New preprint: 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).  

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

Press release: 5,000 years of matrilineal continuity in North-Western Tuscany

The city of Lucca as seen from satellite. Source: Google Earth.
The city of Lucca as seen from satellite. Source: Google Earth.

It just came out in American Journal of Physical anthropology our new paper (behind paywall) The female ancestor’s tale: Long‐term matrilineal continuity in a nonisolated region of Tuscany, Result of the collaboration between the University of Ferrara and the University of Florence. Here is an open-access link to the PDF (read-only).

North-Western Tuscany (roughly Lucca and Massa Carrara provinces) has always been a corridor of exchange between Central and North-Western Italy. The region was disputed between the Etruscans and Ligurians, it has been then conquered by the Romans, and in the following centuries underwent several changes of rulers.

We tried to define if and when such complex history entailed matrilinear discontinuity in the local population. We did so by analysing a portion of the mitochondrial DNA in 119 samples from the region, dated from the Copper age (around 5,000 years ago) the Roman period, the Renaissance, modern-day and including some Etruscan sequences from the whole of Tuscany.

tuscany

Using computer simulations we found out that the better explanation for the genetic diversity in our samples is that they belong to the same population, in continuity through time. This is a quite surprising result since similar degrees of long-term continuity have been mostly observed in isolated areas.

A possible explanation of those results that either the historical changes observed in north-western Tuscany (conquers, immigration etc.) mainly lead to foreign males arriving and marrying local females. It is also possible that the rulers from outside (Romans, Lombards, French) and the local population did not mix significantly because they were part of different social groups. Whatever the region may be, modern day Lucca inhabitants appear to be the direct descendants of the women living in the regions millennia ago, teaching us that genetic continuity can not only be found in isolated communities.

New paper: The female ancestor’s tale: Long‐term matrilineal continuity in a nonisolated region of Tuscany

Lucca_GEarth
The city of Lucca as seen from satellite. Source: Google Earth.

It just come out in American Journal of Physical anthropology our new paper (behind paywall) The female ancestor’s tale: Long‐term matrilineal continuity in a nonisolated region of Tuscany, in collaboration with Guido Barbujani, Silvia Ghirotto and Francesca Tassi, in Ferrara, and David Caramelli, Stefania Vai and colleagues in Florence. Open-access link to the PDF (read-only).

Michela Leonardi, Anna Sandionigi, Annalisa Conzato, Stefania Vai, Martina Lari, Francesca Tassi, Silvia Ghirotto, David Caramelli, Guido Barbujani

The female ancestor’s tale: Long‐term matrilineal continuity in a nonisolated region of Tuscany

Objectives: With the advent of ancient DNA analyses, it has been possible to disentangle the contribution of ancient populations to the genetic pool of the modern inhabitants of many regions. Reconstructing the maternal ancestry has often highlighted genetic continuity over several millennia, but almost always in isolated areas. Here we analyze North‐western Tuscany, a region that was a corridor of exchanges between Central Italy and the Western Mediterranean coast.

Materials and methods: We newly obtained mitochondrial HVRI sequences from 28 individuals, and after gathering published data, we collected genetic information for 119 individuals from the region. Those span five periods during the last 5,000 years: Prehistory, Etruscan age, Roman age, Renaissance, and Present‐day. We used serial coalescent simulations in an approximate Bayesian computation framework to test for continuity between the mentioned groups.

Results: Our analyses always favor continuity over discontinuity for all groups considered, with the Etruscans being part of the genealogy. Moreover, the posterior distributions of the parameters support very small female effective population sizes.

Conclusions: The observed signals of long‐term genetic continuity and isolation are in contrast with the history of the region, conquered several times (Etruscans, Romans, Lombards, and French). While the Etruscans appear as a local population, intermediate between the prehistoric and the other samples, we suggest that the other conquerors—arriving from far—had a consistent social or sex bias, hence only marginally affecting the maternal lineages. At the same time, our results show that long‐term genealogical continuity is not necessarily linked to geographical isolation.

Am J Phys Anthropol2018;110. https://doi.org/10.1002/ajpa.23679 

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