Genetic Monitoring for Managers


Types of GEM

Category II GeM Project Example: Population Structure

Blackwell Publishing Ltd Congruent population structure inferred from dispersal behaviour and intensive genetic surveys of the threatened Florida scrub-jay (Aphelocoma coerulescens)

Coulon et al. 2008

This example illustrates how genetic information, coupled with Bayesian cluster analysis, can be used to identify distinct genetic groups within a species. The Florida scrub-jay (Aphelocoma coerulescens) is

type structrue fig 1
The Florida scrub-jay is endemic to Florida, and classified as a Threatened species there.

a non-migratory bird endemic to Florida that is federally listed as a threatened species. The species is restricted to early successional, fire-maintained xeric oak scrub (Woolfenden and Fitzpatrick 1984) that has declined substantially due to land-type conversion and suppression of fire. As a result, scrub-jay populations are believed to be at approximately 3% of historical levels (Pranty 1996) and are continuing to decline. Recovery of the species must be based on habitat restoration as well as on knowledge of the species' dispersal capabilities and genetic structure.

For this study, Coulon et al. (2008) collected blood samples from the brachial vein of one or both wings on 1028 scrub-jays collected widely across Florida. They genotyped the individuals using PCR analysis at 20 microsatellite loci that were previously developed for the Florida scrub-jay.

Following this, they delineated 8 - 13 genetically distinct groups using Bayesian clustering algorithms from two different programs, STRUCTURE (Pritchard et al. 2000) and GENELAND (Guillot et al. 2005). Further analysis suggested 10 genetically distinct groups across the range of the species.

type structure fig 2
Study area showing relevant landscape characteristics [from Coulon et al. 2008]

Prior to the study by Coulon et al. (2008), Stith et al. (1996) had delineated 42 meta-populations of Florida scrub-jay based on dispersal probabilities. Their model was based on observed dispersal distances, coupled with knowledge about land-use types that scrub-jays use or avoid during dispersal.

One of the fundamental questions asked by Coulon et al. (2008) was whether these dispersal-based meta-populations showed any relationship to the groups that they identified through genetic analysis.

Nearly all of the meta-populations defined by Stith et al. (1996) are embedded within the genetic groups defined by Couloun et al. (2008), and no metapopulation is genetically subdivided. The close congruence between dispersal-defined metapopulations and genetically-distinct groups suggests genuine genetic boundaries.


sytpe structure fig 3
Polygons are minimum convex polygons (MCP) delineating the area shared by individuals belonging to the same genetic group as determined with GENELAND and color coded accordingly. [from Coulon et al. 2008]

As noted by Koenig and Walters (2008) this study represents a substantial accomplishment by identifying nearly identical patterns with two distinct methods (genetic and demographic surveys). Population genetic structure obtained via these methods is of high enough quality to inform conservation efforts and provides a new tool in the management of a threatened species over large areas.



Population structure of Columbia spotted frogs (Rana luteiventris) is strongly affected by the landscape.

Funk et al. 2005

funk fig 4 pop struct2
Model of population structure in Columbia spotted frogs. Large circles represent low elevation populations with large effective population sizes. Arrow thickness denotes the relative level of geneflow among populations.

Animal dispersal and subsequent geneflow among populations may be affected by a multitude of landscape features. Highways, rivers, and mountains are just a few factors that influence how animals move. Significant features may even lead to isolation, hence impacting evolutionary trajectories.

Funk et al. (2005) examined genetic variation in Columbia spotted frogs (Rana luteiventris) from 28 breeding ponds in western Montana and Idaho, USA, in order to investigate the effects of landscape structure on patterns of gene flow. Amphibians are thought to have limited ability to disperse and may therefore be especially vulnerable to isolation. Specifically, they wanted to look at the influence of elevational changes and topographical features (i.e., ridges) on geneflow, and whether ponds equate to a randomly mating population.

Using six microsatellites, the authors used pairwise Fst to qualitatively assess the effects of topographic features on genetic divergence. They used program ARLEQUIN version 2.001 (Schneider et al. 2000) to examine broad geographical subdivisions using analysis of molecular variance with Fst (amova; Excoffier et al. 1992). They then used Mantel tests (Mantel 1967) and partial Mantel tests (Smouse et al. 1986) to examine the effect of straight-line distance, river distance, elevational differences, and mountain ridges.

Their results suggested that gene flow is restricted by ridges and elevation in this species. However, they found that frog populations generally included more than a single pond except for very isolated ponds. Their results also suggested surprisingly high levels of gene flow among ponds separated by large distances at low elevations.

funk fig 3 pop struct1
Green circles contain animals grouped into populations defined by both exact tests and a clustering algorithm (Pritchard et al. 2000). Blue circles are by exact tests only, yellow circles by clustering algorithm only.

Genetic variation within populations was strongly negatively correlated with elevation, suggesting effective population sizes are much smaller at high elevation than at low elevation.

Finally, the authors concluded that low elevation populations may act as important sources of immigrants for high elevation populations. As such, extinction of low elevation populations may have direct impacts on the persistence of high elevation popualations as well by isolating them as effective islands.

Given that lower elevation areas are typically the first to be degraded, isolated, and infested with exotic species, such a scenario is far too likely and has been observed already in multiple frog populations.