Matthew J. Christmas
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View article: Whole genome resequencing of Megachile rotundata
Whole genome resequencing of Megachile rotundata Open
Social insects have exceptionally high rates of crossing over . We gain insight into the evolutionary causes of these extreme recombination rates by comparing recombination rate variation across the genome of a social and solitary bee. We …
View article: Large Inversions Shape Diversification and Genome Evolution in Common Quails
Large Inversions Shape Diversification and Genome Evolution in Common Quails Open
Chromosomal inversions, by suppressing recombination, can profoundly shape genome evolution and drive adaptation. In the common quail ( Coturnix coturnix ), a highly mobile bird with a vast Palearctic breeding range, we previously identifi…
View article: Vocal learning–associated convergent evolution in mammalian proteins and regulatory elements
Vocal learning–associated convergent evolution in mammalian proteins and regulatory elements Open
Vocal production learning (“vocal learning”) is a convergently evolved trait in vertebrates. To identify brain genomic elements associated with mammalian vocal learning, we integrated genomic, anatomical, and neurophysiological data from t…
View article: The Genomic Basis of Adaptation to High Elevations in Africanized Honey Bees
The Genomic Basis of Adaptation to High Elevations in Africanized Honey Bees Open
A range of different genetic architectures underpin local adaptation in nature. Honey bees (Apis mellifera) in the Eastern African Mountains harbor high frequencies of two chromosomal inversions that likely govern adaptation to this high-e…
View article: Using evolutionary constraint to define novel candidate driver genes in medulloblastoma
Using evolutionary constraint to define novel candidate driver genes in medulloblastoma Open
Current knowledge of cancer genomics remains biased against noncoding mutations. To systematically search for regulatory noncoding mutations, we assessed mutations in conserved positions in the genome under the assumption that these are mo…
View article: Integrating gene annotation with orthology inference at scale
Integrating gene annotation with orthology inference at scale Open
Annotating coding genes and inferring orthologs are two classical challenges in genomics and evolutionary biology that have traditionally been approached separately, limiting scalability. We present TOGA (Tool to infer Orthologs from Genom…
View article: Evolutionary constraint and innovation across hundreds of placental mammals
Evolutionary constraint and innovation across hundreds of placental mammals Open
Zoonomia is the largest comparative genomics resource for mammals produced to date. By aligning genomes for 240 species, we identify bases that, when mutated, are likely to affect fitness and alter disease risk. At least 332 million bases …
View article: Three-dimensional genome rewiring in loci with human accelerated regions
Three-dimensional genome rewiring in loci with human accelerated regions Open
Human accelerated regions (HARs) are conserved genomic loci that evolved at an accelerated rate in the human lineage and may underlie human-specific traits. We generated HARs and chimpanzee accelerated regions with an automated pipeline an…
View article: Insights into mammalian TE diversity through the curation of 248 genome assemblies
Insights into mammalian TE diversity through the curation of 248 genome assemblies Open
We examined transposable element (TE) content of 248 placental mammal genome assemblies, the largest de novo TE curation effort in eukaryotes to date. We found that although mammals resemble one another in total TE content and diversity, t…
View article: A genomic timescale for placental mammal evolution
A genomic timescale for placental mammal evolution Open
The precise pattern and timing of speciation events that gave rise to all living placental mammals remain controversial. We provide a comprehensive phylogenetic analysis of genetic variation across an alignment of 241 placental mammal geno…
View article: Relating enhancer genetic variation across mammals to complex phenotypes using machine learning
Relating enhancer genetic variation across mammals to complex phenotypes using machine learning Open
Protein-coding differences between species often fail to explain phenotypic diversity, suggesting the involvement of genomic elements that regulate gene expression such as enhancers. Identifying associations between enhancers and phenotype…
View article: The contribution of historical processes to contemporary extinction risk in placental mammals
The contribution of historical processes to contemporary extinction risk in placental mammals Open
Species persistence can be influenced by the amount, type, and distribution of diversity across the genome, suggesting a potential relationship between historical demography and resilience. In this study, we surveyed genetic variation acro…
View article: Leveraging base-pair mammalian constraint to understand genetic variation and human disease
Leveraging base-pair mammalian constraint to understand genetic variation and human disease Open
Thousands of genomic regions have been associated with heritable human diseases, but attempts to elucidate biological mechanisms are impeded by an inability to discern which genomic positions are functionally important. Evolutionary constr…
View article: Comparative genomics of Balto, a famous historic dog, captures lost diversity of 1920s sled dogs
Comparative genomics of Balto, a famous historic dog, captures lost diversity of 1920s sled dogs Open
We reconstruct the phenotype of Balto, the heroic sled dog renowned for transporting diphtheria antitoxin to Nome, Alaska, in 1925, using evolutionary constraint estimates from the Zoonomia alignment of 240 mammals and 682 genomes from dog…
View article: The functional and evolutionary impacts of human-specific deletions in conserved elements
The functional and evolutionary impacts of human-specific deletions in conserved elements Open
Conserved genomic sequences disrupted in humans may underlie uniquely human phenotypic traits. We identified and characterized 10,032 human-specific conserved deletions (hCONDELs). These short (average 2.56 base pairs) deletions are enrich…
View article: Chiropterans Are a Hotspot for Horizontal Transfer of DNA Transposons in Mammalia
Chiropterans Are a Hotspot for Horizontal Transfer of DNA Transposons in Mammalia Open
Horizontal transfer of transposable elements (TEs) is an important mechanism contributing to genetic diversity and innovation. Bats (order Chiroptera) have repeatedly been shown to experience horizontal transfer of TEs at what appears to b…
View article: Leveraging Base Pair Mammalian Constraint to Understand Genetic Variation and Human Disease
Leveraging Base Pair Mammalian Constraint to Understand Genetic Variation and Human Disease Open
Although thousands of genomic regions have been associated with heritable human diseases, attempts to elucidate biological mechanisms are impeded by a general inability to discern which genomic positions are functionally important. Evoluti…
View article: Evolutionary constraint and innovation across hundreds of placental mammals
Evolutionary constraint and innovation across hundreds of placental mammals Open
Evolutionary constraint and acceleration are powerful, cell-type agnostic measures of functional importance. Previous studies in mammals were limited by species number and reliance on human-referenced alignments. We explore the evolution o…
View article: Evolution of the ancestral mammalian karyotype and syntenic regions
Evolution of the ancestral mammalian karyotype and syntenic regions Open
Decrypting the rearrangements that drive mammalian chromosome evolution is critical to understanding the molecular bases of speciation, adaptation, and disease susceptibility. Using 8 scaffolded and 26 chromosome-scale genome assemblies re…
View article: A genomic and morphometric analysis of alpine bumblebees: Ongoing reductions in tongue length but no clear genetic component
A genomic and morphometric analysis of alpine bumblebees: Ongoing reductions in tongue length but no clear genetic component Open
Over the last six decades, populations of the bumblebees Bombus sylvicola and Bombus balteatus in Colorado have experienced decreases in tongue length, a trait important for plant‐pollinator mutualisms. It has been hypothesized that this o…
View article: Genomic, Habitat, and Leaf Shape Analyses Reveal a Possible Cryptic Species and Vulnerability to Climate Change in a Threatened Daisy
Genomic, Habitat, and Leaf Shape Analyses Reveal a Possible Cryptic Species and Vulnerability to Climate Change in a Threatened Daisy Open
Olearia pannosa is a plant species listed as vulnerable in Australia. Two subspecies are currently recognised (O. pannosa subsp. pannosa (silver daisy) and O. pannosa subsp. cardiophylla (velvet daisy)), which have overlapping ranges but d…
View article: Genetic Barriers to Historical Gene Flow between Cryptic Species of Alpine Bumblebees Revealed by Comparative Population Genomics
Genetic Barriers to Historical Gene Flow between Cryptic Species of Alpine Bumblebees Revealed by Comparative Population Genomics Open
Evidence is accumulating that gene flow commonly occurs between recently diverged species, despite the existence of barriers to gene flow in their genomes. However, we still know little about what regions of the genome become barriers to g…
View article: A genomic and morphometric analysis of alpine bumblebees: ongoing reductions in tongue length but no clear genetic component
A genomic and morphometric analysis of alpine bumblebees: ongoing reductions in tongue length but no clear genetic component Open
Over the last six decades, populations of the bumblebees Bombus sylvicola and Bombus balteatus in Colorado have experienced decreases in tongue length, a trait important for plant-pollinator mutualisms. It has been hypothesized that this o…
View article: Site preparation impacts on soil biotic and abiotic properties, weed control, and native grass establishment
Site preparation impacts on soil biotic and abiotic properties, weed control, and native grass establishment Open
In severely degraded systems active restoration is required to overcome legacies of past land use and to create conditions that promote the establishment of target plant communities. While our understanding of the importance of soil microb…
View article: Increased Genetic Diversity via Gene Flow Provides Hope for Acacia whibleyana, an Endangered Wattle Facing Extinction
Increased Genetic Diversity via Gene Flow Provides Hope for Acacia whibleyana, an Endangered Wattle Facing Extinction Open
In this paper we apply a conservation genomics approach to make evidence-based management recommendations for Acacia whibleyana, an endangered shrub endemic to Eyre Peninsula, South Australia. We used population genomic analysis to assess …
View article: Functional acclimation across microgeographic scales in Dodonaea viscosa
Functional acclimation across microgeographic scales in Dodonaea viscosa Open
Intraspecific plant functional trait variation provides mechanistic insight into persistence and can infer population adaptive capacity. However, most studies explore intraspecific trait variation in systems where geographic and environmen…