Abstract Meiotic recombination in vertebrates is concentrated in hotspots throughout the genome. The location and stability of hotspots have been linked to the presence or absence of PRDM9, leading to two primary models for hotspot evolution derived from mammals and birds. Species with PRDM9-directed recombination have rapid turnover of hotspots concentrated in intergenic regions (i.e., mammals), whereas hotspots in species lacking PRDM9 are concentrated in functional regions and have greater stability over time (i.e., birds). Snakes possess PRDM9, yet virtually nothing is known about snake recombination. Here, we examine the recombination landscape and test hypotheses about the roles of PRDM9 in rattlesnakes. We find substantial variation in recombination rate within and among snake chromosomes, and positive correlations between recombination rate and gene density, GC content, and genetic diversity. Like mammals, snakes appear to have a functional and active PRDM9, but rather than being directed away from genes, snake hotspots are concentrated in promoters and functional regions—a pattern previously associated only with species that lack a functional PRDM9. Snakes therefore provide a unique example of recombination landscapes in which PRDM9 is functional, yet recombination hotspots are associated with functional genic regions—a combination of features that defy existing paradigms for recombination landscapes in vertebrates. Our findings also provide evidence that high recombination rates are a shared feature of vertebrate microchromosomes. Our results challenge previous assumptions about the adaptive role of PRDM9 and highlight the diversity of recombination landscape features among vertebrate lineages.
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Genome-wide data implicate terminal fusion automixis in king cobra facultative parthenogenesis
Abstract Facultative parthenogenesis (FP) is widespread in the animal kingdom. In vertebrates it was first described in poultry nearly 70 years ago, and since then reports involving other taxa have increased considerably. In the last two decades, numerous reports of FP have emerged in elasmobranch fishes and squamate reptiles (lizards and snakes), including documentation in wild populations of both clades. When considered in concert with recent evidence of reproductive competence, the accumulating data suggest that the significance of FP in vertebrate evolution has been largely underestimated. Several fundamental questions regarding developmental mechanisms, nonetheless, remain unanswered. Specifically, what is the type of automixis that underlies the production of progeny and how does this impact the genomic diversity of the resulting parthenogens? Here, we addressed these questions through the application of next-generation sequencing to investigate a suspected case of parthenogenesis in a king cobra ( Ophiophagus hannah ). Our results provide the first evidence of FP in this species, and provide novel evidence that rejects gametic duplication and supports terminal fusion as a mechanism underlying parthenogenesis in snakes. Moreover, we precisely estimated heterozygosity in parthenogenetic offspring and found appreciable retained genetic diversity that suggests that FP in vertebrates has underappreciated evolutionary significance.
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- Award ID(s):
- 1812310
- NSF-PAR ID:
- 10386915
- Date Published:
- Journal Name:
- Scientific Reports
- Volume:
- 11
- Issue:
- 1
- ISSN:
- 2045-2322
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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In this study, two parthenogenetic events within a family of the whitespotted bambooshark
Chiloscyllium plagiosum are reported. A captive female produced multiple parthenogens. Unexpectedly, a single specimen of a total of nine parthenogens displayed external claspers characterizing the male sex in chondrichthyans. Upon dissection, internal sexual organs of this specimen were malformed or absent; however, the presence of claspers in this study challenges the as yet assumed sex determination system in this shark species. Even more remarkable was that one of the female parthenogens reproduced asexually again producing viable offspring. As far as is known, this is the first genetically confirmed evidence for second‐generation facultative parthenogenesis in vertebrates. These results support the evolutionary significance of parthenogenesis as an alternative to sexual reproduction. -
Pickett, Brett E. ; Jurado, Kellie (Ed.)ABSTRACT Data that catalogue viral diversity on Earth have been fragmented across sources, disciplines, formats, and various degrees of open sharing, posing challenges for research on macroecology, evolution, and public health. Here, we solve this problem by establishing a dynamically maintained database of vertebrate-virus associations, called The Global Virome in One Network (VIRION). The VIRION database has been assembled through both reconciliation of static data sets and integration of dynamically updated databases. These data sources are all harmonized against one taxonomic backbone, including metadata on host and virus taxonomic validity and higher classification; additional metadata on sampling methodology and evidence strength are also available in a harmonized format. In total, the VIRION database is the largest open-source, open-access database of its kind, with roughly half a million unique records that include 9,521 resolved virus “species” (of which 1,661 are ICTV ratified), 3,692 resolved vertebrate host species, and 23,147 unique interactions between taxonomically valid organisms. Together, these data cover roughly a quarter of mammal diversity, a 10th of bird diversity, and ∼6% of the estimated total diversity of vertebrates, and a much larger proportion of their virome than any previous database. We show how these data can be used to test hypotheses about microbiology, ecology, and evolution and make suggestions for best practices that address the unique mix of evidence that coexists in these data. IMPORTANCE Animals and their viruses are connected by a sprawling, tangled network of species interactions. Data on the host-virus network are available from several sources, which use different naming conventions and often report metadata in different levels of detail. VIRION is a new database that combines several of these existing data sources, reconciles taxonomy to a single consistent backbone, and reports metadata in a format designed by and for virologists. Researchers can use VIRION to easily answer questions like “Can any fish viruses infect humans?” or “Which bats host coronaviruses?” or to build more advanced predictive models, making it an unprecedented step toward a full inventory of the global virome.more » « less
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Abstract Although systematic reviews are intended to provide trusted scientific knowledge to meet the needs of decision-makers, their reliability can be threatened by bias and irreproducibility. To help decision-makers assess the risks in systematic reviews that they intend to use as the foundation of their action, we designed and tested a new approach to analyzing the evidence selection of a review: its coverage of the primary literature and its comparison to other reviews. Our approach could also help anyone using or producing reviews understand diversity or convergence in evidence selection. The basis of our approach is a new network construct called the inclusion network, which has two types of nodes: primary study reports (PSRs, the evidence) and systematic review reports (SRRs). The approach assesses risks in a given systematic review (the target SRR) by first constructing an inclusion network of the target SRR and other systematic reviews studying similar research questions (the companion SRRs) and then applying a three-step assessment process that utilizes visualizations, quantitative network metrics, and time series analysis. This paper introduces our approach and demonstrates it in two case studies. We identified the following risks: missing potentially relevant evidence, epistemic division in the scientific community, and recent instability in evidence selection standards. We also compare our inclusion network approach to knowledge assessment approaches based on another influential network construct, the claim-specific citation network, discuss current limitations of the inclusion network approach, and present directions for future work.
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Several consensus reports cite a critical need to dramatically increase the number and diversity of STEM graduates over the next decade. They conclude that a change to evidence-based instructional practices, such as concept-based active learning, is needed. Concept-based active learning involves the use of activity-based pedagogies whose primary objectives are to make students value deep conceptual understanding (instead of only factual knowledge) and then to facilitate their development of that understanding. Concept-based active learning has been shown to increase academic engagement and student achievement, to significantly improve student retention in academic programs, and to reduce the performance gap of underrepresented students. Fostering students' mastery of fundamental concepts is central to real world problem solving, including several elements of engineering practice. Unfortunately, simply proving that these instructional practices are more effective than traditional methods for promoting student learning, for increasing retention in academic programs, and for improving ability in professional practice is not enough to ensure widespread pedagogical change. In fact, the biggest challenge to improving STEM education is not the need to develop more effective instructional practices, but to find ways to get faculty to adopt the evidence-based pedagogies that already exist. In this project we seek to propagate the Concept Warehouse, a technological innovation designed to foster concept-based active learning, into Mechanical Engineering (ME) and to study student learning with this tool in five diverse institutional settings. The Concept Warehouse (CW) is a web-based instructional tool that we developed for Chemical Engineering (ChE) faculty. It houses over 3,500 ConcepTests, which are short questions that can rapidly be deployed to engage students in concept-oriented thinking and/or to assess students’ conceptual knowledge, along with more extensive concept-based active learning tools. The CW has grown rapidly during this project and now has over 1,600 faculty accounts and over 37,000 student users. New ConcepTests were created during the current reporting period; the current numbers of questions for Statics, Dynamics, and Mechanics of Materials are 342, 410, and 41, respectively. A detailed review process is in progress, and will continue through the no-cost extension year, to refine question clarity and to identify types of new questions to fill gaps in content coverage. There have been 497 new faculty accounts created after June 30, 2018, and 3,035 unique students have answered these mechanics questions in the CW. We continue to analyze instructor interviews, focusing on 11 cases, all of whom participated in the CW Community of Practice (CoP). For six participants, we were able to compare use of the CW both before and after participating in professional development activities (workshops and/or a community or practice). Interview results have been coded and are currently being analyzed. To examine student learning, we recruited faculty to participate in deploying four common questions in both statics and dynamics. In statics, each instructor agreed to deploy the same four questions (one each for Rigid Body Equilibrium, Trusses, Frames, and Friction) among their overall deployments of the CW. In addition to answering the question, students were also asked to provide a written explanation to explain their reasoning, to rate the confidence of their answers, and to rate the degree to which the questions were clear and promoted deep thinking. The analysis to date has resulted in a Work-In-Progress paper presented at ASEE 2022, reporting a cross-case comparison of two instructors and a Work-In-Progress paper to be presented at ASEE 2023 analyzing students’ metacognitive reflections of concept questions.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1038/s41598-021-86373-1
