Preprints
Filtering by Subject: Genomics
Lactate Dehydrogenase as a Candidate Genomic Marker of Climate Change in Mammals?
Published: 2026-07-13
Subjects: Bioinformatics, Comparative and Evolutionary Physiology, Evolution, Genetics, Genomics, Molecular Genetics, Other Ecology and Evolutionary Biology, Population Biology
Climate change imposes metabolic and thermal stress on mammals, yet genomic markers that track lineage specific adaptation remain limited. Lactate dehydrogenase (LDH), a central enzyme in lactate metabolism and anaerobic stress response, has not previously been evaluated for its evolutionary association with climate change induced selection. Here, comparative genomics across 14 mammalian species [...]
Genome-wide strengthening of evolutionary constraint across the volvocine multicellularity gradient
Published: 2026-07-03
Subjects: Computational Biology, Ecology and Evolutionary Biology, Evolution, Genetics and Genomics, Genomics
The evolutionary cost of maintaining somatic cell populations has been hypothesised to drive proteome-wide strengthening of constraint on coding sequence at the origin of multicellularity. Prior work on the volvocine clade has reported lower d_N/d_S in colonial than in unicellular relatives on 55 chloroplast genes (Hu et al. 2019) and on 105 nuclear single-copy orthogroups across colonial species [...]
Inferring genomic landscapes with the integrative sequentially Markov coalescent (iSMC)
Published: 2026-05-27
Subjects: Bioinformatics, Biology, Computational Biology, Genetics and Genomics, Genomics, Life Sciences
The integrative Sequentially Markovian Coalescent (iSMC) is an extension of the sequentially Markovian Coalescent (SMC) model allowing for parameter heterogeneity along the genome, such as recombination and mutation rates. Heterogeneous parameters follow an autocorrelation process that modulates the genealogical process, extending the hidden state space and adding as few as two extra parameters [...]
Making use of oak genomes
Published: 2026-05-13
Subjects: Biodiversity, Botany, Genomics, Life Sciences
This review summarizes the contributions of genomics to our understanding of oak evolution and management, both past and ongoing. Far from being exhaustive given the large number of publications following the publication of the genomes, this review emphasizes work conducted in the decade following publication of the first two complete oak genome assemblies, and major findings and achievements [...]
Incorporating population genomic perspectives into kelp conservation and aquaculture in the Pacific Northwest
Published: 2026-04-01
Subjects: Ecology and Evolutionary Biology, Evolution, Genetics and Genomics, Genomics, Life Sciences, Marine Biology
Recent kelp forest declines and growth in the kelp aquaculture industry have fueled increasing interest in ecological and evolutionary research on kelp forests, including kelp population genomics. While many kelp management activities have inherent genetic and evolutionary implications, kelp management in the Pacific Northwest (PNW) of North America has to date made only limited use of [...]
From Trading Genes to Crafting New Tricks: How Horizontal Gene Transfer Potentiates the Emergence of Novel Functions
Published: 2026-03-17
Subjects: Evolution, Genetics, Genomics, Microbiology
Horizontal gene transfer (HGT), the set of processes by which genetic information is transferred between individuals, has shaped life’s evolution. It is particularly frequent in microbial organisms, where it has driven numerous remarkable adaptations to extreme conditions, anti-microbial agents, or biotic interactions. Its role in spreading novel functions is now documented by countless examples [...]
Evaluation of site frequency spectrum-based demographic inference methods for use in conservation contexts
Published: 2026-03-15
Subjects: Evolution, Genomics
Genomic methods for inferring historical effective population size (Nₑ) trajectories offer valuable tools for conservation, yet their reliability under conditions typical of conservation datasets—small sample sizes, reduced-representation SNP data, and recent demographic change—remains poorly characterised. We evaluated the performance of two widely used site frequency spectrum (SFS)–based [...]
Transposable elements as drivers of reproductive isolation: A framework for testing hybridization-induced escalation of genetic conflicts
Published: 2026-02-26
Subjects: Evolution, Genetics, Genomics, Other Ecology and Evolutionary Biology
Contrary to long-held views, the exchange of genetic diversity between species by hybridization is now recognized as an important process contributing to the evolution of biodiversity. However, hybridization has molecular consequences beyond the exchange of genetic variation. The clash of divergent genomes upon hybridization can escalate genetic conflicts previously resolved in parental species – [...]
A macroevolutionary gene network reveals diapause evolutionary dynamics beyond the circadian clock and predicts microevolution
Published: 2026-02-16
Subjects: Computational Biology, Evolution, Genomics, Other Genetics and Genomics, Population Biology
Diapause is an alternative developmental pathway evolved independently in many insects to synchronize life cycles with resource abundance. While subsets of this essential phenotype have long been studied at a single species level, the genomic basis of the full diapause syndrome remains poorly understood. Remaining unknown is whether convergent diapause syndromes employ shared mechanisms. This [...]
The interplay between epigenetic mechanisms and deleterious mutations: implications for fitness, evolution and conservation
Published: 2026-01-13
Subjects: Biology, Ecology and Evolutionary Biology, Genetics, Genetics and Genomics, Genomics, Life Sciences, Molecular Genetics
Understanding the causal effects of genetic mutations is essential for explaining fitness variation, forecasting evolutionary trajectories and assessing extinction risk, yet remains a fundamental challenge, particularly in natural populations. While amino acid substitutions can alter protein structure and function, mutations affecting gene regulation can also have significant fitness [...]
The weak driver conundrum: data archiving and biological phenomena impact macrogenetic findings
Published: 2025-12-10
Subjects: Biodiversity, Evolution, Genetics, Genomics, Other Ecology and Evolutionary Biology
Macrogenetics seeks to identify the global drivers and patterns in intraspecific genetic diversity, yet many reported patterns are weak or inconsistent. To achieve multispecies global inference, many macrogenetic studies leverage open sequencing data that can suffer from archiving biases. It remains unclear if macrogenetic inconsistencies are innate genetic phenomena, or are the product of open [...]
Complete de novo assembly of Wolbachia endosymbiont of contemporary Drosophila simulans using long-read genome sequencing.
Published: 2025-10-08
Subjects: Evolution, Genomics
We present a contemporary high-quality, complete de novo assembly of Wolbachia pipientis (wRi Merrill 23, CP199298), an alphaproteobacterial endosymbiont of Drosophila simulans. This assembly was generated using long read sequencing of wRi-infected D. simulans embryos collected from the Merrill College at the University of California, Santa Cruz in October 2023.
Epigenetic changes associated with reproductive investment and life-history trade-offs in lekking male black grouse (Lyrurus tetrix)
Published: 2025-10-05
Subjects: Genomics, Molecular Genetics, Other Ecology and Evolutionary Biology
Life-history trade-offs are a central concept in evolutionary biology, yet their underlying molecular mechanisms are not yet fully understood. Whilst much research has focused on genetic variation, epigenetic mechanisms, which regulate gene regulation, may be equally important. To investigate this, we collected blood samples from 50 male black grouse (Lyrurus tetrix) before and after the [...]
Alternative Promoters Expand Transcriptional Complexity of Temperature Stress Responses in Cassava
Published: 2025-09-29
Subjects: Agriculture, Bioinformatics, Genetics and Genomics, Genomics, Plant Biology, Plant Sciences
Plant abiotic stress responses involve two major gene expression regulatory mechanisms: alternative promoter usage and differential expression. Although differentially expressed genes (DEGs) have been extensively studied, alternative promoter genes (APGs) remain poorly characterized despite their potential importance. We systematically compared APGs and DEGs in cassava (Manihot esculenta), a [...]
Project Psyche: Generating and utilising reference genomes for all Lepidoptera in Europe
Published: 2025-09-10
Subjects: Biodiversity, Genetics and Genomics, Genomics, Life Sciences
Project Psyche is a trans-national initiative to generate and study chromosome-level reference genomes of all ca. 11,000 described species of Lepidoptera (butterflies and moths) found in Europe. The Project Psyche community encompasses diverse researchers, amateur lepidopterists, practitioners, and industry experts united by a common vision of the importance of genomics for Lepidoptera. [...]