Biology subjects

Barnes, I.

Publications and source records attributed to Barnes, I..

4 recordsLinked to original sources

bioRxiv2025

Phylogenetic and population genetic analyses reveal patterns of divergence among isolates in the Ceratocystis manginecans complex

The taxonomic boundaries within the Ceratocystis manginecans complex have remained contentious due to limited morphological variation, interfertility in laboratory mating studies, and the application of different species concepts. However, recent studies have highlighted significant differences among isolates, such as host associations and biological traits, all with important implications for disease management. We examined the phylogenetic relationships, genetic diversity, and population structure of isolates treated broadly in the Ceratocystis manginecans complex, specifically those treated as C. eucalypticola and C. manginecans in various studies. This study included a comprehensive dataset of isolates from multiple hosts and regions, including both historical and recent outbreaks of Ceratocystis canker and wilt disease. Detailed morphological comparisons for representative isolates residing in discrete clades were conducted. Phylogenetic analyses of sequence data for seven gene regions, supported by multilocus genotyping of 16 SSR loci, identified two genetically distinct groups that broadly separated isolates having distinct ecological characteristics, the most relevant of which are infections primarily of roots or above ground tree parts. Morphological comparisons also provided support for the two groupings. Although the results supported the existence of two groups in the C. manginecans complex, there was also evidence of hybridization between isolates in the respective groups suggesting incomplete reproductive isolation, leading to taxonomic ambiguity. Isolates in the two groups are, therefore, treated as distinct lineages within the C. manginecans complex, recognizing their divergence while maintaining a conservative taxonomic approach.

evolutionary biology↗

bioRxiv2025

The influence of biosecurity on the diversity and management of a 120-year old joint insect-fungus pest invasion

The woodwasp, Sirex noctilio, and its mutualistic fungal symbiont, Amylostereum areolatum, are native to Eurasia and northern Africa. Sirex noctilio was first reported outside its native range in New Zealand in 1900, Tasmania in 1952 and mainland Australia in 1961. In this study, we consider the invasion history of these organisms across Australasia through population genetic analysis using mitochondrial sequence data and microsatellite markers and compared them with a previously published dataset from global collections. The study included contemporary (n=461) and historical (n=41) samples of S. noctilio dating back to 1952 and fungal (n=176) samples from across the range. No population structure was found in Australian and New Zealand populations of S. noctilio or the fungal symbiont A. areolatum reflecting both the natural (within the countries) and human-assisted (between the countries) spread of these symbionts. The S. noctilio populations in these countries had lower genetic diversity than other populations sampled globally. Amylostereum areolatum populations from Australia and New Zealand clustered separately from all other countries and were highly clonal. While the results suggested multiple early introductions in these two countries, it also reflected an efficient recent quarantine system that isolated these populations and reduced their complexity compared to other parts of the world. The findings also have relevance to the application of biological control for the pest complex.

ecology↗

bioRxiv2022

Comparing the accuracy and efficiency of third generation DNA barcode sequencing: Oxford Nanopore Technologies versus Pacific Biosciences

At times of drastic decrease in biodiversity and loss of species, sometimes referred to as the "sixth mass extinction" or "Holocene extinction", there is a high demand on the development of effective tools for studying and monitoring biodiversity. In the past decade, new promising technologies, such as third generation sequencing (TGS), enabled massive, rapid, and cost-effective data analysis of non-model organisms, accelerating taxonomic identification studies and contributing to conservation applications. Here, we focus on the comparison of the two main TGS providers, Pacific Biosciences (PacBio), and Oxford Nanopore Technologies (ONT), for the purpose of DNA barcoding. For ONT, we also tested selected combinations of different types of flow cells and ligation sequencing kits. Out of five tested combinations (PacBio, ONT Flongle flow cell & SQK-LSK110 kit, R9 flow cell & SQK-LSK109 kit, R9 & SQK-LSK100 kit, and R10 flow cell & Q20+ chemistry kit), ONTs Flongle turned out to be most variable in returning the results, but at the same time the most cost efficient. The highest numbers of successfully sequenced samples were achieved with the ONTs R10 & Q20+ chemistry combination. In terms of library preparation time, ONT protocols are the quickest, whereas regarding cost effectiveness - using Sanger pricing per sample as a cut-off - various technologies become affordable depending on the number of samples used. Although both tested platforms are suitable for DNA barcoding, we further discuss their limitations and applicability to different studies, with a special focus on the price and the number of samples. The pipeline we developed, from whole specimens to final DNA barcode consensuses, can aid planning and budgeting biodiversity studies, maximising the number of specimens sequenced in one run and speeding up the sample processing time.

molecular biology↗

bioRxiv2018

Population Replacement in Early Neolithic Britain

The roles of migration, admixture and acculturation in the European transition to farming have been debated for over 100 years. Genome-wide ancient DNA studies indicate predominantly Anatolian ancestry for continental Neolithic farmers, but also variable admixture with local Mesolithic hunter-gatherers1-9. Neolithic cultures first appear in Britain c. 6000 years ago (kBP), a millennium after they appear in adjacent areas of northwestern continental Europe. However, the pattern and process of the British Neolithic transition remains unclear10-15. We assembled genome-wide data from six Mesolithic and 67 Neolithic individuals found in Britain, dating from 10.5-4.5 kBP, a dataset that includes 22 newly reported individuals and the first genomic data from British Mesolithic hunter-gatherers. Our analyses reveals persistent genetic affinities between Mesolithic British and Western European hunter-gatherers over a period spanning Britains separation from continental Europe. We find overwhelming support for agriculture being introduced by incoming continental farmers, with small and geographically structured levels of additional hunter-gatherer introgression. We find genetic affinity between British and Iberian Neolithic populations indicating that British Neolithic people derived much of their ancestry from Anatolian farmers who originally followed the Mediterranean route of dispersal and likely entered Britain from northwestern mainland Europe.

evolutionary biology↗