Preprints
Filtering by Subject: Genetics and Genomics
Removing the bad apples: a simple bioinformatic method to improve loci-recovery in de novo RADseq data for non-model organisms
Published: 2020-08-31
Subjects: Bioinformatics, Computational Biology, Genetics and Genomics, Genomics, Life Sciences
The restriction site-associated DNA (RADseq) family of protocols involves digesting DNA and sequencing the region flanking the cut site, thus providing a cost and time efficient way for obtaining thousands of genomic markers. However, when working with non-model taxa with few genomic resources, optimization of RADseq wet-lab and bioinformatic tools may be challenging, often resulting in allele [...]
Climate change prompts monitoring and systematic utilization of honey bee diversity in Turkey
Published: 2020-07-28
Subjects: Agriculture, Apiculture, Biodiversity, Ecology and Evolutionary Biology, Entomology, Genetics and Genomics, Life Sciences
Quantitative studies concerning the impact of climate change on pollinators are generally lacking. Relationship between honey bee diversity, present local adaptations and adaptive capacity of subspecies and ecotypes in the face of climate change is an urgent but rather poorly studied topic worldwide. Actually, such an effort lies at the crossroads of various fields of inquiry. Those include [...]
The genomic revolution and species delimitation in birds (and other organisms): gene flow matters, but what about other evolutionary forces?
Published: 2020-04-09
Subjects: Biodiversity, Ecology and Evolutionary Biology, Evolution, Genetics and Genomics, Genomics, Life Sciences
Given the notion that species are population-level lineages and the availability of genomic data to identify separately evolving populations, researchers usually establish species limits based on gene flow or lack thereof. A strict focus on gene flow as the main –or only– criterion to delimit species involves two main complications in practice. First, approaches often used to apply this criterion [...]
Comparing ecological and evolutionary variability within datasets
Published: 2020-01-28
Subjects: Behavior and Ethology, Ecology and Evolutionary Biology, Evolution, Genetics and Genomics, Life Sciences, Other Ecology and Evolutionary Biology, Other Genetics and Genomics, Social and Behavioral Sciences
Many key questions in evolutionary ecology require the use of variance ratios such as heritability, repeatability, and individual resource specialization. These ratios allow to understand how phenotypic variation is structured into genetic and non-genetic components, to identify how much organisms vary in the resources they use or how functional traits structure species communities. Understanding [...]
Honey Bee Diversity Is Swayed by Migratory Beekeeping and Trade Despite Conservation Practices: Genetic Evidences for the Impact of Anthropogenic Factors on Population Structure
Published: 2019-10-14
Subjects: Agriculture, Animal Sciences, Apiculture, Biodiversity, Ecology and Evolutionary Biology, Entomology, Genetics, Genetics and Genomics, Life Sciences, Zoology
The intense admixture of honey bee (Apis mellifera L.) populations at a global scale is mostly attributed to the widespread migratory beekeeping practices and replacement of queens and colonies with non-native races or hybrids of different subspecies. These practices are also common in Anatolia and Thrace, but their influence on the genetic make-up of the five native subspecies of honey bees has [...]
Embedding indigenous principles in genomic research of culturally significant species: a conservation genomics case study
Published: 2019-09-30
Subjects: Genetics and Genomics, Life Sciences, Other Genetics and Genomics
Indigenous peoples around the world are leading discussion regarding genomic research of humans, and more recently, species of cultural significance, to ensure the ethical and equitable use of DNA. Within a Māori (indigenous people of Aotearoa New Zealand) worldview, genomic data obtained from taonga (culturally significant) species has whakapapa – generally defined as genealogy, whakapapa layers [...]
Assessing symbiont extinction risk using cophylogenetic data
Published: 2019-09-25
Subjects: Biodiversity, Ecology and Evolutionary Biology, Genetics and Genomics, Immunology and Infectious Disease, Life Sciences, Other Life Sciences, Parasitology
Symbionts have a unique mode of life that has attracted the attention of ecologists and evolutionary biologists for centuries. As a result of this attention, these disciplines have produced a mature body of literature on host-symbiont interactions. In contrast, the discipline of symbiont conservation is still in a foundational stage. Here, we aim to integrate methodologies on symbiont [...]
Sexual Selection in Bacteria?
Published: 2019-05-08
Subjects: Bacteriology, Ecology and Evolutionary Biology, Environmental Microbiology and Microbial Ecology Life Sciences, Evolution, Genetics and Genomics, Life Sciences, Microbiology
A main mechanism of lateral gene transfer in bacteria is transformation, where cells take up free DNA from the environment which subsequently can be recombined into the genome. Bacteria are also known to actively release DNA into the environment through secretion or lysis, which could aid uptake via transformation. Various evolutionary benefits of DNA uptake and DNA release have been proposed but [...]
Rapid isolation and characterization of microsatellites in the critically endangered Mountain Bongo (Tragelaphus eurycerus isaaci)
Published: 2019-01-15
Subjects: Ecology and Evolutionary Biology, Genetics and Genomics, Life Sciences, Molecular Genetics
High-throughput sequencing tools promise to revolutionize many aspects of genetics research, e.g. by allowing the identification of functional adaptive genetic variation. However, the expense and expertise required to apply these tools to basic conservation questions is a challenge for applications outside academia, resulting in a so-called “conservation genomics gap” (Shafer et al. 2015). The [...]
DNA methylation patterns in the round goby hypothalamus support an on-the-spot decision scenario for territorial behaviour
Published: 2018-12-11
Subjects: Genetics and Genomics, Genomics, Life Sciences
How early life experiences are stored on a molecular level and affect behavioural phenotypes later in life is not well understood. In fish, reproductive phenotypes are often easily discernible and frequently depend on previous life experiences. DNA methylation is an epigenetic mechanism which is both sensitive to environmental conditions and stable across cell divisions. In this study, we [...]