Biology subjects

Travis, J. M.

Publications and source records attributed to Travis, J. M..

5 recordsLinked to original sources

bioRxiv2024

Chromosome-scale genome assembly and linkage map for Silene uniflora reveal the recombination landscape in a rapidly evolving plant species

The genus Silene is an important model system for fields as diverse as sex chromosome evolution, speciation and disease ecology. However, genomic resources remain scarce in the genus. Here, we present a chromosome-scale genome assembly for S. uniflora, a hermaphroditic/gynodioecious species which is an important model for rapid adaptation to anthropogenic disturbance and the role of phenotypic plasticity in adaptive evolution. Using a combination of long-read and Hi-C sequencing technologies, we generated a 1,268 Mb genome assembly with a scaffold N50 of 40.72 Mb and 682 Mb assembled into 12 chromosomes. We annotated the genome using evidence from transcriptome and protein mapping in combination with ab initio gene prediction, resulting in 41,603 protein-coding genes and a BUSCO completeness score of 91%. We also present a linkage map which we used to validate the genome assembly and estimate local recombination rate across the genome. Comparison to the only two other Silene species with chromosome-scale genome assemblies reveals widespread genome rearrangements in the genus, suggesting Silene may be a promising study system for the role of genome rearrangement in evolution, particularly in the evolution of sex chromosomes and adaptation. Significance statementPlant species in the genus Silene (campions) are important study organisms in multiple areas of ecology and evolution. Sea campion (Silene uniflora) is an important model for investigations into rapid adaptation, phenotypic plasticity and parallel evolution. However, only two species have high-quality genome assemblies available, hampering studies of their genetics and evolution. We present a high-quality genome assembly, genetic map and gene annotation for sea campion. These will be important genomic resources for future studies of sea campion, other species in the genus Silene and the family Caryophyllaceae more generally.

evolutionary biology↗

bioRxiv2022

MerMADE: Coupled biophysical, eco-evolutionary modelling for predicting population dynamics, movement and dispersal evolution in the marine environment

In order to understand patterns in species distributions, we need to understand the underlying mechanisms of dispersal, demography and evolutionary capability of these species. In the marine environment, few models combine these three key components likely due both to the computational challenges involved and the inherent challenges in data collection for parameterisation. To fill this gap, we have developed MerMADE, an individual-based, spatially explicit, eco-evolutionary coupled biophysical model for predicting population dynamics, dispersal and movement evolution in the marine environment (or aquatic environments in general). MerMADE combines dispersal in a 3D, hydrodynamically informed environment with population dynamics, demography and evolutionary functionality in order to investigate questions of connectivity, population persistence and evolution under environmental change and anthropogenic pressure. We illustrate its range of behavioural and physiological functionality using the lesser sandeel, Ammodytes marinus, as a case-study species in an invasion scenario. MerMADEs flexibility in species-specific parameterisation makes it a widely applicable, exciting tool in future sustainable management and conservation of aquatic species under environmental change.

ecology↗

bioRxiv2021

Evolution of reduced dormancy during range expansions

There is increasing evidence that life-history traits can evolve rapidly during range expansion and that this evolution can impact the ecological dynamics of population spread. While dispersal evolution during range expansion has received substantial attention, dormancy (dispersal in time) has not. Here, we use an individual-based model to investigate the evolution of seed dormancy during range expansion. When a population is at spatial equilibrium our model produces results that are consistent with previous theoretical studies: seed dormancy evolves due to kin competition and the degree of dormancy increases as temporal environmental variation increases. During range expansions we consistently observe evolution towards reduced rates of dormancy at the front. Behind the front there is selection for higher rates of dormancy. Notably, the decreased dormancy towards the expanding margin reduces the regional resilience of recently expanded populations to a series of harsh years. We discuss how dormancy evolution during range expansion, and its consequences for spatial population dynamics, may impact other evolutionary responses to environmental change. We end with suggestions for future theoretical and empirical work.

evolutionary biology↗

bioRxiv2020

RangeShifter 2.0: An extended and enhanced platform for modelling spatial eco-evolutionary dynamics and species' responses to environmental changes.

O_LIProcess-based models are becoming increasingly used tools for understanding how species are likely to respond to environmental changes and to potential management options. RangeShifter is one such modelling platform, which has been used to address a range of questions including identifying effective reintroduction strategies, understanding patterns of range expansion and assessing population viability of species across complex landscapes. C_LIO_LIHere we introduce a new version, RangeShifter 2.0, which incorporates important new functionality. It is now possible to simulate dynamics over user-specified, temporally changing landscapes. Additionally, the genetic and evolutionary capabilities have been strengthened, notably by introducing an explicit genetic modelling architecture, which allows for simulation of neutral and adaptive genetic processes. Furthermore, emigration, transfer and settlement rules can now all evolve, allowing for sophisticated simulation of the evolution of dispersal. We illustrate the potential application of RangeShifter 2.0s new functionality by two examples. The first illustrates the range expansion of a virtual species across a dynamically changing UK landscape. The second demonstrates how the software can be used to explore the concept of evolving connectivity in response to land-use modification, by examining how movement rules come under selection over landscapes of different structure and composition. C_LIO_LIRangeShifter 2.0 is built using object-oriented C++ providing computationally efficient simulation of complex individual-based, eco-evolutionary models. The code has been redeveloped to enable use across operating systems, including on high performance computing clusters, and the Windows GUI has been enhanced. Furthermore, the recoding of the package has supported the development of a new version running under the R platform, RangeShiftR. C_LIO_LIRangeShifter 2.0 will facilitate the development of in-silico assessments of how species will respond to environmental changes and to potential management options for conserving or controlling them. By making the code available open source, we hope to inspire further collaborations and extensions by the ecological community. C_LI

ecology↗

bioRxiv2020

MetaConnect, a new platform for population viability modelling to assist decision makers in conservation and urban planning

In a context of global change, scientists and policy-makers require tools to address the issue of biodiversity loss. Population viability analysis (PVA) has been the main tool to deal with this problem. However, the tools developed during the 90s poorly integrate recent scientific advances in landscape genetics and dispersal. We developed a flexible and modular modelling platform for PVA that addresses many of the limitations of existing software. MetaConnect is an individual-based, process-based and PVA-oriented modelling platform which could be used as a research or a decision-making tool. Here, we present the core base modelling of MetaConnect. We demonstrate its potential use through a case study illustrating the platforms capability for performing integrated PVA including extinction probability estimation, genetic differentiation and landscape connectivity analysis. We used MetaConnect to assess the impact of infrastructure works on the natterjack toad metapopulation functioning.

ecology↗