Bayesian Skyline Plots disagree with range size changes based on Species Distribution Models for Holarctic birds

Abstract

During the Quaternary, large climate oscillations impacted the distribution and demography of species globally. Two approaches have played a major role in reconstructing changes through time: Bayesian Skyline Plots (BSPs), which reconstruct population fluctuations based on genetic data, and Species Distribution Models (SDMs), which allow us to back‐cast the range occupied by a species based on its climatic preferences. In this paper, we contrast these two approaches by applying them to a large data set of 102 Holarctic bird species, for which both mitochondrial DNA sequences and distribution maps are available, to reconstruct their dynamics since the Last Glacial Maximum (LGM). Most species experienced an increase in effective population size (Ne, as estimated by BSPs) as well as an increase in geographical range (as reconstructed by SDMs) since the LGM; however, we found no correlation between the magnitude of changes in Ne and range size. The only clear signal we could detect was a later and greater increase in Ne for wetland birds compared to species that live in other habitats, a probable consequence of a delayed and more extensive increase in the extent of this habitat type after the LGM. The lack of correlation between SDM and BSP reconstructions could not be reconciled even when range shifts were considered. We suggest that this pattern might be linked to changes in population densities, which can be independent of range changes, and caution that interpreting either SDMs or BSPs independently is problematic and potentially misleading.

pastclim: an R package to easily access and use paleoclimatic reconstructions

“…The analyses presented will focus on comparing the climate associated with observations to the one from the whole region of interest, and they may represent exploratory steps prior to species distribution modelling (e.g. Miller et al 2021b).…”

“…e . ecology (Miller et al 2021a, b), paleoecology (Leonardi et al 2018, 2020, Somveille et al 2020, Chen et al 2021, Schap et al 2021, Thorup et al 2021), conservation (Beyer and Manica 2021), population genetics (Maisano Delser et al 2021), archaeology (Racimo et al 2020, Betti et al 2020, Beyer et al 2021, Krzyzanska et al 2021, Park and Marwick 2022, Cerasoni et al 2022, Timbrell et al 2022), the evolution of the genus Homo (Will et al 2021, Timmermann et al 2022), anthropology (Leonardi et al 2017, Padilla-Iglesias et al 2021) and linguistics (Beyer et al 2019).…”

Genetic demography: What does it mean and how to interpret it, with a case study on the Neolithic transition

“…There have been attempts at solving this problem by comparing effective population size with the potential range of species reconstructed based on climatic data. While there seems to be some level of correlation between the two in some cases (Lorenzen et al 2011), this is not always true (Miller et al 2021).…”

Demographic expansions and the emergence of host specialization in genetically distinct strains of the tick-transmitted bacteriumAnaplasma phagocytophilum

“…An increase in the effective population size (N e ) of the mainland European roe deer population is estimated to have occurred between 3,932 and 7,919 years ago (Baker & Hoelzel 2014), possibly reflecting this range expansion as well as increases in the continent-wide roe deer census population size. Although relationships between estimates of N e and census population sizes have been shown to lack consistent correlation (Pierson et al 2008), in natural systems sustained increases in N e generally only occur as the result of a corresponding increase in census population size (Ho & Shapiro 2011, Miller et al 2021). More recently, the reductions of forest cover corresponding to increases in agricultural practices across Europe starting roughly 1,500 years ago led to a dramatic increase in edge habit (Kaplan et al 2009, Fyfe et al 2015, Zanon et al 2018).…”

“…Although relationships between estimates of Ne and census population sizes have been shown to lack consistent correlation (Pierson et al 2008), in natural systems sustained increases in Ne generally only occur as the result of a corresponding increase in census population size (Ho & Shapiro 2011, Miller et al 2021. More recently, the reductions of forest cover corresponding to increases in agricultural practices across Europe starting roughly 1,500 years ago led to a dramatic increase in edge habit (Kaplan et al 2009, Fyfe et al 2015, Zanon et al 2018).…”