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Abstract Broad paradigms of vertebrate genomic repeat element evolution have been largely shaped by analyses of mammalian and avian genomes. Here, based on analyses of genomes sequenced from over 60 squamate reptiles (lizards and snakes), we show that patterns of genomic repeat landscape evolution in squamates challenge such paradigms. Despite low variance in genome size, squamate genomes exhibit surprisingly high variation among species in abundance (ca. 25–73% of the genome) and composition of identifiable repeat elements. We also demonstrate that snake genomes have experienced microsatellite seeding by transposable elements at a scale unparalleled among eukaryotes, leading to some snake genomes containing the highest microsatellite content of any known eukaryote. Our analyses of transposable element evolution across squamates also suggest that lineage-specific variation in mechanisms of transposable element activity and silencing, rather than variation in species-specific demography, may play a dominant role in driving variation in repeat element landscapes across squamate phylogeny.
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Deconstructing the Gestalt: New concepts and tests of homology, as exemplified by a re‐conceptualization of “microstomy” in squamates
Abstract Snakes—a subset of lizards—have traditionally been divided into two major groups based on feeding mechanics: “macrostomy,” involving the ingestion of proportionally large prey items; and “microstomy,” the lack of this ability. “Microstomy”—considered present in scolecophidian and early‐diverging alethinophidian snakes—is generally viewed as a symplesiomorphy shared with non‐snake lizards. However, this perspective of “microstomy” as plesiomorphic and morphologically homogenous fails to recognize the complexity of this condition and its evolution across “microstomatan” squamates. To challenge this problematic paradigm, we formalize a new framework for conceptualizing and testing the homology of overall character complexes, or “morphotypes,” which underlies our re‐assessment of “microstomy.” Using micro‐computed tomography (micro‐CT) scans, we analyze the morphology of the jaws and suspensorium across purported “microstomatan” squamates (scolecophidians, early‐diverging alethinophidians, and non‐snake lizards) and demonstrate that key components of the jaw complex are not homologous at the level of primary character state identity across these taxa. Therefore, rather than treating “microstomy” as a uniform condition, we instead propose that non‐snake lizards, early‐diverging alethinophidians, anomalepidids, leptotyphlopids, and typhlopoids each exhibit a unique and nonhomologous jaw morphotype: “minimal‐kinesis microstomy,” “snout‐shifting,” “axle‐brace maxillary raking,” “mandibular raking,” and “single‐axle maxillary raking,” respectively. The lack of synapomorphy among scolecophidians is inconsistent with the notion of scolecophidians representing an ancestral snake condition, and instead reflects a hypothesis of the independent evolution of fossoriality, miniaturization, and “microstomy” in each scolecophidian lineage. We ultimately emphasize that a rigorous approach to comparative anatomy is necessary in constructing evolutionary hypotheses that accurately reflect biological reality.
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- Award ID(s):
- 1902242
- PAR ID:
- 10448999
- Publisher / Repository:
- Wiley Blackwell (John Wiley & Sons)
- Date Published:
- Journal Name:
- The Anatomical Record
- Volume:
- 304
- Issue:
- 10
- ISSN:
- 1932-8486
- Format(s):
- Medium: X Size: p. 2303-2351
- Size(s):
- p. 2303-2351
- Sponsoring Org:
- National Science Foundation
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