Biology subjects

Lanigan, L. T.

Publications and source records attributed to Lanigan, L. T..

6 recordsLinked to original sources

bioRxiv2026

The Genomic Landscape of Post-Black Death Epidemics in Northern Europe and the Caucasus

One of the most devastating events in human history, the Black Death (c.1347-1353), marked the beginning of the Second Plague Pandemic. After initially receding, plague returned in intermittent outbreaks throughout Europe, beginning with the pestis secunda. Despite its significance, the post-Black Death epidemiology of Yersinia pestis remains poorly understood. Here, we report 23 new Y. pestis genomes recovered from Second Plague Pandemic contexts across Scandinavia, the Netherlands, Iceland, and Armenia, spanning approximately 270 years. Applying a reproducible mutation-filtering pipeline to assess genetic diversity, we report both Black Death and post-Black Death lineages and document multiple waves of plague at individual cemetery sites. We identify four pestis secunda genomes, including three from Armenia, supporting the eastward dissemination of this lineage prior to its disappearance from Europe. We also resolve a previously under-characterised Branch 1A sub-lineage of Y. pestis and provide the first genomic evidence of plague in Iceland, resolving longstanding uncertainty over its presence on the island. Finally, by calling variants against a reconstructed ancestral reference, we identify clade-defining mutations, including nonsynonymous changes in metabolic and biofilm-related genes with predicted structural effects that may have contributed to shaping the epidemiological dynamics of the Second Plague Pandemic.

genetics↗

bioRxiv2026

The population structure and genetic health of European wolves

Once nearly eradicated from Europe, grey wolves (Canis lupus) have recently undergone a remarkable demographic recovery, but their long-term survival remains precarious. By analyzing 1,001 genomes, we uncover a mosaic of distinct evolutionary lineages, not a single recovering population. Northern populations exhibit Asian wolf ancestry, while southern populations preserve ancient Holocene lineages, with dog introgression varying by region. Isolated wolves from the Scandinavian, Italian, and Iberian peninsulas harbored particularly high levels of inbreeding and fixed deleterious mutations. Signatures of genome erosion were widespread across Europe, with many populations falling well short of the minimum size recommended for long-term survival. Our study reveals the complex tapestry of wolf ancestry and variation across Europe, which calls for nuanced, regional conservation plans founded in genetic monitoring.

genomics↗

bioRxiv2024

Digesting the data: Proper validation in ancient metagenomic studies is essential

In a recent publication in this journal, Reynoso-Garcia et al. [1] used shotgun sequencing to analyze human coprolites (paleofeces) from two pre-Columbian contexts in Puerto Rico to reconstruct the diet of the islands Indigenous population before the arrival of Europeans. Based on the results, the team claim to have identified various edible New World plant species, including maize (Zea mays), sweet potato (Ipomoea batatas), chili pepper (Capsicum annuum), peanut (Arachis spp.), papaya (Carica papaya), and tomato (Solanum lycopersicum), as well as other cultivars such as cotton (Gossypium barbadense) and tobacco (Nicotiana sylvestris) [1]. Reynoso-Garcia et al. [1] also claim to have identified edible fungi, including Ustilago spp., which according to the authors, further supports their findings and points to the consumption of huitlacoche or corn smut, a known delicacy in Mexico today that is believed to have originated in Aztec times [2]. Shotgun DNA sequencing of archaeological samples, such as dental calculus or coprolites, provides a powerful tool to reconstruct ancient microbial communities and to study the evolution of the human microbiome [e.g. 3,4-6]. In some instances, shotgun sequencing results can also provide insights into the diet and subsistence strategies of past communities [e.g. 7,8]. However, identifying DNA from dietary sources in complex shotgun metagenomic datasets is far from straightforward. As has been discussed previously [9,10], and as we demonstrate below, one of the main challenges is the risk of false positives. Any potential dietary signals should, therefore, be carefully assessed. Unfortunately, we feel that Reynoso-Garcia et al.s study [1] falls short in that regard and we conclude that while it is entirely possible (and even likely, based on other evidence [e.g. 11,12]) that the Indigenous inhabitants of Puerto Rico subsisted on a diet that included some, or even all of the edible plant taxa the team identified, the DNA results they present do not, in and of themselves, support that claim.

genomics↗

bioRxiv2023

Conservation implications of elucidating the Korean wolf taxonomic ambiguity through whole-genome sequencing

The taxonomic status of the now likely extirpated Korean Peninsula wolf has been extensively debated, with some arguing it represents an independent wolf lineage, Canis coreanus. To investigate the Korean wolf genetic affiliations and their taxonomic implications, we sequenced and analysed the genomes of a historical Korean wolf dated to the beginning of the 20th century, and a captive wolf originally located at the Pyongyang Central Zoo. Our results indicated that the Korean wolf bears similar genetic ancestry to other regional East Asian populations, therefore suggesting it is not a distinct taxonomic lineage. We identified regional patterns of wolf population structure and admixture in East Asia with potential conservation consequences in the Korean Peninsula and on a regional scale. We find the Korean wolf has similar diversity and inbreeding to other East Asian wolves. Finally, we show that, in contrast to the historical sample, the captive wolf is more genetically similar to wolves from the Tibetan Plateau, hence, Korean wolf conservation programs might not benefit from the inclusion of this specimen.

evolutionary biology↗

bioRxiv2022

Genomes of the extinct Sicilian wolf reveal a complex history of isolation and admixture with ancient dogs

The Sicilian wolf represented the only population of wolves living on a Mediterranean island until the first half of the twentieth century (1930s-1960s) 1-7. Previous studies hypothesised that they remained isolated from mainland wolves from the end of the Last Glacial Maximum (LGM) 8,9, until human persecutions led them to extinction 1-7. There are only seven known Sicilian wolf specimens from the 19th and 20th century preserved in museums in Italy and recent morphometric analyses assigned them to the new subspecies Canis lupus cristaldii 10. To better understand the origins of the Sicilian wolf, and its relationship to other wolf populations, we sequenced four whole genomes (3.8x-11.6x) and five mitogenomes. We investigated the relationship between Sicilian wolves and other modern breeds to identify potential admixture. Furthermore, considering that the last land-bridge between Sicily and Italy disappeared after the LGM 11, around 17 kya, we explored the possibility that the Sicilian wolf retained ancestry from ancient wolf and dog lineages. Additionally, we explored whether the long-term isolation might have affected the genomic diversity, inbreeding levels and genetic load of the Sicilian wolf. Our findings show that the Sicilian wolves shared most ancestry with the modern Italian wolf population but are better modelled as admixed with European dog breeds, and shared traces of Eneolithic and Bronze age European dogs. We also find signatures of severe inbreeding and low genomic diversity at population and individual levels due to long-term isolation and drift, suggesting also low effective population size.

genomics↗

bioRxiv2018

Stone Age \"chewing gum\" yields 5,700 year-old human genome and oral microbiome

We present a complete ancient human genome and oral microbiome sequenced from a piece of resinous \"chewing gum\" recovered from a Stone Age site on the island of Lolland, Denmark, and directly dated to 5,8585,661 cal. BP (GrM13305;5,007{+/-}11). We sequenced the genome to an average depth-of coverage of 2.3x and find that the individual who chewed the resin was female and genetically more closely related to western hunter gatherers from mainland Europe, than hunter gatherers from central Scandinavia. We use imputed genotypes to predict physical characteristics and find that she had dark skin and hair, and blue eyes. Lastly, we also recovered microbial DNA that is characteristic of an oral microbiome and faunal reads that likely associate with diet. The results highlight the potential for this type of sample material as a new source of ancient human and microbial DNA.

genomics↗