Latent spatial models and sampling design for landscape genetics

Hanks, Ephraim M.; Hooten, Melvin B.; Knick, Steven T.; Oyler‐McCance, Sara J.; Fike, Jennifer A.; Cross, Todd B.; Schwartz, Michael K.

doi:10.1214/16-aoas929

Cited by 11 publications

(6 citation statements)

References 43 publications

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“…Optimal spatial designs (Mateu & Müller, 2012) balance distributing the sampling locations uniformly over the study domain (e.g. a space-filling design) to maximize coverage for spatial interpolation, and clustering sample locations to permit estimation of the spatial correlation function (Fortin, Drapeau, & Legendre, 1990;Hanks et al, 2016;Royle & Nychka, 1998;Ver Hoef, 2012). Several two-stage designs have been proposed (Guillera-Arroita, Ridout, & Morgan, 2014;Pacifici, Reich, Dorazio, & Conroy, 2016) that first analyse data from an initial sample, and then add more observations based on the interim results to target areas of uncertainty remaining after the first stage.…”

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confidence: 99%

Integrating auxiliary data in optimal spatial design for species distribution modelling

2018

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Traditional surveys used to create species distribution maps and estimate ecological relationships are expensive and time consuming. Citizen science offers a way to collect a massive amount of data at negligible cost and has been shown to be a useful supplement to traditional analyses. However, there remains a need to conduct formal surveys to firmly establish ecological relationships and trends. In this paper, we investigate the use of auxiliary (e.g. citizen science) data as a guide to designing more efficient ecological surveys. Our aim is to explore the use of opportunistic data to inform spatial survey design through a novel objective function that minimizes misclassificaton rate (i.e. false positives and false negatives) of the estimated occupancy maps. We use an initial occupancy estimate from auxiliary data as the prior in a Bayesian spatial occupancy model, and an efficient posterior approximation that accounts for spatial dependence, covariate effects, and imperfect detection in an exchange algorithm to search for the optimal set of sampling locations to minimize misclassification rate. We examine the optimal design as a function of the detection rate and quality of the citizen‐science data, and compare this optimal design with several common ad hoc designs via an extensive simulation study. We then apply our method to eBird data for the brown‐headed nuthatch in the Southeast US. We argue that planning a survey with the use of auxiliary data improves estimation accuracy and may significantly reduce the costs of sampling.

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confidence: 99%

Integrating auxiliary data in optimal spatial design for species distribution modelling

2018

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“…In addition, a small number of blood samples collected by other researchers as part of separate radio telemetry and GPS tracking field research were made available to us for use in this study. The spatial distribution of our sampling was optimized as described in Hanks et al [ 25 ]. Briefly, following a pilot sample, we used a latent spatial model to identify spatial trends in genetic variation.…”

Section: Methodsmentioning

confidence: 99%

New strategies for characterizing genetic structure in wide-ranging, continuously distributed species: A Greater Sage-grouse case study

et al. 2022

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Characterizing genetic structure across a species’ range is relevant for management and conservation as it can be used to define population boundaries and quantify connectivity. Wide-ranging species residing in continuously distributed habitat pose substantial challenges for the characterization of genetic structure as many analytical methods used are less effective when isolation by distance is an underlying biological pattern. Here, we illustrate strategies for overcoming these challenges using a species of significant conservation concern, the Greater Sage-grouse (Centrocercus urophasianus), providing a new method to identify centers of genetic differentiation and combining multiple methods to help inform management and conservation strategies for this and other such species. Our objectives were to (1) describe large-scale patterns of population genetic structure and gene flow and (2) to characterize genetic subpopulation centers across the range of Greater Sage-grouse. Samples from 2,134 individuals were genotyped at 15 microsatellite loci. Using standard STRUCTURE and spatial principal components analyses, we found evidence for four or six areas of large-scale genetic differentiation and, following our novel method, 12 subpopulation centers of differentiation. Gene flow was greater, and differentiation reduced in areas of contiguous habitat (eastern Montana, most of Wyoming, much of Oregon, Nevada, and parts of Idaho). As expected, areas of fragmented habitat such as in Utah (with 6 subpopulation centers) exhibited the greatest genetic differentiation and lowest effective migration. The subpopulation centers defined here could be monitored to maintain genetic diversity and connectivity with other subpopulation centers. Many areas outside subpopulation centers are contact zones where different genetic groups converge and could be priorities for maintaining overall connectivity. Our novel method and process of leveraging multiple different analyses to find common genetic patterns provides a path forward to characterizing genetic structure in wide-ranging, continuously distributed species.

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“…The spatial distribution of our sampling was optimized as described in Hanks et al. (), following a smaller pilot sample. Feather samples were collected from leks using noninvasive methods (Bush, Vinsky, Aldridge, & Paszkowski, ; Segelbacher, ) after having been dropped by sage‐grouse during breeding activity, while blood samples were collected from sage‐grouse on leks as part of radiotelemetry field research.…”

Section: Methodsmentioning

confidence: 99%

The genetic network of greater sage‐grouse: Range‐wide identification of keystone hubs of connectivity

Cross

Schwartz

Naugle

et al. 2018

Ecology and Evolution

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Genetic networks can characterize complex genetic relationships among groups of individuals, which can be used to rank nodes most important to the overall connectivity of the system. Ranking allows scarce resources to be guided toward nodes integral to connectivity. The greater sage‐grouse (Centrocercus urophasianus) is a species of conservation concern that breeds on spatially discrete leks that must remain connected by genetic exchange for population persistence. We genotyped 5,950 individuals from 1,200 greater sage‐grouse leks distributed across the entire species’ geographic range. We found a small‐world network composed of 458 nodes connected by 14,481 edges. This network was composed of hubs—that is, nodes facilitating gene flow across the network—and spokes—that is, nodes where connectivity is served by hubs. It is within these hubs that the greatest genetic diversity was housed. Using indices of network centrality, we identified hub nodes of greatest conservation importance. We also identified keystone nodes with elevated centrality despite low local population size. Hub and keystone nodes were found across the entire species’ contiguous range, although nodes with elevated importance to network‐wide connectivity were found more central: especially in northeastern, central, and southwestern Wyoming and eastern Idaho. Nodes among which genes are most readily exchanged were mostly located in Montana and northern Wyoming, as well as Utah and eastern Nevada. The loss of hub or keystone nodes could lead to the disintegration of the network into smaller, isolated subnetworks. Protecting both hub nodes and keystone nodes will conserve genetic diversity and should maintain network connections to ensure a resilient and viable population over time. Our analysis shows that network models can be used to model gene flow, offering insights into its pattern and process, with application to prioritizing landscapes for conservation.

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Latent spatial models and sampling design for landscape genetics

Cited by 11 publications

References 43 publications

Integrating auxiliary data in optimal spatial design for species distribution modelling

Integrating auxiliary data in optimal spatial design for species distribution modelling

New strategies for characterizing genetic structure in wide-ranging, continuously distributed species: A Greater Sage-grouse case study

The genetic network of greater sage‐grouse: Range‐wide identification of keystone hubs of connectivity

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