Cynthia Steiner
A5050264657- Genomics and Phylogenetic Studies
- Genetic diversity and population structure
- Chromosomal and Genetic Variations
- Evolution and Paleontology Studies
- Genetic and phenotypic traits in livestock
- Bat Biology and Ecology Studies
- Genetic Mapping and Diversity in Plants and Animals
- RNA and protein synthesis mechanisms
- Genomics and Chromatin Dynamics
- Wildlife Ecology and Conservation
- Animal Genetics and Reproduction
- Biochemical Analysis and Sensing Techniques
- Amphibian and Reptile Biology
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Epigenetics and DNA Methylation
- Animal Ecology and Behavior Studies
- melanin and skin pigmentation
- Fish Ecology and Management Studies
- Identification and Quantification in Food
- Animal Behavior and Reproduction
- Reproductive biology and impacts on aquatic species
- Molecular Biology Techniques and Applications
- Primate Behavior and Ecology
- Estrogen and related hormone effects
- Marine animal studies overview
Zoological Society of San Diego
2011-2025
San Diego Zoo Institute for Conservation Research
2014-2025
Digital Research Alliance of Canada
2023-2024
Howard Hughes Medical Institute
2023
University of California, Santa Cruz
2023
University of California, Riverside
2023
Broad Institute
2023
Morningside College
2023
University of Massachusetts Chan Medical School
2023
Science for Life Laboratory
2023
Molecular phylogenetic analysis, calibrated with fossils, resolves the time frame of mammalian radiation.
Using next-generation sequencing technology alone, we have successfully generated and assembled a draft sequence of the giant panda genome. The contigs (2.25 gigabases (Gb)) cover approximately 94% whole genome, remaining gaps (0.05 Gb) seem to contain carnivore-specific repeats tandem repeats. Comparisons with dog human showed that genome has lower divergence rate. assessment genes potentially underlying some its unique traits indicated bamboo diet might be more dependent on gut microbiome...
Phylogenetic relationships, divergence times, and patterns of biogeographic descent among primate species are both complex contentious. Here, we generate a robust molecular phylogeny for 70 genera 367 based on concatenation 69 nuclear gene segments ten mitochondrial sequences, most which were extracted from GenBank. Relaxed clock analyses times with 14 fossil-calibrated nodes suggest that living Primates last shared common ancestor 71–63 Ma, divergences within Strepsirrhini Haplorhini...
Little is known about the genetic basis of ecologically important morphological variation such as diverse color patterns mammals. Here we identify changes contributing to an adaptive difference in pattern between two subspecies oldfield mice (Peromyscus polionotus). One mainland has a cryptic dark brown dorsal coat, while younger beach-dwelling lighter coat produced by natural selection for camouflage on pale coastal sand dunes. Using genome-wide linkage mapping, identified three chromosomal...
The PacBio® HiFi sequencing method yields highly accurate long-read datasets with read lengths averaging 10-25 kb and accuracies greater than 99.5%. These long reads can be used to improve results for complex applications such as single nucleotide structural variant detection, genome assembly, assembly of difficult polyploid or repetitive genomes, metagenomes. Currently, there is a need sample data sets both evaluate the benefits these well development bioinformatic tools including...
Zoonomia is the largest comparative genomics resource for mammals produced to date. By aligning genomes 240 species, we identify bases that, when mutated, are likely affect fitness and alter disease risk. At least 332 million (~10.7%) in human genome unusually conserved across species (evolutionarily constrained) relative neutrally evolving repeats, 4552 ultraconserved elements nearly perfectly conserved. Of 101 significantly constrained single bases, 80% outside protein-coding exons half...
Annotating coding genes and inferring orthologs are two classical challenges in genomics evolutionary biology that have traditionally been approached separately, limiting scalability. We present TOGA (Tool to infer Orthologs from Genome Alignments), a method integrates structural gene annotation orthology inference. implements different paradigm orthologous loci, improves ortholog detection of conserved compared with state-of-the-art methods, handles even highly fragmented assemblies. scales...
The precise pattern and timing of speciation events that gave rise to all living placental mammals remain controversial. We provide a comprehensive phylogenetic analysis genetic variation across an alignment 241 mammal genome assemblies, addressing prior concerns regarding limited genomic sampling species. compared neutral genome-wide phylogenomic signals using concatenation coalescent-based approaches, interrogated chromosomes, analyzed extensive catalogs structural variants. Interordinal...
Human accelerated regions (HARs) are conserved genomic loci that evolved at an rate in the human lineage and may underlie human-specific traits. We generated HARs chimpanzee with automated pipeline alignment of 241 mammalian genomes. Combining deep learning chromatin capture experiments neural progenitor cells, we discovered a significant enrichment topologically associating domains containing variants change three-dimensional (3D) genome organization. Differential gene expression between...
Species persistence can be influenced by the amount, type, and distribution of diversity across genome, suggesting a potential relationship between historical demography resilience. In this study, we surveyed genetic variation single genomes 240 mammals that compose Zoonomia alignment to evaluate how effective population size (
Understanding the regulatory landscape of human genome is a long-standing objective modern biology. Using reference-free alignment across 241 mammalian genomes produced by Zoonomia Consortium, we charted evolutionary trajectories for 0.92 million candidate cis-regulatory elements (cCREs) and 15.6 transcription factor binding sites (TFBSs). We identified 439,461 cCREs 2,024,062 TFBSs under constraint. Genes near constrained perform fundamental cellular processes, whereas genes...
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 enhancers and phenotypes is challenging because enhancer activity can be tissue-dependent functionally conserved despite low sequence conservation. We developed Tissue-Aware Conservation Inference Toolkit (TACIT) associate candidate with species' using predictions from machine learning...
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) are enriched for brain functions across genetic, epigenomic, transcriptomic datasets. Using massively parallel reporter assays six cell types, we discovered 800 hCONDELs conferring significant differences regulatory activity, half of which enhance rather than disrupt function....
Abstract The most dynamic and repetitive regions of great ape genomes have traditionally been excluded from comparative studies 1–3 . Consequently, our understanding the evolution species is incomplete. Here we present haplotype-resolved reference analyses six species: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan siamang. We achieve chromosome-level contiguity with substantial sequence accuracy (<1 error in 2.7 megabases) completely 215 gapless chromosomes...
Convergent evolution is a widespread phenomenon seen in diverse organisms inhabiting similar selective environments. However, it unclear if phenotypes are produced by the same or different genes and mutations. Here we analyze molecular mechanisms underlying convergent pigment pattern among subspecies of beach mouse (Peromyscus polionotus) Gulf Atlantic coasts Florida. In these two geographic regions, separated more than 300 km, "beach mice" have lighter colored coats do their mainland...
The evolution of perissodactyls (rhinoceroses, tapirs, and horses) has been well studied primarily because their extensive fossil record. Nevertheless, controversy persists regarding relationships some the extant taxa, reflecting inconsistencies between molecular morphological studies. Here we examine phylogenetic 16 living perissodactyl species by concatenating two mitochondrial nine nuclear genes, estimate divergence times using a relaxed Bayesian clock approach. Our analyses recovered...
Only five species of the once-diverse Rhinocerotidae remain, making reconstruction their evolutionary history a challenge to biologists since Darwin. We sequenced genomes from rhinoceros (three extinct and two living), which we compared existing data remaining three living range outgroups. identify an early divergence between extant African Eurasian lineages, resolving key debate regarding phylogeny rhinoceroses. This Miocene (∼16 million years ago [mya]) split post-dates land bridge...
Abstract Small populations are often exposed to high inbreeding and mutational load that can increase the risk of extinction. The Sumatran rhinoceros was widespread in Southeast Asia, but is now restricted small isolated on Sumatra Borneo, most likely extinct Malay Peninsula. Here, we analyse 5 historical 16 modern genomes from these investigate genomic consequences recent decline, such as increased load. We find Peninsula population experienced shortly before extirpation, which possibly...
Decrypting the rearrangements that drive mammalian chromosome evolution is critical to understanding molecular bases of speciation, adaptation, and disease susceptibility. Using 8 scaffolded 26 chromosome-scale genome assemblies representing 23/26 mammal orders, we computationally reconstructed ancestral karyotypes syntenic relationships at 16 nodes along phylogeny. Three different reference genomes (human, sloth, cattle) phylogenetically distinct superorders were used assess bias in expand...
We present haplotype-resolved reference genomes and comparative analyses of six ape species, namely: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran siamang. achieve chromosome-level contiguity with unparalleled sequence accuracy (<1 error in 500,000 base pairs), completely sequencing 215 gapless chromosomes telomere-to-telomere. resolve challenging regions, such as the major histocompatibility complex immunoglobulin loci, providing more in-depth evolutionary insights. Comparative...
Due to their small population sizes, threatened and endangered species frequently suffer from a lack of genetic diversity, potentially leading inbreeding depression reduced adaptability.1Frankham R. Conservation genetics.Annu. Rev. Genet. 1995; 29: 305-327Crossref PubMed Scopus (886) Google Scholar During the latter half twentieth century, North America's largest soaring bird,2Finkelstein M. Kuspa Z. Snyder N.F. Schmitt N.J. California condor (Gymnogyps californianus), version 1.0.in:...
The critically endangered northern white rhinoceros is believed to be extinct in the wild, with recent death of last male leaving only two remaining individuals captivity. Its extinction would appear inevitable, but development advanced cell and reproductive technologies such as cloning by nuclear transfer artificial production gametes via stem cells differentiation offer a second chance for its survival. In this work, we analyzed genome-wide levels genetic diversity, inbreeding, population...