News

michelaleonardi Articles, Research

Genetics and ecology do not agree in reconstructing how birds reacted to past climate changes

A new paper in which I took part is now available in Molecular Ecology

Eleanor F. Miller, Rhys E. Green, Andrew Balmford, Pierpaolo Maisano Delser, Robert Beyer, Marius Somveille, Michela Leonardi, William Amos, Andrea Manica
Bayesian Skyline Plots disagree with range size changes based on Species Distribution Models for Holarctic birds
Molecular Ecology, Volume 30, Issue 16 August 2021 Pages 3993-4004

We analysed more than 100 species of Holarctic birds finding that genetics and ecology do not agree in reconstructing how more they reacted to past climatic fluctuations.

Why should we care? The reconstructions compared in our paper (one based on genetic data, the other on ecological modelling) are widely used to assess how well species can react to the ongoing climate emergency.

In our study, we show that when we systematically compare them for a lot of species they tend to tell us quite different stories. This does not mean that they are wrong: different methods are based on different assumptions, and each of them is likely to be missing a small but significant part of the whole story.

So, when we use these methods, the key is interdisciplinarity: integrating into the analyses different lines of evidence help tackle these limitations and get more reliable results.

Article

Eleanor F. Miller, Rhys E. Green, Andrew Balmford, Pierpaolo Maisano Delser, Robert Beyer, Marius Somveille, Michela Leonardi, William Amos, Andrea Manica
Bayesian Skyline Plots disagree with range size changes based on Species Distribution Models for Holarctic birds
Molecular Ecology, Volume 30, Issue 16 August 2021 Pages 3993-4004 https://doi.org/10.1111/mec.16032

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.

michelaleonardi Outreach, Videos

Pint of Science 2021: Climate change and conservation after COVID-19: what’s next?

Yesterday I had the pleasure to host the Pint of Science Cambridge event “Climate change and conservation after COVID-19: what’s next?”, an online roundtable with the geographer Chris Sandbrook, geoengineer Hugh Hunt, and Eleanor Bladon, zoologist and broadcaster.

It was a lively debate in which we discussed a lot of questions. What is happening with climate change and conservation? What are the next steps to be taken? Has the COVID-19 pandemic disrupted our efforts towards a greener world? How can technology help us? Look at the video below to find the answers proposed by our experts.

michelaleonardi Preprints, Research

A new explanation for the genetic structure of the Yellow Warbler

A new preprint to which I have contributed is now out on bioRxiv.

When temperate species living in the northern hemisphere are genetically differentiated for no apparent reason, it is likely due to what happened during the last Ice Age.

The expansion of the ice sheets around 21,000 years ago led many species to move to the so-called “glacial refugia”, areas further south where the climate remained milder. If there were multiple refugia isolated from each other, what was previously a single population could divide and differentiate, and then maintain this genetic structure when returning north after the end of the glaciation.

This has happened to many species. It is important, however, not to assume that it’s the reason behind the genetic structure of any species. We tested this hypothesis for the Yellow Warbler (Setophaga petechia), a small passerine bird living in North America.

Male Yellow Warbler (Setophaga petechia).
Photo by Alan Vernon on Flickr. Distributed under the CC BY-NC-SA 2.0 license

A study on this species found a clear genetic structure: Eastern and Western populations west are quite different from each other, while those living in the middle have intermediate characteristics.

In our study, we explicitly simulated the genetic history of this little bird over the past 50,000 years. In this way, we were able to test whether during the glacial maximum (around 21,000 years ago) the species moved to single or multiple refugia, and what happened during the repopulation of North America after the end of the Ice Age.

Immagine

By doing so, we were able to demonstrate that the yellow warbler had only one glacial refugium; the observed genetic diversity observed is the result of an asymmetric expansion. Ice sheets retreated at different times in the East and the West, and populations moved northward at different times, which created the genetic structure we see today.

It is important to remember that multiple glacial refugia are only one of the possible explanations for modern-day genetic structure: instead of assuming it we should test if it is the most likely explanation for any species of interest.

Preprint

Eleanor F. Miller, Michela Leonardi, Robert Beyer, Mario Krapp, Marius Somveille, Gian Luigi Somma, Pierpaolo Maisano Delser, Andrea Manica
Post-glacial expansion dynamics, not refugial isolation, shaped the genetic structure of a migratory bird, the Yellow Warbler (Setophaga petechia)
bioRxiv 2021.05.10.443405; doi: https://doi.org/10.1101/2021.05.10.443405

ABSTRACT

During the glacial periods of the Pleistocene, swathes of the Northern Hemisphere were covered by ice sheets, tundra and permafrost leaving large areas uninhabitable for temperate and boreal species. The glacial refugia paradigm proposes that, during glaciations, species living in the Northern Hemisphere were forced southwards, forming isolated, insular populations that persisted in disjunct regions known as refugia. According to this hypothesis, as ice sheets retreated, species recolonised the continent from these glacial refugia, and the mixing of these lineages is responsible for modern patterns of genetic diversity. However, an alternative hypothesis is that complex genetic patterns could also arise simply from heterogenous post-glacial expansion dynamics, without separate refugia. Both mitochondrial and genomic data from the North American Yellow warbler (Setophaga petechia) shows the presence of an eastern and western clade, a pattern often ascribed to the presence of two refugia. Using a climate-informed spatial genetic modelling (CISGeM) framework, we were able to reconstruct past population sizes, range expansions, and likely recolonisation dynamics of this species, generating spatially and temporally explicit demographic reconstructions. The model captures the empirical genetic structure despite including only a single, large glacial refugium. The contemporary population structure observed in the data was generated during the expansion dynamics after the glaciation and is due to unbalanced rates of northward advance to the east and west linked to the melting of the icesheets. Thus, modern population structure in this species is consistent with expansion dynamics, and refugial isolation is not required to explain it, highlighting the importance of explicitly testing drivers of geographic structure.

michelaleonardi Outreach, Videos

Webinar: Darwin Day AIRIcerca 2021 (in Italian)

Every year the evolutionary biology community celebrates Darwin Day. On the 12th of February, the birthday of Charles Darwin, events are organised all over the world to celebrate the scientist and his legacy.

This year, I have organised and moderated an online seminar (in Italian) for AIRIcerca Cambridge.

“Discovering the first Italian edition of “On the Origin of Species”

Speakers: Marco Ferraguti (evolutionary biologist) e Chiara Ceci (science communicator)

You can find below the whole video of the event (in Italian).