An Efficient and User-Friendly Implementation of the Founder Analysis Methodology

Vieira, Daniel; Almeida, Mafalda Sofia Tavares Gomes de; Richards, Martin B.; Soares, Pedro

doi:10.1007/978-3-030-23873-5_15

Cited by 2 publications

(2 citation statements)

References 16 publications

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“…Our results indicate that whilst this region contributed only a small fraction to the number of slaves forcibly taken into North America, its impact on South America was much greater. This corroborates the results from genome-wide analysis by Gouveia et al [ 53 ] and the identity-by-descent approach of Micheletti et al [ 54 ], which also suggested a substantially higher percentage of Southern African ancestry in South Americans of African descent.…”

Section: Discussionsupporting

confidence: 91%

Phylogeography of Sub-Saharan Mitochondrial Lineages Outside Africa Highlights the Roles of the Holocene Climate Changes and the Atlantic Slave Trade

Sá

Almeida

Azonbakin

et al. 2022

IJMS

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Despite the importance of ancient DNA for understanding human prehistoric dispersals, poor survival means that data remain sparse for many areas in the tropics, including in Africa. In such instances, analysis of contemporary genomes remains invaluable. One promising approach is founder analysis, which identifies and dates migration events in non-recombining systems. However, it has yet to be fully exploited as its application remains controversial. Here, we test the approach by evaluating the age of sub-Saharan mitogenome lineages sampled outside Africa. The analysis confirms that such lineages in the Americas date to recent centuries—the time of the Atlantic slave trade—thereby validating the approach. By contrast, in North Africa, Southwestern Asia and Europe, roughly half of the dispersal signal dates to the early Holocene, during the “greening” of the Sahara. We elaborate these results by showing that the main source regions for the two main dispersal episodes are distinct. For the recent dispersal, the major source was West Africa, but with two exceptions: South America, where the fraction from Southern Africa was greater, and Southwest Asia, where Eastern Africa was the primary source. These observations show the potential of founder analysis as both a supplement and complement to ancient DNA studies.

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Section: Discussionsupporting

confidence: 91%

Phylogeography of Sub-Saharan Mitochondrial Lineages Outside Africa Highlights the Roles of the Holocene Climate Changes and the Atlantic Slave Trade

Sá

Almeida

Azonbakin

et al. 2022

IJMS

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“…By excluding singletons, we confirmed that the founders were haplotypes established within the sink population with at least one hypothetical epidemiological link (i.e., we inferred at least one transmission within the sink population). We analyzed all of the networks phylogeographically and considered all hypothetical intercontinental founders (as direct matches or inferred matches) [36,37]. To establish the direction of the movements, we considered three parameters: (a) the polarity of the tree topology (which depended on the rooting) to establish the origin of the ancestral clade that contains the founder; (b) the observed diversity of the clade in both the hypothetical source and sink, mostly in early detected samples of the clade; (c) the time of detection of the clade in both locations, source, and sink/s.…”

Section: Methodsmentioning

confidence: 99%

Phylogeography of 27,000 SARS-CoV-2 Genomes: Europe as the Major Source of the COVID-19 Pandemic

et al. 2020

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The novel coronavirus SARS-CoV-2 emerged from a zoonotic transmission in China towards the end of 2019, rapidly leading to a global pandemic on a scale not seen for a century. In order to cast fresh light on the spread of the virus and on the effectiveness of the containment measures adopted globally, we used 26,869 SARS-CoV-2 genomes to build a phylogeny with 20,247 mutation events and adopted a phylogeographic approach. We confirmed that the phylogeny pinpoints China as the origin of the pandemic with major founders worldwide, mainly during January 2020. However, a single specific East Asian founder underwent massive radiation in Europe and became the main actor of the subsequent spread worldwide during March 2020. This lineage accounts for the great majority of cases detected globally and even spread back to the source in East Asia. Despite an East Asian source, therefore, the global pandemic was mainly fueled by its expansion across and out of Europe. It seems likely that travel bans established throughout the world in the second half of March helped to decrease the number of intercontinental exchanges, particularly from mainland China, but were less effective between Europe and North America where exchanges in both directions are visible up to April, long after bans were imposed.

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An Efficient and User-Friendly Implementation of the Founder Analysis Methodology

Cited by 2 publications

References 16 publications

Phylogeography of Sub-Saharan Mitochondrial Lineages Outside Africa Highlights the Roles of the Holocene Climate Changes and the Atlantic Slave Trade

Phylogeography of Sub-Saharan Mitochondrial Lineages Outside Africa Highlights the Roles of the Holocene Climate Changes and the Atlantic Slave Trade

Phylogeography of 27,000 SARS-CoV-2 Genomes: Europe as the Major Source of the COVID-19 Pandemic

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