michelaleonardi Preprints, Research

Low ecological differentiation in leopard subspecies

It is now out in bioRxiv the preprint resulting from the part II project of Sidney Leedham:

Sidney Leedham, Johanna L. A. Paijmans, Andrea Manica, Michela Leonardi
Niche conservatism in a generalist felid: low differentiation of the climatic niche among subspecies of the leopard (Panthera pardus)
bioRxiv 2023.01.26.525491

The leopard (Panthera pardus) is a generalist species with a very wide geographic range: it can be found in most of Africa and part of Eurasia. It is subdivided into one African and eight Asian subspecies, which are the result of an ancient expansion from Africa.

We collected published observations of leopards across the entire historical range to see if the Asian subspecies live in the same climate as the African one, or if, in their expansion, they adapted to new climatic conditions.

We visualised the niche occupied by each subspecies in the climate space and compared them to see how much the Asian subspecies diverged from the African one. In most cases, there is great or total overlap, with the exception of the Persian leopard which suggests niche expansion.

This is supported by the fact that, when modelling the range of the species using only African presences, only the most northern part of the distribution is not retrieved.

These results help us better understand how the ecology of the leopard varies across its range, a knowledge that is vital for the effective conservation of its most distinct and vulnerable populations.

Preprint

Sidney Leedham, Johanna L. A. Paijmans, Andrea Manica, Michela Leonardi
Niche conservatism in a generalist felid: low differentiation of the climatic niche among subspecies of the leopard (Panthera pardus)
bioRxiv 2023.01.26.525491. doi: https://doi.org/10.1101/2023.01.26.525491

Abstract

Aim Species distribution modelling can be used to reveal if the ecology of a species varies across its range, to investigate if range expansions entailed niche shifts, and to help assess ecological differentiation: the answers to such questions are vital for effective conservation. The leopard (Panthera pardus spp.) is a generalist species composed of one African and eight Asian subspecies, reflecting dispersal from an ancestral African range. This study uses species distribution models to compare the niches of leopard subspecies, to investigate if they conserved their niches when moving into new territories or adapted to local conditions and shifted niche.

Location Africa and Eurasia

Methods We assembled a database of P. pardus spp. presences. We then associated them with bioclimatic variables to identify which are relevant in predicting the distribution of the leopard. We then constructed a species distribution model and compared the distribution predicted from models based on presences from all subspecies versus the ones built only using African leopards. Finally, we used multivariate analysis to visualise the niche occupied by each subspecies in the climate space, and to compare niche overlaps to assess ecological differentiation.

Results Niche comparisons and model predictions suggest a general lack of niche separation between all subspecies. Most Asian subspecies have overlapping niches and occupy subsets of the niche of the African leopard. Nevertheless, we found the Persian leopard Panthera pardus saxicolor to have the most distinct niche, giving some evidence for niche expansion in more Northern Asian subspecies.

Main conclusions These results suggest little ecological differentiation among leopard subspecies and a lack of adaptation to novel climates after dispersal from Africa. This finding complements recent genetic studies in implying that the taxonomy of Asian leopards may not reflect biological differentiation, an issue that is important to resolve due to its relevance for the conservation of the species.

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 Preprints, Research

mtDNA-based reconstructions of change in effective population sizes of Holarctic birds do not agree with their reconstructed range sizes based on paleoclimates

European robin (Erithacus rubecula), picture by Michela Leonardi
European robin (Erithacus rubecula), one of the species analysed in the study.
Picture by Michela Leonardi

A new preprint to which I collaborated was just submitted to BioRxiv: mtDNA-based reconstructions of change in effective population sizes of Holarctic birds do not agree with their reconstructed range sizes based on paleoclimates. The work is led by Eleanor Miller, and was performed under the supervision of Andrea Manica and Bill Amos (University of Cambridge). 

In this article we have studied 102 bird species living in different environments of Eurasia and North America, trying to understand how the climatic changes that occurred after the last glacial maximum (around 21,000 years ago) influenced their demographics . In fact, during the last glacial maximum the climate was much colder, perennial ice covered a large part of the northern hemisphere, and some environments were much more widespread (for example the steppe and cold prairies) while others were much less widespread (for example example forests). For this reason, a difference in the demographic response of species living in different environments could be expected.

Reconstructing the demographics of the past is a very difficult task, there is no method that allows you to do it directly. What can be done is to use different methods that calculate measures that can give us indirect information on what the number of individuals could have been at a given moment. In our article, we used two of these methods, which are based on different data and different assumptions, in order to maximize the amount of information obtained.

The first of these approaches are Bayesian Skyline Plots, which reconstruct the effective population size over time based on mitochondrial DNA. Although the name may be misleading, this measure is not strictly linked to the number of individuals, rather it indicates the degree of genetic variability present in the population. It is based on the assumption that all individuals have the possibility of interbreeding with each other, and the same probability of reproducing: under these conditions, a population with more individuals has a higher genetic variability, for this reason the reconstructions of the effective size are considered informative on demographics. However, they must be interpreted carefully because they can also be influenced by the degree of geographical isolation, by the presence of geographical barriers between groups of individuals, and by many other factors. I will soon be publishing a book chapter on this subject, which clears up some of the more frequent mistakes that can be made in interpreting this kind of information.

The second method is ecological modeling of species distribution (Species Distribution Modelling). This class of methods associates the observations of a species with the environmental or climatic characteristics in which it lives, to reconstruct the potential distribution area both in the present and in the past (or in the future) when simulations of the climate of other periods are available. Again, the size of the distribution area is not directly related to the number of individuals, but this measure is often used as a proxy for demographics assuming that larger distribution areas can support a greater number of individuals.

Our analyses show that when it comes to demographics of the past it is essential not to consider the information drawn from a single method, and to remember that behind every model or measure there are important assumptions that must be tested from time to time. Reality is always more complex than the methods we use to reconstruct it, which is why it is necessary to integrate different approaches in order to be able to have the most complete picture of the situation possible.

Eleanor F. Miller, Rhys E. Green, Andrew Balmford, Robert Beyer, Marius Somveille, Michela Leonardi, William Amos, Andrea Manica

mtDNA-based reconstructions of change in effective population sizes of Holarctic birds do not agree with their reconstructed range sizes based on paleoclimates

During the Quaternary, large climate oscillations had profound impacts on the distribution, demography and diversity of species globally. Birds offer a special opportunity for studying these impacts because surveys of geographical distributions, publicly-available genetic sequence data, and the existence of species with adaptations to life in structurally different habitats, permit large-scale comparative analyses. We use Bayesian Skyline Plot (BSP) analysis of mitochondrial DNA to reconstruct profiles depicting how effective population size (Ne) may have changed over time, focussing on variation in the effect of the last deglaciation among 102 Holarctic species. Only 3 species showed a decline in Ne since the Last Glacial Maximum (LGM) and 7 showed no sizeable change, whilst 92 profiles revealed an increase in Ne. Using bioclimatic Species Distribution Models (SDMs), we also estimated changes in species potential range extent since the LGM. Whilst most modelled ranges also increased, we found no correlation across species between the magnitude of change in range size and change in Ne. The lack of correlation between SDM and BSP reconstructions could not be reconciled even when range shifts were considered. We suggest the lack of agreement between these measures might be linked to changes in population densities which can be independent of range changes. We caution that interpreting either SDM or BSPs independently is problematic and potentially misleading. Additionally, we found that Ne of wetland species tended to increase later than species from terrestrial habitats, possibly reflecting a delayed increase in the extent of this habitat type after the LGM.

bioRxiv 2019.12.13.870410; doi: https://doi.org/10.1101/2019.12.13.870410