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bioRxiv2018

Bacterial virulence against an oceanic bloom-forming phytoplankter is mediated by algal DMSP

Emiliania huxleyi is a bloom forming microalga that impacts the global sulfur cycle by producing large amounts of dimethylsulfoniopropionate (DMSP) and its volatile metabolic product dimethyl sulfide (DMS). Top-down regulation of E. huxleyi blooms is attributed to viruses and grazers, however, the possible involvement of algicidal bacteria in bloom demise is still elusive. We isolated from a North Atlantic E. huxleyi bloom a Roseobacter strain, Sulfitobacter D7, which exhibited algicidal effects against E. huxleyi upon co-culturing. Both the alga and the bacterium were found to co-occur during a natural E. huxleyi bloom, therefore establishing this host-pathogen system as an attractive, ecologically relevant model for studying alga-bacterium interaction in the oceans. During interaction, Sulfitobacter D7 consumed and metabolized algal DMSP to produce high amounts of methanethiol, an alternative product of DMSP catabolism. We revealed a unique strain-specific response, in which E. huxleyi strains that exuded higher amounts of DMSP were more susceptible to Sulfitobacter D7 infection. Intriguingly, exogenous application of DMSP enhanced bacterial virulence and induced susceptibility in a resistant algal strain to the bacterial pathogen. This DMSP-dependent pathogenicity was highly specific as compared to supplementation of propionate and glycerol. We propose a novel function for DMSP, in addition to its central role in mutualistic interactions, as a mediator of bacterial virulence that may regulate E. huxleyi blooms.

microbiology↗

bioRxiv2018

Genomic insights into metabolism and phylogeography of the mesophilic Thermotogae genus Mesotoga

The genus Mesotoga, the only described mesophilic Thermotogae lineage, is common in mesothermic anaerobic hydrocarbon-rich environments. Besides mesophily, Mesotoga displays lineage-specific phenotypes, such as no or little H2 production and dependence on sulfur-compound reduction, which may influence its ecological role. We used comparative genomics of 18 Mesotoga strains (pairwise 16S rRNA identity > 99%) and a transcriptome of M. prima to investigate how life at moderate temperatures affects phylogeography and to interrogate the genomic features of its lineage-specific metabolism. We propose that Mesotoga accomplish H2 oxidation and thiosulfate reduction using a sulfide dehydrogenase and a hydrogenase-complex and that a pyruvate:ferredoxin oxidoreductase acquired from Clostridia is responsible for oxidizing acetate. Phylogenetic analysis revealed three distinct Mesotoga lineages (89.6-99.9% average nucleotide identity [ANI] within lineages, 79.3-87.6% ANI between lineages) having different geographic distribution patterns and high levels of intra-lineage recombination but little geneflow between lineages. Including data from metagenomes, phylogeographic patterns suggest that geographical separation historically has been more important for Mesotoga than hyperthermophilic Thermotoga and we hypothesize that distribution of Mesotoga is constrained by their anaerobic lifestyle. Our data also suggest that recent anthropogenic activities and environments (e.g., wastewater treatment, oil exploration) have expanded Mesotoga habitats and dispersal capabilities.\n\nOriginality-Significance StatementThis study comprises one of the first whole-genome-based phylogeographic analyses of anaerobic mesophiles, and our data suggest that such microbes are more restricted by geography than are thermophiles (and mesophilic aerobes). This is likely to be a general trait for similar anaerobic organisms - and therefore broadly relevant to and testable in other environments. Moreover, Mesotoga bacteria are part of the largely understudied subsurface ecosystem that has relatively recently been recognized as a new and important biosphere. Understanding the forces responsible for the distribution of organisms in the subsurface, as well as the identification of genes responsible for Mesotogas distinct metabolism, will contribute to the understanding of these communities.

evolutionary biology↗

bioRxiv2018

The multidrug resistance efflux pump MexCD-OprJ is a switcher of the Pseudomonas aeruginosa quorum sensing response

Most antibiotic resistance genes acquired by human pathogens originate from environmental microorganisms. Therefore, understanding the additional functions of these genes, other than conferring antibiotic resistance, is relevant from an ecological point of view. We examined the effect that overexpression of the MexCD-OprJ multidrug efflux pump has in the physiology of the environmental opportunistic pathogen Pseudomonas aeruginosa. Overexpression of this intrinsic resistance determinant shuts down the P. aeruginosa quorum sensing (QS) response. Impaired QS response is due to the extrusion of 4-hydroxy-2-heptylquinoline (HHQ), the precursor of the Pseudomonas Quinolone Signal (PQS), leading to low PQS intracellular levels and reduced production of QS signal molecules. The P. aeruginosa QS response induces the expression of hundreds of genes, which can be costly unless such activation becomes beneficial for the bacterial population. While it is known that the QS response is modulated by population density, information on additional signals/cues that may alert the cells about the benefits of mounting the response is still scarce. It is possible that MexCD-OprJ plays a role in this particular aspect; our results indicate that, upon overexpression, MexCD-OprJ can act as a switcher in the QS population response. If MexCD-OprJ alleviate the cost associated to trigger the QS response when un-needed, it could be possible that MexCD-OprJ overproducer strains might be eventually selected even in the absence of antibiotic selective pressure, acting as antibiotic resistant cheaters in heterogeneous P. aeruginosa populations. This possibility may have potential implications for the treatment of P. aeruginosa chronic infections.

microbiology↗

bioRxiv2018

Did a plant-herbivore arms race drive chemical diversity in Euphorbia?

The genus Euphorbia is among the most diverse and species-rich plant genera on Earth, exhibiting a near-cosmopolitan distribution and extraordinary chemical diversity, especially across highly toxic macro-and polycyclic diterpenoids. However, very little is known about drivers and evolutionary origins of chemical diversity within Euphorbia. Here, we investigate 43 Euphorbia species to understand how geographic separation over evolutionary time has impacted chemical differentiation. We show that the structurally highly diverse Euphorbia diterpenoids are significantly reduced in species native to the Americas, compared to the Eurasian and African continents, where the genus originated. The localization of these compounds to young stems and roots suggest ecological relevance in herbivory defense and immunomodulatory defense mechanisms match diterpenoid levels, indicating chemoevolutionary adaptation to reduced herbivory pressure.\n\nOne Sentence SummaryGlobal chemo-evolutionary adaptation of Euphorbia affected immunomodulatory defense mechanisms.

evolutionary biology↗

bioRxiv2018

Microscopy quantification of microbial birth and death dynamics

Microbes live in dynamic environments where nutrient concentrations fluctuate. Quantifying fitness (birth and death) in a wide range of environments is critical for understanding microbial evolution as well as ecological interactions where one species alters the fitness of another. Here, using high-throughput time-lapse microscopy, we have quantified how Saccharomyces cerevisiae mutants incapable of synthesizing an essential metabolite grow or die in various concentrations of the required metabolite. We establish that cells normally expressing fluorescent proteins lose fluorescence upon death and that the total fluorescence in an imaging frame is proportional to the number of live cells even when cells form multiple layers. We validate our microscopy approach of measuring birth and death rates using flow cytometry, cell counting, and chemostat culturing. For lysine-requiring cells, very low concentrations of lysine are not detectably consumed and do not support cell birth, but delay the onset of death phase and reduce the death rate. In contrast, in low hypoxanthine, hypoxanthine-requiring cells can produce new cells, yet also die faster than in the absence of hypoxanthine. For both strains, birth rates under various metabolite concentrations are better described by the sigmoidal-shaped Moser model than the well-known Monod model, while death rates depend on the metabolite concentration and can vary with time. Our work reveals how time-lapse microscopy can be used to discover non-intuitive microbial dynamics and to quantify growth rates in many environments.

microbiology↗

bioRxiv2018

Archaeal, bacterial, and eukaryal microbial community structure of sediment and seawater in a coastal region near Puerto Nuevo, Baja California

Microbial communities control numerous biogeochemical processes critical for ecosystem function and health, particularly in coastal ecosystems. However, comparatively little is known about microbial community structure in coastal regions, such that basic patterns of microbial biodiversity, such as species richness and community composition, are generally understudied. To better understand the global patterns of microbial biodiversity in coastal ecosystems, we characterized sediment and seawater microbial communities for three sites near Puerto Nuevo (Baja California, Mexico) using 16S and 18S rRNA gene amplicon sequencing methods. We found that sediment bacteria, archaea, and eukaryote microbial communities contained approximately 5 x 10^2 fold greater operational taxonomic units (OTUs) than their seawater-based counterparts (p < 0.001). Further, distinct bacterial, archaeal and eukaryal phyla were found in sediment and seawater samples. The phyla Acidobacteria, Chlorobi, and Chloroflexi were found to be abundant and unique to the sediment and Cyanobacteria, Spirochaetae, and Woesearchaeota to the seawater environment. Apicomplexa and Arthropoda were abundant eukaryal phyla found uniquely in the sediment whereas the Cryptomonadales and Protalveolata were detected only in the seawater. Furthermore, bacterial and archaeal communities were statistically different by site (p < 0.05) in both seawater and sediment samples for the Major Outlet site, the site closest to a residential area. In contrast, eukaryal microbial communities were only different among sites in the seawater samples. Overall, these results suggest that our understanding of coastal microbial biodiversity patterns require spatially robust sampling. This study contributes to a growing body of foundational microbial biodiversity and ecology knowledge, providing context to the global change that is induced by urban development.

microbiology↗

bioRxiv2018

A novel oceanic uncultured temperate cyanophage lineage

Marine cyanobacteria are important contributors to primary production in the ocean and their viruses (cyanophages) affect the ocean microbial communities. Despite reports of lysogeny in marine cyanobacteria, the genome sequence of such temperate cyanophages remains unknown although genomic analysis indicate potential for lysogeny in certain marine cyanophages. Using assemblies from Red Sea and Tara Oceans metagenomes, we recovered genomes of a novel uncultured marine cyanophage lineage, which contain, in addition to common cyanophage genes, a phycobilisome degradation protein NblA, an integrase and a split DNA polymerase. The DNA polymerase forms a monophyletic clade with a DNA polymerase from a genomic island in Synechococcus WH8016. The island contains a relic prophage that does not resemble any previously reported cyanophage but shares several genes with the newly identified cyanophages reported here. Metagenomic recruitment indicates that the novel cyanophages are widespread, albeit at low abundance. Here we describe a novel potentially lysogenic cyanophage family, their abundance and distribution in the marine environment.\n\nOriginality-Significance StatementMarine cyanobacteria are major contributors to primary production in the ocean. Despite reports of lysogeny in marine cyanobacteria, genomes from lysogenic marine cyanophages have not been reported yet. Using metagenomics assemblies, we recovered complete genomes of a novel uncultured marine cyanophage lineage. Remarkably, the DNA polymerase of these uncultured phages forms a monophyletic clade with the DNA polymerase from a genomic island in Synechococcus WH8016. The genomic island contains a putative relic prophage that does not resemble any known cultured cyanophage but shares several genes with the newly identified cyanophage family. These findings provide both phylogenomic and abundance estimates that are missing from current ecological models of this important group of marine viruses.

microbiology↗

bioRxiv2018

Social organization and biting performance in Fukomys mole-rats (Bathyergidae, Rodentia)

A caste system, based on work activity and reproduction, has been proposed in the two African mole-rat species which are generally considered eusocial, Heterocephalus glaber and Fukomys damarensis. Social behaviour in other Fukomys species is key to understanding evolution of sociality within bathyergids, which display a social continuum among species from solitary to eusocial. Furthermore, insight in the social structure of colonies may be instrumental in understanding the observed, extensive intraspecific morphological variation and ultimately help species delimitation. For the first, time social organisation was studied in a colony of wild-caught Fukomys micklemi (Sekute cytotype) from Zambia. Data were collected on work behaviour and analysed against morphological variables and biting performance. Although there was considerable variation in the amount of work performed by each individual, clearly distinguishable castes were not found. Castes might represent an artificial subdivision, which does not necessarily reflect the dynamic changes within a colony. Variation in work may be the result of an ongoing process of continuous change, whereby a colony undergoes a certain evolution that is reflected in developmental patterns of individuals. Ecological factors will undoubtedly play an important role in colony evolution. Consequently, predictions made according to the Aridity Food Distribution Hypothesis should be tested, taking into account the possibility of a dynamic model as described here. The relation between biting performance and behavioural traits was investigated for the first time. Whereas differences in biting performance were strongly correlated with morphological parameters, relation between work and biting performance remains unclear.

evolutionary biology↗

bioRxiv2018

Finding CRISPR’s Niche: Oxygen and Temperature Shape the Incidence of Adaptive Immunity

Bacteria and archaea are locked in a near-constant battle with their viral pathogens. Despite previous mechanistic characterization of numerous prokaryotic defense strategies, the underlying ecological drivers of different strategies remain largely unknown and predicting which species will take which strategies remains a challenge. Here, we focus on the CRISPR immune strategy and develop a phylogenetically-corrected machine learning approach to build a predictive model of CRISPR incidence using data on over 100 traits across over 2600 species. We discover a strong but hitherto-unknown negative interaction between CRISPR and aerobicity, which we hypothesize may result from interference between CRISPR associated proteins and non-homologous end-joining DNA repair due to oxidative stress. Our predictive model also quantitatively confirms previous observations of an association between CRISPR and temperature. Finally, we contrast the environmental associations of different CRISPR system types (I, II, III) and restriction modification systems, all of which act as intracellular immune systems.

microbiology↗

bioRxiv2018

Taxonomy, phylogeny and biogeography of African spurfowls (Galliformes, Phasianidae, Coturnicinae, Pternistis spp.)

During much of the 20th Century, partridge/quail-like, Afro-Asian phasianine birds referred to commonly as African spurfowls, francolins and/or partridges had a tortuous taxonomic history. Because of striking autapomorphic differences in plumage, vocalizations and ecology in some of these taxa, as many as nine genera and nearly 200 clinal and/or idiosyncratic subspecies, embedded within a polyphyletic Perdicinae, were recognized. In 1963, two clades, 28 francolin and spurfowl species (fisante in Afrikaans) and 13 Afro-Asiatic francolins and partridges (patryse in Afrikaans), were combined into a single genus (Francolinus) - the largest within the Galliformes - comprising about 100 subspecies. Furthermore, fisante and patryse were partitioned into several unnamed \"Groups\" and four \"Unplaced\" species. Here, we use morphological, behavioural and DNA evidence to produce: a comprehensive revision of the taxonomy and phylogeny of the fisante clade; a stable classification system for tis component taxa; and hypotheses vis-a-vis eco-biogeographical processes that promoted their speciation and cladogenesis. We shift Francolinus spp. sensu stricto (members of the Spotted Group) and the Unplaced Francolinus gularis from the fisante clade to the patryse [discussed in Mandiwana-Neudani et al., in review]. An Unplaced fisant, F. nahani, is linked with Ptilopachus petrosus (another African endemic partridge ) within the Odontophoridae (New World Quails ). We recognize 25 species of fisante (hereafter spurfowls), including seven with subspecies. They comprise 34 terminal taxa placed within a single genus, Pternistis, sister to Ammoperdix and Perdicula spp., Coturnix quails and Alectoris partridges , within the now monophyletic Coturnicinae. Only one of four putative Groups of spurfowls, the Bare-throated Group, is monophyletic. The other three Groups (Montane, Scaly and Vermiculated) are para- or polyphyletic. Several species pairs of spurfowls, most notably P. afer and cranchii, hybridize in para/sympatry. One Bare-throated spurfowl, P. rufopictus, may be the product of stabilized hybridization between P. afer and/or cranchii and P. leucoscepus.

evolutionary biology↗

bioRxiv2018

Physiological starvation increases EGF-Ras-MAPK pathway activity during C. elegans vulval induction

Studying how molecular pathways respond to ecologically relevant environmental variation is fundamental to understand organismal development and its evolution. Here we characterize how starvation modulates Caenorhabditis elegans vulval cell fate patterning - an environmentally sensitive process, with a nevertheless robust output. Past research has shown many vulval mutants affecting EGF-Ras-MAPK, Delta-Notch and Wnt pathways to be suppressed by environmental factors, such as starvation. Here we aimed to resolve previous, seemingly contradictory, observations on how starvation modulates levels of vulval induction. Using the strong starvation suppression of the Vulvaless phenotype of lin-3/egf reduction-of-function mutations as an experimental paradigm, we first tested for a possible involvement of the sensory system in relaying starvation signals to affect vulval induction: mutation of various sensory inputs, DAF-2/Insulin or DAF-7/TGF-{beta} signaling did not abolish lin-3(rf) starvation suppression. In contrast, nutrient deprivation induced by mutation of the intestinal peptide transporter gene pept-1 or the TOR pathway component rsks-1 (the orthologue of mammalian P70S6K) very strongly suppressed lin-3(rf) mutant phenotypes. Therefore, physiologically starved animals induced by these mutations tightly recapitulated the effects of external starvation on vulval induction. While both starvation and pept-1 RNAi were sufficient to increase Ras and Notch pathway activities in vulval cells, the highly penetrant Vulvaless phenotype of a tissue-specific null allele of lin-3 was not suppressed by either condition. This and additional results indicate that partial lin-3 expression is required for starvation to affect vulval induction. These results suggest a cross-talk between nutrient deprivation, TOR-S6K and EGF-Ras-MAPK signaling during C. elegans vulval induction.

genetics↗

bioRxiv2018

Strategic allocation of working memory resource

Visual working memory (VWM), the brief retention of past visual information, supports a range of cognitive functions (Fukuda, Vogel, Mayr, & Awh, 2010; Johnson et al., 2013). The resource that supports VWM is limited, raising the question of how the brain allocates this limited resource to different objects. This question is even more interesting in ecological settings, in which objects are not equally important. In a psychophysical experiment, participants remembered the location of four targets with different probabilities of being tested after a delay. We then measured their memory accuracy of one of the targets. We found that participants allocated more resource to memoranda with higher priority, but underallocated resource to high- and overallocated to low-priority targets relative to the true probe probabilities. These results are well explained by a computational model in which resource is allocated to minimize expected estimation error. We replicated this finding in a second experiment in which participants bet on their memory fidelity after making the location estimate. The results of this experiment show that people 1) use information about memory quality and 2) minimize error even with an incentivized, alternative resource allocation strategy. Humans may mitigate the behavioral effects of a limited VWM through knowledge of memory fidelity and strategic resource allocation.

neuroscience↗

bioRxiv2018

Animal models with group-specific additive genetic variances: extending genetic group models

1. The animal model is a key tool in quantitative genetics and has been used extensively to estimate fundamental parameters, such as additive genetic variance, heritability, or inbreeding effects. An implicit assumption of animal models is that all founder individuals derive from a single population. This assumption is commonly violated, for instance in cross-bred livestock breeds, when an observed population receive immigrants, or when a meta-population is split into genetically differentiated subpopulations. Ignoring genetic differences among different source populations of founders may lead to biased parameter estimates, in particular for the additive genetic variance.\n\n2. To avoid such biases, genetic group models, extensions to the animal model that account for the presence of more than one genetic group, have been proposed. As a key limitation, the method to date only allows that the breeding values differ in their means, but not in their variances among the groups. Methodology previously proposed to account for group-specific variances included terms for segregation variance, which rendered the models infeasibly complex for application to most real study systems.\n\n3. Here we explain why segregation variances are often negligible when analyzing the complex polygenic traits that are frequently the focus of evolutionary ecologists and animal breeders. Based on this we suggest an extension of the animal model that permits estimation of group-specific additive genetic variances. This is achieved by employing group-specific relatedness matrices for the breeding value components attributable to different genetic groups. We derive these matrices by decomposing the full relatedness matrix via the generalized Cholesky decomposition, and by scaling the respective matrix components for each group. To this end, we propose a computationally convenient approximation for the matrix component that encodes for the Mendelian sampling variance. Although convenient, this approximation is not critical.\n\n4. Simulations and an example from an insular meta-population of house sparrows in Norway with three genetic groups illustrate that the method is successful in estimating group-specific additive genetic variances and that segregation variances are indeed negligible in the empirical example.\n\n5. Quantifying differences in additive genetic variance within and among populations is of major biological interest in ecology, evolution, and animal and plant breeding. The proposed method allows to estimate such differences for subpopulations that form a connected meta-population, which may also be useful to study temporal or spatial variation of additive genetic variance.

evolutionary biology↗

bioRxiv2018

Thermosipho spp. immune system differences affect variation in genome size and geographical distributions

Thermosipho species inhabit thermal environments such as marine hydrothermal vents, petroleum reservoirs and terrestrial hot springs. A 16S rRNA phylogeny of available Thermosipho spp. sequences suggested habitat specialists adapted to living in hydrothermal vents only, and habitat generalists inhabiting oil reservoirs, hydrothermal vents and hotsprings. Comparative genomics of 15 Thermosipho genomes separated them into three distinct species with different habitat distributions: the widely distributed T. africanus and the more specialized, T. melanesiensis and T. affectus. Moreover, the species can be differentiated on the basis of genome size, genome content and immune system composition. For instance, the T. africanus genomes are largest and contained the most carbohydrate metabolism genes, which could explain why these isolates were obtained from ecologically more divergent habitats. Nonetheless, all the Thermosipho genomes, like other Thermotogae genomes, show evidence of genome streamlining. Genome size differences between the species could further be correlated to differences in defense capacities against foreign DNA, which influence recombination via HGT. The smallest genomes are found in T. affectus that contain both CRISPR-cas Type I and III systems, but no RM system genes. We suggest that this has caused these genomes to be almost devoid of mobile elements, contrasting the two other species genomes that contain a higher abundance of mobile elements combined with different immune system configurations. Taken together, the comparative genomic analyses of Thermosipho spp. revealed genetic variation allowing habitat differentiation within the genus as well as differentiation with respect to invading mobile DNA.

microbiology↗

bioRxiv2018

Conservation and Divergence in the Asexual Sporulation Gene Regulatory Network Across a Genus of Filamentous Fungi

Asexual sporulation is fundamental to the ecology and lifestyle of filamentous fungi and can facilitate both plant and human infection. In Aspergillus, the production of asexual spores is primarily governed by the BrlA[->]AbaA[->]WetA regulatory cascade. The final step in this cascade is controlled by the WetA protein and not only governs the morphological differentiation of spores but also the production and deposition of diverse metabolites into spores. While WetA is conserved across the genus Aspergillus, the structure and degree of conservation of the wetA gene regulatory network (GRN) remains largely unknown. We carried out comparative transcriptome analyses between wetA null mutant and wild type asexual spores in three representative species spanning the diversity of the genus Aspergillus: A. nidulans, A. flavus, and A. fumigatus. We discovered that WetA regulates asexual sporulation in all three species via a negative feedback loop that represses BrlA, the cascades first step. Furthermore, ChIP-seq experiments in A. nidulans asexual spores suggest that WetA is a DNA-binding protein that interacts with a novel regulatory motif. Several global regulators known to bridge spore production and the production of secondary metabolites show species-specific regulatory patterns in our data. These results suggest that the BrlA[->]AbaA[->]WetA cascades regulatory role in cellular and chemical asexual spore development is functionally conserved, but that the wetA-associated GRN has diverged during Aspergillus evolution.

microbiology↗

bioRxiv2018

Genetic characterization of invasive house mouse populations on small islands

House mice (Mus musculus) have dispersed to nearly every major landmass around the globe as a result of human activity. They are a highly successful invasive species, but their presence can be devastating for native ecosystems. This is particularly true on small offshore islands where mouse populations may grow unchecked by predators. Here we use genome-wide SNP genotypes to examine ancestry and population structure on two islands of ecological interest - Southeast Farallon Island, near San Francisco, CA; and Floreana Island in the Galapagos - in the context of a total cohort of 520 mice with diverse geographic origins, as a first step towards genetically-based eradication campaigns. We show that Farallon and Floreana mice, like those from previously-studied islands in both the Atlantic and Pacific Oceans, are of admixed European ancestry. We find that these populations are on average more inbred than mainland ones and passed through a strong colonization bottleneck with little subsequent genetic exchange. Finally we show that rodenticide resistance alleles present in parts of Europe are absent from all island populations studied. Our results add nuance to previous studies of island populations based on mitochondrial sequences or small numbers of microsatellites and will be useful for future eradication and monitoring efforts.

genetics↗

bioRxiv2018

Utilising the boundary layer to help restore the connectivity of fish habitats and populations

SignificanceHabitat fragmentation is a significant contributor to the worldwide decline of freshwater ecosystem health, the most pervasive cause of which is culverts. Culverts act as a barrier to fish movement, impacting feeding, predator avoidance, spawning, and community structures. Here we show that a common remediation strategy that involves baffles, is detrimental to the successful passage of small bodied and juvenile fish at high velocities. To remedy this widespread problem, we present a novel remediation design that benefits a range of small-bodied species and juvenile fish at the same high velocities, regardless of morphology or ecological niche. The application of this remediation design may be expanded to any smooth surfaced anthropogenic structure, to improve fish passage and restore ecosystem functionality.\n\nAbstractCulverts are a major cause of habitat fragmentation in freshwater ecosystems, are a barrier to fish movement, and are regarded as a significant contributor in the decline of freshwater fish populations globally. To try to address this, various culvert remediation designs have been implemented, including the installation of vertical baffles and the provision of naturalistic (rock) substrates. While remediation strategies generally aim to reduce the velocity of water flowing through the structure, there is often resistance to their use because the resultant reduction in culvert discharge can negatively impact upstream flooding while also resulting in debris clogging and increased culvert maintenance costs. In addition, baffles markedly increase water turbulence that may be detrimental to passage by some fish species or size classes. Here we present some novel remediation designs that exploit the reduced water velocity in boundary layers along the culvert wall to enhance fish passage without significantly compromising discharge capacity. These longitudinal designs produce an expanded reduced velocity zone along the culvert margins that generate minimal turbulence. We show that these novel designs are significantly advantageous to the swimming endurance and traversability for six small-bodied Australian fish species. We also provide data on how and why some culvert baffle designs may impede small-bodied fish passage. This data scales with increasing water velocity, encompassing inter-specific differences in swimming capacity. These results have broad implications for fish community structure and the requirement of juvenile cohort of large-bodied commercially important species where baffles have been implemented to facilitate fish passage.

animal behavior and cognition↗

bioRxiv2018

Extreme and rapid bursts of functional adaptations shape bite force in amniotes

Adaptation is the fundamental driver of functional and biomechanical evolution and can be linked to rates of phenotypic trait evolution. Significant shifts in evolutionary rates are seen as instances of exceptional adaptation. However, whether or not signatures of exceptional adaptations (elevated rates) can be distinguished from general adaptations (background rate) in biomechanical traits remains to be tested in a robust statistical framework. Here, we apply a recently developed phylogenetic statistical approach for detecting exceptional adaptations in bite force, in a large group of terrestrial vertebrates, the amniotes. Our results show that bite force in amniotes evolved through multiple bursts of exceptional changes, whereby whole groups - including Darwin';s finches, maniraptoran dinosaurs (group of non-avian dinosaurs including birds), anthropoids and hominins (the group of species including modern humans) - experienced significant rate increases compared to the background rate. However, in most parts of the amniote tree of life we find no exceptional rate increases, indicating that coevolution with body size was primarily responsible for the patterns observed in bite force. Our approach represents a template for future studies in functional morphology and biomechanics, where exceptional functional adaptations can be quantified and potentially linked to specific ecological factors underpinning major evolutionary radiations.

evolutionary biology↗