Publications by Andrew Gottscho
Molecular Phylogenetics and Evolution, 2017
Multi-locus nuclear DNA data were used to delimit species of fringe-toed lizards of the Uma notat... more Multi-locus nuclear DNA data were used to delimit species of fringe-toed lizards of the Uma notata complex, which are specialized for living in wind-blown sand habitats in the deserts of southwestern North America, and to infer whether Quaternary glacial cycles or Tertiary geological events were important in shaping the historical biogeography of this group. We analyzed ten nuclear loci collected using Sanger sequencing and genome-wide sequence/single-nucleotide polymorphism (SNP) data collected using restriction-associated DNA (RAD) sequencing. A combination of species discovery methods (concatenated phylogenies, parametric and non-parametric clustering algorithms) and species validation approaches (coalescent-based species tree/isolation-with-migration models) were used to delimit species, infer phylogenetic relationships, and to estimate effective population sizes, migration rates, and speciation times. Uma notata, U. inornata, U. cowlesi, and an undescribed species from Mohawk Dunes, Arizona (U. sp.) were supported as distinct in the concatenated analyses and by clustering algorithms, and all operational taxonomic units were decisively supported as distinct species by ranking hierarchical nested speciation models with Bayes factors based on coalescent-based species tree methods. However, significant unidirectional gene flow (2NM > 1) from U. cowlesi and U. notata into U. rufopunctata was detected under the isolation-with-migration model. Therefore, we conservatively delimit four species-level lineages within this complex (U. inornata, U. notata, U. cowlesi, and U. sp.), treating U. rufopunctata as a hybrid population (U. notata  cowlesi). Both concatenated and coalescent-based estimates of speciation times support the hypotheses that speciation within the complex occurred during the late Pleistocene, and that the geological evolution of the Colorado River delta during this period was an important process shaping the observed phylogeographic patterns.
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Abstract: Genetic diversity within species provides the raw material for adaptation and evolution... more Abstract: Genetic diversity within species provides the raw material for adaptation and evolution. Just as regions of high species diversity are conservation targets, identifying regions containing high genetic diversity and divergence within and among populations may be important to protect future evolutionary potential. When multiple co-distributed species show spatial overlap in high genetic diversity and divergence, these regions can be considered evolutionary hotspots. We mapped spatial population genetic structure for 17 animal species across the Mojave Desert, USA. We analyzed these in concurrence and located 10 regions of high genetic diversity, divergence or both among species. These were mainly concentrated along the western and southern boundaries where ecotones between mountain, grassland and desert habitat are prevalent, and along the Colorado River. We evaluated the extent to which these hotspots overlapped protected lands and utility-scale renewable energy development projects of the Bureau of Land Management. While 30–40% of the total hotspot area was categorized as protected, between 3–7% overlapped with proposed renewable energy project footprints, and up to 17% overlapped with project footprints combined with transmission corridors. Overlap of evolutionary hotspots with renewable energy development mainly occurred in 6 of the 10 identified hotspots. Resulting GIS-based maps can be incorporated into ongoing landscape planning efforts and highlight specific regions where further investigation of impacts to population persistence and genetic connectivity may be warranted.
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Sequence capture and restriction site associated DNA sequencing (RADseq) are popularmethods for o... more Sequence capture and restriction site associated DNA sequencing (RADseq) are popularmethods for obtaining large numbers of loci for phylogenetic analysis. These methods are typically used to collect data at different evolutionary timescales; sequence capture is primarily used for obtaining conserved loci, whereas RADseq is designed for discovering single nucleotide polymorphisms (SNPs) suitable for population genetic or phylogeographic analyses. Phylogenetic questions that span both “recent” and “deep” timescales could benefit from either type of data, but studies that directly compare the two approaches are lacking.Wecompared phylogenies estimated from sequence capture and double digest RADseq (ddRADseq) data for North American phrynosomatid lizards, a speciesrich and diverse group containing nine genera that began diversifying approximately 55Ma. Sequence capture resulted in 584 loci that provided a consistent and strong phylogeny using concatenation and species tree inference. However, the phylogeny estimated from the ddRADseq data was sensitive to the bioinformatics steps used for determining homology, detecting paralogs, and filtering missing data. The topological conflicts among the SNP trees were not restricted to any particular timescale, but instead were associated with short internal branches. Species tree analysis of the largest SNP assembly, which also included the most missing data, supported a topology that matched the sequence capture tree. This preferred phylogeny provides strong support for the paraphyly of the earless lizard genera Holbrookia and Cophosaurus, suggesting that the earless morphology either evolved twice or evolved once and was subsequently lost in Callisaurus.
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The purpose of this article is to provide an ultimate tectonic explanation for several well-studi... more The purpose of this article is to provide an ultimate tectonic explanation for several well-studied zoogeographic boundaries along the west coast of North America, specifically, along the boundary of the North American and Pacific plates (the San Andreas Fault system). By reviewing 177 references from the plate tectonics and zoogeography literature, I demonstrate that four Great Pacific Fracture Zones (GPFZs) in the Pacific plate correspond with distributional limits and spatially concordant phylogeographic breaks for a wide variety of marine and terrestrial animals, including invertebrates, fish, amphibians, reptiles, birds, and mammals. These boundaries are: (1) Cape Mendocino and the North Coast Divide, (2) Point Conception and the Transverse Ranges, (3) Punta Eugenia and the Vizcaíno Desert, and (4) Cabo Corrientes and the Sierra Transvolcanica. However, discussion of the GPFZs ismostly absent from the zoogeography and phylogeography literature likely due to a disconnect between biologists and geologists. I argue that the four zoogeographic boundaries reviewed here ultimately originated via the same geological process (triple junction evolution). Finally, I suggest how a comparative phylogeographic approach can be used to test the hypothesis presented here.
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The North American deserts were impacted by both Neogene plate tectonics and Quaternary climatic ... more The North American deserts were impacted by both Neogene plate tectonics and Quaternary climatic fluctuations, yet it remains unclear how these events influenced speciation in this region. We tested published hypotheses regarding the timing and mode of speciation, population structure, and demographic history of the Mojave Fringe-toed Lizard ( Uma scoparia ), a sand dune specialist endemic to the Mojave Desert of California and Arizona. We sampled 109 individual lizards representing 22 insular dune localities, obtained DNA sequences for 14 nuclear loci, and found that U. scoparia has low genetic diversity relative to the U. notata species complex, comparable to that of chimpanzees and southern elephant seals. Analyses of genotypes using Bayesian clustering algorithms did not identify discrete populations within U. scoparia. Using isolation- with-migration (IM) models and a novel coalescent-based hypothesis testing approach, we estimated that U. scoparia diverged from U. notata in the Pleistocene epoch. The likelihood ratio test and the Akaike Information Criterion consistently rejected nested speciation models that included parameters for migration and population growth of U. scoparia. We reject the Neogene vicariance hypothesis for the speciation of U. scoparia and define this species as a single evolutionarily significant unit for conservation purposes.
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Papers by Andrew Gottscho
<i> Uma thurmanae</i> sp. nov. Mohawk Dunes Fringe-toed Lizards Figs 5–8<b> Hol... more <i> Uma thurmanae</i> sp. nov. Mohawk Dunes Fringe-toed Lizards Figs 5–8<b> Holotype.</b> Adult female ( USNM 590033; Figs 5–6) collected on 29 March 2015 by A. D. Gottscho at 17:28 hours. Type locality: the north end of the Mohawk Dunes (~ 2.2 km south of Interstate 8), Yuma County, Arizona, United States of America ( 32°41.698 N; 113° 48.935 W; WGS-84 datum). Deposited at the National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.<b> Paratypes</b>. USNM 590034 adult female, USNM 590035 adult male, USNM 590036 adult male, USNM 590037 juvenile female, USNM 590038 adult female, USNM 590039 juvenile female, USNM 590040 adult male, USNM 590041 adult male, USNM 590042 juvenile female, USNM 590043 adult male. Collected 25 and 26 March 2016 by A.D. Gottscho, J. Rabbers, and S. Harrington from Mohawk Dunes, Yuma County, AZ, USA. Deposited at the National Museum of Natural History, Washington, DC, USA.<b> Diagnosis.</b><i> Uma thurmanae</i> is a morphologically cryptic species that doesn't exhibit any known fixed morphological differences from other species in the complex, but it can be distinguished from those other species both by statistical differences in morphological characters ( Table 5, Fig. 3) and in multivariate morphospace ( Fig. 4). It can also be distinguished from all other members of the<i> U. notata</i> complex by nucleotide substitutions in three mtDNA loci ( Table 8).<b> Description of holotype</b>. Adult female; SVL= 68 mm; tail length= 77 mm; head width= 12 mm; head length= 15 mm; head height= 8 mm. Scalation: dorsal head scales smooth, slightly raised; parietal eye present, centrally located in a circular interparietal scale; enlarged post-parietal scales present with three scales separating post-parietal scales from inter-parietal scale; five enlarged anterior auricular scales; four superciliaries; 12 lower festoons; three suboculars, with the third being substantially larger and more elongated than the first two; five enlarged anterior auricular scales; two canthals; four [...]
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FIGURE 8. (A) An individual of U. thurmanae in its natural habitat. (B) Sand dune habitat of U. t... more FIGURE 8. (A) An individual of U. thurmanae in its natural habitat. (B) Sand dune habitat of U. thurmanae (camera pointed east with the Mohawk Dunes in the midground and the Mohawk Mountains in the background). Photographs by A. Gottscho.
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FIGURE 5. (A) Dorsal and (B) ventral view of the adult female holotype (USNM 590033) of Uma thurm... more FIGURE 5. (A) Dorsal and (B) ventral view of the adult female holotype (USNM 590033) of Uma thurmanae. Photographs by E. Langan and J. Poindexter.
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FIGURE 7. Satellite map of collecting localities for the type series of Uma thurmanae. Locations ... more FIGURE 7. Satellite map of collecting localities for the type series of Uma thurmanae. Locations where specimens were collected, denoted by red stars, lie along the Mohawk Dunes, a long strip running northwest to southeast. The lizards are isolated in this dune system by the parallel Mohawk Mountains to the east, the Gila River and Interstate-8 to the north, and alluvial fans to the west and south, ultimately resulting in speciation. Source: "Mohawk Dunes," 32° 34' N, 113° 38' W, Google Earth. Imagery date: May 29, 2016. Accessed: July 3, 2018.
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FIGURE 4. Locations of Uma specimens in the morphospace defined by the first two axes of a Discri... more FIGURE 4. Locations of Uma specimens in the morphospace defined by the first two axes of a Discriminant Function Analysis of morphological characters. Top: when specimens with broken tails are included and TL excluded (n=57), U. inornata can still be distinguished from other OTUs, but U. notata overlaps considerably with U. rufopunctata and U. cowlesi overlaps considerably with U. sp. Bottom: analysis of only the specimens with intact tails such that tail length (TL) could be measured (n=32) allows each OTU to be distinguished.
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FIGURE 6. Holotype (USNM 590033) of Uma thurmanae showing (A) dorsal and (B) ventral head; (C) do... more FIGURE 6. Holotype (USNM 590033) of Uma thurmanae showing (A) dorsal and (B) ventral head; (C) dorsal right hindfoot and (D) dorsal right forefoot showing toe fringes. Photographs by E. Langan and J. Poindexter.
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FIGURE 3. Box-and-whisker plots for discrete morphological characters that exhibited significant ... more FIGURE 3. Box-and-whisker plots for discrete morphological characters that exhibited significant pairwise differences between OTUs. See Appendix 2 for details of how the characters were measured. SPLB=Supralabial Scales; SPCIL=Supraciliary Scales; INS=Internasal Scales; FP=Femoral Pores.
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FIGURE 2. Maximum likelihood phylogeny of the concatenated mitochondrial DNA sequences estimated ... more FIGURE 2. Maximum likelihood phylogeny of the concatenated mitochondrial DNA sequences estimated with RAxML. Bootstrap support values greater than 50% are shown adjacent to relevant nodes.
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FIGURE 1. Approximate geographic distributions of members of the U. notata species complex and it... more FIGURE 1. Approximate geographic distributions of members of the U. notata species complex and its sister species, U. scoparia (adapted from Gottscho et al. 2017). Actual geographic distributions are more fragmented than shown by the shaded areas as the lizards are restricted to windblown sand habitats within those areas.
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Genome Biology and Evolution, 2015
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Publications by Andrew Gottscho
Papers by Andrew Gottscho