methylation in naturally diverging populations

Epigenetic mechanisms such as DNA methylation (DNAme) are thought to comprise an invaluable adaptive toolkit in the early stages of local adaptation, especially when genetic diversity is constrained. However, the link between genetic diversity and DNAme has been scarcely examined in natural populations, despite its potential to shed light on the evolutionary forces acting on methylation state. Here, we analysed reduced-representation bisulfite sequencing and whole genome pool-seq data from marine and freshwater stickleback populations to examine the relationship between DNAme variation (between- and within-population), and nucleotide diversity in the context of freshwater adaptation. We find that sites that are differentially methylated between populations have higher underlying standing genetic variation, with diversity higher among sites that gained methylation in freshwater than those that lost it. Strikingly, while nucleotide diversity is generally lower in the freshwater population as expected from a population bottleneck, this is not the case for sites which lost methylation which instead have elevated nucleotide diversity in freshwater compared to marine. Subsequently, we show that nucleotide diversity is higher among sites with ancestrally variable methylation and also positively correlates with the sensitivity to environmentally induced methylation change. Both suggest that as selection on the control of methylation state becomes relaxed, so too does selection against mutations at the sites themselves. Increased epigenetic variance in a population is therefore likely to precede genetic diversification.

evolutionary biology↗

bioRxiv2019

Non-coding rather than coding regions underpin avian bill shape diversification at macroevolutionary scales

Recent progress has been made in identifying genomic regions implicated in trait evolution on a microevolutionary scale in many species, but whether these are relevant over macroevolutionary time remains unclear. Here, we directly address this fundamental question using bird beak shape, a key evolutionary innovation linked to patterns of resource use, divergence and speciation, as a model trait. We integrate class-wide geometric-morphometric analyses with evolutionary sequence analyses of 10,322 protein coding genes as well as 229,001 genomic regions spanning 72 species. We identify 1,434 protein coding genes and 39,806 noncoding regions for which molecular rates were significantly related to rates of bill shape evolution. We show that homologs of the identified protein coding genes as well as genes in close proximity to the identified noncoding regions are involved in craniofacial embryo development in mammals. They are associated with embryonic stem cells pathways, including BMP and Wnt signalling, both of which have repeatedly been implicated in the morphological development of avian beaks. This suggests that identifying genotype-phenotype association on a genome wide scale over macroevolutionary time is feasible. While the coding and noncoding gene sets are associated with similar pathways, the actual genes are highly distinct, with significantly reduced overlap between them and bill-related phenotype associations specific to noncoding loci. Evidence for signatures of recent diversifying selection on our identified noncoding loci in Darwin finch populations further suggests that regulatory rather than coding changes are major drivers of morphological diversification over macroevolutionary times.

evolutionary biology↗

bioRxiv2018

Programmed DNA elimination of germline development genes in songbirds

Genomes can vary within individual organisms. Programmed DNA elimination leads to dramatic changes in genome organisation during the germline-soma differentiation of ciliates1, lampreys2, nematodes3,4, and various other eukaryotes5. A particularly remarkable example of tissue-specific genome differentiation is the germline-restricted chromosome (GRC) in the zebra finch which is consistently absent from somatic cells6. Although the zebra finch is an important animal model system7, molecular evidence from its large GRC (>150 megabases) is limited to a short intergenic region8 and a single mRNA9. Here, we combined cytogenetic, genomic, transcriptomic, and proteomic evidence to resolve the evolutionary origin and functional significance of the GRC. First, by generating tissue-specific de-novo linked-read genome assemblies and re-sequencing two additional germline and soma samples, we found that the GRC contains at least 115 genes which are paralogous to single-copy genes on 18 autosomes and the Z chromosome. We detected an amplification of [≥]38 GRC-linked genes into high copy numbers (up to 308 copies) but, surprisingly, no enrichment of transposable elements on the GRC. Second, transcriptome and proteome data provided evidence for functional expression of GRC genes at the RNA and protein levels in testes and ovaries. Interestingly, the GRC is enriched for genes with highly expressed orthologs in chicken gonads and gene ontologies involved in female gonad development. Third, we detected evolutionary strata of GRC-linked genes. Developmental genes such as bicc1 and trim71 have resided on the GRC for tens of millions of years, whereas dozens have become GRC-linked very recently. The GRC is thus likely widespread in songbirds (half of all bird species) and its rapid evolution may have contributed to their diversification. Together, our results demonstrate a highly dynamic evolutionary history of the songbird GRC leading to dramatic germline-soma genome differences as a novel mechanism to minimise genetic conflict between germline and soma.

evolutionary biology↗

bioRxiv2018

Sexual selection rewires reproductive protein networks

Polyandry drives postcopulatory sexual selection (PCSS), resulting in rapid evolution of male ejaculate traits. Critical to male and female fitness, the ejaculate is known to contain rapidly evolving seminal fluid proteins (SFPs) produced by specialized male secretory accessory glands. The evidence that rapid evolution of some SFPs is driven by PCSS, however, is indirect, based on either plastic responses to changes in the sexual selection environment or correlative macroevolutionary patterns. Moreover, such studies focus on SFPs that represent but a small component of the accessory gland proteome. Neither how SFPs function with other reproductive proteins, nor how PCSS influences the underlying secretory tissue adaptations and content of the accessory gland, has been addressed at the level of the proteome. Here we directly test the hypothesis that PCSS results in rapid evolution of the entire male accessory gland proteome and protein networks by taking a system-level approach, combining divergent experimental evolution of PCSS in Drosophila pseudoobscura (Dpse), high resolution mass spectrometry (MS) and proteomic discovery, bioinformatics and population genetic analyses. We demonstrate that PCSS influences the abundance of over 200 accessory gland proteins, including SFPs. A small but significant number of these proteins display molecular signatures of positive selection. Divergent PCSS also results in fundamental and remarkably compartmentalized evolution of accessory gland protein networks in which males subjected to strong PCSS invest in protein networks that serve to increase protein production whereas males subjected to relaxed PCSS alters protein networks involved in protein surveillance and quality. These results directly demonstrate that PCSS is a key evolutionary driver that shapes not only individual reproductive proteins, but rewires entire reproductive protein networks.\n\nThe abbreviations used are

evolutionary biology↗

bioRxiv2018

Exploring the unmapped DNA and RNA reads in a songbird genome

BackgroundA widely used approach in next-generation sequencing projects is the alignment of reads to a reference genome. A significant percentage of reads, however, frequently remain unmapped despite improvements in the methods and hardware, which have enhanced the efficiency and accuracy of alignments. Usually unmapped reads are discarded from the analysis process, but significant biological information and insights can be uncovered from this data. We explored the unmapped DNA (normal and bisulfite treated) and RNA sequence reads of the great tit (Parus major) reference genome individual. From the unmapped reads we generated de novo assemblies. The generated sequence contigs were then aligned to the NCBI non-redundant nucleotide database using BLAST, identifying the closest known matching sequence.\n\nResultsMany of the aligned contigs showed sequence similarity to sequences from different bird species and genes that were absent in the great tit reference assembly. Furthermore, there were also contigs that represented known P. major pathogenic species. Most interesting were several species of blood parasites such as Plasmodium and Trypanosoma.\n\nConclusionsOur analyses revealed that meaningful biological information can be found when further exploring unmapped reads. It is possible to discover sequences that are either absent or misassembled in the reference genome and sequences that indicate infection or sample contamination. In this study we also propose strategies to aid the capture and interpretation of this information from unmapped reads.

genomics↗