Genetic networks in ecology: A guide to population, relatedness, and pedigree networks and their applications in conservation biology

Jones, Teri B.; Manseau, Micheline

doi:10.1016/j.biocon.2022.109466

Cited by 10 publications

(15 citation statements)

References 80 publications

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“…As a flexible and highly scalable approach for analyzing individualbased genetic relationships, a kinship network was constructed. The advantage of using an individual-based metric over a populationbased one such as F ST is that no a priori assumptions are made about (meta-)population structure and thus allowing the data to directly inform the fine-grain genetic structure (Jones & Manseau, 2022).…”

Section: Kinship Networkmentioning

confidence: 99%

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Bactrocera dorsalis in the Indian Ocean: A tale of two invasions

Deschepper

Vanbergen

Zhang

et al. 2022

Evolutionary Applications

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An increasing number of invasive fruit fly pests are colonizing new grounds. With this study, we aimed to uncover the invasion pathways of the oriental fruit fly, Bactrocera dorsalis into the islands of the Indian Ocean. By using genome-wide SNP data and a multipronged approach consisting of PCA, ancestry analysis, phylogenetic inference, and kinship networks, we were able to resolve two independent invasion pathways. A western invasion pathway involved the stepping-stone migration of B. dorsalis from the east African coast into the Comoros, along Mayotte and into Madagascar with a decreasing genetic diversity. The Mascarene islands (Reunion and Mauritius), on the contrary, were colonized directly from Asia and formed a distinct cluster. The low nucleotide diversity suggests that only a few genotypes invaded the Mascarenes. The presence of many long runs of homozygosity (ROH) in the introduced populations is indicative of population bottlenecks, with evidence of a more severe bottleneck for populations along the western migration pathway than on the Mascarene islands. More strict phytosanitary regulations are recommended in order to prevent the further spread of B. dorsalis.

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Section: Kinship Networkmentioning

confidence: 99%

“…By imposing a significance level α = 0.05 or 0.10, the links that carry weights that are not different than under the null hypothesis can be pruned from the network. This method is preferred above a global weight threshold pruning method and reveals the multilayered and often complex nature of the network (Jones & Manseau, 2022).…”

Section: Kinship Networkmentioning

confidence: 99%

Bactrocera dorsalis in the Indian Ocean: A tale of two invasions

Deschepper

Vanbergen

Zhang

et al. 2022

Evolutionary Applications

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“…In familial networks, individuals with higher-closeness centrality come either from more connected families, or larger families with more generations captured during sampling. These three centrality measures capture different network characteristics and topology from the measure of individual influence in the alpha centrality, the direct familial connections in the degree centrality, and the well-connected nodes in the closeness centrality (Jones and Manseau, 2022).…”

Section: Network Centralitymentioning

confidence: 99%

“…Each centrality measure was standardized between 0 and 1. To validate the familial network centrality measures used in these models (due to the lack of independence of data points present in network data), 10,000 random familial networks with a burn-in of 1,000 networks were generated using permutations (Jones and Manseau, 2022). Each network was created by swapping mothers or fathers and swapping offspring.…”

Section: Familial Network and Densitymentioning

confidence: 99%

“…To investigate these factors on density and density response, we first used 10.3389/fevo.2022.956834 noninvasive genetic sampling and spatial capture-recapture (SCR) modeling to generate a spatially explicit caribou density raster layer using landscape covariates to create a heterogeneous density surface. Using the same genetic data, we constructed familial networks and calculated individual recruitment and dispersal rates along with a range of networks metrics to assess the contribution of individual boreal caribou to the population (McFarlane et al, 2021;Jones and Manseau, 2022). We have previously shown spatial variation in individual measures of network centrality (a node's position within a network; Jones and Manseau, 2022) across Saskatchewan, with animals in the southern part of their range presenting higher numbers of parent-offspring relationships, along with connections to other highly connected individuals (McFarlane et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

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Identification of familial networks reveals sex-specific density dependence in the dispersal and reproductive success of an endangered ungulate

et al. 2022

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Density is an important demographic parameter that is commonly overlooked in studies of wild populations. Here, we examined the effects of variable spatially explicit density on a range of demographic parameters in a wild population of a cryptic ungulate, boreal woodland caribou (Rangifer tarandus caribou). Using non-invasive genetic sampling, we applied spatial capture–recapture methods with landscape covariates to estimate the density of boreal woodland caribou across a 108,806 km2 study area. We then created a familial network from the reconstructed parent–offspring relationships to determine whether spatial density influenced sex-specific individual reproductive success, female pregnancy status, and dispersal distance. We found that animal density varied greatly in response to land cover types and disturbance; animal density was most influenced by landscape composition and distance to roads varying from 0 in areas with >20% deciduous cover to 270 caribou per 1,000 km2 in areas presenting contiguous older coniferous cover. We found that both male and female reproductive success varied with density, with males showing a higher probability of having offspring in higher-density areas, and the opposite for females. No differences were found in female pregnancy rates occurring in high- and low-density areas. Dispersal distances varied with density, with offspring moving shorter distances when parents were found in higher-density areas. Familial networks showed lower-closeness centrality and lower-degree centrality for females in higher-density areas, indicating that females found in higher-density areas tend to be less broadly associated with animals across the range. Although high-density areas do reflect good-quality caribou habitat, the observed decreased closeness and degree centrality measures, dispersal rates, and lower female recruitment rates suggest that remnant habitat patches across the landscape may create population sinks.

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Limited effects of population age on the genetic structure of spatially isolated forest herb populations in temperate Europe

Huang,

Feigs,

Holzhauer

et al. 2024

Ecology and Evolution

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Due to multiple land‐cover changes, forest herb populations residing in forest patches embedded in agricultural landscapes display different ages and, thus, experience differences in genetic exchange, mutation accumulation and genetic drift. The extent of divergence in present‐day population genetic structure among these populations of different ages remains unclear, considering their diverse breeding systems and associated pollinators. Answering this question is essential to understand these species' persistence, maintenance of evolutionary potential and adaptability to changing environments. We applied a multi‐landscape setup to compare the genetic structure of forest herb populations across forest patches of different ages (18–338 years). We studied the impact on three common slow‐colonizer herb species with distinct breeding systems and associated pollinators: Polygonatum multiflorum (outcrossing, long‐distance pollinators), Anemone nemorosa (outcrossing, short‐distance pollinators) and Oxalis acetosella (mixed breeding). We aimed to assess if in general older populations displayed higher genetic diversity and lower differentiation than younger ones. We also anticipated that P. multiflorum would show the smallest while O. acetosella the largest difference, between old and young populations. We found that older populations had a higher observed heterozygosity (Ho) but a similar level of allelic richness (Ar) and expected heterozygosity (He) as younger populations, except for A. nemorosa, which exhibited higher Ar and He in younger populations. As populations aged, their pairwise genetic differentiation measured by DPS decreased independent of species identity while the other two genetic differentiation measures showed either comparable levels between old and young populations (G"ST) or inconsistency among three species (cGD). The age difference of the two populations did not explain their genetic differentiation. Synthesis: We found restricted evidence that forest herb populations with different ages differ in their genetic structure, indicating that populations of different ages can reach a similar genetic structure within decades and thus persist in the long term after habitat disturbance. Despite their distinct breeding systems and associated pollinators, the three studied species exhibited partly similar genetic patterns, suggesting that their common characteristics, such as being slow colonizers or their ability to propagate vegetatively, are important in determining their long‐term response to land‐cover change.

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Genetic networks in ecology: A guide to population, relatedness, and pedigree networks and their applications in conservation biology

Cited by 10 publications

References 80 publications

Bactrocera dorsalis in the Indian Ocean: A tale of two invasions

Bactrocera dorsalis in the Indian Ocean: A tale of two invasions

Identification of familial networks reveals sex-specific density dependence in the dispersal and reproductive success of an endangered ungulate

Limited effects of population age on the genetic structure of spatially isolated forest herb populations in temperate Europe

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