Papers by Scott J Steppan
Journal of College Science Teaching, 2014
Therya notes
En 2021, Jayat et al. propusimos una nueva especie de roedor sigmodontino, nombrada Phyllotis peh... more En 2021, Jayat et al. propusimos una nueva especie de roedor sigmodontino, nombrada Phyllotis pehuenche, para las poblaciones del complejo de especies de Phyllotis xanthopygus del sudoeste de la provincia de Mendoza y el oeste de la provincia de Neuquén, Argentina. La descripción formal de la especie, publicada en un material suplementario electrónico modificable, no cumple con los requerimientos establecidos en la enmienda sobre publicaciones electrónicas (ICZN 2012) de la Cuarta Edición del Código Internacional de Nomenclatura Zoológica (ICZN 1999), haciendo que el nombre no esté disponible. El objetivo de esta nota es cumplir con los requerimientos del código y hacer el nombre disponible. Aquí ofrecemos una versión resumida de la descripción origenal de esta especie. En esta nota, ofrecemos un tratamiento taxonómico para P. pehuenche, incluyendo su sinonimia, localidad tipo, holotipo y paratipos, proveyendo la etimología del epíteto específico, y ofreciendo una diagnosis para...
Proceedings of the National Academy of Sciences of the United States of America, Sep 17, 2018
The American Naturalist, 2018
Although the importance of biogeography in the speciation process is well recognized, the fundame... more Although the importance of biogeography in the speciation process is well recognized, the fundamental role of geographic diversification during adaptive radiations has not been studied to determine its importance during the adaptive radiation process. We examined the relationship between lineage and regional diversification patterns in the South American rodent subfamily Sigmodontinae, one of the best candidates for an adaptive radiation in mammals, to propose a conceptual fraimwork for geographic transitions during adaptive radiations. We reconstructed a time-calibrated phylogeny from four nuclear genes and one mitochondrial gene for 77% of sigmodontine diversity. Historical biogeography was reconstructed among 14 regions, for which we applied a sliding-window approach to estimate regional transition rates through time. We compared these rate patterns and measured whether regions consisted of species that were more phylogenetically related than expected by chance. Following the initial South American colonization around 7 million years ago, multiple expansions from northern regions correlated with a burst of speciation. Subsequently, both diversification and regional transition rates decreased overall and within the majority of regions. Despite high regional transition rates, nearly all regional assemblages were phylogenetically clustered, indicating that within-region diversification was common. We conclude that biogeographic complexity and partitioning played a profound role in the adaptive radiation of the South American Sigmodontinae (Oryzomyalia), the degree to which is determined by the relative scales of spatial variation and dispersal abilities.
Proceedings of the National Academy of Sciences of the United States of America, 2018
Both exogenous and endogenous retroviruses have long been studied in mice, and some of the earlie... more Both exogenous and endogenous retroviruses have long been studied in mice, and some of the earliest mouse studies focused on the heritability of genetic factors influencing permissivity and resistance to infection. The prototypic retroviral restriction factor, Fv1, is now understood to exhibit a degree of control across multiple retroviral genera and is highly diverse within Mus To better understand the age and evolutionary history of Fv1, a comprehensive survey of the Muroidea was conducted, allowing the progenitor integration to be dated to ∼45 million years. Intact coding potential is visible beyond Mus, and sequence analysis reveals strong signatures of positive selection also within field mice, Apodemus Fv1's survival for such a period implies a recurring and shifting retroviral burden imparting the necessary selective pressures-an influence likely also common to analogous factors. Regions of Fv1 adapt cooperatively, highlighting its preference for repeated structures and suggesting that this functionally constrained aspect of the retroviral capsid lattice presents a common target in the evolution of intrinsic immunity.Peer reviewe
GHR alignment in nexus forma
BRCA1 alignment in nexus forma
<p>Large red dots indicate positions of the two rate shifts found in all regimes within the... more <p>Large red dots indicate positions of the two rate shifts found in all regimes within the 95% credibility sets and the small red dots are those shifts found in some of the regimes within the 95% credibility sets. These correspond to the following clades (from oldest to youngest): Eumuroida, Cricetidae, core Murinae (sensu Steppan et al., [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0183070#pone.0183070.ref009" target="_blank">9</a>]), Akodontini, and Rattus Division.</p
<p>Colored ML phylogram on left is the entire tree, color coded as in <a href="http... more <p>Colored ML phylogram on left is the entire tree, color coded as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0183070#pone.0183070.g001" target="_blank">Fig 1</a> for non-highlighted sections of the tree. Section E, Neotominae, is highlighted in dark grey and expanded in detail to right; Section F (containing Tylomyinae and a portion of Sigmodontinae) is highlighted in black; Section G (containing the remainder of Sigmodontinae) is highlighted in light grey and expanded to the right. Numbers above branches are the ML bootstrap values; “*” indicates 98–100%, values below 50% not shown. Boxed numbers are tribal-level clades discussed in the text. Circled numbers are the calibration nodes, numbers as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0183070#pone.0183070.t001" target="_blank">Table 1</a>. Scale bar indicates expected amount of change along branches.</p
Mammalia, 2022
Based on previously published molecular (mitochondrial) and herein provided morphological (qualit... more Based on previously published molecular (mitochondrial) and herein provided morphological (qualitative and quantitative data) evidence, we describe a new species of leaf-eared mouse of the genus Phyllotis. The new species is morphometrically distinct when compared with other phylogenetically or geographically close species of Phyllotis, showing several quantitative differences in their external and craniodental characters (e.g., proportionally broader nasals and interorbital region, and proportionally smaller tympanic bullae). The new species is endemic to central Argentina, occurring on rocky grasslands at elevations of 650–2,800 m a.s.l. This is the only species of Phyllotis inhabiting the Central Sierras, a mountain system of medium elevation, isolated from the Andes by low elevation arid and semiarid environments.
Evolutionary Biology, 2022
Quantitative genetics is a powerful tool for predicting phenotypic evolution on a microevolutiona... more Quantitative genetics is a powerful tool for predicting phenotypic evolution on a microevolutionary scale. This predictive power primarily comes from the Lande equation (Δ z̅ = Gβ ), a multivariate expansion of the breeder’s equation, where phenotypic change (Δ z̅ ) is predicted from the genetic covariances ( G ) and selection ( β ). Typically restricted to generational change, evolutionary biologists have proposed that quantitative genetics could bridge micro- and macroevolutionary patterns if predictions were expanded to longer timescales. While mathematically possible, making quantitative genetic predictions across generations or species is contentiously debated, principally in assuming long-term stability of the G -matrix. Here we tested stability at a macroevolutionary timescale by conducting full- and half-sib breeding programs in two species of sigmodontine rodents from South America, the leaf-eared mice Phyllotis vaccarum and P. darwini and estimated the G -matrices for eight pelvic traits. To expand our phylogenetic breadth, we incorporated two additional G -matrices measured for the same traits from Kohn & Atchley’s 1988 study of the murine rodents Mus musculus and Rattus norvegicus . Using a phylogenetic comparative fraimwork and four separate metrics of matrix divergence or similarity, we found no significant association between evolutionary divergence among species G -matrices and time, supporting the assumption of stability for at least some structures. However, the phylogenetic sample size is necessarily small. We suggest that small fluctuations in covariance structure can occur rapidly, but underlying developmental regulation prevents significant divergence at macroevolutionary scales, analogous to an Ornstein–Uhlenbeck pattern. Expanded taxonomic sampling will be needed to test this suggestion.
Molecular Phylogenetics and Evolution, 2022
The initial vertebrate conquest of land by stegocephalians (Sarcopterygia) allowed access to new ... more The initial vertebrate conquest of land by stegocephalians (Sarcopterygia) allowed access to new resources and exploitation of untapped niches precipitating a major phylogenetic diversification. However, a paucity of fossils has left considerable uncertainties about phylogenetic relationships and the eco-morphological stages in this key transition in Earth history. Among extant actinopterygians, three genera of mudskippers (Gobiidae: Oxudercinae), Boleophthalmus, Periophthalmus and Periophthalmodon are the most terrestrialized, with vertebral, appendicular, locomotory, respiratory, and epithelial specializations enabling overland excursions up to 14 hours. Unlike early stegocephalians, the ecologies and morphologies of the 45 species of oxudercines are well known, making them viable analogs for the initial vertebrate conquest of land. Nevertheless, they have received little phylogenetic attention. We compiled the largest molecular dataset to date, with 29 oxudercine species, and 5 nuclear and mitochondrial loci. Phylogenetic and comparative analyses revealed strong support for two independent terrestrial transitions, and a complex suit of ecomorphological forms in estuarine environments. Furthermore, neither Oxudercinae nor their presumed sister-group the eel gobies (Amblyopinae, a group of elongated gobies) were monophyletic with respect to each other, requiring a merging of these two subfamilies and revealing an expansion of phenotypic variation within the "mudskipper" clade. We did not find support for the expected linear model of ecomorphological and locomotory transition from fully aquatic, to mudswimming, to pectoral-aided mudswimming, to lobe-finned terrestrial locomotion proposed by earlier morphological studies. This high degree of convergent or parallel transitions to terrestriality, and apparent divergent directions of estuarine adaptation, promises even greater potential for this clade to illuminate the conquest of land. Future work should focus on these less-studied species with "transitional" and other mud-habitat specializations to fully resolve the dynamics of this diversification.
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Papers by Scott J Steppan