The phylogenetic systematics of blue‐tailed skinks (Plestiodon) and the family Scincidae

Blue‐tailed skinks (genus Plestiodon) are a common component of the terrestrial herpetofauna throughout their range in eastern Eurasia and North and Middle America. Plestiodon species are also frequent subjects of ecological and evolutionary research, yet a comprehensive, well‐supported phylogenetic framework does not yet exist for this genus. We construct a comprehensive molecular phylogeny of Plestiodon using Bayesian phylogenetic analyses of a nine‐locus data set comprising 8308 base pairs of DNA, sampled from 38 of the 43 species in the genus. We evaluate potential gene tree/species tree discordance by conducting phylogenetic analyses of the concatenated and individual locus data sets, as well as employing coalescent‐based methods. Specifically, we address the placement of Plestiodon within the evolutionary tree of Scincidae, as well as the phylogenetic relationships between Plestiodon species, and their taxonomy. Given our sampling of major Scincidae lineages, we also re‐evaluate ‘deep’ relationships within the family, with the goal of resolving relationships that have been ambiguous in recent molecular phylogenetic analyses. We infer strong support for several scincid relationships, including a major clade of ‘scincines’ and the inter‐relationships of major Mediterranean and southern African genera. Although we could not estimate the precise phylogenetic affinities of Plestiodon with statistically significant support, we nonetheless infer significant support for its inclusion in a large ‘scincine’ clade exclusive of Acontinae, Lygosominae, Brachymeles, and Ophiomorus. Plestiodon comprises three major geographically cohesive clades. One of these clades is composed of mostly large‐bodied species inhabiting northern Indochina, south‐eastern China (including Taiwan), and the southern Ryukyu Islands of Japan. The second clade comprises species inhabiting central China (including Taiwan) and the entire Japanese archipelago. The third clade exclusively inhabits North and Middle America and the island of Bermuda. A vast majority of interspecific relationships are strongly supported in the concatenated data analysis, but there is nonetheless significant conflict amongst the individual gene trees. Coalescent‐based gene tree/species tree analyses indicate that incongruence amongst the nuclear loci may severely obscure the phylogenetic inter‐relationships of the primarily small‐bodied Plestiodon species that inhabit the central Mexican highlands. These same analyses do support the sister relationship between Plestiodon marginatus Hallowell, 1861 and Plestiodon stimpsonii (Thompson, 1912), and differ with the mitochondrial DNA analysis that supports Plestiodon elegans (Boulenger, 1887) + P. stimpsonii. Finally, because the existing Plestiodon taxonomy is a poor representation of evolutionary relationships, we replace the existing supraspecific taxonomy with one congruent with our phylogenetic results. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 165 , 163–189.     

Chronic catchment nitrogen enrichment and stoichiometric constraints on the bioavailability of dissolved organic matter from leaf leachate

1. Chronic nitrogen (N) deposition may alter the bioavailability of dissolved organic matter (DOM) in streams by multiple pathways. Elevated N deposition may alter the nutrient stoichiometry of DOM as well as nutrient availability in stream water. 2. We evaluated the influence of a decadal‐scale experimental N enrichment on the relative importance of DOM nutrient content and inorganic nutrient availability on the bioavailability of DOM. We measured the consumption of dissolved organic carbon (DOC) and changes in nutrient concentration, DOM components and enzyme activity in a bottle incubation assay with different DOM and nutrient treatments. To evaluate the effect of DOM stoichiometry, we used leaf leachates of different carbon/N/phosphorus (C : N :P) ratio, made from leaf litter sourced in the reference and N‐enriched catchments at the Bear Brook Watershed in Maine (BBWM). We also manipulated the concentration of inorganic N and P to compare the effect of nutrient enrichment with DOM stoichiometry. 3. DOC from the N‐enriched catchment was consumed 14% faster than that from the reference catchment. However, mean DOC consumption for both leachates was more than doubled by the simultaneous addition of N and P, compared to controls, while the addition of N or P alone increased consumption by 42 and 23%, respectively. The effect of N and/or P enrichment consistently had a greater effect than DOM source for all response variables considered. 4. We subsequently conducted DOC uptake measurements using leaf leachate addition under ambient and elevated N and P in the streams draining the reference and N‐enriched catchments at BBWM. In both streams, DOC uptake lengths were shorter when N and P were elevated. 5. Although both DOM stoichiometry and inorganic nutrient availability affect DOM bioavailability, N and P co‐limitation appears to be the dominant driver of reach‐scale processing of DOM.     

Potential agronomic options for energy-efficient sugar beet-based bioethanol production in northern Japan

Sugar beet (Beta vulgaris L. subsp. vulgaris) is deemed to be one of the most promising bioethanol feedstock crops in northern Japan. To establish viable sugar beet‐based bioethanol production systems, energy‐efficient protocols in sugar beet cultivation are being intensively sought. On this basis, the effects of alternative agronomic practices for sugar beet production on total energy inputs (from fuels and agricultural materials during cultivation and transportation) and ethanol yields (estimated from sugar yields) were assessed in terms of (i) direct drilling, (ii) reduced tillage (no moldboard plowing), (iii) no‐fungicide application, (iv) using a high‐yielding beet genotype, (v) delayed harvesting and (vi) root+crown harvesting. Compared with the conventional sugar beet production system used in the Tokachi region of Hokkaido, northern Japan, which makes use of transplants, direct drilling and no‐fungicide application contributed to reduced energy inputs from raising seedlings and fungicides, respectively, but sugar (or ethanol) yields were also reduced by these practices, to a greater equivalent extent than the reductions in energy inputs. Consequently, direct drilling (6.84 MJ L^?1) and no‐fungicide application (7.78 MJ L^?1) worsened the energy efficiency (total energy inputs to produce 1 L of ethanol), compared with conventional sugar beet production practices (5.82 MJ L^?1). Sugar yields under conventional plow‐based tillage and reduced tillage practices were similar, but total energy inputs were reduced as a result of reduced fuel consumption from not plowing. Hence, reduced tillage showed improved energy efficiency (5.36 MJ L^?1). The energy efficiency was also improved by using a high‐yielding genotype (5.23 MJ L^?1) and root+crown harvesting (5.21 MJ L^?1). For these practices, no major changes in total energy inputs were noted, but sugar yields were consistently increased. Neither total energy inputs nor ethanol yields were affected by extending the vegetative growing period by delaying harvesting.     

Phylogenetic relationships, taxonomy, character evolution and biogeography of the lacertid lizards of the genus Takydromus (Reptilia: Squamata): a molecular perspective

Historical relationships were inferred for the oriental lizards of the genus Takydromus Daudin 1802 (Lacertidae) on the basis of DNA sequences. Of the 17 species currently recognized for the genus, 13 species represented by 42 specimens from 29 localities were examined. Maximum-likelihood and maximum-parsimony analyses of data for 829 aligned sites from parts of the mitochondrial 12S and 16S rRNA genes yielded relationships that, while showing no substantial discrepancy with each other, were strikingly different from a currently prevailing phylogenetic hypothesis from a parsimony analysis of morphological characters. Based on the results of these molecular analyses, supplemented by results of the morphological analysis that offered robust evidence for positions of two additional species ( T. khasiensis and T. sylvaticus ), the following interrelationships were hypothesized as the most preferred phylogeny: ( kuehnei ( sexlineatus khasiensis ))( tachydromoides (( smaragdinus ( sauteri ( dorsalis sylvaticus ))) ( amurensis ((( formosanus wolteri ) hsuehshanensis )( toyamai ( septentrionalis stejnegeri )))))). These interrelationships indicate: (1) invalidity of Platyplacopus Boulenger 1917 , which was recently resurrected as a subgenus of Takydromus on the basis of the morphological analysis; (2) homoplasy in states of some morphological characters, such as green dorsal coloration, that were considered as synapomorphs of certain nodes in the morphological analysis; and (3) involvement of the genus in a series of vicariances in both the continental and insular parts of eastern Eurasia. Due to the paucity of available samples, phylogenetic status of T. intermedius and T. haughtonianus remain to be examined in future studies.  © 2002 The Linnean Society of London, Biological Journal of the Linnean Society , 76 , 493–509.     

Development and morphology of rostral cartilages in batoid fishes (Ghondrichthyes: Batoidea), with comments on homology within vertebrates

The rostral cartilages of batoid fishes were examined to elucidate their development, morphology and homology. Comparison of a variety of rostral cartilages among elasmobranchs with other groups of vertebrates shows that rostral cartilages originate embryologically from the trabecula and/or lamina orbitonasalis. Because different morphogenetic patterns of the derivatives of the two embryonic cartilages give rise to a wide variety of forms of rostral cartilages even within elasmobranchs, and because morphogenesis involves complex interactions among participating structures in the ethmo-orbital area, we put forward conceptual and empirical discussions to elucidate the homology of the rostral cartilages in batoid fishes. With six assumptions given in this study and based on recent discussions of biological and historical homology, our discussions centre on: (1) recognition of complex interactions of participating biological entities in development and evolution; (2) elucidation of a set of interacting biological and evolutionary factors to define a given morphological structure; (3) assessment of causal explanations for similarities or differences between homologous structures by determining genetic, epigenetic and evolutionary factors. Examples of conceptual approaches are given to make the approaches testable. Although a paucity of knowledge of rostral cartilage formation is the major obstacle to thorough analysis of the conceptual framework, several tentative conclusions are made on the homology of rostral cartilages that will hopefully attract more research on development and evolution in vertebrate morphology. These are: (1) the rostral cartilage in each group of vertebrates examined can be defined by both developmentally associated and adult structural attributes, yet such data do not allow us to assess homology of a variety of forms of rostral cartilages at higher taxonomic categories; (2) the entire rostral cartilage in elasmobranchs is formed by the contribution of the embryonic trabecula and lamina orbitonasalis. The status of the development and homology of the rostral cartilage in holocephalans remains uncertain; (3) there is no simple picture of evolution of rostral cartilages among three putative monophyletic assemblages of elasmobranchs, galeomorphs, squaloids (possibly plus Squatina, Chlamydoselachus and hexanchoids as the orbitostylic group) and batoid fishes. It is highly likely that rostral cartilages in each subgroup or subgroups of these assemblages may be of phylogenetic significance but that it may not serve as a basis to unite these assemblages into much higher assemblages; (4) the tripodal rostral cartilage is unique in form in the group including some carcharhinoid and lamnoid sharks. The status of the analogous tripodal cartilage in some squaloids remains uncertain. The unfused tripodal cartilage of the electric ray Narke is interpreted as developmentally equivalent to, but not homologous with, the unfused or fused ones in the sharks; (5) the rostral cartilage in the electric ray Torpedo is uniquely formed because of its embryonic origin solely from the ventro-medial part of the lamina orbitonasalis, but it is regarded as homologous with the rostral cartilages which are formed by the trabecula and other components of the lamina orbitonasalis in other batoid fishes; (6) the cornu trabecula contributes to the formation of the ventral stem of the rostral cartilage at least in elasmobranchs, especially to a particular set of rostral cartilages, i.e. the tripodal rostral cartilage in the shark Scyliorhinus and dorso-ventrally flattened rostral shaft in the narcinidid electric rays; (7) there is a unique form of a rostral shaft with rostral appendix in skates and probably guitarfishes; (8) there is no rostral cartilage in adult benthic stingrays, pelagic stingrays Dasyatis violacea and Myliobatidae, although it is present in embryonic stages; (9) there is a unique form of the rostral cartilage as a rostral projection from the dorso-lateral part of the lamina orbitonasalis in pelagic stingrays Rhinopteridae and Mobulidae, which together with part of the pectoral fins, forms a pair of cephalic fins; (10) different developmental mechanisms may be responsible for the absence or loss of rostral cartilages in different groups, i.e. absence of the cartilage derived from the medial area of the trabecula in Torpedo vs absence of the rostral cartilage in benthic stingrays; (11) the rostral cartilages in some placental mammals (cetaceans and sirenians) arise only from the medial area of the trabecula because monotreme and placental mammals do not form the trabecula cranii; (12) some actinopterygians and sacropterygians possess a rostral cartilage which originates only from the medial area of the trabecula. One scombroid group, including Sardini and Thunnini, Scomberomorus, Acanthocybium, Istiophoridae and Xiphias, possesses a unique larval beak composed of the rostral cartilage, ethmoid cartilage and premaxillar bone. The development and homology of other rostral cartilages remain to be further elucidated; (13) urodeles possess a medial rostral process whose anlage is probably developmentally equivalent to that in batoid fishes but the occurrence in urodeles is either atavistic or unique (autapomorphic); (14) the upper jaw of tadpoles is unique in possessing the suprarostral cartilage; the anlage of the cartilage is probably developmentally equivalent to the outgrowth of the cornu trabecula in batoid fishes.     

The jaw apparatus of the Cretaceous ammonite Reesidites

Jaws are preserved within the body chambers of three specimens of a collignoniceratid ammonite Reesidites minimus (Hayasaka and Fukada) from the Upper liuoniaq of Hokkaido, Japan. Light microscopic and SEM observations of sections indicate that both upper and lower jaws consist mainly of a thick, double-walled chitinous lamella with a beak-like anterior projection. The outer chitinous lamella of the lower jaw is covered by a thick calcareous layer. The jaw apparatus of this species morphologically resembles aptychus-type jaws of Jurassic ammonites, but is distinguished by the presence of an anterior beak-like projection with serrated ridges and grooves in the lower jaw. These observations strongly suggest a biting ability in this species.