Mark S. Springer
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Pseudogenes Document Protracted Parallel Regression of Oral Anatomy in Myrmecophagous Mammals Open
Adaptation to ant and/or termite consumption (myrmecophagy) in mammals constitutes a textbook example of convergent evolution, being independently derived in several mammalian lineages. Myrmecophagous species are characterized by striking …
View article: Sky islands of Southwest China. II: Unraveling hidden species diversity of talpid moles using phylogenomics and skull-based deep learning
Sky islands of Southwest China. II: Unraveling hidden species diversity of talpid moles using phylogenomics and skull-based deep learning Open
The sky islands of Southwest China, characterized by dramatic topographical and climatic variations, are prominent hotspots of biodiversity and endemism. Organisms inhabiting middle-to-high elevation habitats in this region are geographica…
View article: Pseudogenes Document Protracted Parallel Regression of Oral Anatomy in Myrmecophagous Mammals
Pseudogenes Document Protracted Parallel Regression of Oral Anatomy in Myrmecophagous Mammals Open
Adaptation to ant and/or termite consumption (myrmecophagy) in mammals constitutes a textbook example of convergent evolution, being independently derived in several mammalian lineages. Myrmecophagous species are characterized by striking …
The effects of ordered multistate morphological characters on phylogenetic analyses of eutherian mammals Open
Multistate morphological characters are routinely used in phylogenetic analyses. Individual multistate characters may be treated as linearly ordered, partially ordered, or unordered. Each option implies a hypothesis of character evolution,…
A new phylogeny for Aves is compromised by pervasive misalignment and homology problems Open
Large volumes of liquid water transiently existed on the surface of Mars more than 3 billion years ago. Much of this water is hypothesized to have been sequestered in the subsurface or lost to space. We use rock physics models and Bayesian…
P12.06 GLP-compliant validation of a FluoroSpot assay to monitor tumor neoantigen vaccinations in preclinical mouse models Open
Background While immunomonitoring as secondary endpoint gets increasingly attractive in neoantigen clinical trials for personalized tumor vaccines, the preclinical testing of neoantigen candidates in animal models may help in neoantigen se…
Molecular Evidence for Relaxed Selection on the Enamel Genes of Toothed Whales (Odontoceti) with Degenerative Enamel Phenotypes Open
Different species of toothed whales (Odontoceti) exhibit a variety of tooth forms and enamel types. Some odontocetes have highly prismatic enamel with Hunter-Schreger bands, whereas enamel is vestigial or entirely lacking in other species.…
Three Blind Moles: Molecular Evolutionary Insights on the Tempo and Mode of Convergent Eye Degeneration in Notoryctes typhlops (Southern Marsupial Mole) and Two Chrysochlorids (Golden Moles) Open
Golden moles (Chrysochloridae) and marsupial moles (Notoryctidae) are textbook examples of convergent evolution. Both taxa are highly adapted to subterranean lifestyles and have powerful limbs for digging through the soil/sand, ears that a…
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…
Genetic excision of the regulatory cardiac troponin I extension in high heart rate mammal clades Open
Mammalian cardiac troponin I (cTnI) contains a highly conserved N-terminal extension harboring protein kinase A targets (Ser 23/24 ) which are phosphorylated during ß-adrenergic stimulation to increase cardiomyocyte relaxation rate. Here, …
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: 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: 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…
Quantification of congruence among gene trees with polytomies using overall success of resolution for phylogenomic coalescent analyses Open
Gene‐tree‐inference error can cause species‐tree‐inference artefacts in summary phylogenomic coalescent analyses. Here we integrate two ways of accommodating these inference errors: collapsing arbitrarily or dubiously resolved gene‐tree br…
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…
Innate Principles and the Digital Object: Insights from Core Knowledge Theory Open
Psychology research reveals that humans possess innate principles that govern how we make sense of objects and object-directed actions. These principles are embedded in interrelated systems of core knowledge that shape behavior. This paper…
Supplemental data for "Assessing congruence among gene trees with polytomies using overall success of resolution for coalescent analyses" Open
Supplemental data for "Assessing congruence among gene trees with polytomies using overall success of resolution for coalescent analyses"
A genomic timescale for placental mammal evolution: Datasets Open
Datasets used in Foley N.M., Mason, V.C., Harris A.J., Bredemeyer K.R., Damas J., Lewin H.A., Eizirik E., Gatesy J., Zoonomia Consortium, Springer M.S., and W.J. Murphy (2022) A genomic timescale for placental mammal evolution. Science. x:…
A genomic timescale for placental mammal evolution: Datasets Open
Datasets used in Foley N.M., Mason, V.C., Harris A.J., Bredemeyer K.R., Damas J., Lewin H.A., Eizirik E., Gatesy J., Zoonomia Consortium, Springer M.S., and W.J. Murphy (2022) A genomic timescale for placental mammal evolution. Science. x:…
A genomic timescale for placental mammal evolution: Datasets Open
Datasets used in Foley N.M., Mason, V.C., Harris A.J., Bredemeyer K.R., Damas J., Lewin H.A., Eizirik E., Gatesy J., Zoonomia Consortium, Springer M.S., and W.J. Murphy (2022) A genomic timescale for placental mammal evolution. Science. x:…
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…
Phylogenomic Coalescent Analyses of Avian Retroelements Infer Zero-Length Branches at the Base of Neoaves, Emergent Support for Controversial Clades, and Ancient Introgressive Hybridization in Afroaves Open
Retroelement insertions (RIs) are low-homoplasy characters that are ideal data for addressing deep evolutionary radiations, where gene tree reconstruction errors can severely hinder phylogenetic inference with DNA and protein sequence data…
Contradictory Phylogenetic Signals in the Laurasiatheria Anomaly Zone Open
Relationships among laurasiatherian clades represent one of the most highly disputed topics in mammalian phylogeny. In this study, we attempt to disentangle laurasiatherian interordinal relationships using two independent genome-level appr…