skip to main content


Search for: All records

Creators/Authors contains: "Pyron, R. Alexander"

Note: When clicking on a Digital Object Identifier (DOI) number, you will be taken to an external site maintained by the publisher. Some full text articles may not yet be available without a charge during the embargo (administrative interval).
What is a DOI Number?

Some links on this page may take you to non-federal websites. Their policies may differ from this site.

  1. Foitzik, Susanne ; Zelditch, Miriam (Ed.)
    Abstract

    Iridescent ultraviolet (IUV) patterns on pierid butterfly wings are phenotypic adaptations commonly used as sexual signals, generated by scales with ultrastructural modifications. Pierid IUV patterns are sexually dichromatic, with reduced size in females, where conspicuous sexual signaling balances courtship against ecological predation. There have been no phylogenetic reconstructions of IUV within Pieridae and little morphological characterization of phenotypic diversity. Our genus-wide characterization of IUV revealed the uniform similarity of stacked lamellar ridges on the dorsal surface of cover scales. We tested a hypothesis of single versus multiple origins by reconstructing a phylogeny of 534 species (~43.2% described species), with all genera represented, and a trait matrix of 734 species (~59.4%) screened for IUV. A single, early dimorphic origin of IUV followed by several losses and gains received strong support, concluding that IUV patterns and structural coloration are old traits. Collectively, these results support the homology of IUV scales and patterns that diversified within several lineages, suggesting an interplay between female-mediated sexual selection and ecological predatory selection.

     
    more » « less
    Free, publicly-accessible full text available October 5, 2024
  2. Abstract

    Bald sea urchin disease (BSUD) is most likely a bacterial infection that occurs in a wide range of sea urchin species and causes the loss of surface appendages. The disease has a variety of additional symptoms, which may be the result of the many bacteria that are associated with BSUD. Previous studies have investigated causative agents of BSUD, however, there are few reports on the surface microbiome associated with the infection. Here, we report changes to the surface microbiome on purple sea urchins in a closed marine aquarium that contracted and then recovered from BSUD in addition to the microbiome of healthy sea urchins in a separate aquarium. 16S rRNA gene sequencing shows that microhabitats of different aquaria are characterized by different microbial compositions, and that diseased, recovered, and healthy sea urchins have distinct microbial compositions, which indicates that there is a correlation between microbial shifts and recovery from disease.

     
    more » « less
  3. Abstract

    Numerous mechanisms can drive speciation, including isolation by adaptation, distance, and environment. These forces can promote genetic and phenotypic differentiation of local populations, the formation of phylogeographic lineages, and ultimately, completed speciation. However, conceptually similar mechanisms may also result in stabilizing rather than diversifying selection, leading to lineage integration and the long‐term persistence of population structure within genetically cohesive species. Processes that drive the formation and maintenance of geographic genetic diversity while facilitating high rates of migration and limiting phenotypic differentiation may thereby result in population genetic structure that is not accompanied by reproductive isolation. We suggest that this framework can be applied more broadly to address the classic dilemma of “structure” versus “species” when evaluating phylogeographic diversity, unifying population genetics, species delimitation, and the underlying study of speciation. We demonstrate one such instance in the Seepage Salamander (Desmognathus aeneus) from the southeastern United States. Recent studies estimated up to 6.3% mitochondrial divergence and four phylogenomic lineages with broad admixture across geographic hybrid zones, which could potentially represent distinct species supported by our species‐delimitation analyses. However, while limited dispersal promotes substantial isolation by distance, microhabitat specificity appears to yield stabilizing selection on a single, uniform, ecologically mediated phenotype. As a result, climatic cycles promote recurrent contact between lineages and repeated instances of high migration through time. Subsequent hybridization is apparently not counteracted by adaptive differentiation limiting introgression, leaving a single unified species with deeply divergent phylogeographic lineages that nonetheless do not appear to represent incipient species.

     
    more » « less
  4. Abstract

    Significant advances have been made in species delimitation and numerous methods can test precisely defined models of speciation, though the synthesis of phylogeography and taxonomy is still sometimes incomplete. Emerging consensus treats distinct genealogical clusters in genome-scale data as strong initial evidence of speciation in most cases, a hypothesis that must therefore be falsified under an explicit evolutionary model. We can now test speciation hypotheses linking trait differentiation to specific mechanisms of divergence with increasingly large data sets. Integrative taxonomy can, therefore, reflect an understanding of how each axis of variation relates to underlying speciation processes, with nomenclature for distinct evolutionary lineages. We illustrate this approach here with Seal Salamanders (Desmognathus monticola) and introduce a new unsupervised machine-learning approach for species delimitation. Plethodontid salamanders are renowned for their morphological conservatism despite extensive phylogeographic divergence. We discover 2 geographic genetic clusters, for which demographic and spatial models of ecology and gene flow provide robust support for ecogeographic speciation despite limited phenotypic divergence. These data are integrated under evolutionary mechanisms (e.g., spatially localized gene flow with reduced migration) and reflected in emergent properties expected under models of reinforcement (e.g., ethological isolation and selection against hybrids). Their genetic divergence is prima facie evidence for species-level distinctiveness, supported by speciation models and divergence along axes such as behavior, geography, and climate that suggest an ecological basis with subsequent reinforcement through prezygotic isolation. As data sets grow more comprehensive, species-delimitation models can be tested, rejected, or corroborated as explicit speciation hypotheses, providing for reciprocal illumination of evolutionary processes and integrative taxonomies. [Desmognathus; integrative taxonomy; machine learning; species delimitation.]

     
    more » « less
  5. null (Ed.)
    Jacob Green was born in 1790 to a prominent New Jersey family of scholars and theologians. He taught at the College of New Jersey (now Princeton University) from 1818 to 1822 before co-founding Jefferson Medical College (now Thomas Jefferson University) in 1825, where he taught Chemistry until his death in 1841. Between 1818 and 1831, he published a series of nine papers on lizards, salamanders, and snakes, authoring the original description of several well-known species of salamanders from the eastern United States. Many of his names are ambiguous; some have been adjudicated by the ICZN, while others are currently treated as nomina dubia. Here, we review all of Green’s publications, report on newly re-discovered or re-interpreted material from several major natural history collections, and resolve most if not all remaining issues through a series of taxonomic actions. In particular, we first designate a neotype for Salamandra nigra Green, 1818. We then place S. sinciput-albida Green, 1818 and S. frontalis Gray in Cuvier, 1831 in synonymy with S. scutata Temminck in Temminck & Schlegel, 1838 and invoke Reversal of Precedence under Article 23.9 to designate them nomina oblita. We also designate a lectotype for S. bislineata Green, 1818. Finally, we resurrect the name S. fusca Green, 1818 as the valid name for the species Desmognathus fuscus, assuming priority over Triturus fuscus Rafinesque, 1820, designating S. fusca Laurenti, 1768 a nomen oblitum, and placing S. nigra Green, 1818 in synonymy. While Green’s herpetological legacy is not as expansive as that of some of his successors such as Holbrook, he is nonetheless a foundational early worker in salamanders, having described some of the most-studied species in the world. 
    more » « less
  6. Ruane, Sara (Ed.)
    Abstract Genome-scale data have the potential to clarify phylogenetic relationships across the tree of life but have also revealed extensive gene tree conflict. This seeming paradox, whereby larger data sets both increase statistical confidence and uncover significant discordance, suggests that understanding sources of conflict is important for accurate reconstruction of evolutionary history. We explore this paradox in squamate reptiles, the vertebrate clade comprising lizards, snakes, and amphisbaenians. We collected an average of 5103 loci for 91 species of squamates that span higher-level diversity within the clade, which we augmented with publicly available sequences for an additional 17 taxa. Using a locus-by-locus approach, we evaluated support for alternative topologies at 17 contentious nodes in the phylogeny. We identified shared properties of conflicting loci, finding that rate and compositional heterogeneity drives discordance between gene trees and species tree and that conflicting loci rarely overlap across contentious nodes. Finally, by comparing our tests of nodal conflict to previous phylogenomic studies, we confidently resolve 9 of the 17 problematic nodes. We suggest this locus-by-locus and node-by-node approach can build consensus on which topological resolutions remain uncertain in phylogenomic studies of other contentious groups. [Anchored hybrid enrichment (AHE); gene tree conflict; molecular evolution; phylogenomic concordance; target capture; ultraconserved elements (UCE).] 
    more » « less
  7. Abstract

    The Tree of Life will be irrevocably reshaped as anthropogenic extinctions continue to unfold. Theory suggests that lineage evolutionary dynamics, such as age since origination, historical extinction filters and speciation rates, have influenced ancient extinction patterns – but whether these factors also contribute to modern extinction risk is largely unknown. We examine evolutionary legacies in contemporary extinction risk for over 4000 genera, representing ~30,000 species, from the major tetrapod groups: amphibians, birds, turtles and crocodiles, squamate reptiles and mammals. We find consistent support for the hypothesis that extinction risk is elevated in lineages with higher recent speciation rates. We subsequently test, and find modest support for, a primary mechanism driving this pattern: that rapidly diversifying clades predominantly comprise range‐restricted, and extinction‐prone, species. These evolutionary patterns in current imperilment may have important consequences for how we manage the erosion of biological diversity across the Tree of Life.

     
    more » « less
  8. Reptiles are still being described worldwide at a pace of hundreds of species a year. While many discoveries are from remote tropical areas, biodiverse arid regions still harbor many novel taxa. Here, we present an updated phylogeny of colubrid snakes from the Western Palearctic by analyzing a supermatrix of all available global snake species with molecular data and report on the discovery of a new genus and species of colubrine snake from southeastern Iran. The new taxon, namedPersiophis fahimiiGen. et sp. nov., is nested within a clade containing Middle Eastern and South Asian ground racers (Lytorhynchus,Rhynchocalamus, Wallaceophis, andWallophis). This species has a derived morphology including an edentulous pterygoid and occurrence of short and blunt teeth on the palatine, maxillae and dentary bones, an elongated snout and a relatively trihedral first supralabial scale that is slightly bigger than the second, and elongated toward the tip of rostral. We also report on the osteology and phylogenetic placement of several poorly studied colubrines:Hierophis andreanus(reassigned toDolichophis) andMuhtarophis barani.

     
    more » « less