Biology subjects

Davinack, A. A.

Publications and source records attributed to Davinack, A. A..

3 recordsLinked to original sources

bioRxiv2026

HapNet: a new Python package for automated population-aware haplotype network analysis and visualization

Haplotype networks are widely used in population genetics and phylogeography to visualize genealogical relationships among DNA sequences and to infer population structure, historical connectivity, and demographic processes. Existing software for haplotype network construction relies primarily on interactive graphical interfaces, which limits reproducibility, automation, and integration into modern bioinformatic workflows. Here, I introduce HapNet, an open-source Python package that enables automated construction, visualization, and summarization of haplotype networks directly from aligned FASTA files. HapNet is the first Python-native package designed specifically for automated, population-aware haplotype network construction and visualization from aligned FASTA files. HapNet implements a minimum-spanning-tree approach based on Hamming distances among haplotypes and incorporates population metadata encoded in sequence headers to produce population-aware network visualizations in which shared haplotypes are represented as pie charts and node sizes scale with haplotype frequency. In addition to a publication-ready network, HapNet generates machine-readable tabular output describing haplotype composition, population membership, and shared versus private haplotypes, facilitating downstream statistical analysis and reproducibility. Here, HapNets utility is demonstrated using mitochondrial DNA sequences from the shell-boring polychaete worm Polydora neocaeca, illustrating how the software reveals patterns of population connectivity and haplotype sharing. HapNet provides a reproducible, scriptable alternative to existing graphical tools and is freely available via the Python Package Index and GitHub.

evolutionary biology↗

bioRxiv2024

Genetic diversity and connectivity of the invasive gastropod, Callinina georgiana (Caenogastropoda: Viviparidae) across a fragmented riverscape: a mitonuclear perspective.

O_LIAquatic Invasive Species (AIS) are a significant threat to global freshwater biodiversity. This study focuses on the banded mystery snail, Callinina georgiana, an invasive species in the Adirondack region of northern New York - an important section of the New York Great Lakes Basin. This project aims to explore the genetic connectivity of C. georgiana within its invasive range using a combination of mitochondrial and nuclear markers. C_LIO_LISampling was conducted in the Raquette River and adjacent waterways, with a total of 229 snails collected from 16 distinct populations distributed across eight different waterbodies. Also included were two populations from the species native range in the southern United States. DNA was extracted, and a 710 bp fragment of the mtDNA marker COI and a 351 bp fragment of nuclear marker Histone-3 (H3) were amplified. Population genetic analyses including haplotype patterning, AMOVA and genetic diversity estimates, neutrality tests and tests for isolation by distance (IBD) were performed to assess connectivity patterns. C_LIO_LIResults showed moderate to high levels of genetic admixture within the snails invasive range as indicated by the lack of geographic patterning of haplotypes and low to moderate levels of genetic differentiation across multiple sites. Demographic analyses combined with high numbers of private haplotypes indicate population expansion. Interestingly, a case of mitonuclear discordance was detected for native and invasive populations as evident by incongruent haplotype patterns for the COI and H3 markers. C_LIO_LICallinina georgiana exhibits a high level of genetic connectivity in its invasive range. The presence of dams does not significantly affect gene flow, indicating that anthropogenic activities, such as boat traffic might be key in dispersing the snails across this fragmented freshwater system. C_LIO_LIThis study offers new insights into the dispersal and genetic structure of an invasive freshwater snail. It highlights the importance of considering anthropogenic factors when confronting complex patterns of genetic diversity. The findings are significant for biodiversity conservation and provide a basis for developing strategies to manage and contain the spread of AIS like C. georgiana, especially in regions with high human activity. C_LI

ecology↗

bioRxiv2023

Worms on the Cape: an integrative survey of polydorid infestation in wild and cultivated oysters (Crassostrea virginica) from Massachusetts, USA

Polydorid infestations pose a significant challenge to shellfish aquaculture by impacting marketability and profitability of farms. In this study, we investigated the prevalence, intensity, identity and biogeography of shell-boring worms infecting both farmed and wild oysters (Crassostrea virginica) from three sites in Wellfleet Harbor, Massachusetts - an economically important shellfishing region in the northeastern United States. DNA barcoding revealed that Polydora websteri was the sole culprit responsible for infecting oysters from all three sites, reaching maximum prevalence (100% infection) and intensity (mean intensity: 38.63) in the Herring River. The oysters in the Herring River are subjected to restricted tidal flow due to the presence of a physical barrier (dike), and this could be responsible for the high infestation levels of P. websteri observed in this population. In addition, a population genetic analysis incorporating COI sequence data from Wellfleet P. websteri in addition to newly published sequences from the Black Sea and the Sea of Azov found very low levels of genetic differentiation across several intercontinental populations (0.000 - 0.399), which is likely being driven by multiple introductory events such as oyster importations. These findings are discussed in relation to the future of shellfish aquaculture in the United States.

zoology↗