Nucleotide diversity patterns of local adaptation at drought‐related candidate genes in wild tomatoes

We surveyed nucleotide diversity at two candidate genes LeNCED1 and pLC30‐15, involved in an ABA (abscisic acid) signalling pathway, in two closely related tomato species Solanum peruvianum and Solanum chilense. Our six population samples (three for each species) cover a range of mesic to very dry habitats. The ABA pathway plays an important role in the plants’ response to drought stress. LeNCED1 is an upstream gene involved in ABA biosynthesis, and pLC30‐15 is a dehydrin gene positioned downstream in the pathway. The two genes show very different patterns of nucleotide variation. LeNCED1 exhibits very low nucleotide diversity relative to the eight neutral reference loci that were previously surveyed in these populations. This suggests that strong purifying selection has been acting on this gene. In contrast, pLC30‐15 exhibits higher levels of nucleotide diversity and, in particular in S. chilense, higher genetic differentiation between populations than the reference loci, which is indicative of local adaptation. In the more drought‐tolerant species S. chilense, one population (from Quicacha) shows a significant haplotype structure, which appears to be the result of positive (diversifying) selection.     

Loss of Nesting Behavior and the Evolution of Viviparity in Reptiles

Presence or absence of nesting behavior during spontaneous or hormone-induced oviposition was determined in captive, oviparous lizards (Anolis carolinensis and Sceloporus undulatus). The occurrence of nesting behavior [digging of a nest cavity, covering the egg(s) with substrate] was determined directly by observation of ovipositing females as well as indirectly by whether eggs were covered (buried). Under uncrowded conditions in large terraria, most females of both species nested. However, under crowded conditions (S. undulatus), or in small cages (A. carolinensis), females oviposited without displaying species-typical nesting behavior. Facultative suppression of nesting behavior during oviposition can occur in nature as well, and this inhibition of behavior may be adaptive. We hypothesize that the absence of nesting behavior in viviparous lizards may be controlled by physiological mechanisms similar to those that control facultative suppression in closely related oviparous species.     

Phylogenetic relationships in the Sceloporus variabilis (Squamata: Phrynosomatidae) complex based on three molecular markers,continuous characters and geometric morphometric data

The monophyly of the Sceloporus variabilis group is well established with five species and two species complexes, but phylogenetic relationships within species complexes are still uncertain. We studied 278 specimens in 20 terminals to sample all taxa in the “variabilis group,” including three subspecies in the “variabilis complex,” and two outgroups (Sceloporus grammicus and Sceloporus megalepidurus). We assembled an extensive morphological data set with discrete and continuous characters (distances and scale counts), including geometric morphometric data (landmark coordinates of three shapes), and a three‐marker molecular data set as well (ND4, 12S and RAG1). We conducted parsimony and Bayesian phylogenetic inferences on these data, including several partitioning and weighting schemes. We suggest elevating three subspecies to full species status. Therefore, we recommend recognition of nine species in the “variabilis group.” First, S. variabilis is sister to Sceloporus teapensis. In turn, Sceloporus cozumelae is sister to Sceloporus olloporus. These four species are a monophyletic group, which is sister to Sceloporus smithi. Finally, Sceloporus marmoratus is sister of the clade of five species. The other species in the “variabilis group” (Sceloporus chrysostictus, Sceloporus couchii and Sceloporus parvus) are a paraphyletic grade at the base of the tree. Our analyses reject the existence of the “variabilis complex.” We conducted a parsimony‐based ancestral reconstruction on body size (snout–vent length), femoral pores and dorsal scales and related morphological changes to geographic distribution of the species. Our phylogenetic hypothesis will allow best designs of comparative studies with species in the “variabilis group,” one of the earliest divergent lineages in the genus.     

Incubation temperature and phenotypic traits of Sceloporus undulatus: implications for the northern limits of distribution

Cold environmental temperature is detrimental to reproduction by oviparous squamate reptiles by prolonging incubation period, negatively affecting embryonic developmental processes, and by killing embryos in eggs directly. Because low soil temperature may prevent successful development of embryos in eggs in nests, the geographic distributions of oviparous species may be influenced by the thermal requirements of embryos. In the present study, we tested the hypothesis that low incubation temperature determines the northern distributional limit of the oviparous lizard Sceloporus undulatus. To compare the effects of incubation temperature on incubation length, egg and hatchling survival, and hatchling phenotypic traits, we incubated eggs of S. undulatus under temperature treatments that simulated the thermal environment that eggs would experience if located in nests within their geographic range at 37°N and north of the species’ present geographic range at latitudes of 44 and 42°N. After hatching, snout–vent length (SVL), mass, tail length, body condition (SVL relative to mass), locomotor performance, and growth rate were measured for each hatchling. Hatchlings were released at a field site to evaluate growth and survival under natural conditions. Incubation at temperatures simulating those of nests at 44°N prolonged incubation and resulted in hatchlings with shorter SVL relative to mass, shorter tails, shorter hind limb span, slower growth, and lower survival than hatchlings from eggs incubated at temperatures simulating those of nests at 37 and 42°N. We also evaluated the association between environmental temperature and the northern distribution of S. undulatus. We predicted that the northernmost distributional limit of S. undulatus would be associated with locations that provide the minimum heat sum (∼495 degree-days) required to complete embryonic development. Based on air and soil temperatures, the predicted northern latitudinal limit of S. undulatus would lie at ∼40.5–41.5°N. Our predicted value closely corresponds to the observed latitudinal limit in the eastern United States of ∼40°N. Our results suggest that soil temperatures at northern latitudes are not warm enough for a sufficient length of time to permit successful incubation of S. undulatus embryos. These results are consistent with the hypothesis that incubation temperature is an important factor limiting the geographic distributions of oviparous reptile species at high latitudes and elevations.     

Long forsaken species diversity in the Middle American lizard Holcosus undulatus (Teiidae)

Numerous reptile species have been divided into subspecies. Although this classification may capture the morphological variation within species, it often conceals significant species diversity because many subspecies actually represent species under lineage‐based species concepts. The lizard Holcosus undulatus is a common, widely distributed, monotypic species in Middle America. However, 12 subspecies of this taxon were recognized until the early 1970s. We used two lineage‐based methods for species delimitation to re‐evaluate species limits within H. undulatus with DNA sequence and morphological data. We included all the previously recognized subspecies of H. undulatus except H. u. miadis. Holcosus undulatus was exclusive. In addition, H. u. amphigrammus, H. u. gaigeae, H. u. hartwegi, H. u. parvus, H. u. pulcher, H. u. sinister, H. u. stuarti, H. u. thomasi and H. u. undulatus were supported as distinct evolutionary lineages based on the molecular and morphological evidence. We therefore elevate all of these subspecies to species rank. In addition, two separate mitochondrial lineages may represent cryptic, undescribed species within H. undulatus. The morphological distinctness and allopatry of H. u. miadis and H. u. pulcher, as well as the high genetic divergence of the latter species, suggest that they also represent distinct evolutionary species. Our results also suggest that additional species diversity may still be hidden within the H. u. amphigrammus, H. u. parvus, H. u. sinister and H. u. undulatus lineages. This work supports resurrection of overlooked diversity within Holcosus, which has important implications for the conservation of this genus in Middle America. © 2015 The Linnean Society of London     

Is physiological performance optimized by thermoregulatory behavior?: a case study of the eastern fence lizard,Sceloporus undulatus

Eastern fence lizards (Sceloporus undulatus) exhibit a distinct thermal preference that might be related to the thermal optimum for physiological performance. Sprint speed and treadmill endurance of S. undulatus were insensitive to body temperature in the ranges of 28–38°C and 25–36°C, respectively. Both locomotor and digestive performances are optimized at the preferred body temperature of S. undulatus, but thermoregulatory behavior is more closely related to the thermal sensitivity of digestive performance than that of locomotor performance.     

Characterization of microsatellite markers for the endemic sand dune lizard,Sceloporus arenicolus

Here we characterize and report on the genetic variability of eight microsatellite loci for the endemic sand dune lizard, Sceloporus arenicolus, that amplified consistently for individuals throughout the species’ range. The number of alleles per locus was high (mean = 13.25) and observed heterozygosities ranged from 0.354 to 0.808. With the exception of a single locus, the loci did not deviate from Hardy–Weinberg expectations. This set of markers is currently being used to examine population structure and landscape genetics in S. arenicolus, a habitat specialist with a restricted range and patchy distribution.     

Age-dependent allozymic variation in a natural population of lizards

An analysis of allozymic variation at 17 loci in a population of the sagebrush lizard (Sceloporus graciosus) in southern Utah yielded an estimate of genic heterozygosity of 0.028. Seven of the loci were variable, but only one, Est-1, was strongly polymorphic. The observation that the frequency of the common genotype (MM) at the Est-1 locus declined monotonically in successive age classes from 0.74 in hatchlings to 0.58 in adults 4 years old or older suggests that allele frequencies at this locus are not independent of selective influences.This research was supported by NSF grant GB-29141 to D.W.T. and NIH grant GM-15769 to R.K.S.     

Morphological convergence and molecular divergence: the taxonomic status of Sceloporus serrifer (squamata,phrynosomatidae) subspecies

Martínez‐Méndez, N., Mejía, O., Rocha‐Gómez, A. & Méndez‐De La Cruz, F. R. (2012) Morphological convergence and molecular divergence: the taxonomic status of Sceloporus serrifer (squamata, phrynosomatidae) subspecies. —Zoologica Scripta, 41, 97–108. The systematics of the subspecies included in Sceloporus serrifer has undergone several taxonomic and nomenclatural rearrangements. This species previously comprised two recognized subspecies, Sceloporus serrifer serrifer and Sceloporus serrifer prezygus, which inhabit contrasting habitats. In this study, we re‐evaluate the taxonomic status of both subspecies using molecular and morphological evidence. Sceloporus serrifer serrifer was recovered as a paraphyletic group, whereas S. s. prezygus was recovered as a polyphyletic group. The molecular results indicate the existence of two independent lineages that diverged at least 1.29 Myr, with the populations currently recognized as S. s. prezygus from the Cuchumatanes Mountains representing a secondary invasion of S. s. serrifer from the lowlands. The lack of meristic differences among the highland populations of different species suggests convergence in similar environments achieved by two different lineages.     

Multilocus analysis of nucleotide variation and speciation in three closely related Populus (Salicaceae) species

Historical tectonism and climate oscillations can isolate and contract the geographical distributions of many plant species, and they are even known to trigger species divergence and ultimately speciation. Here, we estimated the nucleotide variation and speciation in three closely related Populus species, Populus tremuloides, P. tremula and P. davidiana, distributed in North America and Eurasia. We analysed the sequence variation in six single‐copy nuclear loci and three chloroplast (cpDNA) fragments in 497 individuals sampled from 33 populations of these three species across their geographic distributions. These three Populus species harboured relatively high levels of nucleotide diversity and showed high levels of nucleotide differentiation. Phylogenetic analysis revealed that P. tremuloides diverged earlier than the other two species. The cpDNA haplotype network result clearly illustrated the dispersal route from North America to eastern Asia and then into Europe. Molecular dating results confirmed that the divergence of these three species coincided with the sundering of the Bering land bridge in the late Miocene and a rapid uplift of the Qinghai‐Tibetan Plateau around the Miocene/Pliocene boundary. Vicariance‐driven successful allopatric speciation resulting from historical tectonism and climate oscillations most likely played roles in the formation of the disjunct distributions and divergence of these three Populus species.     

Sequences of the lizard cDNAs encoding lactate dehydrogenase (LDH) isozymes A (muscle) and B (heart)

The nucleotide and deduced amino acid sequences of cDNAs encoding L-lactate dehydrogenase (LDH) isozymes A (muscle) and B (heart) from the lizard, Sceloporus undulatus, were determined. The evolutionary relationships among LDH isozymes from animals, plants and bacteria are presented.     

Reproductive ecology of red-chinned lizards (Sceloporus undulatus erythrocheilus) in Southcentral Colorado: comparisons with other populations of a wide-ranging species

Summary We studied the reproductive ecology of a population of Sceloporus undulatus erythrocheilus near Walsenburg, CO during the summers of 1987–1990. Reproductive activity commences soon after emergence in early May and continues until the middle of July. Females mature in their second year following hatching at an age of 20–21 months and a size of 60–63 mm snout-vent length (SVL). Two clutches, averaging10.9 eggs, are produced per year. Larger females produce larger clutches with an increase of one egg per 3 mm SVL. Average SVL of females was 71 mm. Eggs are reasonably large (0.32 g) and relative clutch mass was the largest reported for the species (34% of body mass). A principal component analysis was used to examine relationships among reproductive characters in 12 populations of Sceloporus undulatus. The analysis suggested that patterns of reproduction in this wide-ranging species result from several factors reflecting both adaptive and phylogenetic sources of variation.     

Seasonal variation in metabolic rates and maintenance costs of the eastern fence lizard,Sceloporus undulatus

Metabolic rates of lizards, Sceloporus undulatus, differed between acclimated and acclimatized individuals. Oxygen consumption of field acclimatized Sceloporus undulatus peaked during the early morning and afternoon and was highest overall during spring. Oxygen consumption in the summer was similar to that in the fall. Laboratory acclimated animals collected during spring exhibited significantly lower rates of oxygen consumption than acclimatized individuals. Rates were similar in summer. Oxygen consumption did not vary between spring and summer for acclimated animals. Activity season maintenance costs of adult males based on field body temperatures and seasonal measurements of metabolic rates of acclimatized lizards (23.8 kJ/g) were higher than maintenance costs computed with data for summer lizards (20.6 kJ/g; a difference of 13.4%) and acclimated lizards (15.6 kJ/g; a difference of 34.5%).     

Reproductive cycle of the oviparous lizard Sceloporus jalapae,from Zapotitlán Salinas,Puebla, Mexico

Reproductive patterns vary widely among species and populations of squamates. In general, patterns can be divided into cyclic and acyclic. Cyclic patterns are common in tropical and temperate species of seasonal environments, while acyclic ones are characteristic of tropical species that inhabit less variable environments. We studied the reproductive cycle of Sceloporus jalapae, one of the smallest species of Sceloporus, in an arid environment at Zapotitlán Salinas, Puebla, Mexico. Both sexes mature in the first year following hatching and exhibit a seasonal reproductive pattern with maximum activity in spring and summer that appears to be influenced by temperature. Unlike small species of Sceloporus that inhabit pine–oak and tropical forests, S. jalapae exhibits an extended period of reproductive activity that allows females to produce at least two clutches of 3–7 eggs each, and contrary to other species of Sceloporus, in this species there is no correlation between female length and clutch size. The reproductive pattern of S. jalapae is like that shown by other oviparous species of the genus; nevertheless, some life history traits of this species are shared with oviparous and viviparous species of small size.     

PRIMER NOTE. Using the incomplete genome of the ectomycorrhizal fungus Amanita bisporigera to identify molecular polymorphisms in the related Amanita phalloides

We describe the cross‐genomic isolation of 13 single nucleotide polymorphisms (SNPs) and one variable microsatellite from five loci for the death cap mushroom Amanita phalloides. Microsatellite repeats were identified by searching the partial Amanita bisporigera genome. Flanking primers were designed for 25 of these microsatellite loci and tested for cross‐amplification in A. phalloides. One locus contained an interrupted, compound microsatellite, and four loci contained one to six SNPs. These results demonstrate the usefulness of even an incomplete genome to identify molecular markers for population studies in nonmodel organisms.     

A set of plastid DNA-specific universal primers for flowering plants

MatK and rbcL are recommended as the official barcode loci for higher plants but there remains a need for additional universal markers. We generated a series of 84 new universal primers targeting 42 plastid loci that all yielded single amplicons when applied to DNA templates from 19 diverse higher plant families. Marker utility ultimately depends on sequence variability, with rapidly evolving loci being useful for barcoding or biogeographic applications and more conserved loci being better suited to deep phylogeny reconstruction. Whereas excessive size variation is undesirable for many applications, modest size variability caused by indels and the sequence variation frequently associated with indels are highly desirable. We therefore performed a quick screen of the markers for size and sequence variation using pooled DNA templates from 96 taxonomically diverse species. All markers produced little or no size variation (consistent with the presence of minor indels). The seven regions exhibiting most size variation in pooled templates (rpl23&rpl2.1, 16S, 23S, 4.5S&5S, petB&D and rpl2, rpoC1 and trnK introns) were then amplified for all species individually, confirming the pooled template results. When the most variable loci (introns of trnK and rpoC1) were sequenced for all 96 species, a high level of sequence variation (nucleotide substitutions and indels) was observed among congeneric species groups for both loci. Both markers therefore have potential as supplementary barcode markers.     

Comparative analysis of genome composition in Triticeae reveals strong variation in transposable element dynamics and nucleotide diversity

A 454 sequencing snapshot was utilised to investigate the genome composition and nucleotide diversity of transposable elements (TEs) for several Triticeae taxa, including Triticum aestivum, Hordeum vulgare, Hordeum spontaneum and Secale cereale together with relatives of the A, B and D genome donors of wheat, Triticum urartu (A), Aegilops speltoides (S) and Aegilops tauschii (D). Additional taxa containing the A genome, Triticum monococcum and its wild relative Triticum boeoticum, were also included. The main focus of the analysis was on the genomic composition of TEs as these make up at least 80% of the overall genome content. Although more than 200 TE families were identified in each species, approximately 50% of the overall genome comprised 12–15 TE families. The BARE1 element was the largest contributor to all genomes, contributing more than 10% to the overall genome. We also found that several TE families differ strongly in their abundance between species, indicating that TE families can thrive extremely successfully in one species while going virtually extinct in another. Additionally, the nucleotide diversity of BARE1 populations within individual genomes was measured. Interestingly, the nucleotide diversity in the domesticated barley H. vulgare cv. Barke was found to be twice as high as in its wild progenitor H. spontaneum, suggesting that the domesticated barley gained nucleotide diversity from the addition of different genotypes during the domestication and breeding process. In the rye/wheat lineage, sequence diversity of BARE1 elements was generally higher, suggesting that factors such as geographical distribution and mating systems might play a role in intragenomic TE diversity.     

COMPARISON OF POPULATION STRUCTURE IN CHROMOSOMALLY POLYTYPIC AND MONOTYPIC SPECIES OF SCELOPORUS (SAURIA: IGUANIDAE) IN RELATION TO CHROMOSOMALLY-MEDIATED SPECIATION

Sceloporus grammicus has been used as an example of stasipatric speciation, and some models of chromosomal speciation have assumed that the fission rearrangements which distinguish the chromosome races within this complex are negatively heterotic in the heterozygous state. Consequently, such rearrangements are assumed to be fixed by drift in small, inbred populations. Allelic variation at 19 presumptive gene loci was examined in 13 samples of a chromosomally conservative congener, Sceloporus graciosus, and was compared to an equivalent data set for the chromosomally polytypic S. grammicus. Several estimates of population variability and structure were calculated, and results were inconsistent with models of extreme population subdivision and/or frequent bottlenecks and extinction-colonization events in S. grammicus. For example, mean level of heterozygosity and mean number of alleles per locus were significantly higher in S. grammicus than in S. graciosus, while the average genetic distance (D) was significantly higher in S. graciosus. These results are considered in light of expected “Wrightian” population genetic parameters, and we conclude that S. grammicus does not seem to have the population structure necessary for the fixation of strongly negatively heterotic rearrangements.     

A single nucleotide polymorphism assay for the identification of unisexual Ambystoma salamanders

Unisexual (all female) salamanders in the genus Ambystoma are animals of variable ploidy (2N‐5N) that reproduce via a unique system of ‘leaky’ gynogenesis. As a result, these salamanders have a diverse array of nuclear genome combinations from up to five sexual species: the blue‐spotted (A. laterale), Jefferson (A. jeffersonianum), smallmouth (A. texanum), tiger (A. tigrinum) and streamside (A. barbouri) salamanders. Identifying the genome complement, or biotype, is a critical first step in addressing a broad range of ecological and evolutionary questions about these salamanders. Previous work relied upon genome‐related differences in allele size distributions for specific microsatellite loci, but overlap in these distributions among different genomes makes definitive identification and ploidy determination in unisexuals difficult or impossible. Here, we develop the first single nucleotide polymorphism assay for the identification of unisexual biotypes, based on species‐specific nucleotide polymorphisms in noncoding DNA loci. Tests with simulated and natural unisexual DNA samples show that this method can accurately identify genome complement and estimate ploidy, making this a valuable tool for assessing the genome composition of unisexual samples.     

Size distributions and sex ratios of colonizing lizards

This paper reports the body size distributions and sex ratios of four species of phyrnosomatid lizard that colonized experimentally created density sinks. The experiments were conducted in western Colorado in 1992, and lizards colonizing the habitats in 1993 were compared to those removed in 1992 and those present in 1991. Lizards colonizing the density sinks were able to disperse from adjacent habitat. For two of the species (Urosaurus ornatus and Sceloporus undulatus), colonizing lizards were significantly smaller than either those removed in 1992 or those present in 1991. Two other species (S. graciosus and Uta stansburiana) showed no difference in the size distribution of colonizing and removed lizards. In addition, sex ratios of colonizing lizards did not differ from those removed in 1992 or present in 1991. The results of the experiments have implications for the dynamics of the target populations, rescue of local populations from extinction, the regional persistence of populations subject to turnover in patchy environments, and priority effects in colonization. Received: 3 February 1997 / Accepted: 20 May 1998