Biology subjects

Frantz, L. A. F.

Publications and source records attributed to Frantz, L. A. F..

10 recordsLinked to original sources

bioRxiv2026

Diffuse phenotypic structure in native chickens across Java and Wallacea is consistent with human-mediated connectivity and decentralised selection

Objective: This study aimed to investigate morphometric and plumage-colour variation among native chickens from Wallacea and Java, Indonesia, and to evaluate the contributions of geographic and production-system factors to phenotypic diversity. Methods: Native chickens were sampled from 259 households across eight provinces in Indonesia. Household-level information on production systems and farmer selection practices was collected through structured surveys. Morphometric traits and HSV-derived plumage-colour variables were analysed using principal component analysis (PCA), permutational multivariate analysis of variance (PERMANOVA), and hierarchical variance partitioning to assess phenotypic variation across locations, provinces, and islands. Results: Substantial phenotypic variation was observed among sampled populations, with significant province- and island-level differences detected for several morphometric traits. However, extensive overlap among locations was evident in both morphometric and plumage-colour space, indicating diffuse rather than discrete structuring. Within-location variation accounted for the largest proportion of total phenotypic variance across most traits, consistent with decentralised smallholder management and continued human-mediated exchange. Conclusion: Geographic fragmentation and agroecological heterogeneity alone appear insufficient to generate strongly differentiated phenotypic groups when connectivity among populations is maintained. Whether this phenotypic connectivity corresponds to contemporary gene flow, retained ancestral variation, or convergent environmental responses remains to be tested using genomic data.

ecology↗

bioRxiv2026

Promises and limitations of local ancestry inference in imputed ancient genomes

Recent advances in genome imputation have enabled the application of state-of-the-art statistical methods--originally developed for present-day genomes--to ancient genomes. One class of such methods, known as local ancestry inference (LAI), can model an individuals genome as a mosaic of tracts assigned to different putative ancestral sources, revealing patterns of genetic ancestry across the genome. However, most LAI methods have been designed to study recent admixture events in human history, and they generally assume large panels of present-day genomes. Despite the recent availability of high-quality imputed ancient genomes, it remains unknown to what degree LAI inference is reliable for such datasets. Ancient DNA is often characterized by heterogeneous geographic and temporal sampling, varying degrees of divergence between ancient source proxies and admixing populations, and complex demographic histories. Here, we performed an extensive set of population genetic simulations to evaluate the accuracy of four popular LAI methods-RFMix, FLARE, MOSAIC and simpLAI-under different demographic scenarios, various temporal sampling schemes, sample sizes, and admixture dates. We quantify the accuracy of these methods as a function of different parameters in practically relevant scenarios, and provide general guidelines for future studies utilizing LAI in ancient DNA research.

evolutionary biology↗

bioRxiv2025

Integrative genomics identifies candidate genes underlying trypanotolerance in hybrid African cattle

Integrative genomics combines data from different omic sources to link genotypes and phenotypes with the aim of unravelling biological networks and pathways that undergird complex traits, particularly with respect to disease. In this respect, integrative genomics using population and functional genomic data can be employed to understand evolutionary processes that have shaped adaptation to infectious diseases in domestic cattle. This approach can be particularly informative for African cattle, which exhibit a complex mosaic of Bos taurus (taurine) and Bos indicus (indicine) genomic ancestry. Some African taurine populations have an important evolutionary adaptation known as trypanotolerance, a genetically determined tolerance of infection by trypanosome parasites (Trypanosoma spp.) that cause African animal trypanosomiasis (AAT) disease. AAT is one of the largest constraints to livestock production in sub-Saharan Africa and causes a financial burden of approximately $4.5 billion annually. In this study we identified putative candidate genes underlying trypanotolerance through the integration of local ancestry inference (LAI) from genome-wide SNP data for multiple trypanotolerant and trypanosusceptible hybrid cattle populations with RNA-seq and expression microarray transcriptomics data from multiple tissues collected across time course trypanosome infection experiments. These candidate genes included AGO2, CBL, CNOT1, EDN1, IL1B, NFKB1, RIPK1, and TRAF2. Functional analysis of the gene set outputs from this work highlighted GO terms associated with the immune system (including the major histocompatibility complex - MHC) and cell signalling processes. These results signpost future work to elucidate the cellular networks and pathways that drive trypanotolerance. Author SummaryIntegrative genomics combines different types of data to identify links between genes and traits, particularly with respect to disease. In this respect, integrative genomics can be used to understand the admixture and adaptation to infectious diseases that have shaped the genomes of domestic cattle. This is particularly noticeable in the case of African cattle, which form a complex mosaic of Bos taurus (taurine) and Bos indicus (indicine) ancestry. Some African taurine populations exhibit an evolutionary adaptation known as trypanotolerance, a genetically determined tolerance of infection by trypanosome parasites (Trypanosoma spp.) that cause African animal trypanosomiasis (AAT) disease. AAT is one of the largest constraints to livestock production in sub-Saharan Africa and causes a financial burden of approximately $4.5 billion annually. In this study we identify potential candidate genes underlying trypanotolerance through integration of subchromosomal genomic ancestry data from multiple trypanotolerant and trypanosusceptible hybrid cattle populations with gene expression data from multiple tissues collected across time course trypanosome infection experiments.

genomics↗

bioRxiv2025

Leopard Cats Occupied Human Settlements in China for 3,500 years before the Arrival of Domestic cats in 600-900 CE around the Tang Dynasty

The earliest cats in human settlements in China were not domestic cats (Felis catus), but native leopard cats (Prionailurus bengalensis). To trace when and how domestic cats arrived in East Asia, we analyzed 22 feline bones from 14 sites across China spanning 5,000 years. Nuclear and mitochondrial genomes revealed that leopard cats began occupying anthropogenic scenes around 5,400 years ago and last appeared in 150 CE. Following several centuries gap of archeological feline remains, the first known domestic cat (706-883 CE) in China was identified in Shaanxi during the Tang Dynasty. Genomic analysis suggested a white or partially white coat and a link to a contemporaneous domestic cat from Kazakhstan, indicating a likely dispersal route via the Silk Road. The two felids once independently occupied ancient anthropogenic environments in China but followed divergent paths and reached different destinations in human-animal interactions.

evolutionary biology↗

bioRxiv2024

Genome-wide local ancestry and the functional consequences of admixture in African and European cattle populations

Bos taurus (taurine) and Bos indicus (indicine) cattle diverged at least 150,000 years ago and, since that time, substantial genomic differences have evolved between the two lineages. During the last two millennia, genetic exchange in Africa has resulted in a complex tapestry of taurine-indicine ancestry, with most cattle populations exhibiting varying levels of admixture. Similarly, there are several Southern European cattle populations that also show evidence for historical gene flow from indicine cattle, the highest levels of which are found in the Central Italian White breeds. Here we use two different software tools (MOSAIC and ELAI) for local ancestry inference (LAI) with genome-wide high-and low-density SNP array data sets in hybrid African and Italian cattle populations and obtained broadly similar results despite critical differences in the two LAI methodologies used. Our analyses identified genomic regions with elevated levels of retained or introgressed ancestry from the African taurine, European taurine, Asian indicine lineages. Functional enrichment of genes underlying these ancestry peaks highlighted biological processes relating to immunobiology and olfaction, some of which may relate to differing susceptibilities to infectious diseases, including bovine tuberculosis, East Coast fever, and tropical theileriosis. Notably, for retained African taurine ancestry in admixed trypanotolerant cattle we observed enrichment of genes associated with haemoglobin and oxygen transport. This may reflect positive selection of genomic variants that enhance control of severe anaemia, a debilitating feature of trypanosomiasis disease, which severely constrains cattle agriculture across much of sub-Saharan Africa.

genomics↗

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

Genomic Insights into the Population History and Adaptive Traits of Latin American Criollo Cattle

Criollo cattle, descendants of animals brought by Iberian colonists to the Americas, have been subject to centuries of natural and human-mediated selection in novel tropical agroecological zones. Consequently, these breeds have evolved distinct characteristics such as resistance to disease and exceptional heat tolerance. In addition to European taurine (Bos taurus) ancestry, it has been proposed that gene flow from African taurine and Asian indicine (Bos indicus) cattle has shaped the ancestry of Criollo cattle. In this study, we analysed Criollo breeds from Colombia and Venezuela using whole-genome sequencing (WGS) and single-nucleotide polymorphism (SNP) array data to examine population structure and admixture at high resolution. Analysis of genetic structure and ancestry components provided evidence for African taurine and Asian indicine admixture in Criollo cattle. In addition, using WGS data, we detected selection signatures associated with a myriad of adaptive traits, revealing genes linked to thermotolerance, reproduction, fertility, immunity, and distinct coat and skin coloration traits. This study underscores the remarkable adaptability of Criollo cattle and highlights the genetic richness and potential of these breeds in the face of climate change, habitat flux, and disease challenges. Further research is warranted to leverage these findings for more effective and sustainable cattle breeding programmes.

genomics↗

bioRxiv2020

HAYSTAC: A Bayesian framework for robust and rapid species identification in high-throughput sequencing data

Identification of specific species in metagenomic samples is critical for several key applications, yet many tools available require large computational power and are often prone to false positive identifications. Here we describe High-AccuracY and Scalable Taxonomic Assignment of MetagenomiC data (HAYSTAC), which can estimate the probability that a specific taxon is present in a metagenome. HAYSTAC provides a user-friendly tool to construct databases, based on publicly available genomes, that are used for competitive reads mapping. It then uses a novel Bayesian framework to infer the abundance and statistical support for each species identification and provide per-read species classification. Unlike other methods, HAYSTAC is specifically designed to efficiently handle both ancient and modern DNA data, as well as incomplete reference databases, making it possible to run highly accurate hypothesis-driven analyses (i.e., assessing the presence of a specific species) on variably sized reference databases while dramatically improving processing speeds. We tested the performance and accuracy of HAYSTAC using simulated Illumina libraries, both with and without ancient DNA damage, and compared the results to other currently available methods (i.e., Kraken2/Bracken, KrakenUniq, MALT/HOPS, and Sigma). HAYSTAC identified fewer false positives than both Kraken2/Bracken, KrakenUniq and MALT in all simulations, and fewer than Sigma in simulations of ancient data. It uses less memory than Kraken2/Bracken, KrakenUniq as well as MALT both during database construction and sample analysis. Lastly, we used HAYSTAC to search for specific pathogens in two published ancient metagenomic datasets, demonstrating how it can be applied to empirical datasets. HAYSTAC is available from https://github.com/antonisdim/HAYSTAC Author summaryThe emerging field of paleo-metagenomics (i.e., metagenomics from ancient DNA) holds great promise for novel discoveries in fields as diverse as pathogen evolution and paleoenvironmental reconstruction. However, there is presently a lack of computational methods for species identification from microbial communities in both degraded and nondegraded DNA material. Here, we present "HAYSTAC", a user-friendly software package that implements a novel probabilistic model for species identification in metagenomic data obtained from both degraded and non-degraded DNA material. Through extensive benchmarking, we show that HAYSTAC can be used for accurately profiling the community composition, as well as for direct hypothesis testing for the presence of extremely low-abundance taxa, in complex metagenomic samples. After analysing simulated and publicly available datasets, HAYSTAC consistently produced the lowest number of false positive identifications during taxonomic profiling, produced robust results when databases of restricted size were used, and showed increased sensitivity for pathogen detection compared to other specialist methods. The newly proposed probabilistic model and software employed by HAYSTAC can have a substantial impact on the robust and rapid pathogen discovery in degraded/shallow sequenced metagenomic samples while optimising the use of computational resources.

bioinformatics↗

bioRxiv2018

Selection of appropriate metagenome taxonomic classifiers for ancient microbiome research

Metagenomics enables the study of complex microbial communities from myriad sources, including the remains of oral and gut microbiota preserved in archaeological dental calculus and paleofeces, respectively. While accurate taxonomic assignment is essential to this process, DNA damage, characteristic to ancient samples (e.g. reduction in fragment size), may reduce the accuracy of read taxonomic assignment. Using a set of in silico-generated metagenomic datasets we investigated how the addition of ancient DNA (aDNA) damage patterns influences microbial taxonomic assignment by five widely-used profilers: QIIME/UCLUST, MetaPhlAn2, MIDAS, CLARK-S, and MALT (BLAST-X-mode). In silico-generated datasets were designed to mimic dental plaque, consisting of 40, 100, and 200 microbial species/strains, both with and without simulated aDNA damage patterns. Following taxonomic assignment, the profiles were evaluated for species presence/absence, relative abundance, alpha-diversity, beta-diversity, and specific taxonomic assignment biases. Unifrac metrics indicated that both MIDAS and MetaPhlAn2 provided the most accurate community structure reconstruction. QIIME/UCLUST, CLARK-S, and MALT had the highest number of inaccurate taxonomic assignments; however, filtering out species present at <0.1% abundance greatly increased the accuracy of CLARK-S and MALT. All programs except CLARK-S failed to detect some species from the input file that were in their databases. Ancient DNA damage resulted in minimal differences in species detection and relative abundance between simulated ancient and modern datasets for most programs. In conclusion, taxonomic profiling biases are program-specific rather than damage-dependent, and the choice of taxonomic classification program to use should be tailored to the research question.\n\nImportanceAncient biomolecules from oral and gut microbiome samples have been shown to preserve in the archaeological record. Studying ancient microbiome communities using metagenomic techniques offer a unique opportunity to reconstruct the evolutionary trajectories of microbial communities through time. DNA accumulates specific damage over time, which could potentially affect taxonomic classification and our ability to reconstruct community assemblages accurately. It is therefore necessary to assess whether ancient DNA (aDNA) damage patterns affect metagenomic taxonomic profiling. Here, we assessed biases in community structure, diversity, species detection, and relative abundance estimates by five popular metagenomic taxonomic classification programs using in silico-generated datasets with aDNA damage. Age-related damage patterns had minimal impact on the taxonomic profiles produced by each program, and biases were intrinsic to each program. Therefore, an appropriate classification program should be chosen that minimizes the biases related to the questions being addressed.

microbiology↗

bioRxiv2017

The dental calculus metabolome in modern and historic samples

IntroductionDental calculus is a mineralized microbial dental plaque biofilm that forms throughout life by precipitation of salivary calcium salts. Successive cycles of dental plaque growth and calcification make it an unusually well-preserved, long-term record of host-microbial interaction in the archaeological record. Recent studies have confirmed the survival of authentic ancient DNA and proteins within historic and prehistoric dental calculus, making it a promising substrate for investigating oral microbiome evolution via direct measurement and comparison of modern and ancient specimens.\n\nObjectiveWe present the first comprehensive characterization of the human dental calculus metabolome using a multi-platform approach.\n\nMethodsUltra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) quantified 285 metabolites in modern and historic (200 years old) dental calculus, including metabolites of drug and dietary origin. A subset of historic samples was additionally analyzed by high-resolution gas chromatography-MS (GC-MS) and UPLC- MS/MS for further characterization of polar metabolites and lipids, respectively. Metabolite profiles of modern and historic calculus were compared to identify patterns of persistence and loss.\n\nResultsDipeptides, free amino acids, free nucleotides, and carbohydrates substantially decrease in abundance and ubiquity in archaeological samples, with some exceptions. Lipids generally persist, and saturated and mono-unsaturated medium and long chain fatty acids appear to be well-preserved, while metabolic derivatives related to oxidation and chemical degradation are found at higher levels in archaeological dental calculus than fresh samples.\n\nConclusionsThe results of this study indicate that certain metabolite classes have higher potential for recovery over long time scales and may serve as appropriate targets for oral microbiome evolutionary studies.

microbiology↗