Phylogeographic analysis reveals an ancient East African origin of the human herpes simplexvirus 2 dispersal out-of-Africa.

Human herpes simplex virus 2 (HSV-2) is a globally ubiquitous, slow evolving DNA virus. HSV-2 genomic diversity can be divided into two main groups: an African lineage and worldwide lineage. Competing hypotheses have been put forth to explain the history of HSV-2. HSV-2 may have originated in Africa and then followed the first wave of human migration out of Africa between 50-100 kya. Alternatively, HSV-2 may have migrated out of Africa via the trans-Atlantic slave trade within the last 150-500 years. The lack of HSV-2 genomes from West and Central Africa, combined with a lack of molecular clock signal in HSV-2 has precluded robust testing of these competing hypotheses. Here, we expand the geographic sampling of HSV-2 genomes in order to resolve the geography and timing of divergence events within HSV-2. We analyze 65 newly sequenced HSV-2 genomes collected from primarily West and Central Africa along with 330 previously published genomes sampled over a 47-year period. Evolutionary simulations confirm that the molecular clock in HSV-2 is too slow to be detected using available data. However, phylogeographic analysis indicates that all biologically plausible evolutionary rates would place the ancestor of the worldwide lineage in East Africa, arguing against the trans-Atlantic slave trade as the source of worldwide diversity. The best supported evolutionary rates between 4.2x10-8 and 5.6x10-8 substitutions/site/year suggest a most recent common ancestor for HSV-2 around 90-120 kya and initial dispersal around 21.9-29.3 kya. These dates suggest HSV-2 left Africa during subsequent waves of human migration out of East Africa.

Extensive species diversification and marked geographic phylogenetic structure in the Mesoamerican genus Stenopelmatus (Orthoptera: Stenopelmatidae: Stenopelmatinae) revealed by mitochondrial and nuclear 3RAD data

The Jerusalem cricket subfamily Stenopelmatinae is distributed from south-western Canada through the western half of the United States to as far south as Ecuador. Recently, the generic classification of this subfamily was updated to contain two genera, the western North American Ammopelmatus, and the Mexican, and central and northern South American Stenopelmatus. The taxonomy of the latter genus was also revised, with 5, 13 and 14 species being respectively validated, declared as nomen dubium and described as new. Despite this effort, the systematics of Stenopelmatus is still far from complete. Here, we generated sequences of the mitochondrial DNA barcoding locus and performed two distinct DNA sequence-based approaches to assess the species’ limits among several populations of Stenopelmatus, with emphasis on populations from central and south-east Mexico. We reconstructed the phylogenetic relationships among representative species of the main clades within the genus using nuclear 3RAD data and carried out a molecular clock analysis to investigate its biogeographic history. The two DNA sequence-based approaches consistently recovered 34 putative species, several of which are apparently undescribed. Our estimates of phylogeny confirmed the recent generic update of Stenopelmatinae and revealed a marked phylogeographic structure within Stenopelmatus. Based on our results, we propose the existence of four species-groups within the genus (the faulkneri, talpa, Central America and piceiventris species-groups). The geographic distribution of these species-groups and our molecular clock estimates are congruent with the geological processes that took place in mountain ranges along central and southern Mexico, particularly since the Neogene. Our study emphasises the necessity to continue performing more taxonomic and phylogenetic studies on Stenopelmatus to clarify its actual species richness and evolutionary history in Mesoamerica.

Identification of the Oligocene to early Miocene loricariid catfish †Taubateia paraiba as a member of the Rhinelepinae

Correct identification of fossil taxa is immensely important for dating molecular phylogenies and understanding when and how quickly modern biodiversity evolved. Fossils that are available for a clade of interest and can be directly incorporated in the phylogenetic analysis are considered primary sources of time calibration, whereas calibrations inferred from other studies are secondary (Arroyave et al., 2013). Studies of taxonomic groups that lack fossils must either expand their analyses to include fossilized outgroup lineages, use secondary calibrations, or use more problematic primary calibrations, e.g., vicariant geologic events. The use of vicariant geologic events to calibrate phylogenies poses the risk of circular reasoning, because the goal of many such studies is to determine how geologic events have affected diversification. Near et al. (2012) argued that fossil calibrations external to clades of interest, but still within the broader Actinopterygian (ray-finned fishes) tree, could be used as means of calibrating a generalized molecular clock, but internal calibrations are still valuable for refining such inferences (Arroyave et al., 2013).

Melatonin, Clock Genes, and Mammalian Reproduction: What Is the Link?

Physiological processes and behaviors in many mammals are rhythmic. Recently there has been increasing interest in the role of circadian rhythmicity in the control of reproductive function. The circadian rhythm of the pineal hormone melatonin plays a role in synchronizing the reproductive responses of animals to environmental light conditions. There is some evidence that melatonin may have a role in the biological regulation of circadian rhythms and reproduction in humans. Moreover, circadian rhythms and clock genes appear to be involved in optimal reproductive performance. These rhythms are controlled by an endogenous molecular clock within the suprachiasmatic nucleus (SCN) in the hypothalamus, which is entrained by the light/dark cycle. The SCN synchronizes multiple subsidiary oscillators (clock genes) existing in various tissues throughout the body. The basis for maintaining the circadian rhythm is a molecular clock consisting of transcriptional/translational feedback loops. Circadian rhythms and clock genes appear to be involved in optimal reproductive performance. This mini review summarizes the current knowledge regarding the interrelationships between melatonin and the endogenous molecular clocks and their involvement in reproductive physiology (e.g., ovulation) and pathophysiology (e.g., polycystic ovarian syndrome).

Vasopressin resets the central circadian clock in a manner influenced by sex and vasoactive intestinal polypeptide signaling

Circadian rhythms in behavior and physiology are programmed by the suprachiasmatic nucleus (SCN) of the hypothalamus. A subset of SCN neurons produce the neuropeptide arginine vasopressin (AVP), but it remains unclear whether AVP signaling influences the SCN clock directly. Here we test that AVP signaling acting through V1A and V1B receptors influences molecular rhythms in SCN neurons. V1 receptor agonists were applied ex vivo to PERIOD2::LUCIFERASE SCN slices, allowing for real-time monitoring of changes in molecular clock function. V1A/B agonists reset the phase of the SCN molecular clock in a time-dependent manner, with larger magnitude responses by the female SCN. Further, we find evidence that both Gq and Gs signaling pathways interact with V1A/B-induced SCN resetting, and that this response requires vasoactive intestinal polypeptide (VIP) signaling. Collectively, this work indicates that AVP signaling resets SCN molecular rhythms in conjunction with VIP signaling and in a manner influenced by sex. This highlights the utility of studying clock function in both sexes and suggests that signal integration in central clock circuits regulates emergent properties important for the control of daily rhythms in behavior and physiology.

P-OGC95 Understanding the molecular age of Barrett’s oesophagus in a population-representative sample of patients

Background The incidence of oesophageal adenocarcinoma (OAC) increases dramatically with patient age but only a small proportion of patients with diagnosed Barrett’s oesophagus (BO), the precursor to OAC, will develop dysplasia and/or cancer. Beyond chronological age, biomarkers of progression that capture biological aging offer largely untapped potential for objectively identifying BO patients at highest risk of progression, who could undergo personalised surveillance at shorter intervals. We have developed computational tools to determine tissue-specific aging using genome-wide methylation data as a “molecular clock” for estimating patient-specific BO dwell times at the time of incident diagnosis that cannot be clinically measured by other means. Methods Using the population-based Northern Ireland BO register in a retrospective study, we have identified 46 non-dysplastic BO patients who have 2-4 serial endoscopic biopsies each, and have not progressed to OAC (age range 29-77 years). FFPE biopsies for 10 age-matched patients who had prevalent HGD/OAC at index BO diagnosis were also retrieved. DNA has been extracted, quantified using fluorescence, quality checked through qPCR, and prepared for Illumina EPIC methylation arrays. We created a Python package called “MethylDrift” to determine genome-wide aging rates in patient data. Model outputs are used in the molecular clock for BO tissue age. Results We used MethylDrift to quantify aging rates in both cross-sectional data (population-level epigenetic drift) and longitudinal data within the same patients to obtain individual aging rates. Computational analyses using our previously developed Bayesian framework for the BO molecular clock will be applied to estimate the molecular age of BO in patients, i.e., how long the patient has been living with BO since onset of metaplasia. Results will be compared between age groups, birth cohorts, sex, and importantly between dysplastic and non-dysplastic BO to evaluate biomarker potential. Data analysis is ongoing, and the final results will be presented at the meeting. Conclusions Our results from this nested case-control study demonstrate feasibility and generate pilot data on molecular age as a proxy of BO duration at the time of incident diagnosis, in a large population-based registry of patients with BO. This will inform our computational tools for determining biological aging and can be applied in future work to investigate progression risk according to molecular age. Ultimately, this biomarker could inform surveillance frequency for BO patients, enable earlier detection of neoplastic progression, leading to improved patient outcomes and optimal distribution of limited endoscopy capacity for surveillance.

Evolution of New Zealand's Marine Caddisflies: A Phylogenetic and Phylogeographic Assessment of the Chathamiidae (Insecta: Trichoptera)

<p><b>The Chathamiidae are an interesting family of caddisflies, unusual as all of the five known species are believed to breed entirely within the marine intertidal, comprising one of very few known marine insect groups. Additionally the family approaches almost complete endemicity status in New Zealand, and may represent an ancient lineage representative of ancient vicariance from Gondwana. However one species, the common and widespread Philanisus plebeius is also known to have a disjunct population in New South Wales Australia, hypothesised to represent a recent anthropogenic dispersal. This thesis, using DNA information, examined the Chathamiidae at varying phylogenetic levels.</b></p> <p>Firstly the species Philanisus plebeius was incorporated into a thorough intraspecific phylogeography, including samples from both New Zealand and Australia. The population as a whole was genetically diverse, with the population divisible into two major haplogroups, each restricted to discrete geographic areas with no overlap being observed. One of these groups was restricted to just two localities in the central eastern North Island, whereas the remainder included most remaining samples from both Islands of New Zealand, and also Australia. All Australian samples were found to comprise a single haplotype, differing by a single base pair from the most common haplotype in New Zealand. It was decided that the Australian population therefore represents a recent dispersal event from New Zealand, although unless the Australian haplotype remains undiscovered in New Zealand the level of divergence found is not congruent with a human introduction. One sequence intermediate between the two major haplogroups was identified from a single haplotype from Tauranga. It seemed that much of the population of Philanisus plebeius has been affected by recent demographic expansion, likely due to the effects of the last glacial maximum (LGM).</p> <p>The five species of the Chathamiidae were then analysed in a phylogeny. It was found that the genus Chathamia was polyphyletic, with the species C. integripennis nested within the genus Philanisus. The remaining species, C. brevipennis from the Chatham Islands, was basal to all the remaining members of the family. A strict molecular clock found a recent Pleistocene age (roughly 0.5 Ma) for divergence of the Kermadec Island species Philanisus fasciatus, and a Pliocene-Pleistocene age (roughly 3 Ma) for the Chatham Island species Chathamia brevipennis. For a comparison with the species C. brevipennis, the other Chatham Island caddisfly taxa Oecetis chathamensis, and Hydrobiosis lindsayi were compared with New Zealand relatives; indicated to have late and early Pleistocene ages respectively. A short sequence of the gene COI was amplified for the species Philanisus mataua, however this was found to contain two sequences reflecting either heteroplasmy or sample contamination, inhibiting confident phylogenetic placement. Additionally a larval sample from Sydney was demonstrated to represent C. integripennis, recorded outside of Northern New Zealand for the first time. Finally the Chathamiidae was included in a higher level phylogeny with related families, and was show to comprise a monophyletic group, sister to the Australasian family of the Conoesucidae. A relaxed molecular clock estimated a Cretaceous (roughly 90 Ma) age for the Chathamiidae, congruent with a vicariant age in New Zealand.</p>