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bioRxiv2018

Starvation resistance is associated with developmentally specified changes in sleep, feeding and metabolic rate

Food shortage represents a primary challenge to survival, and animals have adapted diverse developmental, physiological, and behavioral strategies to survive when food becomes unavailable. Starvation resistance is strongly influenced by ecological and evolutionary history, yet the genetic basis for the evolution of starvation resistance remains poorly understood. The fruit fly, Drosophila melanogaster, provides a powerful model for leveraging experimental evolution to investigate traits associated with starvation resistance. While control populations only live a few days without food, selection for starvation resistances results in populations that can survive weeks. We have previously shown that selection for starvation resistance results in increased sleep and reduced feeding in adult flies. Here, we investigate the ontogeny of starvation resistance-associated behavioral and metabolic phenotypes in these experimentally selected flies. We find that selection for starvation resistance results in delayed development and a reduction in metabolic rate in larvae that persists into adulthood, suggesting that these traits may allow for the accumulation of energy stores and an increase in body size within these selected populations. In addition, we find that sleep is largely unaffected by starvation- selection and that feeding increases during the late larval stages, suggesting that experimental evolution for starvation resistance produces developmentally specified changes in behavioral regulation. Together, these findings reveal a critical role for development in the evolution of starvation resistance and indicate that selection can selectively influence behavior during defined developmental timepoints.\n\nSUMMARY STATEMENTDrosophila melanogaster selected for starvation resistance take longer to develop and exhibit development-specific changes in traits associated with the accumulation and conservation of energy stores.

neuroscience↗

bioRxiv2018

Rapid environmental change in games: complications and curiosities

Human-induced rapid environmental change (HIREC) has recently led to alterations in the fitness and behavior of many organisms. Game theory is an important tool of behavioral ecology for analyzing evolutionary situations involving multiple individuals. However, game theory bypasses the details by which behavioral phenotypes are determined, taking the functional perspective straight from expected payoffs to predicted frequencies of behaviors. In contrast with optimization approaches, we identify that to use existing game theoretic models to predict HIREC effects, additional mechanistic details (or assumptions) will often be required. We illustrate this in relation to the hawk-dove game by showing that three different mechanisms, each of which support the same ESS prior to HIREC (fixed polymorphism, probabilistic choice, or cue dependency), can have a substantial effect on behavior (and success) following HIREC. Surprisingly, an increase in the value of resources can lead to a reduction in payoffs (and vice versa), both in the immediate- and long-term following HIREC. An increase in expected costs also increases expected payoffs. Along with these counter-intuitive findings, this work shows that simply understanding the behavioral payoffs of existing games is insufficient to make predictions about the effects of HIREC.\n\nIts the little details that are vital. Little things make big things happen.\n\nJohn Wooden

animal behavior and cognition↗

bioRxiv2018

Genomic signatures of sympatric speciation with historical and contemporary gene flow in a tropical anthozoan

Sympatric diversification is increasingly thought to have played an important role in the evolution of biodiversity around the globe. However, an in situ sympatric origin for co-distributed taxa is difficult to demonstrate empirically because different evolutionary processes can lead to similar biogeographic outcomes-especially in ecosystems with few hard barriers to dispersal that can facilitate allopatric speciation followed by secondary contact (e.g. marine habitats). Here we use a genomic (ddRADseq), model-based approach to delimit a cryptic species complex of tropical sea anemones that are co-distributed on coral reefs throughout the Tropical Western Atlantic. We use coalescent simulations in fastsimcoal2 to test competing diversification scenarios that span the allopatric-sympatric continuum. We recover support that the corkscrew sea anemone Bartholomea annulata (Le Sueur, 1817) is a cryptic species complex, co-distributed throughout its range. Simulation and model selection analyses suggest these lineages arose in the face of historical and contemporary gene flow, supporting a sympatric origin, but an alternative secondary contact model also receives appreciable model support. Leveraging the genome of Exaiptasia pallida we identify five loci under divergent selection between cryptic B. annulata lineages that fall within mRNA transcripts or CDS regions. Our study provides a rare empirical, genomic example of sympatric speciation in a tropical anthozoan-a group that includes reef-building corals. Finally, these data represent the first range-wide molecular study of any tropical sea anemone, underscoring that anemone diversity is under described in the tropics, and highlighting the need for additional systematic studies into these ecologically and economically important species.

evolutionary biology↗

bioRxiv2018

May the phage be with you? Prophage-like elements in the genomes of Soft Rot 3 Pectobacteriaceae (Pectobacterium spp. and Dickeya spp.)

Soft Rot Pectobacteriaceae (SRP; Pectobacterium spp. and Dickeya spp., formerly known as pectinolytic Erwinia spp.) are necrotrophic bacterial pathogens infecting large number of plant species worldwide including agriculturally-important crops. Regardless of the SRP importance in agriculture, little is known about the bacteriophages infecting Pectobacterium spp. and Dickeya spp. and even less about prophages present in SRP genomes. Prophages are recognized as factors underlying bacterial virulence, genomic diversification and ecological fitness and have association with the novel phenotypic properties of bacterial hosts. Likewise, they are recognized as a driving force of bacterial evolution. The aim of this study was to analyze Pectobacterium spp. and Dickeya spp. complete genome sequences downloaded from GenBank (NCBI) for the presence of prophage sequences following their identification and (comparative) characterization with the main focus on current and upcoming perspectives in that field.

microbiology↗

bioRxiv2018

Signatures of negative frequency dependent selection in colonisation factors and the evolution of a multi-drug resistant lineage of Escherichia coli

Escherichia coli is a major cause of bloodstream and urinary tract infections globally. The wide dissemination of multi-drug resistant (MDR) strains of extra-intestinal pathogenic E. coli (ExPEC) poses a rapidly increasing public health burden due to narrowed treatment options and increased risk of failure to clear an infection. Here, we present a detailed population genomic analysis of the ExPEC ST131 clone, in which we seek explanations for its success as an emerging pathogenic strain beyond the acquisition of antimicrobial resistance (AMR) genes. We show evidence for evolution towards separate ecological niches for the main clades of ST131 and differential evolution of anaerobic metabolism, key colonisation and virulence factors. We further demonstrate that negative frequency-dependent selection acting across accessory loci is a major mechanism that has shaped the population evolution of this pathogen.

microbiology↗

bioRxiv2018

Potential for microbial anaerobic hydrocarbon degradation in naturally occurring petroleum-associated deep-sea sediments

The lack of microbial genomes and isolates from the deep seabed means that very little is known about the ecology of this vast habitat. Here, we investigated energy and carbon acquisition strategies of microbial communities from three deep seabed petroleum seeps (3 km water depth) in the Eastern Gulf of Mexico. Shotgun metagenomic analysis revealed that each sediment harbored diverse communities of chemoheterotrophs and chemolithotrophs. We recovered 82 metagenome-assembled genomes affiliated with 21 different archaeal and bacterial phyla. Multiple genomes encoded enzymes for anaerobic oxidation of aliphatic and aromatic compounds, including those of candidate phyla Aerophobetes, Aminicenantes, TA06 and Bathyarchaeota. Microbial interactions are predicted to be driven by acetate and molecular hydrogen. These findings are supported by sediment geochemistry, metabolomics, and thermodynamic modelling. Overall, we infer that deep-sea sediments experiencing thermogenic hydrocarbon inputs harbor phylogenetically and functionally diverse communities potentially sustained through anaerobic hydrocarbon, acetate and hydrogen metabolism.

microbiology↗

bioRxiv2018

The role of land use types and water chemical properties in structuring the microbiome of a connected lakes system

Lakes and other freshwater bodies are intimately connected to the surrounding land, yet to what extent land-use affects the quality of freshwater and the microbial communities living in various freshwater environments is largely unknown. We address this question through an analysis of the land use surrounding 46 inter-connected lakes located within 7 different drainage basins in northern Germany, and the microbiomes of these lakes during early summer. Lake microbiome structure was not determined by the specific drainage basin or by basin size, and bacterial distribution did not seem to be limited by distance. Instead, land use within the drainage basin could predict, to some extent, NO2+NO3 concentrations in the water, which (together with temperature, chlorophyll a and total phosphorus) affected water microbiome structure. Land use directly surrounding the water bodies, however, had little observable effects on water quality or the microbiome. Several microbial lineages, including environmentally important Cyanobacteria and Verrucomicrobia, were differentially partitioned between the lakes. As the amount of available data on land use (e.g. from remote sensing) increases, identifying relationships between land use, aquatic microbial communities and their effect on water quality will be important to better manage freshwater resources worldwide, e.g. by systemically identifying water bodies prone to ecological changes or the presence of harmful organisms.

microbiology↗

bioRxiv2018

Parasite-mediated anorexia increases or decreases virulence evolution, depending on dietary context

Parasite-mediated anorexia is a ubiquitous, but poorly understood component of host-parasite interactions. These temporary but substantial reductions in food intake (range: 4-100%) limit exposure to parasites and alter within-host physiological processes that regulate parasite development, production, and survival, such as energy allocation, immune function, host-microbiota interactions, and gastrointestinal conditions. By altering the duration, severity, and spread of infection, anorexia could substantially alter ecological, evolutionary, and epidemiological dynamics. However, these higher-order implications are typically overlooked and remain poorly understood -- even though medical (e.g., non-steroidal anti-inflammatory drugs, vaccines, targeted signaling pathways, calorie restriction) and husbandry practices (e.g., antibiotic and diet use for rapid growth, nutrient supplementation) often directly or indirectly alter host appetite and nutrient intake. Here, we develop theory that helps elucidate why reduced food intake (anorexia) can enhance or diminish disease severity and illustrates that the population-level outcomes often contrast with the individual-level outcomes: treatments that increase the intake of high quality nutrients (suppressing anorexia), can drive rapid individual-level recovery, but inadvertently increase infection prevalence and select for more virulent parasites. Such a theory-guided approach offers a tool to improve targeting host nutrition to manage disease in both human and livestock populations by revealing a means to predict how nutrient-driven feedbacks will affect both the host and parasite.

evolutionary biology↗

bioRxiv2018

In Silico Identification of Three Types of Integrative and Conjugative Elements (ICEs) in Elizabethkingia anophelis Strains Isolated from Around the World

Elizabethkingia anophelis is an emerging global multidrug-resistant opportunistic pathogen. We assessed the diversity among 13 complete genomes and 23 draft genomes of E. anophelis derived from various environmental settings and human infections from different geographic regions around the world over past decades from 1950s. Thirty-one of these 36 strains harbor integrative and conjugative elements (ICEs). A total of 52 ICEs were identified, and categorized into three ICE types based on the architecture of signature genes in the conjugation module. The type II and III ICEs were found to integrate into regions adjacent to tRNA genes, while type I ICEs used a variety of integration sites, inserting into intergenic regions or even directly into a gene, sometimes disrupting gene function. Integrases such as tyrosine recombinases, serine recombinases and DDE transposases were found in most ICEs. The ICEs carry various cargo genes including transcription regulators and those involved in antibiotic resistance. The CRISPR-Cas system was found in nine strains, including four strains in which CRISPR-Cas machinery and ICEs co-exist. ICE distribution in the strains showed no geographic or temporal patterns. The ICEs in E. anophelis differ in gene structure and sequence from CTnDOT, a well-studied ICE prevalent in Bacteroides spp. This is the first set of ICEs identified in the family Flavobacteriaceae. As a prevalent type of mobile genetic elements in various strains of E. anophelis around the world, the categorization of ICEs will facilitate further investigations such as virulence, genome epidemiology and adaptation genomics of E. anophelis.\n\nImportanceElizabethkingia anophelis is an opportunistic human pathogen, and the genetic diversity between strains from around the world becomes apparent as more genomes are sequenced. The Integrative Conjugative Element (ICE), found in many bacterial species, contains genes for transfer via conjugation and integration into the chromosome, along with various cargo genes. ICEs are identified in 31 of 36 strains and categorized into three types based on architecture of modular genes, integrases, and integration sites. ICE distribution in different strains displays no spatial and temporal patterns. Several ICE-containing strains also possessed CRISPR-Cas units, considered to be the bacterial adaptive immune system providing protection against phage and predatory mobile genetic elements. This co-existence suggests that ICEs are beneficial or at least not harmful to the bacterial cells they inhabit. ICEs as a component of the mobile genetic repertoire enable recipients to resist antibiotics, survive disinfecting agents, and adapt to various ecological niches.

genomics↗

bioRxiv2018

Study of Oak Ridge soils using BONCAT-FACS-Seq reveals that a large fraction of the soil microbiome is active

The ability to link soil microbial diversity to soil processes requires technologies that differentiate active subpopulations of microbes from so-called relic DNA and dormant cells. Measures of microbial activity based on various techniques including DNA labelling have suggested that most cells in soils are inactive, a fact that has been difficult to reconcile with observed high levels of bulk soil activities. We hypothesized that measures of in situ DNA synthesis may be missing the soil microbes that are metabolically active but not replicating, and we therefore applied BONCAT (Bioorthogonal Non Canonical Amino Acid Tagging) i.e. a proxy for activity that does not rely on cell division, to measure translationally active cells in soils. We compared the active population of two soil depths from Oak Ridge (TN) incubated under the same conditions for up to seven days. Depending on the soil, a maximum of 25 - 70% of the cells were active, accounting for 3-4 million cells per gram of soil type, which is an order of magnitude higher than previous estimates. The BONCAT positive cell fraction was recovered by fluorescence activated cell sorting (FACS) and identified by 16S rDNA amplicon sequencing. The diversity of the active fraction was a selected subset of the bulk soil community. Excitingly, some of the same members of the community were recruited at both depths independently from their abundance rank. On average, 86% of sequence reads recovered from the active community shared >97% sequence similarity with cultured isolates from the field site. Our observations are in line with a recent report that, of the few taxa that are both abundant and ubiquitous in soil, 45% are also cultured - and indeed some of these ubiquitous microorganisms were found to be translationally active. The use of BONCAT on soil microbiomes provides evidence that a large portion of the soil microbes can be active simultaneously. We conclude that BONCAT coupled to FACS and sequencing is effective for interrogating the active fraction of soil microbiomes in situ and provides new perspectives to link metabolic capacity to overall soil ecological traits and processes.

microbiology↗

bioRxiv2018

Biogeography and Edaphic Factors Structure Coastal Sediment Microbial Communities More than Vegetation Removal by Sudden Vegetation Dieback

Development of sudden vegetation dieback (SVD), a phenomenon that causes the rapid mortality of salt marsh plants, specifically Spartina alterniflora, has affected large-scale alterations in Atlantic coastal systems, through the often-complete removal of vegetation. In this study, two wetlands that differ in the time since development of SVD were compared in order to study biogeographic and temporal patterns that structure coastal wetland microbial communities and their response to disturbance.\n\nBiogeographic and edaphic factors that distinguished the two wetlands, such as differing salinity, water content, and soil carbon and nitrogen between the sites were more strongly associated with sediment microbial community structure than either sampling date or SVD development. In fact, no OTUs differed in abundance due to the season samples were collected, or vegetation loss due to SVD. This is not to say that SVD did not alter the composition of the microbial communities. The taxonomic composition of sediment communities in SVD-affected sediments was more heterogeneous between samples and a small number of OTUs were enriched in the vegetated sediments. Yet, these data suggest that coastal wetland sediment communities are predominantly shaped by environmental conditions and are generally resilient to temporal cycles or ecosystem disturbances.\n\nImportanceOne of the challenges of microbial ecology is predicting how microbial communities will respond to ecosystem change. Yet, few studies have addressed whether microbial responses to disturbance are consistent over space or time. In this study we employ SVD as a natural vegetation removal experiment and compare the sediment microbial communities between two geographically separated wetlands (ca 125 km). In this manner, we uncover a hierarchical structuring of the microbial communities, being predominantly governed by biogeography, with lesser effects due to disturbance, or temporal dynamics.

microbiology↗

bioRxiv2018

Soil health pilot study in England: outcomes from an on-farm earthworm survey

Earthworms are primary candidates for national soil health monitoring as they are ecosystem engineers that benefit both food production and ecosystem services associated with soil security. Supporting farmers to monitor soil health could help to achieve the policy aspiration of sustainable soils by 2030 in England; however, little is known about how to overcome participation barriers, appropriate methodologies (practical, cost-effective, usefulness) or training needs. This paper presents the results from a pilot #60minworms study which mobilised farmers to assess over >1300 ha farmland soils in spring 2018. The results interpretation framework is based on the presence of earthworms from each of the three ecological groups at each observation (20cm3pit) and spatially across a field (10 soil pits). Results showed that most fields have basic earthworm biodiversity, but 42 % fields may be at risk of over-cultivation as indicated by absence/rarity of epigeic and/or anecic earthworms; and earthworm counting is not a reliable indicator of earthworm biodiversity. Tillage had a negative impact (p < 0.05) on earthworm populations and organic matter management did not mitigate tillage impacts. In terms of farmer participation, Twitter and Farmers Weekly magazine were highly effective channels for recruitment. Direct feedback from participants included excellent scores in trust, value and satisfaction of the protocol (e.g. 100 % would do the test again) and 57 % would use their worm survey results to change their soil management practices. A key training need in terms of earthworm identification skills was reported. The trade-off between data quality, participation rates and fieldwork costs suggests there is potential to streamline the protocol further to #30minuteworms (5 pits), incurring farmer fieldwork costs of approximately {pound}1.48 ha-1. At national scales, {pound}14 million pounds across 4.7 M ha-1 in fieldwork costs per survey could be saved by farmer participation.

scientific communication and education↗

bioRxiv2018

Freshwater diatoms diversify faster than marine in both planktonic and benthic habitats

Many clades that span the marine-freshwater boundary are disproportionately more diverse in the younger, shorter-lived, and scarcer freshwater environments than they are in the marine realm. This disparity is thought to be related to differences in diversification rates between marine and freshwater lineages. However, marine and freshwaters are not ecologically homogeneous, so the study of diversification across the salinity divide should also account for other potentially interacting variables. In diatoms, freshwater and substrate-associated (benthic) lineages are several-fold more diverse than their marine and suspended (planktonic) counterparts. These imbalances provide an excellent system to understand whether these variables interact with diversification. Using multistate hidden-state speciation and extinction models we found that freshwater lineages diversify faster than marine lineages regardless of whether they inhabit the plankton or the benthos. Freshwater lineages also had higher turnover rates (speciation + extinction), suggesting that habitat transitions impact speciation and extinction rates jointly. The plankton-benthos contrast was also consistent with state-dependent diversification, but with modest differences in diversification and turnover rates. Asymmetric, and bidirectional transitions rejected hypotheses about the plankton and freshwaters as absorbing, inescapable habitats. Our results further suggest that the high turnover rate of freshwater diatoms is related to high turnover of freshwater systems themselves.

evolutionary biology↗

bioRxiv2018

Meta-population structure and the evolutionary transition to multicellularity

AO_SCPLOWBSTRACTC_SCPLOWThe evolutionary transition to multicellularity has occurred on numerous occasions, but transitions to complex life forms are rare. While the reasons are unclear, relevant factors include the intensity of within-versus between-group selection that are likely to have shaped the course of life cycle evolution. A highly structured environment eliminates the possibility of mixing between evolving lineages, thus ensuring strong competition between groups. Less structure intensifies competition within groups, decreasing opportunity for group-level evolution. Here, using populations of the bacterium Pseudomonas fluorescens, we report the results of experiments that explore the effect of lineage mixing on the evolution of nascent multicellular groups. Groups were propagated under regimes requiring reproduction via a life cycle replete with developmental and dispersal (propagule) phases, but in one treatment lineages never mixed, whereas in a second treatment, cells from different lineages experienced intense competition during the dispersal phase. The latter treatment favoured traits promoting cell growth at the expense of traits underlying group fitness - a finding that is supported by results from a mathematical model. Together our results show that the transition to multicellularity benefits from ecological conditions that maintain discreteness not just of the group (soma) phase, but also of the dispersal (germline) phase.

evolutionary biology↗

bioRxiv2018

Effects of in-vitro pH decrease on the gametogenesis of the red tree coral, Primnoa pacifica

Primnoa pacifica is the most ecologically important coral species in the North Pacific Ocean where it provides important habitat for commercially important fish and invertebrates. Ocean acidification (OA) is more rapidly increasing in high-latitude seas because anthropogenic CO2 uptake is greater in these regions. This is due to the solubility of CO2 in cold water and the reduced buffering capacity due to low alkalinity of colder waters. Primnoa pacifica colonies were cultured for six to nine months in either pH 7.55 (predicted 2100 pH levels) or pH 7.75 (control). Oocyte development and fecundity in females, and spermatocyst stages in males were measured to assess the effects of pH on gametogenesis. Oocyte diameters were 13.6% smaller and fecundities were 30.9% lower in the Year 2100 samples, indicating that OA may limit oocyte formation, potentially through lipid limitation. A higher proportion of vitellogenic oocytes (65%) were also reabsorbed (oosorption) in the Year 2100 treatment. Lowered pH appeared to advance the process of spermatogenesis with a higher percentage of later stage sperm compared to control controls. There was a laboratory effect observed in all measurement types, however these only significantly affected the analyses of spermatogenesis. These results indicate that reproduction may not be possible in an acidified ocean, or that if spawning could occur, spawned oocytes would not be sufficiently equipped to support the normal development of larvae.

physiology↗

bioRxiv2018

Taxonomic Classification of Ants (Formicidae) from Images using Deep Learning

The well-documented, species-rich, and diverse group of ants (Formicidae) are important ecological bioindicators for species richness, ecosystem health, and biodiversity, but ant species identification is complex and requires specific knowledge. In the past few years, insect identification from images has seen increasing interest and success, with processing speed improving and costs lowering. Here we propose deep learning (in the form of a convolutional neural network (CNN)) to classify ants at species level using AntWeb images. We used an Inception-ResNet-V2-based CNN to classify ant images, and three shot types with 10,204 images for 97 species, in addition to a multi-view approach, for training and testing the CNN while also testing a worker-only set and an AntWeb protocol-deviant test set. Top 1 accuracy reached 62% - 81%, top 3 accuracy 80% - 92%, and genus accuracy 79% - 95% on species classification for different shot type approaches. The head shot type outperformed other shot type approaches. Genus accuracy was broadly similar to top 3 accuracy. Removing reproductives from the test data improved accuracy only slightly. Accuracy on AntWeb protocol-deviant data was very low. In addition, we make recommendations for future work concerning image threshold, distribution, and quality, multi-view approaches, metadata, and on protocols; potentially leading to higher accuracy with less computational effort.

bioinformatics↗

bioRxiv2018

Changes in Microorganisms in the Rhizosphere of Mulberry Genotypes with Differing Resistance to Bacterial Wilt

A close relationship between soil-borne diseases, soil microbial community structure, and functional diversity has been described in the mulberry plant. In the present study, microbial abundance, community structure, and functional diversity in the soil rhizosphere were compared in resistant (Kangqing10) and susceptible (Guisang12) mulberry genotypes using the dilution plate method, micro-ecology technology, and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). The goal of this study was to develop better management methods for mulberry cultivation and preventing and controlling bacterial wilt. Rhizosphere soil microorganisms were more abundant in the resistant normal mulberry genotype than in the susceptible normal mulberry genotype. Carbon source utilization was better in the susceptible normal mulberry genotype. These properties were lower in the resistant sickly mulberry genotype than in the susceptible sickly mulberry genotype. PCR-DGGE indicated that the bacterial and fungal community structures of the resistant genotypes were more stable than those of the susceptible genotypes. Correlation regression analysis implicated mulberry bacterial wilt in the loss of soil nutrients, particularly organic matter and nitrogen, which can disrupt the balance of the soil microbial community. Loss of soil organic matter and nitrogen had a lower impact on resistant genotype plants than on susceptible genotype plants. Therefore, resistant genotype plants displayed some resistance to bacterial wilt. Further insights into the soil rhizosphere microbial diversities of resistant and susceptible genotypes will help in the control and prevention of mulberry bacterial wilt.

microbiology↗

bioRxiv2018

Tree-sequence recording in SLiM opens new horizons for forward-time simulation of whole genomes

There is an increasing demand for evolutionary models to incorporate relatively realistic dynamics, ranging from selection at many genomic sites to complex demography, population structure, and ecological interactions. Such models can generally be implemented as individual-based forward simulations, but the large computational overhead of these models often makes simulation of whole chromosome sequences in large populations infeasible. This situation presents an important obstacle to the field that requires conceptual advances to overcome. The recently developed tree-sequence recording method (Kelleher et al., 2018), which stores the genealogical history of all genomes in the simulated population, could provide such an advance. This method has several benefits: (1) it allows neutral mutations to be omitted entirely from forward-time simulations and added later, thereby dramatically improving computational efficiency; (2) it allows neutral burn-in to be constructed extremely efficiently after the fact, using \"recapitation\"; (3) it allows direct examination and analysis of the genealogical trees along the genome; and (4) it provides a compact representation of a populations genealogy that can be analyzed in Python using the msprime package. We have implemented the tree-sequence recording method in SLiM 3 (a free, open-source evolutionary simulation software package) and extended it to allow the recording of non-neutral mutations, greatly broadening the utility of this method. To demonstrate the versatility and performance of this approach, we showcase several practical applications that would have been beyond the reach of previously existing methods, opening up new horizons for the modeling and exploration of evolutionary processes.

evolutionary biology↗