Jesse M. Meik

Effects of bush encroachment on an assemblage of diurnal lizard species in central Namibia

Bush encroachment is a serious environmental and economic problem in Namibia, but little is known about impacts on native reptile diversity. Area-confined visual surveys were used to examine a diurnal lizard assemblage in central Namibian commercial ranchlands. Surveys were conducted in plots of open savanna habitat and proximal bush-encroached habitat. The following four species comprised 97.5% of all lizard observations: Pedioplanis undata, Mabuya varia, M. striata, and Lygodactylus bradfieldi. Pedioplanis undata was terrestrial, and the remaining three species were largely arboreal in our study plots. Mabuya varia was found in all savanna plots but was absent from all bush-encroached plots. Two species (P. undata and L. bradfieldi) were less abundant in bush-encroached plots. One species (M. striata) was more abundant in bush-encroached plots than in open savanna plots. Arboreal lizards demonstrated an avoidance to invasive woody plant species. Decreased diversity of habitat structure in bush-encroached habitats appears to influence native savanna lizard assemblages. Our results are consistent with accumulating evidence suggesting that bush encroachment and its associated ecological impacts are reorganizing savanna ecosystems throughout southern Africa. # 2002 Elsevier Science Ltd. All rights reserved.

Temporal variation in groundwater quality in the Permian Basin of Texas, a region of increasing unconventional oil and gas development.

The recent expansion of natural gas and oil extraction using unconventional oil and gas development (UD) practices such as horizontal drilling and hydraulic fracturing has raised questions about the potential for environmental impacts. Prior research has focused on evaluations of air and water quality in particular regions without explicitly considering temporal variation; thus, little is known about the potential effects of UD activity on the environment over longer periods of time. Here, we present an assessment of private well water quality in an area of increasing UD activity over a period of 13months. We analyzed samples from 42 private water wells located in three contiguous counties on the Eastern Shelf of the Permian Basin in Texas. This area has experienced a rise in UD activity in the last few years, and we analyzed samples in four separate time points to assess variation in groundwater quality over time as UD activities increased. We monitored general water quality parameters as well as several compounds used in UD activities. We found that some constituents remained stable over time, but others experienced significant variation over the period of study. Notable findings include significant changes in total organic carbon and pH along with ephemeral detections of ethanol, bromide, and dichloromethane after the initial sampling phase. These data provide insight into the potentially transient nature of compounds associated with groundwater contamination in areas experiencing UD activity.

Phylogenetic relationships of the enigmatic longtailed rattlesnakes (Crotalus ericsmithi, C. lannomi, and C. stejnegeri).

The longtailed rattlesnakes of western Mexico represent an enigmatic group of poorly known venomous snake species: Crotalus ericsmithi, C. lannomi, and C. stejnegeri. In the 120 years since their discovery, fewer than twenty individuals have been deposited in natural history collections worldwide. These three species share similar morphological traits, including a particularly long tail that has been interpreted as either an ancestral condition among rattlesnakes or as derived within the longtailed group. An understanding of the phylogenetic distinctiveness and relationships among the longtailed rattlesnakes, and their relationships to other rattlesnake groups, has previously been hampered by a dearth of comparative material and tissues for collection of DNA sequence data. Facilitated by the recent availability of tissue samples from multiple individuals of each species, we estimate the phylogenetic relationships among the longtailed rattlesnakes and their placement among other rattlesnake groups, using DNA sequence data from three mitochondrial and three nuclear gene fragments. We explore phylogenetic signal in our data using Bayesian and maximum likelihood methods, species tree analyses and hypothesis testing. Our results strongly support the monophyly of longtailed rattlesnakes and suggest the three species diverged from each other during the mid to late Pliocene or early Pleistocene (~1.5-5.6 mya). Contrary to prevailing hypotheses, we find no evidence for an early or basal divergence of the longtailed clade within the rattlesnake tree, and instead estimate that it diverged relatively recently (~6.8 mya) from its sister lineage, composed of the diamondback rattlesnakes (C. atrox group) and the prairie rattlesnakes (C. viridis group). With our added sampling of lineages and identification of previously used problematic sequences, we provide a revised hypothesis for relationships among Crotalus species, yet underscore the need for future studies and new data to deliver a well-supported robust estimate of rattlesnake relationships.

Thousands of microsatellite loci from the venomous coralsnake Micrurus fulvius and variability of select loci across populations and related species

Studies of population genetics increasingly use next‐generation DNA sequencing to identify microsatellite loci in nonmodel organisms. There are, however, relatively few studies that validate the feasibility of transitioning from marker development to experimental application across populations and species. North American coralsnakes of the Micrurus fulvius species complex occur in the United States and Mexico, and little is known about their population structure and phylogenetic relationships. This absence of information and population genetics markers is particularly concerning because they are highly venomous and have important implications on human health. To alleviate this problem in coralsnakes, we investigated the feasibility of using 454 shotgun sequences for microsatellite marker development. First, a genomic shotgun library from a single individual was sequenced (approximately 7.74 megabases; 26 831 reads) to identify potentially amplifiable microsatellite loci (PALs). We then hierarchically sampled 76 individuals from throughout the geographic distribution of the species complex and examined whether PALs were amplifiable and polymorphic. Approximately half of the loci tested were readily amplifiable from all individuals, and 80% of the loci tested for variation were variable and thus informative as population genetic markers. To evaluate the repetitive landscape characteristics across multiple snakes, we also compared microsatellite content between the coralsnake and two other previously sampled snakes, the venomous copperhead (Agkistrodon contortrix) and Burmese python (Python molurus).

Body Size Evolution in Insular Speckled Rattlesnakes (Viperidae: Crotalus mitchellii)

Background Speckled rattlesnakes (Crotalus mitchellii) inhabit multiple islands off the coast of Baja California, Mexico. Two of the 14 known insular populations have been recognized as subspecies based primarily on body size divergence from putative mainland ancestral populations; however, a survey of body size variation from other islands occupied by these snakes has not been previously reported. We examined body size variation between island and mainland speckled rattlesnakes, and the relationship between body size and various island physical variables among 12 island populations. We also examined relative head size among giant, dwarfed, and mainland speckled rattlesnakes to determine whether allometric differences conformed to predictions of gape size (and indirectly body size) evolving in response to shifts in prey size. Methodology/Principal Findings Insular speckled rattlesnakes show considerable variation in body size when compared to mainland source subspecies. In addition to previously known instances of gigantism on Ángel de la Guarda and dwarfism on El Muerto, various degrees of body size decrease have occurred frequently in this taxon, with dwarfed rattlesnakes occurring mostly on small, recently isolated, land-bridge islands. Regression models using the Akaike information criterion (AIC) showed that mean SVL of insular populations was most strongly correlated with island area, suggesting the influence of selection for different body size optima for islands of different size. Allometric differences in head size of giant and dwarf rattlesnakes revealed patterns consistent with shifts to larger and smaller prey, respectively. Conclusions/Significance Our data provide the first example of a clear relationship between body size and island area in a squamate reptile species; among vertebrates this pattern has been previously documented in few insular mammals. This finding suggests that selection for body size is influenced by changes in community dynamics that are related to graded differences in area over what are otherwise similar bioclimatic conditions. We hypothesize that in this system shifts to larger prey, episodic saturation and depression of primary prey density, and predator release may have led to insular gigantism, and that shifts to smaller prey and increased reproductive efficiency in the presence of intense intraspecific competition may have led to insular dwarfism.

The Phenotypic Effects of Spontaneous Mutations in Different Environments

Understanding the context dependence of mutation represents the current frontier of mutation research. In particular, understanding how traits vary in their abilities to accrue mutational variation and how the environment influences expression of mutant phenotypes yields insight into evolutionary processes. We conducted phenotypic assays in four environments using a set of Daphnia pulex mutation accumulation lines to examine the context dependence of mutation. Life-history traits accrued mutational variance faster than morphological traits when considered in individual environments. Across environments, the mutational variance in plasticity was also greater for life-history traits than for morphological traits, although this pattern was less robust. In addition, the expression of mutational variance depended on the environment, which resulted in changes in the rank order of genotype performance across environments in some cases. Such cryptic genetic variation resulting from mutation may maintain genetic diversity and allow for rapid adaptation in spatially or temporally variable environments.

Coding meristic characters for phylogenetic analysis: a comparison of step-matrix gap-weighting and generalized frequency coding.

Meristic characters, or counts of discrete serially ho-mologous structures, are a distinctive and ubiquitousclass of quantitative organismal variation. Meristic char-acters share many properties with morphometric char-acters (i.e., measurements, proportions, etc.): they arereadily described numerically, they usually vary withinand among taxa, and they often appear to follow similarunderlying frequency distributions (e.g., Burbrink, 2001;Allsteadt et al., 2006). Based on these similarities, meris-tic characters are generally lumped with morphometriccharactersintothebroadercategoryof“quantitativecon-tinuouscharacters”forphylogenyreconstruction.Meris-tic characters also exhibit properties that differ subtly,butperhapsimportantly,frommorphometriccharacters.It has been increasingly recognized that morphologicalsystematists often code intrinsically quantitative char-acters as qualitative by artificially compartmentalizingvariation into relatively few ordered states (e.g., inter-clavicle,medianprocess:0=normallength;1=reduced;Etheridge and de Queiroz, 1988). This practice alwaysproduces arbitrary character states with morphometricdata. In contrast, meristic characters may be viewed asdiscrete traits that, depending on the range of variation,showacontinuumfrombinarytransformations,throughmultistate polymorphic characters, to quasicontinu-ous variation analogous to morphometric data (Wiens,2001).Arguments both for and against the inclusion ofquantitative continuous characters are prevalent in thesystematics literature and are beyond the scope of thisarticle (see Rae, 1998; Swiderski et al., 1998; Thiele,1993). Regardless, various authors have shown thatsuch characters do provide substantial phylogenetic in-formation despite the potential for increased levels ofhomoplasy, and thus remain relevant to empirical sys-tematics (e.g., Campbell and Frost, 1993; Wiens, 1995;WiensandServedio,1998).Severalcodingmethodshavebeen developed for incorporating meristic characters inphylogenetic analysis and dealing with the problem ofpartially overlapping character states across taxa. For bi-nary characters, frequency bins have most often beenused; whereas polymorphic multistate characters havebeen analyzed using majority methods, segment cod-ing, gap coding, gap weighting, step matrices, and var-ious statistical similarity analyses (e.g., Colless, 1980;Mabee and Humphries, 1993; Mickevich and Johnson,1976; Swiderski et al., 1998; Thiele, 1993; Wiens, 1993).Wiens (1998, 2000) and Wiens and Servedio (1997, 1998)evaluated several classes of coding methods and con-cluded that frequency methods were generally most ef-fective. In recent years, two methods that augment andimprove on previous approaches have become widelyused for coding meristic (and other quantitatively de-fined) characters for phylogenetic analysis: step-matrixgap-weighting (SMGW; Wiens, 2001) and general-ized frequency coding (GFC; Smith and Gutberlet,2001).SMGW is an application of step matrices (Wiens,1995) to the gap-weighting method introduced by Thiele(1993). In gap weighting, taxa are assigned states basedon range-standardized mean values of a trait, with thenumber of possible states scaled to the maximum num-ber allowed by the software used to infer phylogenies(e.g.,32statesforPAUP*;Swofford,1993).Gapsbetweenmeans are weighted based on the magnitude of theirdifferences so that larger differences in trait means be-tween taxa translate into larger weights. A limitation ofthe step-matrix approach is that the number of distinctstates is potentially restricted by the software used tobuild phylogenies (e.g., PAUP* only allows 32 states, sodata sets with over 32 taxa would likely not be amenableto SMGW). The purported advantage of SMGW is thatstep matrices allow more fine-grained weighting thansimple gap weighting by increasing the trait range from32 states to 1000 states (the maximum cost betweenstatesinastepmatrixusingPAUP*).Thus,charactersaretreated as approximations of a continuous scale (Wiens,2001).GFC can be viewed as a method that combines ele-ments of both gap weighting (as implemented by Thiele,1993) and the frequency bins method of Wiens (1993).In GFC, each quantitative character is divided into sub-charactersthatcorrespondwitheachcharacterstate.Thefrequency of specimens falling into a given subcharac-ter is described with frequency bins; the overall effectis that cumulative frequency distributions of characterstates per taxa are constructed for each character. A po-tential advantage of GFC is that frequency distributionsare simply translated into phlyogenetically analyzabledata, maximizing information content while eliminat-ing the need for further data manipulation (Smith andGutberlet, 2001). The primary operational difference be-tween these methods is that character states within taxaare coded using estimates of cumulative frequencies of

Point source attribution of ambient contamination events near unconventional oil and gas development

We present an analysis of ambient benzene, toluene, and xylene isomers in the Eagle Ford shale region of southern Texas. In situ air quality measurements using membrane inlet mobile mass spectrometry revealed ambient benzene and toluene concentrations as high as 1000 and 5000 parts-per-billion, respectively, originating from specific sub-processes on unconventional oil and gas well pad sites. The detection of highly variant contamination events attributable to natural gas flaring units, condensate tanks, compressor units, and hydrogen sulfide scavengers indicates that mechanical inefficiencies, and not necessarily the inherent nature of the extraction process as a whole, result in the release of these compounds into the environment. This awareness of ongoing contamination events contributes to an enhanced knowledge of ambient volatile organic compounds on a regional scale. While these reconnaissance measurements on their own do not fully characterize the fluctuations of ambient BTEX concentrations that likely exist in the atmosphere of the Eagle Ford Shale region, they do suggest that contamination events from unconventional oil and gas development can be monitored, controlled, and reduced.

Evolutionary morphology of the rattlesnake style

BackgroundThe rattlesnake rattling system is an evolutionary novelty that includes anatomical, behavioral, and physiological modifications of the generalized pitviper tail. One such modification, the formation of a bony clublike style at the terminal region of the caudal vertebrae, has not previously been examined in a phylogenetic context. Here we used skeletal material, cleared and stained preparations, and radiographs of whole preserved specimens to examine interspecific variation in style morphology among 34 rattlesnake species.ResultsEvolutionary Principal Components Analysis revealed an inverse relationship between caudal segmental counts and style size, supporting the hypothesis that bone from caudal vertebral elements was reallocated to style formation during the evolution of this structure. Most of the basal rattlesnake species have small styles consisting of few compacted vertebral elements; however, early in the rattlesnake radiation there appears to have been two independent transitions to relatively large, pronged styles consisting of multiple coalesced vertebrae (once in Sistrurus catenatus, and once in Crotalus following the divergence of the Mexican long-tailed rattlesnakes). In terms of style shape, the two most divergent species, C. catalinensis and C. ericsmithi, provide insight into the possible relationship between style and rattle matrix morphology and lineage-specific evolutionary strategies for retaining rattle segments.ConclusionThe considerable interspecific variation in rattle morphology appears to correspond to variation in the bony style. We hypothesize that style morphology evolves indirectly as an integrated module responding to adaptive evolution on matrix morphology.

NEW DISTRIBUTION RECORDS FOR THE QUERÉTERO DUSKY RATTLESNAKE CROTALUS AQUILUS (VIPERIDAE), WITH COMMENTS ON MORPHOLOGY AND HABITAT USE

Abstract We provide the 1st documented accounts of the Mexican endemic rattlesnake Crotalus aquilus from the state of México. The new records extend the known distribution of the species into a region where it may be sympatric with the superficially similar C. triseriatus. Because these taxa have previously been subject to some taxonomic confusion, we performed a preliminary morphological comparison using individuals of both species obtained from proximal localities. Our analyses support the supposition that these taxa are morphologically distinct. The new localities for C. aquilus are situated in high valleys that have been extensively modified by human settlement and agriculture.