Large predators, large data, large conservation issues

We are a diverse group here at The Molecular Ecologist. Melissa writes love letters to sponges. Stacy takes you on exotic kelp road trips. Arun gives you another excuse to spend the afternoon playing with R. I feel that it is my duty to hold down the fort for charismatic megafauna every once in a while.
So here you go, two new studies that use genetic data to solve some “big” animal problems in wildlife conservation.
The conservation challenge of accurate effective population sizes
The effective population size (Ne) is one of those foundational parameters in molecular ecology. It is also a sort of wolf in sheep’s clothing: a parameter so fundamental to other calculations, yet difficult to estimate accurately in the first place. In reality, generations overlap, sampling rarely takes place over long periods of time, and age-specific survival isn’t an easy metric to come by.
Measuring Ne is especially important in conservation scenarios, when the effective population size reveals much more about the evolutionary potential of a population than simply monitoring population sizes. In the most recent issue of Molecular Ecology, Kamath et al. use grizzly bears, a historical figurehead for predator conservation, to test the efficacy of different Ne estimators. The grizzly bear system in the Greater Yellowstone Ecosystem makes for a model group to determine Ne: isolated from other populations (no gene flow) and sampled intensively throughout multiple generations.
Fifty years of grizzly bear samples (N = 729) were genotypes at 20 microsats and Ne estimations were compared to those from corresponding demographic data. Estimators of Ne included:

  • Parentage assignments (EPA)
  • linage disequilibrium (LDne)
  • Sibship estimator (SA in COLONY)
  • Variance Ne (in NEESTIMATOR)
  • Temporal Approach (in GONe)
  • Likelihood-based temporal (in MLNe)

So, what’s best? Well, it depends on your data of course. Small sample sizes greatly reduce the power of EPA and SA methods compared to LD methods. However, EPA methods are one of the only approaches that is applicable to age-structured populations. Essentially, knowing the strengths and weaknesses of all these methods and comparing their results can increase your confidence in the “right” Ne.
The good news for you megafauna lovers out there, regardless of methodology: grizzly bears have bounced back in a big way by almost quadrupling their effective population size in just a few decades. Predictably, this new data also has some eager to knock that number back down.
Outbreeding and the demise of the dingo
The hybridization of native and introduced species can cause an avalanche of sticky conservation issues. What if the hybrids are better off than either species? What if the hybrids aren’t likely to spread around? What if hybridization results in complete extinction of a native species? A particularly interesting application of this native/introduced hybrid scenario is also featured in the recent issue of Molecular Ecology: Australian dingoes and domestic dogs.
Ever since dogs came to Australia with European settlers two hundred years ago, interbreeding between dingoes and dogs has been observed and the proportion of hybrid animals corresponds to those areas where dogs (and humans) have been the longest. Unlike some other hybrids between native and invasive species, the traits that we humans have selected for in domestic dogs (smaller brains, weaker jaws, reduced hearing ability) are likely bad news for dingoes, which currently occupy an ecologically-important role as a trophic regulator across most of Australia.
Stephens et al. conduct a continent-wide survey of hybridization between dingoes and dogs using both Bayesian clustering and log-of-odds methods that were compared to simulated hybrid data. They find that almost half of their 3,600 samples can be classified as “pure” dingos, but all regions demonstrate some percentage of introgression from domestic dogs. This introgression in much more pronounced in eastern and coastal Australia, where human influence provides the highest density of domestic dogs and the longest periods of interaction.

Figure taken from Stephens et al. (2015). Displays

Figure taken from Stephens et al. (2015). Displays the “purity” of dingos across Australia as assessed by log-of-odds (left) and Bayesian clustering (right)

While the result seems hopeful (there are still refugia for pure dingoes), the sheer spread of this hybridization and the likelihood of further human-assisted interactions between dogs and dingoes is intimidating. However, the documentation of this pattern now may prevent the headline of the future: “Scientists: the pure dingo is no more”
Kamath, P. L., Haroldson, M. A., Luikart, G., Paetkau, D., Whitman, C., & Manen, F. T. (2015). Multiple estimates of effective population size for monitoring a long‐lived vertebrate: an application to Yellowstone grizzly bears. Molecular Ecology.
*Stephens, D., Wilton, A. N., Fleming, P. J., & Berry, O. (2015). Death by sex in an Australian icon: a continent‐wide survey reveals extensive hybridisation between dingoes and domestic dogs. Molecular Ecology.
*Postscript: Current leader, by a wide margin, for my favorite title of the year.

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