Publications by authors named "Nina Marchi"

11 Publications

  • Page 1 of 1

No evidence for female kin association, indications for extragroup paternity, and sex-biased dispersal patterns in wild western gorillas.

Ecol Evol 2021 Jun 25;11(12):7634-7646. Epub 2021 May 25.

UMR7206 Eco-anthropologie Muséum national d'Histoire naturelle CNRS Université de Paris; Musée de l'Homme Paris France.

Characterizing animal dispersal patterns and the rational behind individuals' transfer choices is a long-standing question of interest in evolutionary biology. In wild western gorillas (), a one-male polygynous species, previous genetic findings suggested that, when dispersing, females might favor groups with female kin to promote cooperation, resulting in higher-than-expected within-group female relatedness. The extent of male dispersal remains unclear with studies showing conflicting results. To investigate male and female dispersal patterns and extragroup paternity, we analyzed long-term field observations, including female spatial proximity data, together with genetic data (10 autosomal microsatellites) on individuals from a unique set of four habituated western gorilla groups, and four additional extragroup males (49 individuals in total). The majority of offspring (25 of 27) were sired by the group male. For two offspring, evidence for extragroup paternity was found. Contrarily to previous findings, adult females were not significantly more related within groups than across groups. Consistently, adult female relatedness within groups did not correlate with their spatial proximity inferred from behavioral data. Adult females were similarly related to adult males from their group than from other groups. Using statistics, we found significant genetic structure and a pattern of isolation by distance, indicating limited dispersal in this species. Comparing relatedness among females and among males revealed that males disperse farer than females, as expected in a polygamous species. Our study on habituated western gorillas shed light on the dispersal dynamics and reproductive behavior of this polygynous species and challenge some of the previous results based on unhabituated groups.
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http://dx.doi.org/10.1002/ece3.7596DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8216920PMC
June 2021

fastsimcoal2: demographic inference under complex evolutionary scenarios.

Bioinformatics 2021 Jun 23. Epub 2021 Jun 23.

Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.

Motivation: fastsimcoal2 extends fastsimcoal, a continuous time coalescent-based genetic simulation program, by enabling the estimation of demographic parameters under very complex scenarios from the site frequency spectrum under a maximum-likelihood framework.

Results: Other improvements include multi-threading, handling of population inbreeding, extended input file syntax facilitating the description of complex demographic scenarios, and more efficient simulations of sparsely structured populations and of large chromosomes.

Availability: fastsimcoal2 is freely available on http://cmpg.unibe.ch/software/fastsimcoal2/. It includes console versions for Linux, Windows and MacOS, additional scripts for the analysis and visualization of simulated and estimated scenarios, as well as a detailed documentation and ready-to-use examples.
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http://dx.doi.org/10.1093/bioinformatics/btab468DOI Listing
June 2021

Demographic inference.

Curr Biol 2021 03;31(6):R276-R279

CMPG, Institute of Ecology and Evolution, University of Berne, Berne, Switzerland; Swiss Institute of Ecology and Evolution, 1015 Lausanne, Switzerland. Electronic address:

In the last ten years, the next generation sequencing revolution has multiplied the amount of genetic data for many organisms by orders of magnitude. This has not only led to evolutionary biologists having more data available but also to new and different types of data: from a handful of allozyme markers in the 70s, we got dozens of restriction fragment length polymorphisms (RFLPs) in the 80s, hundreds of microsatellites in the 90s, thousands to hundreds of thousands of single nucleotide polymorphisms (SNPs) in the 2000s, a few full genomes in the 2010s, and thousands of full genomes in the 2020s. These data have provided information not only on the genetic diversity and evolution of the organisms studied but also on genome-wide patterns of selection, linkage disequilibrium, as well as recombination and mutation processes. Below, we will describe how these new genomic data can be used to infer the past demographic history of populations.
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http://dx.doi.org/10.1016/j.cub.2021.01.053DOI Listing
March 2021

Gene flow as a simple cause for an excess of high-frequency-derived alleles.

Evol Appl 2020 Oct 2;13(9):2254-2263. Epub 2020 Jun 2.

CMPG Institute of Ecology and Evolution University of Berne Berne Switzerland.

Most human populations exhibit an excess of high-frequency variants, leading to a U-shaped site-frequency spectrum (uSFS). This pattern has been generally interpreted as a signature of ongoing episodes of positive selection, or as evidence for a mis-assignment of ancestral/derived allelic states, but uSFS has also been observed in populations receiving gene flow from a ghost population, in structured populations, or after range expansions. In order to better explain the prevalence of high-frequency variants in humans and other populations, we describe here which patterns of gene flow and population demography can lead to uSFS by using extensive coalescent simulations. We find that uSFS can often be observed in a population if gene flow brings a few ancestral alleles from a well-differentiated population. Gene flow can either consist in single pulses of admixture or continuous immigration, but different demographic conditions are necessary to observe uSFS in these two scenarios. Indeed, an extremely low and recent gene flow is required in the case of single admixture events, while with continuous immigration, uSFS occurs only if gene flow started recently at a high rate or if it lasted for a long time at a low rate. Overall, we find that a neutral uSFS occurs under more restrictive conditions in populations having received single pulses of gene flow than in populations exposed to continuous gene flow. We also show that the uSFS observed in human populations from the 1000 Genomes Project can easily be explained by gene flow from surrounding populations without requiring past episodes of positive selection. These results imply that uSFS should be common in non-isolated populations, such as most wild or domesticated plants and animals.
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http://dx.doi.org/10.1111/eva.12998DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7513730PMC
October 2020

Why and when was lactase persistence selected for? Insights from Central Asian herders and ancient DNA.

PLoS Biol 2020 06 8;18(6):e3000742. Epub 2020 Jun 8.

Eco-anthropologie, Muséum national d'Histoire naturelle, CNRS, Université de Paris, Paris, France.

The genetic adaptation of humans to the consumption of milk from dairying animals is one of the most emblematic cases of recent human evolution. While the phenotypic change under selection, lactase persistence (LP), is known, the evolutionary advantage conferred to persistent individuals remains obscure. One informative but underappreciated observation is that not all populations whose ancestors had access to milk genetically adapted to become lactase persistent. Indeed, Central Asian herders are mostly lactase nonpersistent, despite their significant dietary reliance on dairy products. Investigating the temporal dynamic of the -13.910:C>T Eurasian mutation associated with LP, we found that, after its emergence in Ukraine 5,960 before present (BP), the T allele spread between 4,000 BP and 3,500 BP throughout Eurasia, from Spain to Kazakhstan. The timing and geographical progression of the mutation coincides well with the migration of steppe populations across and outside of Europe. After 3,000 BP, the mutation strongly increased in frequency in Europe, but not in Asia. We propose that Central Asian herders have adapted to milk consumption culturally, by fermentation, and/or by colonic adaptation, rather than genetically. Given the possibility of a nongenetic adaptation to avoid intestinal symptoms when consuming dairy products, the puzzle then becomes this: why has LP been selected for at all?
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http://dx.doi.org/10.1371/journal.pbio.3000742DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7302802PMC
June 2020

Author Correction: 137 ancient human genomes from across the Eurasian steppes.

Nature 2018 11;563(7729):E16

Buketov Karaganda State University, Saryarka Archaeological Institute, Karaganda, Kazakhstan.

with In this Article, Angela M. Taravella and Melissa A. Wilson Sayres have been added to the author list (associated with: School of Life Sciences, Center for Evolution and Medicine, The Biodesign Institute, Arizona State University, Tempe, AZ, USA). The author list and Author Information section have been corrected online.
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http://dx.doi.org/10.1038/s41586-018-0488-1DOI Listing
November 2018

Close inbreeding and low genetic diversity in Inner Asian human populations despite geographical exogamy.

Sci Rep 2018 06 20;8(1):9397. Epub 2018 Jun 20.

Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, 75016, Paris, France.

When closely related individuals mate, they produce inbred offspring, which often have lower fitness than outbred ones. Geographical exogamy, by favouring matings between distant individuals, is thought to be an inbreeding avoidance mechanism; however, no data has clearly tested this prediction. Here, we took advantage of the diversity of matrimonial systems in humans to explore the impact of geographical exogamy on genetic diversity and inbreeding. We collected ethno-demographic data for 1,344 individuals in 16 populations from two Inner Asian cultural groups with contrasting dispersal behaviours (Turko-Mongols and Indo-Iranians) and genotyped genome-wide single nucleotide polymorphisms in 503 individuals. We estimated the population exogamy rate and confirmed the expected dispersal differences: Turko-Mongols are geographically more exogamous than Indo-Iranians. Unexpectedly, across populations, exogamy patterns correlated neither with the proportion of inbred individuals nor with their genetic diversity. Even more surprisingly, among Turko-Mongols, descendants from exogamous couples were significantly more inbred than descendants from endogamous couples, except for large distances (>40 km). Overall, 37% of the descendants from exogamous couples were closely inbred. This suggests that in Inner Asia, geographical exogamy is neither efficient in increasing genetic diversity nor in avoiding inbreeding, which might be due to kinship endogamy despite the occurrence of dispersal.
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http://dx.doi.org/10.1038/s41598-018-27047-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6010435PMC
June 2018

137 ancient human genomes from across the Eurasian steppes.

Nature 2018 05 9;557(7705):369-374. Epub 2018 May 9.

Buketov Karaganda State University, Saryarka Archaeological Institute, Karaganda, Kazakhstan.

For thousands of years the Eurasian steppes have been a centre of human migrations and cultural change. Here we sequence the genomes of 137 ancient humans (about 1× average coverage), covering a period of 4,000 years, to understand the population history of the Eurasian steppes after the Bronze Age migrations. We find that the genetics of the Scythian groups that dominated the Eurasian steppes throughout the Iron Age were highly structured, with diverse origins comprising Late Bronze Age herders, European farmers and southern Siberian hunter-gatherers. Later, Scythians admixed with the eastern steppe nomads who formed the Xiongnu confederations, and moved westward in about the second or third century BC, forming the Hun traditions in the fourth-fifth century AD, and carrying with them plague that was basal to the Justinian plague. These nomads were further admixed with East Asian groups during several short-term khanates in the Medieval period. These historical events transformed the Eurasian steppes from being inhabited by Indo-European speakers of largely West Eurasian ancestry to the mostly Turkic-speaking groups of the present day, who are primarily of East Asian ancestry.
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http://dx.doi.org/10.1038/s41586-018-0094-2DOI Listing
May 2018

Sex-specific genetic diversity is shaped by cultural factors in Inner Asian human populations.

Am J Phys Anthropol 2017 04 3;162(4):627-640. Epub 2017 Feb 3.

Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, F-75016, Paris, France.

Objectives: Sex-specific genetic structures have been previously documented worldwide in humans, even though causal factors have not always clearly been identified. In this study, we investigated the impact of ethnicity, geography and social organization on the sex-specific genetic structure in Inner Asia. Furthermore, we explored the process of ethnogenesis in multiple ethnic groups.

Methods: We sampled DNA in Central and Northern Asia from 39 populations of Indo-Iranian and Turkic-Mongolic native speakers. We focused on genetic data of the Y chromosome and mitochondrial DNA. First, we compared the frequencies of haplogroups to South European and East Asian populations. Then, we investigated the genetic differentiation for eight Y-STRs and the HVS1 region, and tested for the effect of geography and ethnicity on such patterns. Finally, we reconstructed the male demographic history, inferred split times and effective population sizes of different ethnic groups.

Results: Based on the haplogroup data, we observed that the Indo-Iranian- and Turkic-Mongolic-speaking populations have distinct genetic backgrounds. However, each population showed consistent mtDNA and Y chromosome haplogroups patterns. As expected in patrilocal populations, we found that the Y-STRs were more structured than the HVS1. While ethnicity strongly influenced the genetic diversity on the Y chromosome, geography better explained that of the mtDNA. Furthermore, when looking at various ethnic groups, we systematically found a genetic split time older than historical records, suggesting a cultural rather than biological process of ethnogenesis.

Conclusions: This study highlights that, in Inner Asia, specific cultural behaviors, especially patrilineality and patrilocality, leave a detectable signature on the sex-specific genetic structure.
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http://dx.doi.org/10.1002/ajpa.23151DOI Listing
April 2017

Mitochondrial Genetic Diversity of Eurasian Red Squirrels (Sciurus vulgaris) from Denmark.

J Hered 2015 Nov-Dec;106(6):719-27. Epub 2015 Oct 30.

From the Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark (Madsen, Vilstrup, Fernández, Marchi, and Orlando); the Eco-Anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Université Paris Diderot, Sorbonne Paris Cité, France (Marchi); the Danmarks Naturfredningsforening, Masnedøgade 20, 2100 Copenhagen, Denmark (Håkansson); the Naturstyrelsen, Naturstyrelsen på Fyn, Sollerupsvej 22, 5600 Faaborg, Denmark (Krog); Department of BioScience, Aarhus University, Grenåvej 14, 8410 Rønde, Denmark (Asferg); and the Zoological Museum, Natural History Museum of Denmark, Universitetsparken 15, 2100 Copenhagen, Denmark (Baagøe).

Melanistic Eurasian red squirrels Sciurus vulgaris are commonly found on the Danish island of Funen. They are thought to represent native Danish squirrel types and are presently under threat from admixture with introduced red squirrels. In response, a conservation program was started in 2009 that involves the translocation of melanistic squirrels from Funen to the squirrel-free island of Langeland. Using mitochondrial DNA of 101 historical and modern samples from throughout Denmark, we assess for the first time population structure and mitochondrial genetic diversity of Danish squirrels compared to its larger pan-Eurasian distribution. We find that Danish squirrels have low levels of genetic diversity, especially melanistic individuals. Bayesian skyline reconstructions show that Danish squirrels have most probably experienced a severe bottleneck within the last 200 years. Also, fine-scale genetic structure was found between squirrels from the regions of Funen, Zealand and Jutland, which mimics the insular geography of Denmark. Additional nuclear DNA analyses will be required to determine the precise admixture levels between original Danish and introduced squirrels and to locate unmixed candidate populations for specific conservation efforts.
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http://dx.doi.org/10.1093/jhered/esv074DOI Listing
April 2016

Confirmation of a founder effect in a Northern European population of a new β-globin variant: HBB:c.23_26dup (codons 8/9 (+AGAA)).

Eur J Hum Genet 2015 Sep 3;23(9):1158-64. Epub 2014 Dec 3.

Service d'Hématologie, Hôpital St Vincent de Paul, Université Catholique de Lille, GHICL, Lille, France.

β-Thalassemia is a genetic disease caused by a defect in the production of the β-like globin chain. More than 200 known different variants can lead to the disease and are mainly found in populations that have been exposed to malaria parasites. We recently described a duplication of four nucleotides in the first exon of β-globin gene in several families of patients living in Nord-Pas-de-Calais (France). Using the genotypes at 12 microsatellite markers surrounding the β-globin gene of four unrelated variant carriers plus an additional one recently discovered, we found that they shared a common haplotype indicating a founder effect that was estimated to have taken place 225 years ago (nine generations). In order to determine whether this variant arose in this region of Northern Europe or was introduced by migrants from regions of the world where thalassemia is endemic, we genotyped the first 4 unrelated variant carriers and 32 controls from Nord-Pas-de-Calais for 97 European ancestry informative markers (EAIMs). Using these EAIMs and comparing with population reference panels, we demonstrated that the variant carriers were very similar to the controls and were closer to North European populations than to South European or Middle-East populations. Rare β-thalassemia variants have already been described in patients sampled in non-endemic regions, but it is the first proof of a founder effect in Northern Europe.
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http://dx.doi.org/10.1038/ejhg.2014.263DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4538212PMC
September 2015
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