Biology subjects

Bougiouri, K.

Publications and source records attributed to Bougiouri, K..

3 recordsLinked to original sources

bioRxiv2024

Imputation of ancient canid genomes reveals inbreeding history over the past 10,000 years

The multi-millenia long history between dogs and humans has placed them at the forefront of archeological and genomic research. Despite ongoing efforts including the analysis of ancient dog and wolf genomes, many questions remain regarding their geographic and temporal origins, and the microevolutionary processes that led to the diversity of breeds today. Although ancient genomes provide valuable information, their use is hindered by low depth of coverage and post-mortem damage, which inhibits confident genotype calling. In the present study, we assess how genotype imputation of ancient dog and wolf genomes, utilising a large reference panel, can improve the resolution provided by ancient datasets. Imputation accuracy was evaluated by down-sampling high coverage dog and wolf genomes to 0.05-2x coverage and comparing concordance between imputed and high coverage genotypes. We measured the impact of imputation on principal component analyses and runs of homozygosity. Our findings show high (R2>0.9) imputation accuracy for dogs with coverage as low as 0.5x and for wolves as low as 1.0x. We then imputed a dataset of 90 ancient dog and wolf genomes, to assess changes in inbreeding during the last 10,000 years of dog evolution. Ancient dog and wolf populations generally exhibited lower inbreeding levels than present-day individuals. Interestingly, regions with low ROH density maintained across ancient and present-day samples were significantly associated with genes related to olfaction and immune response. Our study indicates that imputing ancient canine genomes is a viable strategy that allows for the use of analytical methods previously limited to high-quality genetic data.

evolutionary biology↗

bioRxiv2023

Heteroplasmy and tandem repeats reveal adaptation to elevation in the New World Jays (Aves: Corvidae)

Advances in high-throughput sequencing (HTS) and bioinformatic tools have enabled the quick and cost-efficient assembly of complete mitochondrial genomes (mitogenomes) in non-model organisms. Consequently, new evidence of heteroplasmy, recombination and paternal leakage in mitogenomes has increased. In this study, we utilized HTS data from whole-genome sequencing to assemble the first complete mitogenomes of nine species of New World Jays (NWJs), covering all genera. We further investigated the evolution of heteroplasmy, tandem repeats (TRs) and signatures of natural selection. Our results showed a molecular shift in the adaptation to low elevation in the NWJs. Among the species studied, we found 10 heteroplasmic sites either containing TRs in the same site or 1 to 300 nucleotides adjacent; one species-specific TR in a transfer RNA (tRNA-P) potentially associated with low elevation; one phylogenetic branch with evidence of episodic positive selection also associated with low elevation; and 5 codon sites with strong support for positive selection. We referred to the heteroplasmy-TR interaction and its possible role with regulation, recombination and paternal leakage in the mitogenomes. Finally, phylogenetic relationships were in agreement with previous studies and we discussed how selective pressure on genes from the oxidative phosphorylation pathway (OXPHOS) may benefit species from low-elevation habitats. Although these findings in the NWJs require further investigation, this study offers promising insights about the evolution of mitogenomes in birds.

genomics↗

bioRxiv2023

Clearwing butterflies challenge the thermal melanism hypothesis

In contrast to most butterflies harboring opaque wing colorations, some species display large transparent patches on their wings. Wing transparency, which entails a dramatic reduction of pigmentation, raises the question of potential costs for vital functions, such as thermoregulation, especially along climatic gradients. The thermal melanism hypothesis posits that darker colorations should be favored in colder environments, which enables them to absorb more radiation and maintain a body temperature compatible with activity. This prediction extends to the near infrared (NIR) range, which represents a large proportion of solar radiation. Here we assess the implications of wing transparency for light absorption and thermal properties in 42 butterfly species from the neotropical tribe Ithomiini that range the extent of transparency, from fully opaque to highly transparent, and we test whether those species conform to the prediction of the thermal melanism hypothesis. We find that transparent wings are less efficient than opaque wings to absorb light across UV, Visible and NIR wavelength ranges, and are also less efficient to collect heat. Moreover, dark coloration occupies a lower proportion of wing area as altitude increases, and ithomiine species harbor more transparency at higher altitudes, where climatic conditions are colder, going strongly against the prediction of the thermal melanism hypothesis. We discuss these surprising results in light of recent studies suggesting that factors other than adaptation to cold, such as predation pressure, physiology or behavior, may have driven the evolution of wing patterns in Ithomiini. Significance StatementThe thermal melanism hypothesis predicts that organisms should be darker and absorb solar radiation more efficiently in colder environments. The Neotropical butterflies Ithomiini are unusual in that many species harbor large transparent patches on their wings, raising questions related to their efficacy of solar radiation absorption and heating capacities. We investigate optical and thermal properties of several ithomiine species along a climatic gradient. We find that transparent wings are less efficient at absorbing radiation and collecting heat. Unexpectedly, the proportion of transparent species increases with altitude, challenging the thermal melanism hypothesis and suggesting that factors other than adaptation to cold, such as predation pressure, may have driven the evolution of wing patterns in Ithomiini.

evolutionary biology↗