Long-term climatic stability drives accumulation and maintenance of divergent freshwater fish lineages in a temperate biodiversity hotspot.

Anthropogenic climate change is forecast to drive regional climate disruption and instability across the globe. These impacts are likely to be exacerbated within biodiversity hotspots, both due to the greater potential for species loss but also to the possibility that endemic lineages might not have experienced significant climatic variation in the past, limiting their evolutionary potential to respond to rapid climate change. We assessed the role of climatic stability on the accumulation and persistence of lineages in an obligate freshwater fish group endemic to the southwest Western Australia (SWWA) biodiversity hotspot. Using 19,426 genomic (ddRAD-seq) markers and species distribution modelling, we explored the phylogeographic history of western (Nannoperca vittata) and little (Nannoperca pygmaea) pygmy perches, assessing population divergence and phylogenetic relationships, delimiting species and estimating changes in species distributions from the Pliocene to 2100. We identified two deep phylogroups comprising three divergent clusters, which showed no historical connectivity since the Pliocene. We conservatively suggest these represent three isolated species with additional intraspecific structure within one widespread species. All lineages showed long-term patterns of isolation and persistence owing to climatic stability but with significant range contractions likely under future climate change. Our results highlighted the role of climatic stability in allowing the persistence of isolated lineages in the SWWA. This biodiversity hotspot is under compounding threat from ongoing climate change and habitat modification, which may further threaten previously undetected cryptic diversity across the region.

Evaluating conserved domains and motifs of decapod gonadotropin-releasing hormone G protein-coupled receptor superfamily.

G protein-coupled receptors (GPCRs) are an ancient family of signal transducers that are both abundant and consequential in metazoan endocrinology. The evolutionary history and function of the GPCRs of the decapod superfamilies of gonadotropin-releasing hormone (GnRH) are yet to be fully elucidated. As part of which, the use of traditional phylogenetics and the recycling of a diminutive set of mis-annotated databases has proven insufficient. To address this, we have collated and revised eight existing and three novel GPCR repertoires for GnRH of decapod species. We developed a novel bioinformatic workflow that included clustering analysis to capture likely GnRH receptor-like proteins, followed by phylogenetic analysis of the seven transmembrane-spanning domains. A high degree of conservation of the sequences and topology of the domains and motifs allowed the identification of species-specific variation (up to ~70%, especially in the extracellular loops) that is thought to be influential to ligand-binding and function. Given the key functional role of the DRY motif across GPCRs, the classification of receptors based on the variation of this motif can be universally applied to resolve cryptic GPCR families, as was achieved in this work. Our results contribute to the resolution of the evolutionary history of invertebrate GnRH receptors and inform the design of bioassays in their deorphanization and functional annotation.

Cognitive Load Influences Drop Jump Landing Mechanics During Cognitive-Motor-Simulated Shooting.

INTRODUCTION: Military duties require immense cognitive-motor multitasks that may predispose soldiers to musculoskeletal injury. Most cognitive challenges performed in the research laboratory are not tactical athlete specific, limiting generalizability and transferability to in-field scenarios. The purpose of this study was to determine the impact of a cognitive-motor multitask (forward drop jump landing while simultaneously performing simulated shooting) on knee kinetics and kinematics. METHODS: Twenty-four healthy collegiate Reserve Officer's Training Corps members (18 males and 6 females, 20.42 ± 1.28 years, 174.54 ± 10.69 cm, 78.11 ± 14.96 kg) volunteered, and knee kinetics and kinematics were assessed between baseline and cognitive-loaded conditions. Repeated measures ANOVAs were conducted for each dependent variable with the within-subject factor of condition (baseline vs. cognitive load). RESULTS: Univariate ANOVAs indicated that knee flexion angle at initial contact (IC) (decreased 6.07°; d = 3.14), knee flexion displacement (increased 6.78°; d = 1.30), knee abduction angle at IC (increased 2.3°; d = 1.46), peak knee abduction angle (increased 3.04°; d = 0.77), and peak vertical ground reaction force (increased 0.81 N/kg; d = 2.13) were significant between conditions (P < .001). Therefore, cognitive load resulted in decreased knee flexion and increased knee abduction angle at IC and greater peak vertical ground reaction force, all factors commonly associated with knee injury risk. Peak knee flexion angle and knee abduction displacement were not significant between conditions (P > .05). CONCLUSIONS: Cognitive challenge induced knee landing biomechanics commonly associated with injury risk. Injury risk screening or return-to-training or duty assessments in military personnel might consider both baseline and cognitive conditions.

Variation in intraspecific demography drives localised concordance but species-wide discordance in response to past climatic change.

BACKGROUND: Understanding how species biology may facilitate resilience to climate change remains a critical factor in detecting and protecting species at risk of extinction. Many studies have focused on the role of particular ecological traits in driving species responses, but less so on demographic history and levels of standing genetic variation. Additionally, spatial variation in the interaction of demographic and adaptive factors may further complicate prediction of species responses to environmental change. We used environmental and genomic datasets to reconstruct the phylogeographic histories of two ecologically similar and largely co-distributed freshwater fishes, the southern (Nannoperca australis) and Yarra (N. obscura) pygmy perches, to assess the degree of concordance in their responses to Plio-Pleistocene climatic changes. We described contemporary genetic diversity, phylogenetic histories, demographic histories, and historical species distributions across both species, and statistically evaluated the degree of concordance in co-occurring populations. RESULTS: Marked differences in contemporary genetic diversity, historical distribution changes and historical migration were observed across the species, with a distinct lack of genetic diversity and historical range expansion suggested for N. obscura. Although several co-occurring populations within a shared climatic refugium demonstrated concordant demographic histories, idiosyncratic population size changes were found at the range edges of the more spatially restricted species. Discordant responses between species were associated with low standing genetic variation in peripheral populations. This might have hindered adaptive potential, as documented in recent demographic declines and population extinctions for the two species. CONCLUSION: Our results highlight both the role of spatial scale in the degree of concordance in species responses to climate change, and the importance of standing genetic variation in facilitating range shifts. Even when ecological traits are similar between species, long-term genetic diversity and historical population demography may lead to discordant responses to ongoing and future climate change.

Cognitive Load Impairs Time to Initiate and Complete Shooting Tasks in ROTC Members.

INTRODUCTION: Multitasking typically requires an individual to simultaneously process cognitive information while performing a motor task. Cognitive motor interference (CMi) is encountered when cognitive challenges negatively impact motor task performance. Military personnel encounter cognitively taxing situations, especially during combat or other tactical performance scenarios, which may lead to injury or motor performance deficits (i.e., shooting inaccuracy, delayed stimulus-response time, and slowed movement speed). The purpose of the current study was to develop four cognitive motor shooting paradigms to determine the effects of cognitive load on shooting performance in healthy Reserve Officers' Training Corps (ROTC) cadets. METHODS: Thirty-two healthy collegiate ROTC members (24 male and 8 female; 20.47 ± 1.24 years, 174.95 ± 10.58 cm, and 77.99 ± 13.90 kg) were recruited to complete four simulated shooting tasks with additional "motor" challenge (180° turn, gait, weighted, and unweighted landing) and with and without a "cognitive" decision-making challenge requiring response selection and inhibition to both auditory and visual stimuli, totaling eight multi-task cognitive motor shooting conditions. The current study was approved by the university's Institutional Review Board. Task initiation (seconds), task completion (seconds), and number of misses were calculated to determine marksmanship efficiency and accuracy. For each task, a multivariate repeated-measures analysis of variance (ANOVA) was conducted for the combined dependent variables. If the overall multivariate repeated-measures ANOVA was significant, follow-up univariate ANOVAs were conducted for each dependent variable. Alpha was set at α = 0.05 for all analyses. RESULTS: Task initiation increased for the cognitive condition for the 180° turn (4.29 ± 1.22 seconds baseline, 5.09 ± 1.39 seconds cognitive; P < .05), gait (2.76 ± .60 seconds baseline, 3.93 ± .62 seconds cognitive; P < .05), unweighted (1.27 ± .57 seconds baseline, 3.39 ± .63 seconds cognitive; P < .05), and weighted landing (1.46 ± .72 seconds baseline, 3.35 ± .60 seconds cognitive; P < .05). Task completion time increased for the cognitive condition for the 180° turn (3.48 ± 1.53 seconds baseline, 4.85 ± 1.24 seconds cognitive; P < .05), gait (7.84 ± 2.07 seconds baseline, 9.23 ± 1.76 seconds cognitive; P < .05), unweighted (5.98 ± 1.55 seconds baseline, 7.45 ± 1.51 seconds cognitive; P < .05), and weighted landing (6.09 ± 1.42 seconds baseline, 7.25 ± 1.79 seconds cognitive; P < .05). There were no statistically significant differences in the number of misses for any of the tasks between conditions (P > .05). CONCLUSIONS: The addition of a cognitive load increased both task initiation and task completion times during cognitive motor simulated shooting. Adding cognitive loads to tactical performance tasks can result in CMi and negatively impact tactical performance. Thus, consideration for additional cognitive challenges into training may be warranted to reduce the potential CMi effect on tactical performance.

The roles of aridification and sea level changes in the diversification and persistence of freshwater fish lineages.

While the influence of Pleistocene climatic changes on divergence and speciation has been well-documented across the globe, complex spatial interactions between hydrology and eustatics over longer timeframes may also determine species evolutionary trajectories. Within the Australian continent, glacial cycles were not associated with changes in ice cover and instead largely resulted in fluctuations from moist to arid conditions across the landscape. We investigated the role of hydrological and coastal topographic changes brought about by Plio-Pleistocene climatic changes on the biogeographic history of a small Australian freshwater fish, the southern pygmy perch Nannoperca australis. Using 7958 ddRAD-seq (double digest restriction-site associated DNA) loci and 45,104 filtered SNPs, we combined phylogenetic, coalescent and species distribution analyses to assess the various roles of aridification, sea level and tectonics and associated biogeographic changes across southeast Australia. Sea-level changes since the Pliocene and reduction or disappearance of large waterbodies throughout the Pleistocene were determining factors in strong divergence across the clade, including the initial formation and maintenance of a cryptic species, N. 'flindersi'. Isolated climatic refugia and fragmentation due to lack of connected waterways maintained the identity and divergence of inter- and intraspecific lineages. Our historical findings suggest that predicted increases in aridification and sea level due to anthropogenic climate change might result in markedly different demographic impacts, both spatially and across different landscape types.

Application of the random forest algorithm to Streptococcus pyogenes response regulator allele variation: from machine learning to evolutionary models.

Group A Streptococcus (GAS) is a globally significant bacterial pathogen. The GAS genotyping gold standard characterises the nucleotide variation of emm, which encodes a surface-exposed protein that is recombinogenic and under immune-based selection pressure. Within a supervised learning methodology, we tested three random forest (RF) algorithms (Guided, Ordinary, and Regularized) and 53 GAS response regulator (RR) allele types to infer six genomic traits (emm-type, emm-subtype, tissue and country of sample, clinical outcomes, and isolate invasiveness). The Guided, Ordinary, and Regularized RF classifiers inferred the emm-type with accuracies of 96.7%, 95.7%, and 95.2%, using ten, three, and four RR alleles in the feature set, respectively. Notably, we inferred the emm-type with 93.7% accuracy using only mga2 and lrp. We demonstrated a utility for inferring emm-subtype (89.9%), country (88.6%), invasiveness (84.7%), but not clinical (56.9%), or tissue (56.4%), which is consistent with the complexity of GAS pathophysiology. We identified a novel cell wall-spanning domain (SF5), and proposed evolutionary pathways depicting the 'contrariwise' and 'likewise' chimeric deletion-fusion of emm and enn. We identified an intermediate strain, which provides evidence of the time-dependent excision of mga regulon genes. Overall, our workflow advances the understanding of the GAS mga regulon and its plasticity.

Lessons Learnt From Using the Machine Learning Random Forest Algorithm to Predict Virulence in Streptococcus pyogenes.

Group A Streptococcus is a globally significant human pathogen. The extensive variability of the GAS genome, virulence phenotypes and clinical outcomes, render it an excellent candidate for the application of genotype-phenotype association studies in the era of whole-genome sequencing. We have catalogued the distribution and diversity of the transcription regulators of GAS, and employed phylogenetics, concordance metrics and machine learning (ML) to test for associations. In this review, we communicate the lessons learnt in the context of the recent bacteria genotype-phenotype association studies of others that have utilised both genome-wide association studies (GWAS) and ML. We envisage a promising future for the application GWAS in bacteria genotype-phenotype association studies and foresee the increasing use of ML. However, progress in this field is hindered by several outstanding bottlenecks. These include the shortcomings that are observed when GWAS techniques that have been fine-tuned on human genomes, are applied to bacterial genomes. Furthermore, there is a deficit of easy-to-use end-to-end workflows, and a lag in the collection of detailed phenotype and clinical genomic metadata. We propose a novel quality control protocol for the collection of high-quality GAS virulence phenotype coupled to clinical outcome data. Finally, we incorporate this protocol into a workflow for testing genotype-phenotype associations using ML and 'linked' patient-microbe genome sets that better represent the infection event.

In silico characterisation of stand-alone response regulators of Streptococcus pyogenes.

Bacterial "stand-alone" response regulators (RRs) are pivotal to the control of gene transcription in response to changing cytosolic and extracellular microenvironments during infection. The genome of group A Streptococcus (GAS) encodes more than 30 stand-alone RRs that orchestrate the expression of virulence factors involved in infecting multiple tissues, so causing an array of potentially lethal human diseases. Here, we analysed the molecular epidemiology and biological associations in the coding sequences (CDSs) and upstream intergenic regions (IGRs) of 35 stand-alone RRs from a collection of global GAS genomes. Of the 944 genomes analysed, 97% encoded 32 or more of the 35 tested RRs. The length of RR CDSs ranged from 297 to 1587 nucleotides with an average nucleotide diversity (π) of 0.012, while the IGRs ranged from 51 to 666 nucleotides with average π of 0.017. We present new evidence of recombination in multiple RRs including mga, leading to mga-2 switching, emm-switching and emm-like gene chimerization, and the first instance of an isolate that encodes both mga-1 and mga-2. Recombination was also evident in rofA/nra and msmR loci with 15 emm-types represented in multiple FCT (fibronectin-binding, collagen-binding, T-antigen)-types, including novel emm-type/FCT-type pairings. Strong associations were observed between concatenated RR allele types, and emm-type, MLST-type, core genome phylogroup, and country of sampling. No strong associations were observed between individual loci and disease outcome. We propose that 11 RRs may form part of future refinement of GAS typing systems that reflect core genome evolutionary associations. This subgenomic analysis revealed allelic traits that were informative to the biological function, GAS strain definition, and regional outbreak detection.

Phylogenomic history of enigmatic pygmy perches: implications for biogeography, taxonomy and conservation.

Pygmy perches (Percichthyidae) are a group of poorly dispersing freshwater fishes that have a puzzling biogeographic disjunction across southern Australia. Current understanding of pygmy perch phylogenetic relationships suggests past east-west migrations across a vast expanse of now arid habitat in central southern Australia, a region lacking contemporary rivers. Pygmy perches also represent a threatened group with confusing taxonomy and potentially cryptic species diversity. Here, we present the first study of the evolutionary history of pygmy perches based on genome-wide information. Data from 13 991 ddRAD loci and a concatenated sequence of 1 075 734 bp were generated for all currently described and potentially cryptic species. Phylogenetic relationships, biogeographic history and cryptic diversification were inferred using a framework that combines phylogenomics, species delimitation and estimation of divergence times. The genome-wide phylogeny clarified the biogeographic history of pygmy perches, demonstrating multiple east-west events of divergence within the group across the Australian continent. These results also resolved discordance between nuclear and mitochondrial data from a previous study. In addition, we propose three cryptic species within a southwestern species complex. The finding of potentially new species demonstrates that pygmy perches may be even more susceptible to ecological and demographic threats than previously thought. Our results have substantial implications for improving conservation legislation of pygmy perch lineages, especially in southwestern Western Australia.

In silico characterisation of the two-component system regulators of Streptococcus pyogenes.

Bacteria respond to environmental changes through the co-ordinated regulation of gene expression, often mediated by two-component regulatory systems (TCS). Group A Streptococcus (GAS), a bacterium which infects multiple human body sites and causes multiple diseases, possesses up to 14 TCS. In this study we examined genetic variation in the coding sequences and non-coding DNA upstream of these TCS as a method for evaluating relationships between different GAS emm-types, and potential associations with GAS disease. Twelve of the 14 TCS were present in 90% of the genomes examined. The length of the intergenic regions (IGRs) upstream of TCS coding regions varied from 39 to 345 nucleotides, with an average nucleotide diversity of 0.0064. Overall, IGR allelic variation was generally conserved with an emm-type. Subsequent phylogenetic analysis of concatenated sequences based on all TCS IGR sequences grouped genomes of the same emm-type together. However grouping with emm-pattern and emm-cluster-types was much weaker, suggesting epidemiological and functional properties associated with the latter are not due to evolutionary relatedness of emm-types. All emm5, emm6 and most of the emm18 genomes, all historically considered rheumatogenic emm-types clustered together, suggesting a shared evolutionary history. However emm1, emm3 and several emm18 genomes did not cluster within this group. These latter emm18 isolates were epidemiologically distinct from other emm18 genomes in study, providing evidence for local variation. emm-types associated with invasive disease or nephritogenicity also did not cluster together. Considering the TCS coding sequences (cds), correlation with emm-type was weaker than for the IGRs, and no strong correlation with disease was observed. Deletion of the malate transporter, maeP, was identified that serves as a putative marker for the emm89.0 subtype, which has been implicated in invasive outbreaks. A recombination-related, subclade-forming DNA motif was identified in the putative receiver domain of the Spy1556 response regulator that correlated with throat-associated emm-pattern-type A-C strains.

In silico prediction of the G-protein coupled receptors expressed during the metamorphic molt of Sagmariasus verreauxi (Crustacea: Decapoda) by mining transcriptomic data: RNA-seq to repertoire.

Against a backdrop of food insecurity, the farming of decapod crustaceans is a rapidly expanding and globally significant source of food protein. Sagmariasus verreauxi spiny lobster, the subject of this study, are decapods of underdeveloped aquaculture potential. Crustacean neuropeptide G-protein coupled receptors (GPCRs) mediate endocrine pathways that are integral to animal fecundity, growth and survival. The potential use of novel biotechnologies to enhance GPCR-mediated physiology may assist in improving the health and productivity of farmed decapod populations. This study catalogues the GPCRs expressed in the early developmental stages, as well as adult tissues, with a view to illuminating key neuropeptide receptors. De novo assembled contiguous sequences generated from transcriptomic reads of metamorphic and post metamorphic S. verreauxi were filtered for seven transmembrane domains, and used as a reference for iterative re-mapping. Subsequent putative GPCR open reading frames (ORFs) were BLAST annotated, categorised, and compared to published orthologues based on phylogenetic analysis. A total of 85 GPCRs were digitally predicted, that represented each of the four arthropod subfamilies. They generally displayed low-level and non-differential metamorphic expression with few exceptions that we examined using RT-PCR and qPCR. Two putative CHH-like neuropeptide receptors were annotated. Three dimensional structural modelling suggests that these receptors exhibit a conserved extracellular ligand binding pocket, providing support to the notion that these receptors co-evolved with their ligands across Decapoda. This perhaps narrows the search for means to increase productivity of farmed decapod populations.

The case for investing in family planning in the Pacific: costs and benefits of reducing unmet need for contraception in Vanuatu and the Solomon Islands.

BACKGROUND: Unmet need for family planning in the Pacific is among the highest in the world. Better understanding of required investments and associated benefits of increased access to family planning in the Pacific may assist prioritisation and funding. METHODS: We modelled the costs and associated health, demographic and economic impacts of reducing unmet need for family planning between 2010-2025 in Vanuatu and the Solomon Islands. Baseline data were obtained from census reports, Demographic and Health Surveys, and UN agency reports. Using a demographic modelling program we compared a scenario of "no change in unmet need" with two distinct scenarios: 1) all family planning needs met by 2020; and, 2) all needs met by 2050. RESULTS: Meeting family planning needs by 2020 would increase prevalence of modern contraception in 2025 from 36.8 to 65.5% in Vanuatu and 28.5 to 37.6% in the Solomon Islands. Between 2010-2025 the average annual number of unintended pregnancies would decline by 68% in Vanuatu and 50% in the Solomon Islands, and high-risk births would fall by more than 20%, averting 2,573 maternal and infant deaths. Total fertility rates would fall from 4.1 to 2.2 in Vanuatu and 3.5 in the Solomon Islands, contributing to slowed population growth and lower dependency ratios. The direct cost of reducing unmet need by 2020 was estimated to be $5.19 million for Vanuatu and $3.36 million for the Solomon Islands between 2010-2025. Preventing unintended pregnancies would save $112 million in health and education expenditure. CONCLUSIONS: In small island developing states such as Vanuatu and the Solomon Islands, increasing investment in family planning would contribute to improved maternal and infant outcomes and substantial public sector savings.