| 1. |
- Orlando, Ludovic, et al.
(författare)
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Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse
- 2013
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 499:7456, s. 74-
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Tidskriftsartikel (refereegranskat)abstract
- The rich fossil record of equids has made them a model for evolutionary processes(1). Here we present a 1.12-times coverage draft genome from a horse bone recovered from permafrost dated to approximately 560-780 thousand years before present (kyr BP)(2,3). Our data represent the oldest full genome sequence determined so far by almost an order of magnitude. For comparison, we sequenced the genome of a Late Pleistocene horse (43 kyr BP), and modern genomes of five domestic horse breeds (Equus ferus caballus), a Przewalski's horse (E. f. prze-walskii) and a donkey (E. asinus). Our analyses suggest that the Equus lineage giving rise to all contemporary horses, zebras and donkeys originated 4.0-4.5 million years before present (Myr BP), twice the conventionally accepted time to the most recent common ancestor of the genus Equus(4,5). We also find that horse population size fluctuated multiple times over the past 2 Myr, particularly during periods of severe climatic changes. We estimate that the Przewalski's and domestic horse populations diverged 38-72 kyr BP, and find no evidence of recent admixture between the domestic horse breeds and the Przewalski's horse investigated. This supports the contention that Przewalski's horses represent the last surviving wild horse population(6). We find similar levels of genetic variation among Przewalski's and domestic populations, indicating that the former are genetically viable and worthy of conservation efforts. We also find evidence for continuous selection on the immune system and olfaction throughout horse evolution. Finally, we identify 29 genomic regions among horse breeds that deviate from neutrality and show low levels of genetic variation compared to the Przewalski's horse. Such regions could correspond to loci selected early during domestication.
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| 2. |
- Feng, Shaohong, et al.
(författare)
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Dense sampling of bird diversity increases power of comparative genomics
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 587:7833
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Tidskriftsartikel (refereegranskat)abstract
- Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity(1-4). Sparse taxon sampling has previously been proposed to confound phylogenetic inference(5), and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species. A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.
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| 3. |
- Jarvis, Erich D., et al.
(författare)
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Whole-genome analyses resolve early branches in the tree of life of modern birds
- 2014
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 346:6215, s. 1320-1331
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Tidskriftsartikel (refereegranskat)abstract
- To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.
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| 4. |
- Zhang, Guojie, et al.
(författare)
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Comparative genomics reveals insights into avian genome evolution and adaptation
- 2014
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 346:6215, s. 1311-1320
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Tidskriftsartikel (refereegranskat)abstract
- Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.
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| 5. |
- Boesen, Amanda H., et al.
(författare)
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Assessment of the LeadCare® Plus for Use on Scandinavian Brown Bears (Ursus arctos)
- 2019
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Ingår i: Frontiers in Veterinary Science. - : Frontiers Media S.A.. - 2297-1769. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- Lead (Pb) exposure is associated with adverse health effects in both humans and wildlife. Blood lead levels (BLL) of sentinel wildlife species can be used to monitor environmental lead exposure and ecosystem health. BLL analyzers, such as the LeadCare (R), are validated for use in humans, assessed for use in some avian species and cattle, and are increasingly being used on wildlife to monitor lead exposure. The LeadCare (R) analyzers use a technique called anodic stripping voltammetry (ASV). Species-specific conversion equations have been proposed to approximate the levels found with gold standard measuring methods such as inductively coupled plasma mass spectrometry (ICP-MS) because the ASV method has been shown to underestimate BLL in some species. In this study we assessed the LeadCare (R) Plus (LCP) for use on Scandinavian brown bears (Ursus arctos). LCP measurements were correlated with ICP-MS with a Bland-Altman analyzed bias of 16.3-22.5%, showing a consistent overestimation of BLL analyzed with LCP. Based on this analysis we provide conversion equations for calculating ICP-MS BLL based on the LCP results in Scandinavian brown bears. Our study shows that the LeadCare (R) Plus can be used for monitoring of lead exposure by approximating gold standard levels using conversion equations. This enables comparison with other gold standard measured BLL within the observed range of this study (38.20-174.00 mu g/L). Our study also found that Scandinavian brown bears are highly exposed to environmental lead.
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| 6. |
- Holm, Sonja L., et al.
(författare)
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HEIMDAL : A thermal neutron powder diffractometer with high and flexible resolution combined with SANS and neutron imaging - Designed for materials science studies at the European Spallation Source
- 2016
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Ingår i: Nuclear Instruments and Methods in Physics Research, Section A: Accelerators, Spectrometers, Detectors and Associated Equipment. - : Elsevier BV. - 0168-9002. ; 828, s. 229-241
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Tidskriftsartikel (refereegranskat)abstract
- HEIMDAL will be a multi length scale neutron scattering instrument for the study of structures covering almost nine orders of magnitude from 0.01 nm to 50 mm. The instrument is accepted for construction at the European Spallation Source (ESS) and features a variable resolution thermal neutron powder diffractometer (TNPD), combined with small angle neutron scattering (SANS) and neutron imaging (NI). The instrument uses a novel combination of a cold and a thermal guide to fulfill the diverse requirements for diffraction and SANS. With an instrument length of 170 m, HEIMDAL will take advantage of the high neutron flux of the long pulse at ESS, whilst maintaining a high q-resolution due to the long flight path. The q-range coverage is up to 20 Å-1 allowing low-resolution PDF analysis. With the addition of SANS, HEIMDAL will be able to cover a uniquely broad length scale within a single instrumental set-up. HEIMDAL will be able to accommodate modern materials research in a broad variety of fields, and the task of the instrument will be to study advanced functional materials in action, as in situ and in operandi at multiple length scales (0.01-100 nm) quasi simultaneously. The instrument combines state-of-the-art neutron scattering techniques (TNPD, SANS, and NI) with the goal of studying real materials, in real time, under real conditions. This article describes the instrument design ideas, calculations and results of simulations and virtual experiments.
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