Preprints
Filtering by Subject: Genetics
IQ2MC: A New Framework to Infer Phylogenetic Time Trees Using IQ-TREE 3 and MCMCTree with Mixture Models
Published: 2025-05-05
Subjects: Bioinformatics, Computational Biology, Ecology and Evolutionary Biology, Evolution, Genetics, Genetics and Genomics, Genomics, Life Sciences
IQ-TREE and MCMCTree are two widely used phylogenetic tools to infer phylogenetic trees and estimate divergence times, respectively. As MCMCTree performs fast approximate Markov Chain Monte Carlo sampling to obtain the times along a fixed tree topology, it would be natural to use IQ-TREE to obtain the tree. However, it is currently not possible to integrate these tools seamlessly, as MCMCTree [...]
Plant genomic variation and its implications for proposed EU NGT legislation
Published: 2025-04-09
Subjects: Biotechnology, Ecology and Evolutionary Biology, Evolution, Genetics, Genetics and Genomics, Genomics, Life Sciences, Molecular Genetics, Plant Breeding and Genetics Life Sciences, Plant Sciences
The European Commission proposal for New Genomic Techniques (NGTs) of July 2023 specifies that NGT1 plants, which are considered equivalent to conventional plants, may differ from the recipient or parental plant by no more than 20 insertions, which cannot be longer than 20 bp; deletions can be of any size and number. Here, we examine the proposed 20/20 NGT1 limit against the background of the [...]
The molecular evolutionary basis of species formation revisited
Published: 2025-04-09
Subjects: Ecology and Evolutionary Biology, Evolution, Genetics, Genetics and Genomics, Life Sciences
How do new species arise? This is among the most fundamental questions in evolutionary biology. The first genetic model for how reproductive barriers leads to the origin of new species was proposed nearly 90 years ago. However, empirical evidence for the genetic mechanisms that cause reproductive barriers took many decades to accumulate. In 2010, Presgraves presented a comprehensive review of the [...]
Conservation macrogenetics reveals the potential hidden consequences of the 2019-2020 Black Summer fires on Australian biodiversity
Published: 2025-03-17
Subjects: Biodiversity, Genetics, Genomics, Life Sciences, Molecular Genetics, Other Ecology and Evolutionary Biology, Population Biology
The use of genetic analyses has become ubiquitous in conservation planning and management as biodiversity is increasingly threatened globally. Typically, such analyses are employed at the species-level, though as genetic data accrue, it is now possible to consider the genetic composition of multiple species across landscapes. Such macrogenetic perspectives can reveal the potential genetic [...]
Winds of change: Charting a pathway to ecosystem monitoring using airborne environmental DNA
Published: 2025-03-06
Subjects: Genetics
Airborne environmental DNA (airborne eDNA) analysis leverages the globally ubiquitous medium of air to deliver broad species distribution data and support ecosystem monitoring across diverse environments. As this emerging technology matures, addressing critical challenges and seizing key opportunities will be essential to fully realise its potentially transformative impact. In June 2024, the [...]
Beyond the obstetric dilemma: evolutionary maternal-fetal conflict causes health problems in pregnancy and childbirth
Published: 2025-03-03
Subjects: Anthropology, Biological and Physical Anthropology, Ecology and Evolutionary Biology, Evolution, Genetics, Life Sciences, Maternal and Child Health, Medicine and Health Sciences, Translational Medical Research
In excellent recent work, Webb and colleagues challenged the so-called “obstetric dilemma”—the long-standing hypothesis that human childbearing is particularly dangerous because we have a narrow pelvis but large infant heads (we are bipedal and smart). They showed that humans and chimpanzees have a comparable fetal-pelvic squeeze. What, then, causes risky childbirth in humans? Webb and colleagues [...]
Transferable approaches to CRISPR-Cas9 induced genome editing in non-model insects: a brief guide
Published: 2025-02-27
Subjects: Animal Experimentation and Research, Animal Sciences, Entomology, Genetics, Life Sciences, Molecular Genetics, Other Genetics and Genomics, Zoology
Despite the large variety of insect species with divergent morphological, developmental and physiological features questions on gene function could for a long time only be addressed in few model species. The adoption of the bacterial CRISPR-Cas system for genome editing in eukaryotic cells widened the scope of the field of functional genetics: for the first time the creation of heritable genetic [...]
Simple maternal effect animal models provide biased estimates of additive genetic and maternal variation
Published: 2024-12-16
Subjects: Ecology and Evolutionary Biology, Genetics, Zoology
Maternal effects (the consistent effect of a mother on her offspring) can inflate estimates of additive genetic variation (V_A) if not properly accounted for. As they are typically assumed to cause similarities only among maternal siblings, they are often accounted for by modelling maternal identity effects. However, if maternal effects have a genetic basis, they create additional similarities [...]
Evolutionary rescue by aneuploidy in tumors exposed to anti-cancer drugs
Published: 2024-07-31
Subjects: Ecology and Evolutionary Biology, Evolution, Genetics, Life Sciences
Evolutionary rescue happens when a population survives a sudden environmental change that initially causes the population to decline toward extinction. A prime example of evolutionary rescue is the ability of cancer to survive exposure to treatment. One evolutionary mechanism by which a population of cancer cells can adapt to chemotherapy is aneuploidy. Aneuploid cancer cells can be fitter in an [...]
Hijackers, hitchhikers, or co-drivers? The mysteries of microbial mobilizable genetic elements
Published: 2024-04-26
Subjects: Bacteriology, Evolution, Genetics, Life Sciences, Molecular Biology
Mobile genetic elements shape microbial gene repertoires and population dynamics, but their mechanisms of horizontal transmission are often unknown. Recent results reveal that many, possibly most, bacterial mobile genetic elements require helper elements to transfer between (or within) genomes. We refer to these non-autonomous, albeit mobile, elements as Hitcher Genetic Elements (hitchers or [...]
Evolution and maintenance of mtDNA gene content across eukaryotes
Published: 2024-04-22
Subjects: Evolution, Genetics, Genomics
Across eukaryotes, most genes required for mitochondrial function have been transferred to, or otherwise acquired by, the nucleus. Encoding genes in the nucleus has many advantages. So why do mitochondria retain any genes at all? Why does the set of mtDNA genes vary so much across different species? And how do species maintain functionality in the mtDNA genes they do retain? In this review we [...]
Why there are so many definitions of fitness in models
Published: 2024-04-11
Subjects: Biology, Computational Biology, Ecology and Evolutionary Biology, Evolution, Genetics, Genetics and Genomics, Life Sciences, Population Biology
“Fitness” quantifies the ability to survive and reproduce, but is operationalized in many different ways. Generally, short-term fitness (e.g., expected number of surviving offspring) is assigned to genotypes or phenotypes, and used to non-trivially derive longer-term operationalizations of fitness (e.g. fixation probability or sojourn time), providing insight as to which organismal strategies [...]
Datathons: fostering equitability in data reuse in ecology
Published: 2024-04-04
Subjects: Biodiversity, Biology, Environmental Microbiology and Microbial Ecology Life Sciences, Genetics, Genetics and Genomics, Genomics, Life Sciences, Microbiology
Approaches to rapidly collect global biodiversity data are increasingly important, but biodiversity blindspots persist. We organized a three-day Datathon event to improve the openness of local biodiversity data, and facilitate data reuse by local researchers. The first Datathon, organized among microbial ecologists in Uruguay and Argentina assembled the largest microbiome dataset in the region to [...]
Covariance reaction norms: A flexible method for estimating complex environmental effects on trait (co)variances
Published: 2023-11-21
Subjects: Behavior and Ethology, Biology, Ecology and Evolutionary Biology, Evolution, Genetics, Integrative Biology, Life Sciences, Population Biology, Research Methods in Life Sciences, Zoology
Estimating quantitative genetic and phenotypic (co)variances is crucial for investigating evolutionary ecological phenomena such as developmental integration, life history tradeoffs, and niche specialization, as well as for describing selection and predicting multivariate evolution in the wild. While most studies assume (co)variances are fixed over short timescales, environmental heterogeneity [...]
Uneven genetic data limits biodiversity assessments in protected areas globally
Published: 2023-10-26
Subjects: Biodiversity, Ecology and Evolutionary Biology, Environmental Policy, Genetics, Life Sciences
Increasing the extent of protected areas (PA) through 30x30 and other area-based conservation initiatives can help to achieve global biodiversity conservation goals across all biodiversity levels. However, intraspecific genetic variation, the foundational level of biodiversity, is rarely explicitly considered in PA design or quality performance assessments. Repurposing existing genetic data could [...]