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Ne curiosity about effective population size?

About the authors:

Miranda Wade received her B.S. in Biological Science from Colorado State University and her dual PhD in Integrative Biology and Ecology, Evolutionary Biology, and Behavior from Michigan State University. During her time in Mariah Meek’s lab at MSU, her work consisted of using ‘omics to address various conservation questions in both a rare desert place facing land-use change and the molecular consequences of microplastics exposure in a model fish species. She is currently the fearless associate editor for this blog and will begin a PostDoc at the University of Hong Kong in early 2024.

Erin E. Collins studied ecology and wildlife management at Michigan Technological University and conducted her PhD research on Antarctic Sea spider systematics and phylogeography at Central Michigan University. She subsequently worked as a fisheries geneticist for the Columbia River Inter-Tribal Fish Commission, where she investigated the genetic mechanisms associated with the migration of steelhead and Chinook salmon in the Columbia River Basin to inform conservation management of these fishes. She is currently a postdoc in Dr. Mariah Meek’s lab at Michigan State University researching the conservation genomics of Chinook salmon in California’s Central Valley. Her research interests lie in uncovering genetic diversity and population dynamics to aid conservation efforts of imperiled organisms.

Why should Ne-one care?

Effective population size (Ne) describes existing genetic variation and context for the expected genetic health of a population. Evolutionary change is also reflected in Ne estimates as an evaluation of genetic drift, selection, mutation, and gene flow at the population level. Ne is one of the most useful statistics conservation planning because it is integral to establishing minimum viable population size to prevent extirpation.

Does Ne-one find this metaphor illuminating?

Figure 1: Chat GPT likes lifeboats, apparently. Also, this lifeboat was made by AI!

From ChatGPT: ‘Ne can be metaphorically compared to the size of a lifeboat in a vast ocean. Just as a lifeboat’s capacity determines how many people it can save and sustain in the event of a shipwreck, Ne represents the number of individuals within a population that contribute to the genetic diversity and long-term survival of the species. A larger lifeboat (or Ne) provides a better chance of preserving genetic diversity and adapting to changing environmental conditions, while a smaller lifeboat (or Ne) may lead to a higher risk of genetic drift and reduced resilience in the face of challenges.’

Are there Ne examples using this statistic?

In this post, we (briefly) delve into two examples from the AGA’s Journal of Heredity; impacts of fire events on an ESA threatened sand skink population (Schrey et al. 2016) and an assessment of inbreeding in a physically and genetically distinctive killer whale population (Foote et al. 2023). You can find a blog post from earlier this year with a general overview of type D killer whales here.

Figure 1: photo of a Florida sand skink courtesy of the Florida Fish and Wildlife Conservation Commission

Habitat disturbance events such as fires can limit gene flow between populations. Central Florida’s scrub habitat is adapted to a natural cycle of fires to maintain native vegetation. Because of this, managers in this region often use controlled fires to mimic this natural cycle. However, the effects of this management on species diversity and abundance needs investigation. Ne estimates of Florida Sand Skink (Plestiodon reynoldsi) populations before and after fires revealed genetic diversity consequences (Schrey et al. 2016). Both Ne and abundance estimates decreased with the number of fires. Contrastingly, the Ne estimates increased with the time interval between fires. Importantly, this study shows that using managed fires to preserve the vegetation of Florida scrub habitat and implementing strategies for skink conservation require a balance that not just Ne-one can accomplish.

Figure 2: Graphical abstract featuring round-headed type D killer whales

Foote et al. (2023) used Ne to provide insight into the genetic nature of type D killer whales, which are a distinct population that occurs in the Southern Ocean surrounding the Antarctic continent. Type D killer whales differ from other orcas due to their distinct ecotype featuring a reduced eyepatch and super round head (Figure 2). The authors found that Ne estimates of type D killer whales were particularly low compared to other populations, and that Ne has long been low in these killer whales. They also found evidence of long-term inbreeding in the type D killer whales and no instances of sudden population collapse. Understanding historical patterns of low Ne estimates allows for speculation on the cause of this inbreeding outside of the tight-knit nature of killer whales, such as habitat changes. These and other genomic signatures, along with the distinct ecotype found in type D killer whales, may suggest this population is well on its way through the process of speciation.

In conclusion, Ne is a metric with important uses in understanding both the evolutionary past and future trajectory of populations. We hope you learned a bit or simply enjoyed some small bits of information about some charismatic organisms. Also, we are not sorry for the puns (or at least Miranda is not). Ne-way, if Robin Waples somehow sees this, please go easy on us, we are not Ne-where as versed on this topic as you.


Aaron W Schrey, Alexandria K Ragsdale, Earl D McCoy, Henry R Mushinsky, Repeated Habitat Disturbances by Fire Decrease Local Effective Population Size, Journal of Heredity, Volume 107, Issue 4, July 2016, Pages 336–341.

Andrew D Foote, Alana Alexander, Lisa T Ballance, Rochelle Constantine, Bárbara Galletti Vernazzani Muñoz, Christophe Guinet, Kelly M Robertson, Mikkel-Holger S Sinding, Mariano Sironi, Paul Tixier, John Totterdell, Jared R Towers, Rebecca Wellard, Robert L Pitman, Phillip A Morin, “Type D” killer whale genomes reveal long-term small population size and low genetic diversity, Journal of Heredity, Volume 114, Issue 2, March 2023, Pages 94–109.

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