Biology subjects

Hoban, S.

Publications and source records attributed to Hoban, S..

7 recordsLinked to original sources

bioRxiv2026

Challenges and opportunities for integrating genetic diversity monitoring in megadiverse countries: reflections from Mexico

Megadiverse countries concentrate most of the World's biodiversity. These countries encompass different levels of research infrastructure, and nearly all of them have been historically committed to the Convention of Biological Diversity, often setting precedents and leading new approaches. Here, we ask whether the assessment of genetic diversity indicators provide novel insights for biodiversity management and conservation in one of those countries, Mexico. We evaluated the first national application of the Kunming-Montreal Global Biodiversity Framework (GBF), genetic diversity indicators in Mexico. The data covered 97 taxa across diverse ecosystem types and taxonomic groups, including crop wild relatives, to assess the capacity of genetic diversity indicators to provide novel insights, as well as their relevance for strengthening national conservation strategies. We calculated two indicators: the proportion of populations with an effective population size greater than 500 (Ne 500) and the proportion of populations maintained (PM). Data were sufficient to estimate the Ne 500 indicator for 47 taxa and the PM for 28 taxa, with mean indicator values of 0.217 and 0.936, respectively. Species' geographic range was positively associated with Ne 500, whereas national endemicity had no significant effect. Comparisons with the IUCN Red List and Mexico's national extinction-risk legislation revealed that genetic vulnerability occurs even among taxa not currently recognized as threatened. Our findings highlight a gap in legal recognition of genetic diversity protection that could be strengthened by incorporating population-level assessments focused on maintaining adaptive potential in the long-term. Additionally, the indicators allowed to highlight conservation concerns within crop wild relatives, though fully realizing their potential requires integrating the entire wild-to-domesticated complex. The Mexican experience highlights that the main challenge for scaling the monitoring of genetic diversity is not only generating new data, but integrating existing information into systems that strengthen collaboration and communication among researchers, local communities, and government institutions.

evolutionary biology↗

bioRxiv2026

Chromosome-scale Juglans genomes focus fungal defense gene divergence in gene presence and absence instead of copy number

Butternut (Juglans cinerea) is a North American hardwood in steep decline, driven largely by an introduced fungal pathogen that causes butternut canker disease. Tolerance exists within the genus, with the Asian Juglans ailantifolia comparatively tolerant and hybridizing readily with J. cinerea, yet the genomic basis of that difference is poorly resolved. Chromosome-scale reference genomes are presented for J. ailantifolia and for a second J. cinerea accession from the species primary range, with independent scaffolding and uniform annotation across all compared assemblies. Gene family evolution was assessed across twelve Juglandaceae genomes, one per species, and a four accession pangenome was built from J. ailantifolia and J. mandshurica representing section Cardiocaryon and two J. cinerea accessions, Brenton and New Brunswick, representing section Trachycaryon. Neither J. cinerea accession is a putative tolerant selection, so their contrast provides a null against which section-level differences are calibrated. Spanning two sections separated by approximately 30 My, the pangenome partitions many tandem arrays by accession instead of by gene, so copy number is interpreted after merging homology nodes representing the same gene. Section-level variation resides primarily in gene presence and absence, where pathogenesis-related proteins, cysteine-rich receptor-like kinases, wall-associated kinases and lectin-domain receptor kinases are over-represented in the lineage-specific complement of both sections, indicating rapid bidirectional turnover. A smaller set of families is asymmetric, with chitinases and chitin-binding proteins and NB-LRR receptors biased toward the tolerant section and dehydrins, pectin-modifying enzymes and the CBF regulon toward the susceptible one. The largest copy number difference in the dataset separates the two conspecific accessions, at a senescence-associated cysteine protease. The two butternuts are further distinguished by their demographic histories and by the functional composition of their accession-specific gene content: the northern New Brunswick accession retains lower heterozygosity, a distinct coalescent trajectory, and enrichment for calcium transport across channels, pumps and homeostasis, for salt stress response regulation, and for raffinose family oligosaccharide biosynthesis, spanning both the perception and the cryoprotective effectors of freezing tolerance. These findings support recognition of the northern population as a cryptic glacial refugium and a conservation priority.

genomics↗

bioRxiv2023

Conserving a threatened North American walnut: a chromosome-scale reference genome for butternut (Juglans cinerea)

With the advent of affordable and more accurate third generation sequencing technologies and the associated bioinformatic tools, it is now possible to sequence, assemble, and annotate more species of conservation concern than ever before. Juglans cinerea, commonly known as butternut or white walnut, is a member of the walnut family, native to the Eastern United States and Southeastern Canada. The species is currently listed as Endangered on the IUCN Red List due to decline from an invasive fungus known as Ophiognomonia clavigignenti-juglandacearum (Oc-j) that causes butternut canker. Oc-j creates visible sores on the trunks of the tree which essentially starves and slowly kills the tree. Natural resistance to this pathogen is rare. Conserving butternut is of utmost priority due to its critical ecosystem role and cultural significance. As part of an integrated undergraduate and graduate student training program in biodiversity and conservation genomics, the first reference genome for Juglans cinerea is described here. This chromosome-scale 539 Mb assembly was generated from over 100X coverage of Oxford Nanopore long reads and scaffolded with the Juglans mandshurica genome. Scaffolding with a closely related species oriented and ordered the sequences in a manner more representative of the structure of the genome without altering the sequence. Comparisons with sequenced Juglandaceae revealed high levels of synteny and further supported J. cinereas recent phylogenetic placement. Comparative assessment of gene family evolution revealed a significant number of contracting families, including several associated with biotic stress response.

genomics↗

bioRxiv2022

Practical application of indicators for genetic diversity in CBD post-2020 Global Biodiversity Framework implementation

Genetic diversity is a key aspect of biological variation for the adaptability and survival of populations of species, which must be monitored to assure maintenance. We used data from the Swedish Red-List 2020 and a recent government report to apply three indicators for genetic diversity proposed for the post-2020 Global Biodiversity Framework of the Convention on Biological Diversity (CBD). We made more detailed indicator assessments for mammals and herptiles. For indicator 1, the proportion of populations with effective population size Ne>500, 33% of 22557 investigated species had a population estimate. For herptiles and mammals, 70% and 49%, respectively likely had Ne>500. For indicator 2, the proportion of populations or range remaining within species, 20% of all species evaluated for the Red-List have data. Meanwhile, 32% of the herptile and 84% of the mammal populations are maintaining their populations/range. For indicator 3, the number of species/populations in which genetic diversity is monitored using DNA-based methods, there are studies on 3% of species, and 0.3% are monitored. In contrast 68% of mammals and 29% of herptiles are studied using DNA, and 8% of mammals and 24% of herptiles are genetically monitored. We conclude that the Red List provide data suitable for evaluating the genetic indicators, but the data quality can be improved. There is a synergy in estimating the genetic indicators in parallel with the Red-Listing process. We propose that indicator values could be included in national Red-Listing as a new category - "genetically threatened", based on the genetic indicators.

genetics↗

bioRxiv2021

Reduced representation sequencing to understand the evolutionary history of Torrey pine (Pinus torreyana Parry) with implications for rare species conservation

Understanding the contribution of neutral and adaptive evolutionary processes to population differences is often necessary for better informed management and conservation of rare species. In this study, we focused on Pinus torreyana Parry (Torrey pine), one of the worlds rarest pines, endemic to one island and one mainland population in California. Small population size, low genetic diversity, and susceptibility to abiotic and biotic stresses suggest Torrey pine may benefit from inter-population genetic rescue to preserve the species evolutionary potential. We leveraged reduced representation sequencing to tease apart the respective contributions of stochastic and deterministic evolutionary processes to population differentiation. We applied these data to model spatial and temporal demographic changes in effective population sizes and genetic connectivity, to assess loci possibly under selection, and evaluate genetic rescue as a potential conservation strategy. Overall, we observed exceedingly low standing variation reflecting consistently low effective population sizes across time and limited genetic differentiation suggesting maintenance of gene flow following divergence. However, genome scans identified more than 2000 SNPs candidates for divergent selection. Combined with previous observations indicating population phenotypic differentiation, this indicates that natural selection has likely contributed to population genetic differences. Thus, while reduced genetic diversity, small effective population size, and genetic connectivity between populations suggest genetic rescue could mitigate the adverse effect of rarity, divergent selection between populations indicates that genetic mixing could disrupt adaptation. Further work evaluating the fitness consequences of inter-population admixture is necessary to empirically evaluate the trade-offs associated with genetic rescue in Torrey pine.

genomics↗

bioRxiv2020

Preventing extinctions post-2020 requires recovery actions and transformative change

Stopping human-induced extinctions will require strong policy commitments that comprehensively address threats to species. In 2021, a new Global Biodiversity Framework will be agreed by the Convention on Biological Diversity. Here we investigate how the suggested targets could contribute to reducing threats to threatened vertebrates, invertebrates, and plants, and assess the importance of a proposed target to implement recovery actions for threatened species. We find that whilst many of the targets benefit species, extinction risk for over one third of threatened species would not be reduced sufficiently without a target on recovery actions, including ex situ conservation, reintroductions and other species-specific interventions. A median of 41 threatened species per country require such actions, and they are found in most countries of the world. To prevent future extinctions, policy commitments must include recovery actions for the most threatened species in addition to broader transformative change.

ecology↗

bioRxiv2020

Reporting to the Convention on Biology Diversity: How are countries assessing and protecting their genetic diversity?

Genetic diversity is critically important for all species-domesticated and wild- to adapt to environmental change, and for ecosystem resilience to extreme events. International agreements such as the Convention on Biological Diversity (CBD) have committed to conserve and sustainably and equitably use all levels of biodiversity-genes, species and ecosystems-globally. However, assessment and monitoring of genetic diversity are often overlooked, and there are large knowledge and policy gaps regarding genetic diversity conservation. In this study, we present the first quantitative analysis of genetic diversity assessments conducted by Parties to the CBD. We conducted a detailed, systematic analysis of 114 CBD 5th (submitted 2014) and 6th (submitted 2018) National Reports to quantitatively assess actions, progress on targets, values and indicators related to genetic diversity. First, we found that the importance of genetic diversity is recognised by most Parties to the CBD, and that recognition increased over time. However, genetic targets mainly addressed genetic diversity within cultivated plants, farm animals, and crop wild relatives, with little focus on other wild species. Also, actions for conserving genetic diversity primarily concerned ex-situ facilities and policy, rather than monitoring and intervention for maintaining genetic diversity in situ. The most commonly used indicators of genetic diversity status were the number of genetic resources in conservation facilities, number of threatened breeds, and Red List Index, which are not well correlated to genetic erosion in most species -- highlighting that genetic change is poorly monitored by current indicators. Lastly, analyses of genetic data observations, indigenous use and knowledge of genetic diversity, and strategies being developed and implemented to conserve genetic diversity are highly under-reported. We make several recommendations for the post-2020 CBD Biodiversity Framework to improve awareness, assessment, and monitoring, and facilitate consistent and complete reporting of progress of genetic diversity in future National Reports. Article Impact StatementAn analysis of genetic diversity in CBD National Reports neglects non-domesticated species and demonstrates need for sufficient indicators.

scientific communication and education↗