Ryan W. Norris

A shifted repertoire of endocannabinoid genes in the zebrafish (Danio rerio).

The zebrafish has served as a model organism for developmental biology. Sequencing its genome has expanded zebrafish research into physiology and drug-development testing. Several cannabinoid pharmaceuticals are in development, but expression of endocannabinoid receptors and enzymes remains unknown in this species. We conducted a bioinformatics analysis of the zebrafish genome using 17 human endocannabinoid genes as a reference set. Putative zebrafish orthologs were identified in filtered BLAST searches as reciprocal best hits. Orthology was confirmed by three in silico methods: phylogenetic testing, synteny analysis, and functional mapping. Zebrafish expressed orthologs of cannabinoid receptor 1, transient receptor potential channel vanilloid receptor 4, GPR55 receptor, fatty acid amide hydrolase 1, monoacylglycerol lipase, NAPE-selective phospholipase D, abhydrolase domain-containing protein 4, and diacylglycerol lipase alpha and beta; and paired paralogs of cannabinoid receptor 2, fatty acid amide hydrolase 2, peroxisome proliferator-activated receptor alpha, prostaglandin-endoperoxide synthase 2, and transient receptor potential cation channel subtype A1. Functional mapping suggested the orthologs of transient receptor potential vanilloid receptor 1 and peroxisome proliferator-activated receptor gamma lack specific amino acids critical for cannabinoid ligand binding. No orthologs of N-acylethanolamine acid amidase or protein tyrosine phosphatase, non-receptor type 22 were identified. In conclusion, the zebrafish genome expresses a shifted repertoire of endocannabinoid genes. In vitro analyses are warranted before using zebrafish for cannabinoid development testing.

On the causes of evolutionary transition:transversion bias

Abstract A pattern in which nucleotide transitions are favored several fold over transversions is common in molecular evolution. When this pattern occurs among amino acid replacements, explanations often invoke an effect of selection, on the grounds that transitions are more conservative in their effects on proteins. However, the underlying hypothesis of conservative transitions has never been tested directly. Here we assess support for this hypothesis using direct evidence: the fitness effects of mutations in actual proteins measured via individual or paired growth experiments. We assembled data from 8 published studies, ranging in size from 24 to 757 single-nucleotide mutations that change an amino acid. Every study has the statistical power to reveal significant effects of amino acid exchangeability, and most studies have the power to discern a binary conservative-vs-radical distinction. However, only one study suggests that transitions are significantly more conservative than transversions. In the combined set of 1,239 replacements (544 transitions, 695 transversions), the chance that a transition is more conservative than a transversion is 53 % (95 % confidence interval 50 to 56) compared with the null expectation of 50 %. We show that this effect is not large compared with that of most biochemical factors, and is not large enough to explain the several-fold bias observed in evolution. In short, the available data have the power to verify the “conservative transitions” hypothesis if true, but suggest instead that selection on proteins plays at best a minor role in the observed bias.

Towards a uniform nomenclature for ground squirrels: the status of the Holarctic chipmunks

Abstract The chipmunks are a Holarctic group of ground squirrels currently allocated to the genus Tamias within the tribe Marmotini (Rodentia: Sciuridae). Cranial, postcranial, and genital morphology, cytogenetics, and genetics each separate them into three distinctive and monophyletic lineages now treated as subgenera. These groups are found in eastern North America, western North America, and Asia, respectively. However, available genetic data (mainly from mitochondrial cytochrome b) demonstrate that the chipmunk lineages diverged early in the evolution of the Marmotini, well before various widely accepted genera of marmotine ground squirrels. Comparisons of genetic distances also indicate that the chipmunk lineages are as or more distinctive from one another as are most ground squirrel genera. Chipmunk fossils were present in the late Oligocene of North America and shortly afterwards in Asia, prior to the main radiation of Holarctic ground squirrels. Because they are coordinate in morphological, genetic, and chronologic terms with ground squirrel genera, the three chipmunk lineages should be recognized as three distinct genera, namely, Tamias Illiger, 1811, Eutamias Trouessart, 1880, and Neotamias A. H. Howell, 1929. Each is unambiguously diagnosable on the basis of cranial, post-cranial, and external morphology.

Ancient DNA supports southern survival of Richardson's collared lemming (Dicrostonyx richardsoni) during the last glacial maximum

Collared lemmings (genus Dicrostonyx) are circumpolar Arctic arvicoline rodents associated with tundra. However, during the last glacial maximum (LGM), Dicrostonyx lived along the southern ice margin of the Laurentide ice sheet in communities comprising both temperate and boreal species. To better understand these communities and the fate of these southern individuals, we compare mitochondrial cytochrome b sequence data from three LGM‐age Dicrostonyx fossils from south of the Laurentide ice sheet to sequences from modern Dicrostonyx sampled from across their present‐day range. We test whether the Dicrostonyx populations from LGM‐age continental USA became extinct at the Pleistocene–Holocene transition ~11000 years ago or, alternatively, if they belong to an extant species whose habitat preferences can be used to infer the palaeoclimate along the glacial margin. Our results indicate that LGM‐age Dicrostonyx from Iowa and South Dakota belong to Dicrostonyx richardsoni, which currently lives in a temperate tundra environment west of Hudson Bay, Canada. This suggests a palaeoclimate south of the Laurentide ice sheet that contains elements similar to the more temperate shrub tundra characteristic of extant D. richardsoni habitat, rather than the very cold, dry tundra of the Northern Arctic. While more data are required to determine whether or not the LGM southern population is ancestral to extant D. richardsoni, it seems most probable that the species survived the LGM in a southern refugium.

MORPHOLOGICAL AND MOLECULAR DEFINITION OF CALOMYSCUS HOTSONI (RODENTIA: MUROIDEA: CALOMYSCIDAE)

Abstract The rediscovery of Calomyscus hotsoni in Pakistan is reported. This species had previously been known from a series of specimens taken at the type locality in southwestern Pakistan in 1918 and a series of specimens from 4 localities in southeastern Iran collected in 1962 and reported as this taxon in 2005. Specimens of C. hotsoni were collected from 4 additional locations in southern Pakistan between 1996 and 1999. Partial sequence data from cytochrome b support the recognition of C. hotsoni as a distinct species from the other Calomyscus found in Pakistan, C. baluchi. Material collected from near the type localities of C. hotsoni and C. baluchi demonstrate significant differences in 5 cranial measurements and all external measurements other than ear height. C. hotsoni can be differentiated from C. baluchi by its smaller hind foot. The known distribution of C. hotsoni is greatly expanded and some ecological observations about the species also are reported. Examination of data presented on the distribution and on variation in local abundance suggests that C. hotsoni is currently neither endangered nor threatened.

Bat Diversity in the Simandou Mountain Range of Guinea, with the Description of a New White-Winged Vespertilionid

Tropical West Africa has a high diversity of bats, which are relatively poorly studied. In this baseline biodiversity assessment of bats in the Simandou Mountain Range of southeastern Guinea (Guinea Forestiére), 312 individual bats belonging to 26 species were captured, four of which represent new species records for the country. Combined with the results of a previous survey, 35 bat species have been recorded at Simandou to date, including a new species (Neoromicia sp. nov.), which we describe here, and an additional species potentially new to science. A neotype for Neoromicia tenuipinnis is designated. We present an annotated checklist of the bats at Simandou and neighbouring sites, including some pertinent field notes on their habitat requirements and conservation status. Furthermore, we discuss the estimated maximum species richness and show that Simandou supports one of the most diverse bat communities in tropical Africa. Finally, we outline conservation concerns with respect to bats in the face of the iron ore extraction activities at Simandou.

Bayesian priors for tree calibration: Evaluating two new approaches based on fossil intervals

Background: Studies of diversification and trait evolution increasingly rely on combining molecular sequences and fossil dates to infer time-calibrated phylogenetic trees. Available calibration software provides many options for the shape of the prior probability distribution of ages at a node to be calibrated, but the question of how to assign a Bayesian prior from limited fossil data remains open. Results: We introduce two new methods for generating priors based upon (1) the interval between the two oldest fossils in a clade, i.e., the penultimate gap (PenG), and (2) the ghost lineage length (GLin), defined as the difference between the oldest fossils for each of two sister lineages. We show that PenG and GLin/2 are point estimates of the interval between the oldest fossil and the true age for the node. Furthermore, given either of these quantities, we derive a principled prior distribution for the true age. This prior is log-logistic, and can be implemented approximately in existing software. Using simulated data, we test these new methods against some other approaches. Conclusions: When implemented as approaches for assigning Bayesian priors, the PenG and GLin methods increase the accuracy of inferred divergence times, showing considerably more precision than the other methods tested, without significantly greater bias. When implemented as approaches to post-hoc scaling of a tree by linear regression, the PenG and GLin methods exhibit less bias than other methods tested. The new methods are simple to use and can be applied to a variety of studies that call for calibrated trees.