LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Advanced search

Search results

Result 1 - 10 of total 35

Search options

  1. Article ; Online: Benchmarking the Mantel test and derived methods for testing association between distance matrices.

    Quilodrán, Claudio S / Currat, Mathias / Montoya-Burgos, Juan I

    Molecular ecology resources

    2023  

    Abstract: ... correlations, or when either the response or the explanatory variable(s) is affected by spatial autocorrelation ...

    Abstract Testing the association between objects is central in ecology, evolution, and quantitative sciences in general. Two types of variables can describe the relationships between objects: point variables (measured on individual objects), and distance variables (measured between pairs of objects). The Mantel test and derived methods have been extensively used for distance variables. Yet, these methods have been criticized due to low statistical power and inflated type I error when spatial autocorrelation is present. Here, we assessed the statistical power between different types of tested variables and the type I error rate over a wider range of autocorrelation intensities than previously assessed, both on univariate and multivariate data. We also illustrated the performance of distance matrix statistics through computational simulations of genetic diversity. We show that the Mantel test and derived methods are not affected by inflated type I error when spatial autocorrelation affects only one variable when investigating correlations, or when either the response or the explanatory variable(s) is affected by spatial autocorrelation while investigating causal relationships. As previously noted, with autocorrelation affecting more variables, inflated type I error could be reduced by modifying the significance threshold. Additionally, the Mantel test has no problem of statistical power when the hypothesis is formulated in terms of distance variables. We highlight that transformation of variable types should be avoided because of the potential information loss and modification of the tested hypothesis. We propose a set of guidelines to help choose the appropriate method according to the type of variables and defined hypothesis.
    Language English
    Publishing date 2023-12-02
    Publishing country England
    Document type Journal Article
    ZDB-ID 2406833-0
    ISSN 1755-0998 ; 1755-098X
    ISSN (online) 1755-0998
    ISSN 1755-098X
    DOI 10.1111/1755-0998.13898
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  2. Article ; Online: Temporal Variation in Introgressed Segments' Length Statistics Computed from a Limited Number of Ancient Genomes Sheds Light on Past Admixture Pulses.

    Di Santo, Lionel N / Quilodrán, Claudio S / Currat, Mathias

    Molecular biology and evolution

    2023  Volume 40, Issue 12

    Abstract: Hybridization is recognized as an important evolutionary force, but identifying and timing admixture events between divergent lineages remain a major aim of evolutionary biology. While this has traditionally been done using inferential tools on ... ...

    Abstract Hybridization is recognized as an important evolutionary force, but identifying and timing admixture events between divergent lineages remain a major aim of evolutionary biology. While this has traditionally been done using inferential tools on contemporary genomes, the latest advances in paleogenomics have provided a growing wealth of temporally distributed genomic data. Here, we used individual-based simulations to generate chromosome-level genomic data for a 2-population system and described temporal neutral introgression patterns under a single- and 2-pulse admixture model. We computed 6 summary statistics aiming to inform the timing and number of admixture pulses between interbreeding entities: lengths of introgressed sequences and their variance within genomes, as well as genome-wide introgression proportions and related measures. The first 2 statistics could confidently be used to infer interlineage hybridization history, peaking at the beginning and shortly after an admixture pulse. Temporal variation in introgression proportions and related statistics provided more limited insights, particularly when considering their application to ancient genomes still scant in number. Lastly, we computed these statistics on Homo sapiens paleogenomes and successfully inferred the hybridization pulse from Neanderthal that occurred approximately 40 to 60 kya. The scarce number of genomes dating from this period prevented more precise inferences, but the accumulation of paleogenomic data opens promising perspectives as our approach only requires a limited number of ancient genomes.
    MeSH term(s) Animals ; Genomics ; Paleontology ; Neanderthals/genetics ; Genome ; Biological Evolution
    Language English
    Publishing date 2023-11-22
    Publishing country United States
    Document type Journal Article
    ZDB-ID 998579-7
    ISSN 1537-1719 ; 0737-4038
    ISSN (online) 1537-1719
    ISSN 0737-4038
    DOI 10.1093/molbev/msad252
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  3. Article ; Online: Past human expansions shaped the spatial pattern of Neanderthal ancestry.

    Quilodrán, Claudio S / Rio, Jérémy / Tsoupas, Alexandros / Currat, Mathias

    Science advances

    2023  Volume 9, Issue 42, Page(s) eadg9817

    Abstract: The worldwide expansion of modern humans ( ...

    Abstract The worldwide expansion of modern humans (
    MeSH term(s) Animals ; Humans ; Africa ; Asian People ; Hominidae/genetics ; Neanderthals/genetics ; Phylogeography ; European People/genetics ; Genetic Introgression/genetics
    Language English
    Publishing date 2023-10-18
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2810933-8
    ISSN 2375-2548 ; 2375-2548
    ISSN (online) 2375-2548
    ISSN 2375-2548
    DOI 10.1126/sciadv.adg9817
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  4. Article ; Online: The effect of divergent and parallel selection on the genomic landscape of divergence.

    Ali, Hisham A A / Coulson, Tim / Clegg, Sonya M / Quilodrán, Claudio S

    Molecular ecology

    2023  Volume 33, Issue 3, Page(s) e17225

    Abstract: While the role of selection in divergence along the speciation continuum is theoretically well understood, defining specific signatures of selection in the genomic landscape of divergence is empirically challenging. Modelling approaches can provide ... ...

    Abstract While the role of selection in divergence along the speciation continuum is theoretically well understood, defining specific signatures of selection in the genomic landscape of divergence is empirically challenging. Modelling approaches can provide insight into the potential role of selection on the emergence of a heterogenous genomic landscape of divergence. Here, we extend and apply an individual-based approach that simulates the phenotypic and genotypic distributions of two populations under a variety of selection regimes, genotype-phenotype maps, modes of migration, and genotype-environment interactions. We show that genomic islands of high differentiation and genomic valleys of similarity may respectively form under divergent and parallel selection between populations. For both types of between-population selection, negative and positive frequency-dependent selection within populations generated genomic islands of higher magnitude and genomic valleys of similarity, respectively. Divergence rates decreased under strong dominance with divergent selection, as well as in models including genotype-environment interactions under parallel selection. For both divergent and parallel selection models, divergence rate was higher under an intermittent migration regime between populations, in contrast to a constant level of migration across generations, despite an equal number of total migrants. We highlight that interpreting a particular evolutionary history from an observed genomic pattern must be done cautiously, as similar patterns may be obtained from different combinations of evolutionary processes. Modelling approaches such as ours provide an opportunity to narrow the potential routes that generate the genomic patterns of specific evolutionary histories.
    MeSH term(s) Selection, Genetic ; Genetic Speciation ; Genome ; Biological Evolution ; Genomics ; Gene Flow
    Language English
    Publishing date 2023-12-08
    Publishing country England
    Document type Journal Article
    ZDB-ID 1126687-9
    ISSN 1365-294X ; 0962-1083
    ISSN (online) 1365-294X
    ISSN 0962-1083
    DOI 10.1111/mec.17225
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  5. Article ; Online: Spatially explicit paleogenomic simulations support cohabitation with limited admixture between Bronze Age Central European populations.

    Rio, Jérémy / Quilodrán, Claudio S / Currat, Mathias

    Communications biology

    2021  Volume 4, Issue 1, Page(s) 1163

    Abstract: The Bronze Age is a complex period of social, cultural and economic changes. Recent paleogenomic studies have documented a large and rapid genetic change in early Bronze Age populations from Central Europe. However, the detailed demographic and genetic ... ...

    Abstract The Bronze Age is a complex period of social, cultural and economic changes. Recent paleogenomic studies have documented a large and rapid genetic change in early Bronze Age populations from Central Europe. However, the detailed demographic and genetic processes involved in this change are still debated. Here we have used spatially explicit simulations of genomic components to better characterize the demographic and migratory conditions that may have led to this change. We investigated various scenarios representing the expansion of pastoralists from the Pontic steppe, potentially linked to the Yamnaya cultural complex, and their interactions with local populations in Central Europe, considering various eco-evolutionary factors, such as population admixture, competition and long-distance dispersal. Our results do not support direct competition but rather the cohabitation of pastoralists and farmers in Central Europe, with limited gene flow between populations. They also suggest occasional long-distance migrations accompanying the expansion of pastoralists and a demographic decline in both populations following their initial contact. These results link recent archaeological and paleogenomic observations and move further the debate of genomic changes during the early Bronze Age.
    MeSH term(s) Archaeology ; DNA, Ancient/analysis ; Europe ; Farmers ; Genome, Human ; Human Migration ; Humans
    Chemical Substances DNA, Ancient
    Language English
    Publishing date 2021-10-07
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2399-3642
    ISSN (online) 2399-3642
    DOI 10.1038/s42003-021-02670-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  6. Article ; Online: Air temperature influences early Covid-19 outbreak as indicated by worldwide mortality.

    Quilodrán, Claudio S / Currat, Mathias / Montoya-Burgos, Juan I

    The Science of the total environment

    2021  Volume 792, Page(s) 148312

    Abstract: The Covid-19 outbreak has triggered a global crisis that is challenging governments, health systems and the scientific community worldwide. A central question in the Covid-19 pandemic is whether climatic factors have influenced its progression. To ... ...

    Abstract The Covid-19 outbreak has triggered a global crisis that is challenging governments, health systems and the scientific community worldwide. A central question in the Covid-19 pandemic is whether climatic factors have influenced its progression. To address this question, we used mortality rates during the first three weeks of recorded mortality in 144 countries, during the first wave of the pandemic. We examined the effect of climatic variables, along with the proportion of the population older than 64 years old, the number of beds in hospitals, and the timing and strength of the governmental travel measures to control the spread of the disease. Our first model focuses on air temperature as the central climatic factor and explains 67% of the variation in mortality rate, with 37% explained by the fixed variables considered and 31% explained by country-specific variations. We show that mortality rate is negatively influenced by warmer air temperature. Each additional Celsius degree decreases mortality rate by ~5%. Our second model is centred on the UV Index and follows the same trend as air temperature, explaining 69% of the variation in mortality rate. These results are robust to the exclusion of countries with low incomes, as well as to the exclusion of low- and medium-income countries. We also show that the proportion of vulnerable age classes and access to healthcare are critical factors impacting the mortality rate of this disease. The effects of air temperature at an early stage of the Covid-19 outbreak is a key factor to understand the primary spread of this pandemic, and should be considered in projecting subsequent waves.
    MeSH term(s) COVID-19 ; Disease Outbreaks ; Humans ; Middle Aged ; Pandemics ; SARS-CoV-2 ; Temperature
    Language English
    Publishing date 2021-06-05
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 121506-1
    ISSN 1879-1026 ; 0048-9697
    ISSN (online) 1879-1026
    ISSN 0048-9697
    DOI 10.1016/j.scitotenv.2021.148312
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  7. Article ; Online: Corrigendum

    Claudio S. Quilodrán / Alexandros Tsoupas / Mathias Currat

    Frontiers in Ecology and Evolution, Vol

    The Spatial Signature of Introgression After a Biological Invasion With Hybridization

    2021  Volume 9

    Keywords hybridization ; introgression ; invasive species ; range expansion ; spatially explicit simulations ; Evolution ; QH359-425 ; Ecology ; QH540-549.5
    Language English
    Publishing date 2021-05-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    More links

    Kategorien

  8. Article ; Online: Editorial

    Angela McGaughran / Emiliano Mori / Claudio S. Quilodrán

    Frontiers in Ecology and Evolution, Vol

    The Genomics of Biological Invasion

    2021  Volume 9

    Keywords biological invasion ; genomics ; invasive species ; invasion success ; invasion genomics ; Evolution ; QH359-425 ; Ecology ; QH540-549.5
    Language English
    Publishing date 2021-12-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    More links

    Kategorien

  9. Article ; Online: Harmonizing hybridization dissonance in conservation.

    Quilodrán, Claudio S / Montoya-Burgos, Juan I / Currat, Mathias

    Communications biology

    2020  Volume 3, Issue 1, Page(s) 391

    Abstract: A dramatic increase in the hybridization between historically allopatric species has been induced by human activities. However, the notion of hybridization seems to lack consistency in two respects. On the one hand, it is inconsistent with the biological ...

    Abstract A dramatic increase in the hybridization between historically allopatric species has been induced by human activities. However, the notion of hybridization seems to lack consistency in two respects. On the one hand, it is inconsistent with the biological species concept, which does not allow for interbreeding between species, and on the other hand, it is considered either as an evolutionary process leading to the emergence of new biodiversity or as a cause of biodiversity loss, with conservation implications. In the first case, we argue that conservation biology should avoid the discussion around the species concept and delimit priorities of conservation units based on the impact on biodiversity if taxa are lost. In the second case, we show that this is not a paradox but an intrinsic property of hybridization, which should be considered in conservation programmes. We propose a novel view of conservation guidelines, in which human-induced hybridization may also be a tool to enhance the likelihood of adaptation to changing environmental conditions or to increase the genetic diversity of taxa affected by inbreeding depression. The conservation guidelines presented here represent a guide for the development of programmes aimed at protecting biodiversity as a dynamic evolutionary system.
    MeSH term(s) Adaptation, Physiological/genetics ; Biodiversity ; Biological Evolution ; Conservation of Natural Resources ; Human Activities/trends ; Humans ; Hybridization, Genetic/genetics ; Reproductive Isolation
    Language English
    Publishing date 2020-07-21
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ISSN 2399-3642
    ISSN (online) 2399-3642
    DOI 10.1038/s42003-020-1116-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  10. Article ; Online: Spatially explicit paleogenomic simulations support cohabitation with limited admixture between Bronze Age Central European populations

    Jérémy Rio / Claudio S. Quilodrán / Mathias Currat

    Communications Biology, Vol 4, Iss 1, Pp 1-

    2021  Volume 12

    Abstract: Rio et al. design and utilise spatially explicit simulations of genomic components to investigate the cohabitation or competition hypothesis of Bronze Age Central European human populations. Their results support cohabitation with limited gene flow ... ...

    Abstract Rio et al. design and utilise spatially explicit simulations of genomic components to investigate the cohabitation or competition hypothesis of Bronze Age Central European human populations. Their results support cohabitation with limited gene flow between pastoralists and farmers, linking together palaeogenomic and archaeological observations from the literature.
    Keywords Biology (General) ; QH301-705.5
    Language English
    Publishing date 2021-10-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    More links

    Kategorien

To top