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bioRxiv2018

A multi-species repository of social networks

Social network analysis is an invaluable tool to understand the patterns, evolution, and consequences of sociality. Comparative studies over the spectrum of sociality across taxonomic groups are particularly valuable. Such studies however require quantitative information on social interactions across multiple species which is not easily available. We introduce the Animal Social Network Repository (ASNR) as the first multi-taxonomic repository that collates more than 650 social networks from 47 species, including those of mammals, reptiles, fish, birds, and insects. The repository was created by consolidating social network datasets from the literature on wild and captive animals into a consistent and easy-to-use network data format. The repository is archived at https://bansallab.github.io/asnr/. ASNR has tremendous research potential, including testing hypotheses in the fields of animal ecology, social behavior, epidemiology and evolutionary biology.

animal behavior and cognition↗

bioRxiv2018

Cultural Selection Shapes Network Structure

Cultural evolution relies on the social transmission of cultural traits across a population, along the ties of an underlying social network that emerges from non-random interactions among individuals. Research indicates that the structure of those interaction networks affects information spread, and thus a populations ability for cumulative culture. However, how network structure itself is driven by population-culture co-evolution remains largely unclear. We use a simple but realistic model of complex dynamic social networks to investigate how populations negotiate the trade-off between acquiring new skills and getting better at existing skills, and how this trade-off, in turn, shapes the social structure of the population. Our results reveal unexpected eco-evolutionary feedback from culture onto social network structure and vice versa. We show that selecting for generalists (favouring a broad repertoire of skills) results in sparsely connected networks with highly diverse skill sets, whereas selecting for specialists (favouring skill proficiency) results in densely connected networks and a population that specializes on the same few skills on which everyone is an expert. Surprisingly, cultural selection for specialisation can act as an \"ecological trap\" where it can take a long time for a specialist population to adapt to a generalist world. Our model advances our understanding of the complex feedbacks in cultural evolution and demonstrates how individual-level behaviour can lead to the emergence of population-level structure.

evolutionary biology↗

bioRxiv2018

Plastic multicellular development of Myxococcus xanthus: genotype-environment interactions in a physical gradient

In order to investigate the contribution of the physical environment to variation in multicellular development of Myxococcus xanthus, phenotypes developed by different genotypes in a gradient of substrate stiffness conditions were quantitatively characterized. Statistical analysis showed that plastic phenotypes result from the genotype, the substrate conditions and the interaction between them. Also, phenotypes were expressed with scale- and trait-specificity. Overall, the presented information highlights the constructive role of the physical context in the development of microbial multicellularity, with both ecological and evolutionary implications.

developmental biology↗

bioRxiv2018

Population genomic analyses reveal a highly differentiated genetic cluster of northern goshawks (Accipiter gentilis laingi) in Haida Gwaii

Accurate knowledge of geographic ranges and genetic relationships among populations is important when managing a species or population of conservation concern. In the western Canadian province of British Columbia, a subspecies of the northern goshawk (Accipiter gentilis laingi) is designated as Threatened under the Canadian Species at Risk Act. Historically, the range of this bird of prey has been ambiguous and its genetic distinctness from the other North American subspecies (Accipiter gentilis atricapillus) has not been well established. Given the uncertainty in using morphological traits to assign individual goshawks to these two subspecies, we analyzed genomic relationships in tens of thousands of single nucleotide polymorphisms identified using genotyping-bysequencing of high-quality genetic samples. This genome-wide analysis revealed a genetically distinct population of northern goshawks on the archipelago of Haida Gwaii and subtle genetic structuring among the remainder of our sampling sites within North America. Following from this analysis, we developed targeted genotyping assays for ten loci that are highly differentiated between the two main genetic clusters, allowing the addition of hundreds of low-quality samples to our analysis. This additional information confirmed that the distinct genetic cluster on Haida Gwaii is restricted to that archipelago. As the laingi form was originally described as being based in Haida Gwaii, where the type specimen of that form is from, further study (especially of morphological traits) may indicate a need to restrict this name to the Haida Gwaii genetic cluster. Regardless of taxonomic treatment, our finding of a distinct Haida Gwaii genetic cluster along with the small and historically declining population size of the Haida Gwaii population suggests a high risk of extinction of an ecologically and genetically distinct form of northern goshawk. Outside of Haida Gwaii, sampling regions along the coast of BC and southeast Alaska (often considered regions inhabited by laingi) show some subtle differentiation from other North American regions. We anticipate that these results will increase the effectiveness of conservation management of northern goshawks in northwestern North America. More broadly, other conservation-related studies of genetic variation may benefit from the two-step approach we employed that first surveys genomic variation using high-quality samples and then genotypes low-quality samples at particularly informative loci.

genomics↗

bioRxiv2018

Susceptibility of Spotted Doves (Streptopelia chinensis) to Experimental Infection with the SFTS Phlebovirus

BackgroundSevere fever with thrombocytopenia syndrome virus (SFTSV), an emerging human pathogen naturally transmitted by ticks, has spread widely during the last few years. Although SFTSV has been detected in wild birds, the natural reservoir and amplifying hosts for the virus have not been well-studied.\n\nMethodology/Principle FindingsHere we report an experimental infection of spotted doves (Streptopelia chinensis) with two strains of SFTSV, JS2010-14 (hereafter JS2010), a Chinese lineage strain and JS2014-16 (JS2014) from a Japanese lineage, which represent the main viral genotypes currently circulating in East Asia. We determined that spotted doves were susceptible to SFTSV and the severity of the viremia was dose-dependent. When challenged with 107 and 105 PFU, all doves developed viremia which peaked 3-5 days post-infection (dpi). A subset (25-62.5%) of the birds challenged at 103 PFU, developed viremia. Virulence of SFTSV in spotted doves appeared to be strain-dependent. Infection with the strain of JS2014 led to a death rate of 12.5% and higher viremia titers in experimentally inoculated birds. The doves inoculated with the JS2010 strain survived infection with relatively lower virus titers in the blood.\n\nConclusions/SignificanceOur results suggest that spotted doves, one of the most abundant bird species in China, could be a competent amplifying host of SFTSV, the strain of the Japanese lineage in particular, with higher viremia titers and play an important role in the transmission of SFTSV. Our observations shed light on the ecology of SFTSV which could benefit the implementation of future surveillance and control programs.\n\nAuthor SummarySevere fever with thrombocytopenia syndrome virus (SFTSV), an emerging human pathogen naturally transmitted by ticks. Our recent study have showed that some species of migratory birds, such as swan geese and spotted doves, could be parasitized by H. longicornis, and antibodies against the virus could also be determined in these birds, which showed that migratory birds could be infected by SFTSV naturally. Other studies have reported that migratory bird routes and the distribution of H. longicornis in East Asia overlap with the geographic distribution of SFTSV. Migratory birds are known to be carriers and transmitters of infectious agents, like the causative agents of influenza, West Nile encephalitis, and Lyme disease. Wild birds often travel long distances carrying various parasites, including ticks, which may be infected with viruses and bacteria. It is therefore reasonable to hypothesize that migratory birds may have played an important role in dispersing H. longicornis-borne SFTSV in both scenarios, either the birds are infected directly with the virus or the birds are carriers of parasitic ticks that are infected with the virus. Here we report an experimental infection of spotted doves (Streptopelia chinensis) with two strains of SFTSV, JS2010-14 (hereafter JS2010), a Chinese lineage strain and JS2014-16 (JS2014) from a Japanese lineage, which represent the main viral genotypes currently circulating in East Asia. We determined that spotted doves were susceptible to SFTSV and the severity of the viremia was dose-dependent.\n\nInterestingly, virulence of SFTSV in spotted doves appeared to be strain-dependent. Infection with the strain of JS2014 led to a death rate of 12.5% and higher viremia titers in experimentally inoculated birds. The doves inoculated with the JS2010 strain survived infection with relatively lower virus titers in the blood. These findings provide novel insights for understanding the rapid spread of the virus in a short time span, especially the SFTSV strains from the Japanese lineage (genotype E), which presented cross ocean transmission.

microbiology↗

bioRxiv2018

A phylogenomic framework, evolutionary timeline, and genomic resources for comparative studies of decapod crustaceans

Comprising over 15,000 living species, decapods (crabs, shrimp, and lobsters) are the most instantly recognizable crustaceans, representing a considerable global food source. Although decapod systematics have received much study, limitations of morphological and Sanger sequence data have yet to produce a consensus for higher-level relationships. Here we introduce a new anchored hybrid enrichment kit for decapod phylogenetics designed from genomic and transcriptomic sequences that we used to capture new high-throughput sequence data from 94 species, including 58 of 179 extant decapod families, and 11 of 12 major lineages. The enrichment kit yields 410 loci (>86,000 bp) conserved across all lineages of Decapoda, eight times more molecular data than any prior study. Phylogenomic analyses recover a robust decapod tree of life strongly supporting the monophyly of all infraorders, and monophyly of each of the reptant, lobster, and crab groups, with some results supporting pleocyemate monophyly. We show that crown decapods diverged in the Late Ordovician and most crown lineages diverged in the Triassic-Jurassic, highlighting a cryptic Paleozoic history, and post-extinction diversification. New insights into decapod relationships provide a phylogenomic window into morphology and behavior, and a basis to rapidly and cheaply expand sampling in this economically and ecologically significant invertebrate clade.

evolutionary biology↗

bioRxiv2018

Female variation in allocation of steroid hormones, antioxidants and fatty acids: a multilevel analysis in a wild passerine bird

The environment where an embryo develops can be influenced by components of maternal origin, which can shape offspring phenotypes and therefore maternal fitness. In birds that produce more than one egg per clutch, females differ in the concentration of components they allocate into the yolk along the laying sequence. However, identification of processes that shape female yolk allocation and thus offspring phenotype still remains a major challenge within evolutionary ecology. A way to increase our understanding is by acknowledging that allocation patterns can differ depending on the level of analysis, such as the population versus the among-female (within-population) level. We employed mixed models to analyze at both levels the variation in allocation along the laying sequence of four steroid hormones, three antioxidants, and four groups of fatty acids present in the egg yolks of wild great tits (Parus major). We also quantified repeatabilities for each component to study female consistency. At a population level, the concentrations/proportions of five yolk components varied along the laying sequence, implying that the developmental environment is different for offspring developing in first versus last eggs. Females varied substantially in the mean allocation of components and in their plasticity along the laying sequence. For most components, these two parameters were negatively correlated. Females were also remarkably repeatable in their allocation. Overall, our data emphasize the need to account for female variation in yolk allocation along the laying sequence at multiple levels, as variation at a population level is underpinned by different individual patterns. Our findings also highlight the importance of considering both levels of analysis in future studies investigating the causes and fitness consequences of yolk compounds. Finally, our results on female repeatability confirm that analyzing one egg per nest is a suitable way to address the consequences of yolk resource deposition for the offspring.

physiology↗

bioRxiv2018

Reannotation of the ribonucleotide reductase in a cyanophage reveals life history strategies within the virioplankton

Ribonucleotide reductases (RNRs) are ancient enzymes that catalyze the reduction of ribonucleotides to deoxyribonucleotides. They are required for virtually all cellular life and are prominent within viral genomes. RNRs share a common ancestor and must generate a protein radical for direct ribonucleotide reduction. The mechanisms by which RNRs produce radicals are diverse and divide RNRs into three major classes and several subclasses. The diversity of radical generation methods means that cellular organisms and viruses typically contain the RNR best-suited to the environmental conditions surrounding DNA replication. However, such diversity has also fostered high rates of RNR misannotation within subject sequence databases. These misannotations have resulted in incorrect translative presumptions of RNR biochemistry and have diminished the utility of this marker gene for ecological studies of viruses. We discovered a misannotation of the RNR gene within the Prochlorococcus phage P-SSP7 genome, which caused a chain of misannotations within commonly observed RNR genes from marine virioplankton communities. These RNRs are found in marine cyanopodo- and cyanosiphoviruses and are currently misannotated as Class II RNRs, which are O2-independent and require cofactor B12. In fact, these cyanoviral RNRs are Class I enzymes that are O2-dependent and may require a di-metal cofactor made of Fe, Mn, or a combination of the two metals. The discovery of an overlooked Class I {beta} subunit in the P-SSP7 genome, together with phylogenetic analysis of the and {beta} subunits confirms that the RNR from P-SSP7 is a Class I RNR. Phylogenetic and conserved residue analyses also suggest that the P-SSP7 RNR may constitute a novel Class I subclass. The reannotation of the RNR clade represented by P-SSP7 means that most lytic cyanophage contain Class I RNRs, while their hosts, B12-producing Synechococcus and Prochlorococcus, contain Class II RNRs. By using a Class I RNR, cyanophage avoid a dependence on host-produced B12, a more effective strategy for a lytic virus. The discovery of a novel RNR {beta} subunit within cyanopodoviruses also implies that some unknown viral genes may be familiar cellular genes that are too divergent for homology-based annotation methods to identify.

bioinformatics↗

bioRxiv2018

Phylogenomics, biogeography, and evolution in the American palm genus Brahea

Background and AimsSlow rates of molecular evolution at low taxonomic levels hamper studies of relationships among species, and subsequent biogeographic and evolutionary analyses. An example is the genus Brahea, which is among the most poorly understood lineages of American palms and is characterized by a wide variety of growth forms and intermediate morphological features.\n\nMethodsWe generated approximately 400 kb of genome-scale data from all three genomes for the 11 currently described species of Brahea to infer phylogenetic relationships, reconstruct ancestral growth form, estimate ancestral geographic ranges, and test for niche equivalency among closely related species with geographic overlap.\n\nKey ResultsRelationships receive strong support, and conform to previous subgeneric assignments, except for placement of the dwarf species B. moorei within subgenus Erythea. Our robust phylogenetic hypothesis reveals trends in growth form including an overall increase in height in the B. armata clade, and independent evolution of dwarf forms from taller ancestors in the B. pimo and B. dulcis clades. Ancestral range estimation reveals roles of dispersal (e.g. B. edulis on Guadalupe Island) and sympatric speciation in some cases (e.g. in the B. armata clade), but is equivocal in others (e.g. in the B. pimo clade). We find evidence of niche non-equivalency among species within the B. armata clade in northwestern Mexico, and some evidence of niche non-equivalency between B. berlandieri and B. dulcis, the former of which is synonymized under B. dulcis.\n\nConclusionsOur findings have implications for the complex biogeographic history in Central America and Mexico, suggesting that sympatric speciation and dispersal are the predominant processes of species diversification. Future studies should include population-level sampling across the genus, along with morphological and ecological information, to assess distinctness among species and, particularly, levels of gene flow, in an integrative fashion.

evolutionary biology↗

bioRxiv2018

A retrospective assessment of temperature trends in northern Europe reveals a deep impact on the life cycle of Ixodes ricinus (Acarina: Ixodidae).

1. AbstractThis study modelled the changes in the development processes of the health-threatening tick Ixodes acinus in northern Europe as driven by the trends of temperature (1950-2016). I used the ECA&D dataset of temperature interpolated at a resolution of 0.25o as the base data for further calculations, which were based on a previously developed process-driven model of the tick. I used the annual accumulated temperature in the period 1950-2016 to obtain the development rates of the oviposition, incubation, larva-nymph, and nymph-adult molts. Annual values were used to ascertain the trend in development rates of each stage. The ecological division of northern Europe (LANMAP2) was used to summarize results along large regions. The temperature in the years 1950-2016 clearly increased in every area of the target territory. The largest increase was observed for a wide territory eastern to Baltic countries, north-eastern Sweden and northern Finland. The development rates of every tested life cycle process had a trend to being faster throughout the time series. Moderate to high increase of the oviposition rates (70%-100% faster) resulted in central Sweden, Baltic countries, parts of Finland, and adjacent territories of Russia. Faster (70%-90%) incubation and molting rates were consistently observed in the same territories and also in large areas of western Norway. The trend of temperature in the period 1950-2016 shows a consistent inflection point around the year 1990, when the slope of the time series of temperature drastically rose. A comparison between 1950-1990 and 1991-2016 demonstrated that annual accumulated temperature was 86% and 26% higher in the Alpine regions, 7%-8% in the Atlantic and 157%, 10% and 16% in Boreal, Continental, and Nemoral regions, respectively. It is concluded that (i) accumulated annual temperature is clearly increasing in the studied territory, (ii) changes were larger since approximately the year 1990, and (iii) these changes have a deep impact on the life cycle of the tick I. ricinus. Faster development rates could be part of the processes driving the reported spread of the tick in the target area and should be considered as a serious thread to human health.

epidemiology↗

bioRxiv2018

Eliminating yellow fever epidemics in Africa: vaccine demand forecast and impact modelling

BackgroundTo counter the increasing global risk of Yellow fever (YF), the World Health Organisation initiated the Eliminate Yellow fever Epidemics (EYE) strategy. Estimating YF burden, as well as vaccine impact, while accounting for the features of urban YF transmission such as indirect benefits of vaccination, is key to informing this strategy.\n\nMethods and FindingsWe developed two model variants to estimate YF burden in sub-Saharan Africa, assuming all infections stem from either the sylvatic or the urban cycle of the disease. Both relied on an ecological niche model fitted to the local presence of any YF reported event in 34 African countries. We calibrated under-reporting using independent estimates of transmission intensity provided by 12 serological surveys performed in 11 countries. We calculated local numbers of YF infections, deaths and disability-adjusted life years (DALYs) lost based on estimated transmission intensity while accounting for time-varying vaccination coverage. We estimated vaccine demand and impact of future preventive mass vaccination campaigns (PMVCs) according to various vaccination scenarios.\n\nVaccination activities conducted in Africa between 2005 and 2017 were estimated to prevent from 3.3 (95% CI 1.2-7.7) to 6.1 (95% CI 2.4-13.2) millions of deaths over the lifetime of vaccinees, representing extreme scenarios of all transmission due to the sylvatic or the urban cycle, respectively. By prioritizing provinces based on the risk of urban YF transmission, an average of 37.7 million annual doses for PMVCs over eight years would avert an estimated 9,900,000 (95% CI 7,000,000-13,400,000) infections and 480,000 (180,000-1,140,000) deaths over the lifetime of vaccinees, corresponding to 1.7 (0.7-4.1) deaths averted per 1,000 vaccine doses.\n\nLimitations include substantial uncertainty in the estimates arising from the scarcity of reliable data from surveillance and serological surveys.\n\nConclusionsBy estimating YF burden and vaccine impact over a range of spatial and temporal scales, while accounting for the specificity of urban transmission, our model can be used to inform the current EYE strategy.

epidemiology↗

bioRxiv2018

Discovery of Drosophila melanogaster from Wild African Environments and Genomic Insights into Species History

A long-standing enigma concerns the geographic and ecological origins of the intensively studied vinegar fly, Drosophila melanogaster, a globally widespread species [1] which \"has invariably appeared to be a strict human commensal\" [2]. In spite of its sub-Saharan origins, this species has never been reported from undisturbed wilderness environments that might reflect its pre-commensal niche [3]. Here, we document the collection of 288 D. melanogaster individuals from African wilderness areas in Zambia, Zimbabwe, and Namibia. After sequencing the genomes of 17 flies collected from Kafue National Park, Zambia, we found reduced genetic diversity relative to town populations, elevated chromosomal inversion frequencies, and strong differences at specific genes including known insecticide targets. Combining these new genomes with prior data enabled us to gain novel insights into the history of this species geographic expansion. Our demographic estimates indicated that an expansion from southern Africa began approximately 10,000 years ago, with a Saharan crossing soon after, but expansion from the Middle East into Europe did not begin until roughly 1,400 years ago. This improved model of demographic history will provide a critical resource for future evolutionary and genomic studies of this key model organism. Our results add historical context to the species human association, and the opportunity to study wilderness populations opens the door for future studies on the biological basis of its adaptation to human environments.

genomics↗

bioRxiv2018

Spatial structure arising from chase-escape interactions with crowding

Movement of individuals, mediated by localised interactions, plays a key role in numerous processes including cell biology and ecology. In this work, we investigate an individual-based model accounting for various intraspecies and interspecies interactions in a community consisting of two distinct species. In this framework we consider one species to be chasers and the other species to be escapees, and we focus on chase-escape dynamics where the chasers are biased to move towards the escapees, and the escapees are biased to move away from the chasers. This framework allows us to explore how individual-level directional interactions scale up to influence spatial structure at the macroscale. To focus exclusively on the role of motility and directional bias in determining spatial structure, we consider conservative communities where the number of individuals in each species remains constant. To provide additional information about the individual-based model, we also present a mathematically tractable deterministic approximation based on describing the evolution of the spatial moments. We explore how different features of interactions including interaction strength, spatial extent of interaction, and relative density of species influence the formation of the macroscale spatial patterns.

biophysics↗

bioRxiv2018

Acquired interbacterial defense systems protect against interspecies antagonism in the human gut microbiome

The impact of direct interactions between co-resident microbes on microbiome composition is not well understood. Here we report the occurrence of acquired interbacterial defense (AID) gene clusters in bacterial residents of the human gut microbiome. These clusters encode arrays of immunity genes that protect against type VI secretion toxin-mediated intra- and inter-species bacterial antagonism. Moreover, the clusters reside on mobile elements and we demonstrate that their transfer is sufficient to confer toxin resistance in vitro and in gnotobiotic mice. Finally, we identify and validate the protective capacity of a recombinase-associated AID subtype (rAID-1) present broadly in Bacteroidales genomes. These rAID-1 gene clusters have a structure suggestive of active gene acquisition and include predicted immunity factors of toxins deriving from diverse organisms. Our data suggest that neutralization of contact-dependent interbacterial antagonism via AID systems shapes human gut microbiome ecology.

microbiology↗

bioRxiv2018

A database of egg size and shape from more than 6,700 insect species

1Offspring size is a fundamental trait in disparate biological fields of study. This trait can be measured as the size of plant seeds, animal eggs, or live young, and it influences ecological interactions, organism fitness, maternal investment, and embryonic development. Although multiple evolutionary processes have been predicted to drive the evolution of offspring size, the phylogenetic distribution of this trait remains poorly understood, due to the difficulty of reliably collecting and comparing offspring size data from many species. Here we present a database of 10,449 morphological descriptions of insect eggs, with records for 6,706 unique insect species and representatives from every extant hexapod order. The dataset includes eggs whose volumes span more than eight orders of magnitude. We created this database by partially automating the extraction of egg traits from the primary literature. In the process, we overcame challenges associated with large-scale phenotyping by designing and employing custom bioinformatic solutions to common problems. We matched the taxa in this database to the currently accepted scientific names in taxonomic and genetic databases, which will facilitate the use of this data for testing pressing evolutionary hypotheses in offspring size evolution.

evolutionary biology↗

bioRxiv2018

Insights into the microbiota of Asian seabass (Lates calcarifer) with tenacibaculosis symptoms and description of sp. nov. Tenacibaculum singaporense

Outbreaks of diseases in farmed fish remain a recurring problem despite the development of vaccines and improved hygiene standards on aquaculture farms. One commonly observed bacterial disease in tropical aquaculture of the South-East Asian region is tenacibaculosis, which is attributed to members of the Bacteroidetes genus Tenacibaculum, most notably T. maritimum. The impact of tenacibaculosis on fish microbiota remains poorly understood. In this study, we analysed the microbiota of different tissue types of commercially reared Asian seabass (Lates calcarifer) that showed symptoms of tenacibaculosis and compared the microbial communities to those of healthy and experimentally infected fish that were exposed to diseased farm fish. The microbiota of diseased farm fish was dominated by Proteobacteria (relative abundance{+/-}standard deviation, 74.5%{+/-}22.8%) and Bacteroidetes (18.07%{+/-}21.7%), the latter mainly comprised by a high abundance of Tenacibaculum species (17.6%{+/-}20.7%). In healthy seabass Proteobacteria had also highest relative abundance (48.04%{+/-}0.02%), but Firmicutes (34.2%{+/-}0.02%) and Fusobacteria (12.0%{+/-}0.03%) were the next two major constituents. Experimentally infected fish developed lesions characteristic for tenacibaculosis, but the microbiota was primarily dominated by Proteobacteria (90.4%{+/-}0.2%) and Firmicutes (6.2%{+/-}0.1%). The relative abundance of Tenacibaculum species in experimentally infected fish was significantly lower than in the commercially reared diseased fish and revealed a higher prevalence of different Tenacibaculum species. One strain was isolated and is described here as sp. nov. Tenacibaculum singaporense TLL-A1T (=DSM 106434T, KCTC 62393T). The genome of T. singaporense was sequenced and compared to those of T. maritimum DSM 17995T and the newly sequenced T. mesophilum DSM 13764T.\n\nImportanceFish production from aquaculture facility has become a major source of protein for human consumption and is expected to further grow to meet the growing demands. Devastating fish diseases, such as tenacibaculosis, can eradicate entire stocks of aquaculture fish in a short time and pose a serious threat to individual fish farmers and overall fish production. Understanding the disease processes and the individual microbial players involved has the potential to develop methods to prevent or mitigate infections on aquaculture farms. This study provides important insights into the microbial ecology of tenacibaculosis from an aquaculture facility in Singapore and highlights the complexity of this fish disease at two different disease stages. Furthermore, the isolation of a novel Tenacibaculum species and comparative genome analysis of three different Tenacibaculum species enhance our view of this economically and environmentally important bacterial genus.

microbiology↗

bioRxiv2018

Analysis of structural variants in four African cichlids highlights an association with developmental and immune related genes

African Lakes Cichlids are one of the most impressive example of adaptive radiation. Independently in Lake Victoria, Tanganyika, and Malawi, several hundreds of species arose within the last 10 million to 100,000 years. Whereas most analyses in Cichlids focused on nucleotide substitutions across species to investigate the genetic bases of this explosive radiation, to date, no study has investigated the contribution of structural variants (SVs) to speciation events (through a reduction of gene flow) and adaptation to different ecological niches. Here, we annotate and characterize the repertoires and evolutionary potential of different SV classes (deletion, duplication, inversion, insertions and translocations) in five Cichlid species (Haplochromis burtoni, Metriaclima zebra, Neolamprologus brichardi, Pundamilia nyererei and Oreochromis niloticus). We investigate the patterns of gain/loss across the phylogeny for each SV type enabling the identification of both lineage specific events and a set of conserved SVs, common to all four species in the radiation. Both deletion and inversion events show a significant overlap with SINE elements, while inversions additionally show a limited, but significant association with DNA transposons. Inverted regions are enriched for genes regulating behaviour, or involved in skeletal and visual system development. We also find that duplicated regions show enrichment for genes associated with \"antigen processing and presentation\" (GO:0019882) and other immune related categories. Altogether, we provide the first, comprehensive overview of rearrangement evolution in East African Cichlids, and some initial insights into their possible contribution to adaptation.

evolutionary biology↗

bioRxiv2018

The expendable male hypothesis

Matrilineal descent confers lineage membership via the female line. In matrilineal descent systems, men share lineage membership not with their own children, but with their sisters children. The theoretically influential concept of the matrilineal puzzle posits that men experience tension between the desire to exert control over their natal kin (i.e., the lineage to which they belong) and over their affinal kin (i.e., their spouses and their biological children). The rationale for this puzzle rests on two fundamental assumptions: (i) that men are always in positions of authority over women; and (ii) that men are interested in the outcomes of parenting. In this paper, we suggest that the matrilineal puzzle does not exist from an evolutionary perspective. Instead, we examine what ecological conditions might render men expendable within local kinship configurations-specifically when (i) women, without significant assistance from men, are capable of meeting the subsistence needs of their families; and (ii) men have little to gain from parental investment in children. We conclude that the expendable male hypothesis may explain the evolution of matrilineal descent in numerous cases, and by noting that female-centered approaches that call into doubt assumptions inherent to male-centered models of kinship are justified in evolutionary perspective.\n\nO_QD\"...for some females there exist important advantages for male care ... For many females male parental care has small or negligible effects on female reproductive success, suggesting that as a general explanation for social monogamy, the Male Care is Essential Hypothesis is inadequate.\" - Gowaty 1996 [1]\n\nC_QD

animal behavior and cognition↗