bioRxiv Science⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/330761

HaploVectors: an integrative analytical tool for phylogeography

Duarte, L.·Lima, J.·Maestri, R.·Debastiani, V.·Collevatti, R.
View original source ↗Export metadata ↓

Abstract

Sets of local populations show different degrees of gene flow due to dispersal barriers and environmental constraints, which renders genetic composition gradients among populations (genetic turnover). Unveiling biogeographic correlates of genetic turnover is paramount for phylogeography. While some processes (genetic drift, secondary contact) may erase the historical track of genetic turnover, vicariance or ancient dispersal likely leads to genetic divergence among populations. Yet available analyses do not permit direct inference about mechanisms driving genetic turnover. We propose a novel analytical approach called genvector analysis, which fulfills this gap by decomposing genetic compositional dissimilarities between populations based on either haplotypes or other genetic data into genetic eigenvectors. Such procedure allows exploring genetic turnover among sets of local populations, and analyzing their biogeographic correlates based on null model tests. We evaluate the statistical performance of the method on simulated datasets. We also analyzed biogeographic correlates of genetic turnover of Akodon cursor in the Brazilian Atlantic Forest. Results revealed that genvector analysis is robust to discriminate biogeographic drivers of genetic turnover. For Akodon cursor analysis, we observed that while for the entire species, all predictors considered (except for elevation) explained genetic turnover, within phylogroups some factors varied their importance. Genvector analysis was demonstrated to be useful for several different purposes in phylogeography, and complementary to classic analytical tools widely used by phylogeographers, such as AMOVA or DAPC. The role of ancient versus recent biogeographic events, the relationship between morphological divergence or abiotic variables and genetic turnover can easily be investigated using genvector analysis.

Explore related subjects

ecologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Duarte, L., Lima, J., Maestri, R., Debastiani, V., Collevatti, R.. 2018-05-25. HaploVectors: an integrative analytical tool for phylogeography. https://doi.org/10.1101/330761

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Restoration decisions in highly variable systems: Whether, when, and how to enhance kelp

In highly variable ecosystems, natural variability can obscure signals of decline that warrant intervention, as there is often a lack of long-term data needed to distinguish between declines that are transient and likely to recover naturally and those that would be permanent without intervention. Implementing restoration for a species involves deciding on a threshold condition at which to intervene, duration that this threshold needs to be met before intervening, life stages at introduction, and amounts to introduce. Current bull and giant kelp restoration efforts in California were spurred by persistent kelp loss that started in 2013 following a disease outbreak among predators of the primary herbivore and a marine heatwave. We asked how decisions about intervention cue, threshold, wait time, life stage at introduction, and amount affect population outcomes against a backdrop of environmental variability. We analyzed additional context-dependencies on grazing and climate intensity. To address these questions, we built and parameterized a stochastic stage-structured model for bull and giant kelp, in which we simulated kelp enhancement approaches under a range of grazing and climate scenarios. In a global sensitivity analysis of kelp enhancement decisions, we found that grazing intensity and life stages at introduction were the most influential determinants of kelp biomass and persistence outcomes. The kelp enhancement approach involving temporarily introduced juveniles restored the germ banks of bull and giant kelp, but the two species differed in their responses to that intervention, highlighting that optimal intervention approach is species-dependent. Waiting longer for natural recovery before intervening reduced total intervention effort but also reduced biomass recovery potential. These results support empirical findings from kelp enhancement pilot projects in California and highlight context-dependencies that inform restoration decision-making in kelp forests and other highly variable ecosystems.

ecology↗
bioRxiv2026

Indigenous communities' perceptions of ecosystem services of a montane forest ecosystem in Nigeria: Implications for restoration planning

Restoration of protected areas should aim to maximize outcomes for both biological conservation and local people's livelihoods. In rural Africa, livelihoods are inextricably linked to the provision of ecosystem services (ES) from natural resources, so that community-centred biodiversity conservation must be guided by local perceptions of ES. Our study examined perceptions of ES among eight communities within a 5-km radius of a Nigerian forest reserve characterized by an elevational gradient of 700 m, spanning montane forest, mid-elevation forest, and savannah. The montane forest is noted for its outstanding biodiversity value. We employed semi-structured interviews, focus group discussions and species-use inventories to characterize which ES are recognised, and their perceived importance. We also conducted an ethnobotanical assessment to document community uses of plants and classified the species as savannah or forest species. Across settlements, we observed a three-fold variation in the number of ES recognized, ranging from 6 to 20. Provisioning services, especially food, were ranked higher than regulating, cultural, or supporting services in most settlements. Notably, most provisioning services were from savannah, rather than forest species. Our study adds to growing data on indigenous knowledge about ecosystem services. Implications from these findings are that: i) Landscape-scale management should maintain a mosaic of montane forest and derived savannah to reflect prevailing provisioning needs while enhancing regulating and supporting services. ii) Restoration should prioritise tangible provisioning benefits (e.g., non-timber forest products, medicines and food) alongside regulating and supporting services to align with local priorities. iii) Given potential trade-offs between scientifically derived valuations (biodiversity, regulation) and stakeholder priorities, co-design of restoration objectives and adaptive governance are essential to secure local buy-in and on-going stewardship.

ecology↗
bioRxiv2026

Natural habitats are reservoirs of Fusarium lineages highly pathogenic on Triticum aestivum

Fungal plant diseases are a major cause of crop loss worldwide. Understanding the processes driving these diseases is therefore crucial to anticipate and control epidemics while improving crop yield production. Moreover, the new European Green Deal aims to reduce the use of pesticides, while, few alternatives are currently available on the market. There is therefore an urgent need to better track and anticipate fungal crop epidemics in the current context of fungicide reduction. In light of this, our study aims to understand Fusarium spill overs from non-agricultural habitats in order to better characterise potential non-host Fusarium reservoirs that may be implicated in the emergence of Fusarium diseases. To address this question, we isolated Fusarium lineages from natural populations of Brassica rapa. We characterised their phylogenomic affiliation and found that they display high diversity, with a population structure related to the locality of isolation. By inoculation assays, we identified Fusarium strains from non-agricultural habitats that were highly aggressive on wheat. In addition, we observed a strong effect of wheat variety on disease development. We monitored the Fusarium colonisation through a microscopy approach in both wheat and Brassica plants. We observed that while the fungus is mostly on root surface in Brassica plants, it spreads inter-cellularly in wheat roots with vascular colonisation in the wheat shoots. Finally, we showed that most aggressive Fusarium strains were isolated from Brittany, a French region where wheat is vastly cultivated.

ecology↗