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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). 

Abbiamo appena pubblicato su bioRxiv un nuovo preprint dal titolo: mtDNA-based reconstructions of change in effective population sizes of Holarctic birds do not agree with their reconstructed range sizes based on paleoclimates. La prima autrice è Eleanor Miller, del Dipartimento di Zoologia dell’Università di Cambridge, che ha lavorato sotto la supervisione di Andrea Manica e William Amos (anche loro con la stessa affiliazione).

ATTENZIONE: Questo articolo è un preprint, che vuol dire che non è ancora stato sottoposto a una revisione fra pari (peer-review), per il momento è stato inviato a una rivista scientifica e attende di essere valutato. E’ probabile quindi che la versione finale, dopo il processo di revisione, contenga diversi cambiamenti inclusi nuovi risultati o potenziali nuove analisi a sostegno dei risultati.

In questo articolo abbiamo studiato 102 specie di uccelli che vivono in ambienti diversi di Eurasia e Nord America, cercando di capire in che modo i cambiamenti climatici che sono avvenuti dopo l’ultimo massimo glaciale (intorno ai 21.000 anni fa) hanno influenzato la loro demografia. Infatti durante l’ultimo massimo glaciale il clima era molto più freddo, il ghiaccio perenne copriva gran parte dell’emisfero nord, e alcuni ambienti erano molto più diffusi (ad esempio la steppa e le praterie fredde) mentre altri erano molto meno diffusi (per esempio le foreste). Per questo ci si poteva aspettare una diffrenza nella risposta demografica di specie che vivono in ambienti diversi.

Ricostruire la demografia del passato è un compito molto difficile, non c’è un metodo che permetta di farlo in modo diretto. Quello che si può fare è usare diversi metodi che calcolano delle misure che possano darci informazioni indirette su quello che poteva essere il numero di individui in un determinato momento. Nel nostro articolo abbiamo usato due di questi metodi,  che si basano su dati diversi e assunzioni diverse, in modo da massimizzare la quantità di informazioni ricavate.

Il primo di questi approcci sono i Bayesian Skyline Plot [1], che ricostruiscono la dimensione effettiva della popolazione [2] nel tempo sulla base del DNA mitocondriale. Nonostante il nome possa trarre in inganno, questa misura non è strettamente legata al numero di individui, indica piuttosto il grado di variabilità genetica presente nella popolazione. Si basa sull’assunzione che la tutti gli individui abbiano la possibilità di incrociarsi fra di loro, e la stessa probabilità di riprodursi: in queste condizioni una popolazione con più individui ha una variabilità genetica più alta, per questo motivo le ricostruzioni della dimensione effettiva sono considerate informative sulla demografia. Tuttavia vanno interpretate con attenzione perchè possono essere influenzate anche dal grado di isolamento geografico, dalla presenza di barriere geografiche fra gruppi di individui, e da molti altri fattori. Pubblicherò fra poco un capitolo di libro su questo tema, che mette in chiaro alcuni degli errori più frequenti che si possono fare nell’interpretazione di questo genere di informazioni.

Il secondo metodo è la modellizzazione ecologica della distribuzione delle specie (in inglese Species Distribution Modelling) [3]. Questa classe di metodi associa le osservazioni di una specie con le caratteristiche ambientali o climatiche in cui vive, per ricostruire l’areale di distribuzione potenziale sia nel presente, sia nel passato (o nel futuro) quando sono disponibili simulazioni del clima di altri periodi. Anche in questo caso la dimensione dell’areale di distribuzione non è direttamente correlata al numero di individui, ma spesso si usa questa misura come proxy della demografia presupponendo che areali più grandi possano sostenere un maggior numero di individui. 

Abbiamo confrontato le traiettorie degli skyline plots negli ultimi 21.000 anni con le differenze fra gli areali di distribuzione di 21.000 anni fa e del presente. Nonostante si osservi nella maggior parte delle specie un aumento in entrambe le misure, le traiettorie delle due misure non sono correlate. Probabilmente ci troviamo di fronte a fenomeni che non sono evidenti solo sulla base delle due misure analizzate, come ad esempio dei cambi di densità di popolazione.

Le nostre analisi dimostrano che quando si parla di demografia del passato è fondamentale non considerare le informazioni tratte da un solo metodo, e ricordare che dietro ad ogni modello o misura ci sono delle assunzioni importanti che vanno testate volta per volta. La realtà è sempre più complessa dei metodi che usiamo per ricostruirla, per questo bisogna integrare diversi approcci in modo da riuscire ad avere un quadro della situazione il più completo possibile. 

 

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

New paper: Tracking five millennia of horse management with extensive ancient genome time series

A herd of Kazakh horses in the Pavlodar region of Kazakhstan in August 2016. Credit: Ludovic Orlando
A herd of Kazakh horses in the Pavlodar region of Kazakhstan in August 2016.
Credit: Ludovic Orlando

A new paper to which I collaborated just came out, “Tracking five millennia of horse management with extensive ancient genome time series“, which is the result of a huge collaboration between more than a hundred scientists from many different research centres around the world. The lead authors are Antoine Fages, Kristian Hanghøj and Naveed Khan, and the senior author Ludovic Orlando (University of Toulouse and University of Copenhagen).

Antoine Fages, Kristian Hanghøj, Naveed Khan, Charleen Gaunitz, Andaine Seguin-Orlando, Michela Leonardi, [116 more authors] and Ludovic Orlando

Tracking five millennia of horse management with extensive ancient genome time series
Highlights
  • Two now-extinct horse lineages lived in Iberia and Siberia some 5,000 years ago
  • Iberian and Siberian horses contributed limited ancestry to modern domesticates
  • Oriental horses have had a strong genetic influence within the last millennium
  • Modern breeding practices were accompanied by a significant drop in genetic diversity
Graphical abstract
Graphical abstract

Horse domestication revolutionized warfare and accelerated travel, trade, and the geographic expansion of languages. Here, we present the largest DNA time series for a non-human organism to date, including genome-scale data from 149 ancient animals and 129 ancient genomes (≥1-fold coverage), 87 of which are new. This extensive dataset allows us to assess the modern legacy of past equestrian civilizations. We find that two extinct horse lineages existed during early domestication, one at the far western (Iberia) and the other at the far eastern range (Siberia) of Eurasia. None of these contributed significantly to modern diversity. We show that the influence of Persian-related horse lineages increased following the Islamic conquests in Europe and Asia. Multiple alleles associated with elite-racing, including at the MSTN “speed gene,” only rose in popularity within the last millennium. Finally, the development of modern breeding impacted genetic diversity more dramatically than the previous millennia of human management.

Cell, Volume 177, Issue 6, 30 May 2019, Pages 1419-1435.e31
DOI: https://doi.org/10.1016/j.cell.2019.03.049

New paper: Did Going North Give Us Migraine? An Evolutionary Approach on Understanding Latitudinal Differences in Migraine Epidemiology

Figure 1 from Key et al 2018, showing the populations analysed, their allele frequencies for the variant associated with migraine (in colour), the average temperature, and FST signaturess.
Figure 1 from Key et al 2018, showing the populations analysed, their allele frequencies for the variant associated with migraine (in colour), the average temperature, and FST signatures.

It just came out in Headache our commentary “Did Going North Give Us Migraine? An Evolutionary Approach on Understanding Latitudinal Differences in Migraine Epidemiology”. We discuss a recent publication (Key et al. 2018, Human local adaptation of the TRPM8 cold receptor along a latitudinal cline, PLoS Genet, 14 (5), e1007298) reconstructing the evolutionary history of a genetic polymorphism strongly associated with migraine. We collaborated with Alessandro Viganò and Vittorio di Piero, two medical doctors from the Sapienza University of Rome, to offer to the medical community a commentary piece on the importance of integrating an evolutionary approach into epidemiological studies of migraine, and other potentially genetic-associated diseases.

Alessandro Viganò, Andrea Manica, Vittorio Di Piero, Michela Leonardi

Did Going North Give Us Migraine? An Evolutionary Approach on Understanding Latitudinal Differences in Migraine Epidemiology

This commentary discusses a recent publication by evolutionary biologists with strong implications for migraine experts. The Authors showed that a gene polymorphism associated with migraine gave our ancestors an evolutionary advantage when colonizing northern, and thus colder, territories. They then highlight that the prevalence of migraine may differ among countries because of climatic adaptation. These results may prove useful in planning both epidemiological and physiological studies in the field of migraine.

Headache, 59 (4), 632-634 https://doi.org/10.1111/head.13520

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 

Read-only pdf