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bioRxiv2018

Diversification rates and phylogenies: what are we estimating, and how good are the estimates?

O_LISpecies-specific diversification rates, or \"tip rates\", can be computed quickly from phylogenies and are widely used to study diversification rate variation in relation to geography, ecology, and phenotypes. These tip rates provide a number of theoretical and practical advantages, such as the relaxation of assumptions of rate homogeneity in trait-dependent diversification studies. However, there is substantial confusion in the literature regarding whether these metrics estimate speciation or net diversification rates. Additionally, no study has yet compared the relative performance and accuracy of tip rate metrics across simulated diversification scenarios.\nC_LIO_LIWe compared the statistical performance of three model-free rate metrics (inverse terminal branch lengths; node density metric; DR statistic) and a model-based approach (BAMM). We applied each method to a large set of simulated phylogenies that had been generated under different diversification processes; scenarios included multi-regime time-constant and diversity-dependent trees, as well as trees where the rate of speciation evolves under a diffusion process. We summarized performance in relation to the type of rate variation, the magnitude of rate heterogeneity and rate regime size. We also compared the ability of the metrics to estimate both speciation and net diversification rates.\nC_LIO_LIWe show decisively that model-free tip rate metrics provide a better estimate of the rate of speciation than of net diversification. Error in net diversification rate estimates increases as a function of the relative extinction rate. In contrast, error in speciation rate estimates is low and relatively insensitive to extinction. Overall, and in particular when relative extinction was high, BAMM inferred the most accurate tip rates and exhibited lower error than non-model-based approaches. DR was highly correlated with true speciation rates but exhibited high error variance, and was the best metric for very small rate regimes.\nC_LIO_LIWe found that, of the metrics tested, DR and BAMM are the most useful metrics for studying speciation rate dynamics and trait-dependent diversification. Although BAMM was more accurate than DR overall, the two approaches have complementary strengths. Because tip rate metrics are more reliable estimators of speciation rate, we recommend that empirical studies using these metrics exercise caution when drawing biological interpretations in any situation where the distinction between speciation and net diversification is important.\nC_LI

evolutionary biology↗

bioRxiv2018

Modern wolves trace their origin to a late Pleistocene expansion from Beringia

Grey wolves (Canis lupus) are one of the few large terrestrial carnivores that maintained a wide geographic distribution across the Northern Hemisphere throughout the Pleistocene and Holocene. Recent genetic studies have suggested that, despite this continuous presence, major demographic changes occurred in wolf populations between the late Pleistocene and early Holocene, and that extant wolves trace their ancestry to a single late Pleistocene population. Both the geographic origin of this ancestral population and how it became widespread remain a mystery. Here we analyzed a large dataset of novel modern and ancient mitochondrial wolf genomes, spanning the last 50,000 years, using a spatially and temporally explicit modeling framework to show that contemporary wolf populations across the globe trace their ancestry to an expansion from Beringia at the end of the Last Glacial Maximum - a process most likely driven by the significant ecological changes that occurred across the Northern Hemisphere during this period. This study provides direct ancient genetic evidence that long-range migration has played an important role in the population history of a large carnivore and provides an insight into how wolves survived the wave of megafaunal extinctions at the end of the last glaciation. Moreover, because late Pleistocene grey wolves were the likely source from which all modern dogs trace their origins, the demographic history described in this study has fundamental implications for understanding the geographical origin of the dog.

evolutionary biology↗

bioRxiv2018

Assessing taxonomic metagenome profilers with OPAL

Taxonomic metagenome profilers predict the presence and relative abundance of microorganisms from shotgun sequence samples of DNA isolated directly from a microbial community. Over the past years, there has been an explosive growth of software and algorithms for this task, resulting in a need for more systematic comparisons of these methods based on relevant performance criteria. Here, we present OPAL, a software package implementing commonly used performance metrics, including those of the first challenge of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI), together with convenient visualizations. In addition, OPAL implements diversity metrics from microbial ecology, as well as run time and memory efficiency measurements. By allowing users to customize the relative importance of metrics, OPAL facilitates in-depth performance comparisons, as well as the development of new methods and data analysis workflows. To demonstrate the application, we compared seven profilers on benchmark datasets of the first and second CAMI challenges using all metrics and performance measurements available in OPAL. The software is implemented in Python 3 and available under the Apache 2.0 license on GitHub (https://github.com/CAMI-challenge/OPAL).\n\nAuthor summaryThere are many computational approaches for inferring the presence and relative abundance of taxa (i.e. taxonomic profiling) from shotgun metagenome samples of microbial communities, making systematic performance evaluations a very important task. However, there has yet to be introduced a computational framework in which profiler performances can be compared. This delays method development and applied studies, as researchers need to implement their own custom evaluation frameworks. Here, we present OPAL, a software package that facilitates standardized comparisons of taxonomic metagenome profilers. It implements a variety of performance metrics frequently employed in microbiome research, including runtime and memory usage, and generates comparison reports and visualizations. OPAL thus facilitates and accelerates benchmarking of taxonomic profiling techniques on ground truth data. This enables researchers to arrive at informed decisions about which computational techniques to use for specific datasets and research questions.

bioinformatics↗

bioRxiv2018

The soil microbial foodweb revisited with metatranscriptomics - predatory Myxobacteria as keystone taxon?

Trophic interactions in the microbial food web of soils are crucial for nutrient and carbon cycling. Traditionally, protozoa are considered the major micropredators of bacteria in soil. However, some prokaryotes, such as Myxobacteria and Bdellovibrio are also famous for bacterivorous life style. Until recently, it was impossible to assess the abundance of pro- and eukaryotic micropredators in soils simultaneously. Using a metatranscriptomic three-domain profiling of small subunit ribosomal RNA we investigated the abundance of bacterivores in 28 datasets from eleven European mineral and organic soils of different climatic zones. In all soils, Myxobacteria comprised a significant proportion from 4 - 19% of prokaryotic 16S rRNA transcripts and more than 60% of all bacterivores in most soils. Haliangiaceae and Polyangiaceae were most abundant, while the name-giving Myxococcaceae were barely present. Other bacterial predators like Bdellovibrio were low abundant. Also Protozoan micropredator 18S rRNA transcripts, e.g. from Cercozoa, Amoebozoa and Ciliophora, were on average less abundant, especially in mineral soils. Nematodes were even less abundant. In addition, we applied a longitudinal approach to identify bacterivores during beech litter colonisation. Here, Myxobacteria showed prey-dependent, protozoa-like community dynamics during colonisation. Thus, their broad prey range and high abundance suggests a major influence of Myxobacteria on structuring the prokaryotic community composition in soil, and might warrant their classification as keystone taxon. Our results suggest the presence of an ecologically important \"bacterial loop\" in soil food webs, independent of protozoa and nematodes.

microbiology↗

bioRxiv2018

Fast and general-purpose linear mixed models for genome-wide genetics

Linear mixed effect models are powerful tools used to account for population structure in genome-wide association studies (GWASs) and estimate the genetic architecture of complex traits. However, fully-specified models are computationally demanding and common simplifications often lead to reduced power or biased inference. We describe Grid-LMM (https://github.com/deruncie/GridLMM), an extendable algorithm for repeatedly fitting complex linear models that account for multiple sources of heterogeneity, such as additive and non-additive genetic variance, spatial heterogeneity, and genotype-environment interactions. Grid-LMM can compute approximate (yet highly accurate) frequentist test statistics or Bayesian posterior summaries at a genome-wide scale in a fraction of the time compared to existing general-purpose methods. We apply Grid-LMM to two types of quantitative genetic analyses. The first is focused on accounting for spatial variability and non-additive genetic variance while scanning for QTL; and the second aims to identify gene expression traits affected by non-additive genetic variation. In both cases, modeling multiple sources of heterogeneity leads to new discoveries.\n\nAuthor summaryThe goal of quantitative genetics is to characterize the relationship between genetic variation and variation in quantitative traits such as height, productivity, or disease susceptibility. A statistical method known as the linear mixed effect model has been critical to the development of quantitative genetics. First applied to animal breeding, this model now forms the basis of a wide-range of modern genomic analyses including genome-wide associations, polygenic modeling, and genomic prediction. The same model is also widely used in ecology, evolutionary genetics, social sciences, and many other fields. Mixed models are frequently multi-faceted, which is necessary for accurately modeling data that is generated from complex experimental designs. However, most genomic applications use only the simplest form of linear mixed methods because the computational demands for model fitting can be too great. We develop a flexible approach for fitting linear mixed models to genome scale data that greatly reduces their computational burden and provides flexibility for users to choose the best statistical paradigm for their data analysis. We demonstrate improved accuracy for genetic association tests, increased power to discover causal genetic variants, and the ability to provide accurate summaries of model uncertainty using both simulated and real data examples.

genomics↗

bioRxiv2018

The landscape of coadaptation in Vibrio parahaemolyticus

Investigating fitness interactions in natural populations remains a considerable challenge. We take advantage of the unique population structure of Vibrio parahaemolyticus, a bacterial pathogen of humans and shrimp, to perform a genome-wide screen for coadapted genetic elements. We identified 90 interaction groups involving 1,560 coding genes. 82 of these interaction groups are between accessory genes, many of which have functions related to carbohydrate transport and metabolism. Only 8 interaction groups involve both core and accessory genomes. The largest includes 1,540 SNPs in 82 genes and 338 accessory genome elements, many involved in lateral flagella and cell wall biogenesis. The interactions have a complex hierarchical structure encoding at least four distinct ecological strategies. Preliminary experiments imply that the strategies influence biofilm formation and bacterial growth rate in vitro. One strategy involves a divergent profile in multiple genome regions, implying that strains have irreversibly specialized, while the others involve fewer genes and are more plastic. Our results imply that most genetic alliances are ephemeral but that increasingly complex strategies can evolve and eventually cause speciation.

microbiology↗

bioRxiv2018

Asgard archaea are diverse, ubiquitous, and transcriptionally active microbes

Asgard is a newly proposed archaeal superphylum. Phylogenetic position of Asgard archaea and its relationships to the origin of eukaryotes is attracting increasingly research interest. However, in-depth knowledge of their diversity, distribution, and activity of Asgard archaea remains limited. Here, we used phylogenetic analysis to cluster the publicly available Asgard archaeal 16S rRNA gene sequences into 13 subgroups, including five previously unknown subgroups. These lineages were widely distributed in anaerobic environments, with the majority of 16S rRNA gene sequences (92%) originating from sediment habitats. Co-occurrence analysis revealed potential relationships between Asgard, Bathyarchaeota, and Marine Benthic Group D archaea. Genomic analysis suggested that Asgard archaea are potentially mixotrophic microbes with divergent metabolic capabilities. Importantly, metatranscriptomics confirmed the versatile lifestyles of Lokiarchaeota and Thorarchaeota, which can fix CO2 using the tetrahydromethanopterin Wood-Ljungdahl pathway, perform acetogenesis, and degrade organic matters. Overall, this study broadens the understandings of Asgard archaea ecology, and also provides the first evidence to support a transcriptionally active mixotrophic lifestyle of Asgard archaea, shedding light on the potential roles of these microorganisms in the global biogeochemical cycling.

microbiology↗

bioRxiv2018

SMRT long-read sequencing and Direct Label and Stain optical maps allow the generation of a high-quality genome assembly for the European barn swallow (Hirundo rustica rustica)

BackgroundThe barn swallow (Hirundo rustica) is a migratory bird that has been the focus of a large number of ecological, behavioural and genetic studies. To facilitate further population genetics and genomic studies, here we present a reference genome assembly for the European subspecies (H. r. rustica).\n\nFindingsAs part of the Genome10K (G10K) effort on generating high quality vertebrate genomes, we have assembled a highly contiguous genome assembly using Single Molecule Real-Time (SMRT) DNA sequencing and several Bionano optical map technologies. We compared and integrated optical maps derived both from the Nick, Label, Repair and Stain and from the Direct Label and Stain (DLS) technologies. As proposed by Bionano, the DLS more than doubled the scaffold N50 with respect to the nickase. The dual enzyme hybrid scaffold led to a further marginal increase in scaffold N50 and an overall increase of confidence in the scaffolds. After removal of haplotigs, the final assembly is approximately 1.21 Gbp in size, with a scaffold N50 value of over 25.95 Mbp.\n\nConclusionsThis high-quality genome assembly represents a valuable resource for further studies of population genetics and genomics in the barn swallow, and for studies concerning the evolution of avian genomes. It also represents one of the very first genomes assembled by combining SMRT long-read sequencing with the new Bionano DLS technology for scaffolding. The quality of this assembly demonstrates the potential of this methodology to substantially increase the contiguity of genome assemblies.

genomics↗

bioRxiv2018

High-density linkage map and QTLs for growth in snapper (Chrysophrys auratus)

Characterizing the genetic variation underlying phenotypic traits is a central objective in biological research. This research has been hampered in the past by the limited genomic resources available for most non-model species. However, recent advances in sequencing technology and related genotyping methods are rapidly changing this. Here we report the use of genome-wide SNP data from the ecologically and commercially important marine fish species Chrysophrys auratus (snapper) to 1) construct the first linkage map for this species, 2) scan for growth QTLs, and 3) search for candidate genes in the surrounding QTL regions. The newly constructed linkage map contained ~11K SNP markers and is the densest map to date in the fish family Sparidae. Comparisons with available genome scaffolds indicated that overall marker placement was strongly correlated between the scaffolds and linkage map (R = 0.7), but at fine scales (< 5 cM) there were some precision limitations. Of the 24 linkage groups, which reflect the 24 chromosomes of this species, three were found to contain QTLs with genome-wide significance for growth-related traits. A scan for 13 known candidate growth genes located the genes for growth hormone, parvalbumin, and myogenin within 13.2, 2.6, and 5.0 cM of these genome-wide significant QTLs, respectively. The linkage map and QTLs found in this study will advance the investigation of genome structure and selective breeding in snapper.

evolutionary biology↗

bioRxiv2018

Extreme genetic structure and dynamic range evolution in a montane passerine bird: implications for tropical diversification

AimEmploy phylogeographic analyses of a widespread species complex to examine the role of historical and evolutionary processes in the origin and maintenance of high species diversity in the Neotropical montane region.\n\nLocationNeotropical highlands.\n\nTaxonHenicorhina wood-wrens (Aves, Troglodytidae).\n\nMethodsWe collected mtDNA sequence data for 288 individuals thoroughly covering the range of the Henicorhina leucophrys complex from Mexico to Bolivia. Sequences were employed to characterize population structure, infer phylogenetic relationships among populations and their divergence times, examine lineage accumulation through time, and identify presumptive species using coalescent methods. We also explored the origin of elevational and latitudinal replacements involved in spatial changes in species assemblages in the Andes.\n\nResultsWe found remarkable genetic structure within the complex, which consists of numerous lineages reaching >12% sequence divergence; most divergent populations occur in areas separated by topographic barriers but several of them, typically not sister to each other, co-occur with elevational segregation on mountain slopes or replace each other with latitude along the Andes. Some close relatives occur in areas separated by thousands of kilometers, with more distant relatives occupying intervening areas. The complex likely originated in the Mexican highlands and expanded extensively in South America while diverging rapidly at a constant rate into many different lineages which have persisted for millions of years. Coalescent analyses consistently revealed that the complex may comprise more than 30 species; while we do not suggest these presumptive species should be recognized by taxonomists in the absence of additional data, H. leucophrys is a distant outlier among New World birds in terms of high lineage diversity within a single recognized species.\n\nMain ConclusionsOur study captured wood-wren lineages in the act of building up diversity via divergence and persistence in allopatry, achievement of secondary sympatry, and coexistence at the landscape scale mediated by ecological and evolutionary divergence. Although dispersal by wood-wrens is restricted at present and this likely accounts for strong population structure across topographic barriers, their ranges have been dynamic, managing to disperse over much of the montane Neotropics. Phases of expansion and contraction of ranges and localized extinctions of populations likely account for phylogeographic patterns which are precursors to the origin of new species and the accumulation of diversity in tropical mountains.

evolutionary biology↗

bioRxiv2018

Sexual behavior of the desert locust during intra- and inter-phase interactions

Mating and reproduction behaviors and strategies are fundamental aspects of an organisms evolutionary and ecological success. In locusts, intra- as well as inter-phase reproductive interactions among gregarious and solitarious locust populations have a major impact on the locust population dynamics. However, practically all previous work on locust sexual behavior has been limited to the gregarious phase. Here we provide a first detailed description of pre-copulatory behavior of solitarious desert locusts. We compare our findings with those of previous reports of pre-copulatory behavior of gregarious locusts, focusing on the behavioral elements that serve in inter-sex signaling and communication. We also studied inter-phase (mixed pairs) reproductive interactions. Solitarious males were found to invest more in pre-copulatory courtship and signaling compared to their gregarious counterparts; and the solitarious females played a comparatively more dominant role in the inter-sex communication. The solitarious females were also less prone to demonstrate the typical rejection-related behavioral patterns displayed by the gregarious females. As a consequence of the particular characteristic behavior of each phase, the most successful among intra- and inter-phase pairs were gregarious males with solitary females. Least successful were solitary males encountered with gregarious females, indicating a strong asymmetry in inter-phase reproductive interactions. We discuss these results in the context of non-random or assortative mating in locust mixed or sympatric solitarious-gregarious populations.

animal behavior and cognition↗

bioRxiv2018

Short-term insurance versus long-term bet-hedging strategies as adaptations to variable environments

Understanding how organisms adapt to environmental variation is a key challenge of biology. Central to this are bet-hedging strategies that maximize geometric mean fitness across generations, either by being conservative or diversifying phenotypes. Theoretical models of bet-hedging and the multiplicative fitness effects of environmental variation across generations have traditionally assumed that environmental conditions are constant within lifetimes. However, behavioral ecology has revealed adaptive responses to additive fitness effects of environmental variation within lifetimes, either through insurance or risk-sensitive strategies. Here we explore whether the effects of adaptive insurance interact with the evolution of bet-hedging by varying the position and skew of fitness functions within and between lifetimes. When insurance causes the optimal phenotype to shift from the peak to down the less steeply decreasing side of the fitness function, then conservative bet-hedging does not generally evolve on top of this, even if diversifying bet-hedging can. Canalization to reduce phenotypic variation within a lifetime is almost always favored, except when the tails of the fitness function are steeply convex and produce a novel risk-sensitive increase in phenotypic variance akin to diversifying bet-hedging. Importantly, using skewed fitness functions, we provide the first example of how conservative and diversifying bet-hedging strategies might coexist.

evolutionary biology↗

bioRxiv2018

Out of Africa by spontaneous migration waves

Hominin evolution is characterized by progressive regional differentiation, as well as migration waves, leading to anatomically modern humans that are assumed to have emerged in Africa and spread over the whole world. Why or whether Africa was the source region of modern humans and what caused their spread remains subject of ongoing debate. We present a spatially explicit, stochastic numerical model that includes ongoing mutations, demic diffusion, assortative mating and migration waves. Diffusion and assortative mating alone result in a structured population with relatively homogeneous regions bound by sharp clines. The addition of migration waves results in a power-law distribution of wave areas: for every large wave, many more small waves are expected to occur. This suggests that one or more out-of-Africa migrations would probably have been accompanied by numerous smaller migration waves across the world. The migration waves are considered \"spontaneous\", as the current model excludes environmental or other factors. Large waves preferentially emanate from the central areas of large, compact inhabited areas. During the Pleistocene, Africa was the largest such area most of the time, making Africa the statistically most likely origin of anatomically modern humans, without a need to invoke additional environmental or ecological drivers.

evolutionary biology↗

bioRxiv2018

Stress response, behavior, and development are shaped by transposable element-induced mutations in Drosophila

Mapping genotype to phenotype is challenging because of the difficulties in identifying both the traits under selection and the specific genetic variants underlying these traits. Most of the current knowledge of the genetic basis of adaptive evolution is based on the analysis of single nucleotide polymorphisms (SNPs). Despite increasing evidence for their causal role, the contribution of structural variants to adaptive evolution remains largely unexplored. In this work, we analyzed the population frequencies of 1,615 Transposable Element (TE) insertions in 91 samples from 60 worldwide natural populations of Drosophila melanogaster. We identified a set of 300 TEs that are present at high population frequencies, and located in genomic regions with high recombination rate, where the efficiency of natural selection is high. The age and the length of these 300 TEs are consistent with relatively young and long insertions reaching high frequencies due to the action of positive selection. Indeed, we, and others, found evidence of selective sweeps and/or population differentiation for 65 of them. The analysis of the genes located nearby these 65 candidate adaptive insertions suggested that the functional response to selection is related with the GO categories of response to stimulus, behavior, and development. We further showed that a subset of the candidate adaptive TEs affect expression of nearby genes, and five of them have already been linked to an ecologically relevant phenotypic effect. Our results provide a more complete understanding of the genetic variation and the fitness-related traits relevant for adaptive evolution. Similar studies should help uncover the importance of TE-induced adaptive mutations in other species as well.

evolutionary biology↗

bioRxiv2018

Genome sequence of the wheat stem sawfly, Cephus cinctus, a primitive hymenopteran and wheat pest, illuminates evolution of hymenopteran chemoreceptors

The wheat stem sawfly, Cephus cinctus, is a major pest of wheat and key ecological player in the grasslands of western North America. It also represents a distinctive lineage of sawflies that appeared early during the hymenopteran radiation, but after the clade of Eusymphyta sawflies that is the sister lineage of all other Hymenoptera. We present a high-quality draft genome assembly of 162 Mbp in 1,976 scaffolds with a scaffold N50 of 622 kbp. Automated gene annotation identified 11,210 protein-coding gene models and 1,307 non-coding RNA models. Thirteen percent of the assembly consists of ~58,000 transposable elements partitioned equally between Class-I and Class-II elements. Orthology analysis reveals that 86% of Cephus proteins have identifiable orthologs in other insects. Phylogenomic analysis of conserved subsets of these proteins supports the placement of the Cephidae between the Eusymphyta and the parasitic woodwasp superfamily Orussoidea. Manual annotation and phylogenetic analysis of families of odorant, gustatory, and ionotropic receptors, plus odorant binding proteins, shows that Cephus has representatives for most conserved and expanded gene lineages in the Apocrita (wasps, ants, and bees). Cephus has also maintained several insect gene lineages that have been lost from the Apocrita, most prominently the carbon dioxide receptor subfamily. Furthermore, Cephus encodes a few small lineage-specific chemoreceptor gene family expansions that might be involved in adaptations to new grasses including wheat. These comparative analyses identify gene family members likely to have been present in the hymenopteran ancestor and provide a new perspective on the evolution of the chemosensory gene repertoire.

genomics↗

bioRxiv2018

High-resolution 4D spatiotemporal analysis reveals the contributions of local growth dynamics to contrasting maize root system architectures

Root systems are branched networks that develop from simple growth properties of their individual roots. Yet a mature maize root system has many thousands of roots that each interact with soil structures, water and nutrient patches, and microbial ecologies in the micro-environments surrounding each root tip. Although the plasticity of root growth to these and other environmental factors is well known, how the many local processes contribute over time to global features of root system architecture is hardly understood. We employ an automated 3D root imaging pipeline to capture the growth of maize roots every four hours throughout seven days of seedling development. We model the contrasting architectures of two maize inbred genotypes and their hybrid to derive key parameters that distinguish complex growth patterns as a function of time. The statistical characteristics of local root growth defined the global system properties despite a large range of trait values. \"Computational dissection\" of a single root from each root system identified differences in the size of the root branching zone and lateral branching densities, but not radial patterns, that drove the contrasting root architectures from seedling to maturity. X-ray imaging of mature field-grown root crowns showed that seedling growth trajectories persisted throughout development and could predict eventual architectures, suggesting a strong genetic basis. The work connects individual and systemwide scales of root growth dynamics, providing the means for a function-valued approach to understanding the genetic and genetic x environment conditioning of root growth that will enable breeding for enhanced root traits.\n\nSIGNIFICANCE STATEMENTWhen and where roots grow determines their ability to capture short-lived and patchy water and nutrient resources to support the aboveground organs of the plant. Roots have no known long-distance external sensing mechanisms, but form branched networks that blindly explore the soil and respond to encountered local stimuli. How global architectures form from the many thousands of these local responses, and how they are controlled genetically are major open questions. Here we quantify differences in local root growth patterns of two inbred genotypes of maize that control contrasting systemwide properties. Measurements at the seedling stage were highly correlated with the complex architectures of mature root systems, paving the way for the development of crops with greater resource uptake capacity.

plant biology↗

bioRxiv2018

An Ishihara-style test of animal colour vision

O_LIColour vision mediates ecologically relevant tasks for many animals, such as mate choice, foraging and predator avoidance. However, our understanding of animal colour perception is largely derived from human psychophysics, even though animal visual systems differ from our own. Behavioural tests of non-human animals are required to understand how colour signals are perceived by them.\nC_LIO_LIHere we introduce a novel test of colour vision in animals inspired by the Ishihara colour charts, which are widely used to identify human colour deficiencies. These charts consist of dots that vary in colour, brightness and size, and are designed so that a numeral or letter is distinguishable from distractor dots for humans with normal colour vision. In our method, distractor dots have a fixed chromaticity (hue and saturation) but vary in luminance. Animals can be trained to find single target dots that differ from distractor dots in chromaticity. We provide Matlab code for creating these stimuli, which can be modified for use with different animals.\nC_LIO_LIWe demonstrate the success of this method with triggerfish, Rhinecanthus aculeatus, and highlight behavioural parameters that can be measured, including success of finding the target dot, time to detect dot and error rate. Triggerfish quickly learnt to select target dots that differed from distractors dots regardless of the particular hue or saturation, and proved to use acute colour vision. We measured discrimination thresholds by testing the detection of target colours that were of increasing colour distances ({Delta}S) from distractor dots in different directions of colour space. At least for some colours, thresholds indicated better discrimination than expected from the Receptor Noise Limited (RNL) model assuming 5% Weber fraction for the long-wavelength cone.\nC_LIO_LIThis methodology seems to be highly effective because it resembles natural foraging behavior for the triggerfish and may well be adaptable to a range of other animals, including mammals, birds, bees and freshwater fish. Other questions may be addressed using this methodology, including luminance thresholds, sensory bias, effects of sensory noise in detection tasks, colour categorization and saliency.\nC_LI

animal behavior and cognition↗

bioRxiv2018

The fitness consequences of genetic variation in wild populations of mice

Adaptive evolution can occur when genetic change affects traits subject to natural selection. Although selection is a deterministic process, adaptation can be difficult to predict in finite populations because the functional connections between genotype, phenotype, and fitness are complex. Here, we make these connections using a combination of field and laboratory experiments. We conduct a large-scale manipulative field experiment with wild populations of deer mice in distinct habitats to directly estimate natural selection on pigmentation traits and next test whether this selection drives changes in allele frequency at an underlying pigment locus. We find that divergent cryptic phenotypes are repeatedly favoured in each habitat, leaving footprints of selection in the Agouti gene. Next, using transgenic experiments in Mus, we functionally test one of the Agouti mutations associated with survival, a Serine deletion in exon 2, and find that it causes lighter coat colour via changes in its protein binding properties. Finally, we show significant change in the frequency of this mutation in our field experiment. Together, our findings demonstrate how a sequence variant alters phenotype and show the ensuing ecological consequences that drive changes in population allele frequency, thereby revealing the full process of evolution by natural selection.

evolutionary biology↗