Biology subjects

de Knijff, P.

Publications and source records attributed to de Knijff, P..

3 recordsLinked to original sources

bioRxiv2024

Himalayan whole-genome sequences provide insight into population formation and adaptation

High-altitude environments pose substantial challenges for human survival and reproduction, attracting considerable attention to the demographic and adaptive histories of high-altitude populations. Previous work focused mainly on Tibetans, establishing their genetic relatedness to East Asians and their genetic adaptation to high altitude, especially at EPAS1. Here, we present 87 new whole-genome sequences from 16 Himalayan populations and the insight they provide into the genomic history of the region. We show that population structure in the Himalayas began to emerge as early as 10,000 years ago, predating archaeological evidence of permanent habitation above 2,500 meters by approximately 6,000 years. The high prevalence of the introgressed adaptive EPAS1 haplotype in all high-altitude populations today supports a shared genetic origin and its importance for survival in this region. We also identify additional selection signals in genes associated with hypoxia, physical activity, immunity and metabolism which could have facilitated adaptation to the harsh environment. Over time, increasing genetic structure led to the diverse and strongly differentiated ethnic groups observed today, most of which maintained small population sizes throughout their history or experienced severe bottlenecks. Between 6,000 and 3,000 years ago, a few uniparental lineages became predominant, likely coinciding with the advent of agriculture, although significant population growth was not observed in the Himalayas except in the Tibetans. In more recent times, we detect bidirectional gene flow between high-altitude and lowland groups, occurring on both sides of the Himalayan range. The timing of this admixture aligns with the rise and expansion of historical regional powers, particularly during the Tibetan Empire and the northern Indian Gupta Empire. In the past few centuries, migrations to the Himalayas seem to have occurred alongside conflicts and population displacements in nearby regions and show some sex bias.

genomics↗

bioRxiv2020

DNA metabarcoding successfully quantifies relative abundances of arthropod taxa in songbird diets: a validation study using camera-recorded diets

O_LIEcological research is often hampered by the inability to quantify animal diets. Large-scale changes in arthropod diversity, abundance and phenologies urge the need to understand the consequences for trophic interactions. Diet composition of insectivorous predators can be tracked through DNA metabarcoding of faecal samples, but to validate the quantitative accuracy of metabarcoding, validation using free-living animals for which their diet can be approximated, is needed. C_LIO_LIThis validation study assesses the use of DNA metabarcoding in quantifying diets of an insectivorous songbird. Using camera footage, we documented food items delivered to nestling Pied Flycatchers Ficedula hypoleuca, and subsequently sequenced the Cytochrome Oxidase subunit I (COI) in their faeces. Our special interest was to retrieve the relative contribution of arthropod taxa with a PCR-based protocol. C_LIO_LIAssessment of taxonomic coverage of the invertebrate COI primers LCO1490 and HCO1777, previously applied in insectivorous songbirds, demonstrated that COI barcodes were predominantly assigned to arthropod taxa, however, substantial amounts of reads (2-60%) were assigned to flycatchers. Modified primers reduced vertebrate reads to 0.03%, and yielded more spider DNA without significant changing the recovery of other arthropod taxa. C_LIO_LITo explore digestive biases, contents of stomachs and lower intestines were compared in eight adult male flycatchers, victims of competitors for nest boxes. Similarity in arthropod community composition between stomach and intestines confirmed limited digestive bias. C_LIO_LIWith nest box cameras in 2013, 2015 and 2016, size-adjusted counts of prey items fed to nestlings were recorded, to approximate provided biomass of arthropod orders and families which allowed comparison with abundance of COI barcode reads in nestling faeces. The relative abundances of size-adjusted prey counts and COI reads correlated at R = 0.85 (CI:0.68-0.94) at order level and at R=0.75 (CI:0.67-0.82) at family level. Each common order and all common taxa within Lepidoptera, Diptera and Coleoptera were retrieved in similar proportions, while the taxonomic resolution was higher in barcodes than in camera records. C_LIO_LIThis DNA metabarcoding validation demonstrates that quantitative arthropod diet analyses is possible in songbirds. We discuss the ecological application of our approach in approximating the arthropod diets in insectivorous birds. C_LI

ecology↗

bioRxiv2017

The Beaker Phenomenon And The Genomic Transformation Of Northwest Europe

Bell Beaker pottery spread across western and central Europe beginning around 2750 BCE before disappearing between 2200-1800 BCE. The mechanism of its expansion is a topic of long-standing debate, with support for both cultural diffusion and human migration. We present new genome-wide ancient DNA data from 170 Neolithic, Copper Age and Bronze Age Europeans, including 100 Beaker-associated individuals. In contrast to the Corded Ware Complex, which has previously been identified as arriving in central Europe following migration from the east, we observe limited genetic affinity between Iberian and central European Beaker Complex-associated individuals, and thus exclude migration as a significant mechanism of spread between these two regions. However, human migration did have an important role in the further dissemination of the Beaker Complex, which we document most clearly in Britain using data from 80 newly reported individuals dating to 3900-1200 BCE. British Neolithic farmers were genetically similar to contemporary populations in continental Europe and in particular to Neolithic Iberians, suggesting that a portion of the farmer ancestry in Britain came from the Mediterranean rather than the Danubian route of farming expansion. Beginning with the Beaker period, and continuing through the Bronze Age, all British individuals harboured high proportions of Steppe ancestry and were genetically closely related to Beaker-associated individuals from the Lower Rhine area. We use these observations to show that the spread of the Beaker Complex to Britain was mediated by migration from the continent that replaced >90% of Britains Neolithic gene pool within a few hundred years, continuing the process that brought Steppe ancestry into central and northern Europe 400 years earlier.

genomics↗