A5013931853- Genetic diversity and population structure
- Genomics and Phylogenetic Studies
- Species Distribution and Climate Change
- Wildlife Ecology and Conservation
- Evolution and Paleontology Studies
- Amphibian and Reptile Biology
- Chromosomal and Genetic Variations
- Avian ecology and behavior
- Animal Behavior and Reproduction
- Identification and Quantification in Food
- Environmental DNA in Biodiversity Studies
- Plant and animal studies
- Plant and Fungal Species Descriptions
- Animal Ecology and Behavior Studies
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Evolution and Genetic Dynamics
- Bat Biology and Ecology Studies
- Ecology and Vegetation Dynamics Studies
- Marine and coastal plant biology
- Viral Infections and Vectors
- Conservation Techniques and Studies
- Bird parasitology and diseases
- Advanced biosensing and bioanalysis techniques
- Animal Virus Infections Studies
- Biomedical Text Mining and Ontologies
Museum für Naturkunde
2019-2025
Swedish Museum of Natural History
2017-2024
Australian National University
2013-2024
Centre for Australian National Biodiversity Research
2016-2018
Uppsala University
2017
Harvard University
2013
Max Planck Institute for Ornithology
2013
Building the Tree of Life (ToL) is a major challenge modern biology, requiring advances in cyberinfrastructure, data collection, theory, and more. Here, we argue that phylogenomics stands to benefit by embracing many heterogeneous genomic signals emerging from first decade large-scale phylogenetic analysis spawned high-throughput sequencing (HTS). Such include those most commonly encountered phylogenomic datasets, such as incomplete lineage sorting, but also reticulate processes with greater...
Abstract Genome assemblies are currently being produced at an impressive rate by consortia and individual laboratories. The low costs increasing efficiency of sequencing technologies now enable assembling genomes unprecedented quality contiguity. However, the difficulty in repeat‐rich GC‐rich regions (genomic “dark matter”) limits insights into evolution genome structure regulatory networks. Here, we compare available (short/linked/long reads proximity ligation maps) combinations thereof...
The association of chromosome rearrangements (CRs) with speciation is well established, and there a long history theory evidence relating to "chromosomal speciation." Genomic sequencing has the potential provide new insights into how reorganization genome structure promotes divergence, in model systems demonstrated reduced gene flow rearranged segments. However, are limits what we can understand from small number systems, which each only tell us about one episode chromosomal speciation....
Tropical islands are renowned as natural laboratories for evolutionary study. Lineage radiations across tropical archipelagos ideal systems investigating how colonization, speciation, and extinction processes shape biodiversity patterns. The expansion of the island thrush Indo-Pacific represents one largest yet most perplexing any songbird species. exhibits a complex mosaic pronounced plumage variation its range is arguably world's polytypic bird. It sedentary species largely restricted to...
Abstract Understanding how natural populations will respond to contemporary changes in climate is becoming increasingly urgent and of fundamental importance for the preservation future biodiversity. Among vertebrates, amphibians reptiles are more sensitive environmental perturbations than endotherms ectotherm diversity likely be disproportionally impacted by change. Notwithstanding concerns surrounding change resilience populations, accurately predicting population trajectories based on...
Accurate gene tree inference is an important aspect of species estimation in a summary-coalescent framework. Yet, empirical studies, inferred trees differ accuracy due to stochastic variation phylogenetic signal between targeted loci. Empiricists should, therefore, examine the consistency inference, while accounting for observed heterogeneity resolution phylogenomic data sets. Here, we assess impact error on by screening ${\sim}2000$ exonic loci based prior inference. We focus...
Abstract Targeting phylogenetic diversity (PD) in systematic conservation planning is an efficient way to minimize losses across the Tree of Life. Considering representation genetic below and above species level, also allows robust analyses within systems where taxonomy flux. We use dense sampling phylogeographic for 11 lizard genera, demonstrate how PD can be applied a policy‐ready problem. Our analysis bypasses named taxa, using data directly inform decisions. highlight areas that should...
Abstract Aim The species diversity and endemism of tropical biotas are major contributors to global biodiversity, but the factors underlying formation these systems remain poorly understood. Location world's largest island, New Guinea. Time period Miocene present. Major taxa studied Passerine birds. Methods We first generated a species‐level phylogeny all native breeding passerine birds analyse spatial elevational patterns richness, age phylogenetic diversity. Second, we used an existing...
Abstract Tropical mountains harbor exceptional concentrations of Earth’s biodiversity. In topographically complex landscapes, montane species typically inhabit multiple mountainous regions, but are absent in intervening lowland environments. Here we report a comparative analysis genome-wide DNA polymorphism data for population pairs from eighteen Indo-Pacific bird the Moluccan islands Buru and Seram across island New Guinea. We test how barrier strength relative elevational distribution...
Biological specimens in natural history collections constitute a massive repository of genetic information. Many have been collected areas which they no longer exist or where present-day collecting is not possible. There are also representing populations species that gone extinct. Furthermore, may sampled throughout an extensive time period, particularly valuable for studies change through time. With the advent high-throughput sequencing, museum resources become accessible genomic research....
Satellite DNA (satDNA) is a fast-evolving portion of eukaryotic genomes. The homogeneous and repetitive nature such satDNA causes problems during the assembly genomes, therefore it still difficult to study in detail nonmodel organisms as well across broad evolutionary timescales. Here, we combined use short- long-read data explore diversity evolution between individuals same species genera birds spanning ~40 millions years bird using birds-of-paradise (Paradisaeidae) crow (Corvus) species....
Recent radiations are important to evolutionary biologists, because they provide an opportunity study the mechanisms that link micro- and macroevolution. The role of ecological speciation during adaptive radiation has been intensively studied, but can arise from a diversity processes; in particular, on large continental landmasses where allopatric might frequently precede differentiation. It is therefore establish phylogenetic framework for recent continental-scale species-rich ecologically...
Museum collections harbor millions of samples, largely unutilized for long-read sequencing. Here, we use ethanol-preserved samples containing kilobase-sized DNA to show that amplification-free protocols can yield contiguous genome assemblies. Additionally, using a modified amplification-based protocol, employing an alternative polymerase overcome PCR bias, assembled the 3.1 Gb maned sloth genome, surpassing previous 500 Mb protocol size limit. Our also improves assemblies other...
Museum collections harbor millions of samples, largely unutilized for long-read sequencing. Here, we use ethanol-preserved samples containing kilobase-sized DNA to show that amplification-free protocols can yield contiguous genome assemblies. Additionally, using a modified amplification-based protocol, employing an alternative polymerase overcome PCR bias, assemble the 3.1 Gb maned sloth genome, surpassing previous 500 Mb protocol size limit. Our also improves assemblies other...
West African rainforests are amongst the world’s premier biodiversity hotspots. Over time, size and distribution of these have changed significantly due to fluctuations in climate. However, compared other hotspots, our understanding potential rainforest refugia remains relatively limited. Studies from different disciplines provided valuable insights into location, age evolutionary role. Fossil pollen data comparative biogeography studies revealed cycles contraction expansion linked...
Offspring provisioning and nest defence are important forms of parental care. In birds, parents that engage in behaviour have to interrupt nestling with potentially harmful consequences for offspring growth condition. To maximize fitness, should trade off optimal levels versus defence, but relatively little is known about how allocate their time between these two activities decisions postpone vary as a function the intensity predation risk. We found pairs blue tits, Cyanistes caeruleus,...
Abstract Accurate gene tree inference is an important aspect of species estimation in a summary-coalescent framework. Yet, empirical studies, inferred trees differ accuracy due to stochastic variation phylogenetic signal between targeted loci. Empiricists should therefore examine the consistency inference, while accounting for observed heterogeneity resolution phylogenomic datasets. Here, we assess impact error on by screening ~2000 exonic loci based prior inference. We focus...
Abstract The diverse array of phenotypes and courtship displays exhibited by birds-of-paradise have long fascinated scientists nonscientists alike. Remarkably, almost nothing is known about the genomics this iconic radiation. There are 41 species in 16 genera currently recognized within family (Paradisaeidae), most which endemic to island New Guinea. In study, we sequenced genomes representatives from all five major clades characterize genomic changes that may played a role evolution group's...
The importance of long-distance dispersal (LDD) in shaping geographical distributions has been debated since the nineteenth century. In terrestrial vertebrates, LDD events across large water bodies are considered highly improbable, but organismal traits affecting capacity generally not taken into account. Here, we focus on a recent lizard radiation and combine summary-coalescent species tree based 1225 exons with probabilistic model that links to an evolving trait, investigate whether...
Abstract A taxonomic classification that accurately captures evolutionary history is essential for conservation. Genomics provides powerful tools delimiting species and understanding their relationships. This allows a more accurate detailed view on conservation status compared with other, traditionally used, methods. However, from practical ethical perspective, gathering sufficient samples endangered taxa may be difficult. Here, we use museum specimens to trace the boundaries in an Asian...