Biology subjects

Psonis, N.

Publications and source records attributed to Psonis, N..

3 recordsLinked to original sources

bioRxiv2025

Genetic affinities between an ancient Greek colony and its metropolis: the case of Amvrakia in western Greece

BackgroundDuring the Ancient Greek colonization, Corinth established a stable network of economic and political ties, by founding colonies connecting southern Greece with the mainland of Epirus and reaching as far as the east Adriatic coast. Amvrakia, one of the main Corinthian colonies founded during the 7th century BCE, was characterized by its strong dependence on its metropolis. Here, we aim to investigate the genetic relationships between the Corinthian metropolis and the Amvrakia colony, the contribution of the local population to the founding genetic pool, as well as the demography of Amvrakia in subsequent periods. ResultsDuring its foundation in the Archaic period, Amvrakia appears to have been shaped by genetic influences from at least two different sources. The first source migrated from the Corinth territory, represented by the Archaic Tenea population and is supported via an Identity By Descent (IBD) analysis. The second source shows a direct ancestry from Late Bronze Age (LBA) / Iron Age Greece, including a local LBA population represented by the Ammotopos site located in close proximity to Amvrakia, as shown by a plethora of independent population genomics analyses. During the subsequent Classical and Hellenistic periods, the population of Amvrakia appears to have slightly differentiated, yet evidence of genetic continuity over time is observed. ConclusionsThe migration of Corinthians to Amvrakia contributed to the initial genetic pool of the colony along with the local genetic pool, indicating that the Corinthian colonization included both genetic and cultural transmission between the metropolis and its colony.

evolutionary biology↗

bioRxiv2025

Finding the relatives of a critically endangered island endemic reveals the heterogeneous evolution of land snail mitogenomes (Gastropoda: Helicidae)

We analysed the phylogenetic relationships of Aristena rechingeri, an extremely rare, large, flat-shelled snail from the Aegean island of Karpathos. Low-depth Illumina sequencing data obtained from an empty shell were available, but there was no reference genome or sequences of nuclear loci from the related taxa, so we attempted to resolve the phylogeny with mitogenome sequences. We confirmed that Aristena is sister to the globular-shelled genera Helix and Maltzanella and not to the similarly flat-shelled and geographically proximate Isaurica from Anatolia. Concurrently, we clarified the status of two other flat-shelled taxa (Isaurica callirhoe, Levantina menkhorsti). However, even data from complete mitogenomes do not resolve most of the intergeneric relationships in the tree. The mitogenome sequences show variation in nucleotide compositions and substitution rates among species, making phylogenetic inference difficult even with complex mixture models. In general, our examination of the properties of the mitogenomes point to their dynamic and varied evolution, which misleads phylogenetic analyses even at shallow phylogenetic depths. Furthermore, we found that duplications within the mitogenomes are not very rare and that protein-coding genes followed by tRNAs typically end with an incomplete stop codon. The latter presents an issue for automatic annotation tools.

zoology↗

bioRxiv2024

Read Length Dominates Phylogenetic Placement Accuracy of Ancient DNA Reads

A common problem when analyzing ancient DNA (aDNA) data is to identify the species which corresponds to the recovered aDNA sequence(s). The standard approach is to deploy sequence similarity based tools such as BLAST. However, as aDNA reads may frequently either stem from unsampled taxa due to extinction, it is likely that there is no exact match in any database. As a consequence, these tools may not be able to accurately place such reads in a phylogenetic context. Phylogenetic placement is a technique where a read is placed onto a specific branch of a phylogenetic reference tree, which allows for a substantially finer resolution when identifying reads. Prior applications of phylogenetic placement has deployed only on data from extant sources. Therefore, it is unclear how the aDNA damage affects phylogenetic placements applicability to aDNA data. To investigate how aDNA damage affects placement accuracy, we re-implemented a statistical model of aDNA damage. We deploy this model, along with a modified version of the existing assessment pipeline PEWO, to 7 empirical datasets with 4 leading tools: APPLES, EPA-ng, pplacer, and RAPPAS. We explore the aDNA damage parameter space via a grid search in order to identify the aDNA damage factors that exhibit the largest impact on placement accuracy. We find that the frequency of DNA backbone nicks (and consequently read length) has the by far largest impact on aDNA read placement accuracy, and that other factors, such as misincorporations, have a negligible effect on overall placement accuracy.

bioinformatics↗