skip to main content

Title: Isolation‐by‐distance and isolation‐by‐oceanography in Maroon Anemonefish (Amphiprion biaculeatus)
Obtaining dispersal estimates for a species is key to understanding local adaptation and population dynamics and to implementing conservation actions. Genetic isolation-by-distance (IBD) patterns can be used for estimating dispersal, and these patterns are especially useful for marine species in which few other methods are available. In this study, we genotyped coral reef fish (Amphiprion biaculeatus) at 16 microsatellite loci across eight sites across 210 km in the central Philippines to generate fine-scale estimates of dispersal. All sites except for one followed IBD patterns. Using IBD theory, we estimated a larval dispersal kernel spread of 8.9 km (95% confidence interval of 2.3–18.4 km). Genetic distance to the remaining site correlated strongly with the inverse probability of larval dispersal from an oceanographic model. Ocean currents were a better explanation for genetic distance at large spatial extents (sites greater than 150 km apart), while geographic distance remained the best explanation for spatial extents less than 150 km. Our study demonstrates the utility of combining IBD patterns with oceanographic simulations to understand connectivity in marine environments and to guide marine conservation strategies.  more » « less
Award ID(s):
Author(s) / Creator(s):
; ; ;
Publisher / Repository:
Date Published:
Journal Name:
Evolutionary Applications
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Abstract

    Conservation units (CUs) are an essential tool for maximizing evolutionary potential and prioritizing areas across a species’ range for protection when implementing conservation and management measures. However, current workflows for identifying CUs on the basis of neutral and adaptive genomic variation largely ignore information contained in patterns of isolation by distance (IBD), frequently the primary signal of population structure in highly mobile taxa, such as birds, bats, and marine organisms with pelagic larval stages. While individuals located on either end of a species’ distribution may exhibit clear genetic, phenotypic, and ecological differences, IBD produces subtle changes in allele frequencies across space, making it difficult to draw clear boundaries for conservation purposes in the absence of discrete population structure. Here, we highlight potential pitfalls that arise when applying common methods for delineating CUs to continuously distributed organisms and review existing methods for detecting subtle breakpoints in patterns of IBD that can indicate barriers to gene flow in highly mobile taxa. In addition, we propose a new framework for identifying CUs in all organisms, including those characterized by continuous genomic differentiation, and suggest several possible ways to harness the information contained in patterns of IBD to guide conservation and management decisions.

    more » « less
  2. Abstract

    Human activity continues to impact global ecosystems, often by altering the habitat suitability, persistence, and movement of native species. It is thus critical to examine the population genetic structure of key ecosystemservice providers across human‐altered landscapes to provide insight into the forces that limit wildlife persistence and movement across multiple spatial scales. While some studies have documented declines of bee pollinators as a result of human‐mediated habitat alteration, others suggest that some bee species may benefit from altered land use due to increased food or nesting resource availability; however, detailed population and dispersal studies have been lacking. We investigated the population genetic structure of the Eastern carpenter bee,Xylocopa virginica,across 14 sites spanning more than 450 km, including dense urban areas and intensive agricultural habitat.X. virginicais a large bee which constructs nests in natural and human‐associated wooden substrates, and is hypothesized to disperse broadly across urbanizing areas. Using 10 microsatellite loci, we detected significant genetic isolation by geographic distance and significant isolation by land use, where urban and cultivated landscapes were most conducive to gene flow. This is one of the first population genetic analyses to provide evidence of enhanced insect dispersal in human‐altered areas as compared to semi‐natural landscapes. We found moderate levels of regional‐scale population structure across the study system (GʹST = 0.146) and substantial co‐ancestry between the sampling regions, where co‐ancestry patterns align with major human transportation corridors, suggesting that human‐mediated movement may be influencing regional dispersal processes. Additionally, we found a signature of strong site‐level philopatry where our analyses revealed significant levels of high genetic relatedness at very fine scales (<1 km), surprising givenX. virginica'slarge body size. These results provide unique genetic evidence that insects can simultaneously exhibit substantial regional dispersal as well as high local nesting fidelity in landscapes dominated by human activity.

    more » « less
  3. Abstract

    Dispersal and adaptation are the two primary mechanisms that set the range distributions for a population or species. As such, understanding how these mechanisms interact in marine organisms in particular – with capacity for long‐range dispersal and a poor understanding of what selective environments species are responding to – can provide useful insights for the exploration of biogeographic patterns. Previously, the barnacleNotochthamalus scabrosushas revealed two evolutionarily distinct lineages with a joint distribution that suggests an association with one of the two major biogeographic boundaries (~30°S) along the coast of Chile. However, spatial and genomic sampling of this system has been limited until now. We hypothesized that given the strong oceanographic and environmental shifts associated with the other major biogeographic boundary (~42°S) for Chilean coastal invertebrates, the southern mitochondrial lineage would dominate or go to fixation in locations further to the south. We also evaluated nuclear polymorphism data from 130 single nucleotide polymorphisms to evaluate the concordance of the signal from the nuclear genome with that of the mitochondrial sample. Through the application of standard population genetic approaches along with a Lagrangian ocean connectivity model, we describe the codistribution of these lineages through a simultaneous evaluation of coastal lineage frequencies, an approximation of larval behavior, and current‐driven dispersal. Our results show that this pattern could not persist without the two lineages having distinct environmental optima. We suggest that a more thorough integration of larval dynamics, explicit dispersal models, and near‐shore environmental analysis can explain much of the coastal biogeography of Chile.

    more » « less
  4. Abstract

    Understanding the processes that underlie the development of population genetic structure is central to the study of evolution. Patterns of genetic structure, in turn, can reveal signatures of isolation by distance (IBD), barriers to gene flow, or even the genesis of speciation. However, it is unclear how severe range restriction might impact the processes that dominate the development of genetic structure. In narrow endemic species, is population structure likely to be adaptive in nature, or rather the result of genetic drift? In this study, we investigated patterns of genetic diversity and structure in the narrow endemic Hayden's ringlet butterfly. Specifically, we asked to what degree genetic structure in the Hayden's ringlet can be explained by IBD, isolation by resistance (IBR) (in the form of geographic or ecological barriers to migration between populations), and isolation by environment (in the form of differences in host plant availability and preference). We employed a genotyping‐by‐sequencing (GBS) approach coupled with host preference assays, Bayesian modelling, and population genomic analyses to answer these questions. Our results suggest that despite their restricted range, levels of genetic diversity in the Hayden's ringlet are comparable to those seen in more widespread butterfly species. Hayden's ringlets showed a strong preference for feeding on grasses relative to sedges, but neither larval preference nor potential host availability at sampling sites correlated with genetic structure. We conclude that geography, in the form of IBR and simple IBD, was the major driver of contemporary patterns of differentiation in this narrow endemic species.

    more » « less
  5. Abstract Aim

    To investigate the cryptic diversity and diversification timing in the putatively low‐dispersal Amazonian leaf‐litter lizardLoxopholis osvaldoi, and to ask how geography (rivers, isolation by distance, IBD), ecological drivers (isolation by environment, IBE) and historical factors (climatic refugia) explain intraspecific genetic variation.


    Central Amazonia, Brazil.


    Squamata; Gymnophthalmidae;Loxopholis osvaldoi.


    We sequenced two mitochondrial and two nuclear markers in 157 individuals. Phylogeographic structure and the occurrence of independent evolving lineages where explored through phylogenetic and coalescent analyses. A species tree and divergence dates of lineages were inferred with *BEAST, employing multiple DNA substitution rates. The potential genetic impacts of geographical distance among localities, the environment and the position of localities in relation to main rivers were tested by redundancy analysis (RDA).


    We detected 11 independently evolving and largely divergent intraspecific lineages. Lineage distribution patterns are complex and do not match any conspicuous barrier to gene flow, except for the Amazon River. Most lineages appear to have originated in the lower Miocene and Pliocene, in disagreement with the Pleistocene refuge hypothesis. IBD, IBE and rivers appear to have acted in concert establishing and maintaining genetic structure. However, when controlling for other explanatory variables, IBD explains significantly more variation than rivers, IBE or historical factors.

    Main Conclusions

    Our results strongly suggest thatL.osvaldoiis a species complex. Future taxonomic work should use an integrative approach to explore whether morphological variation is present and congruent with the genetic data. While the use of a sensitive dating analysis allowed us to better describe the diversification history ofL.osvaldoi, the lack of a spatial model of Neogene river dynamics prevents the test of specific, more informative river barrier hypotheses. The data suggest that nonlinear correlation analyses (e.g. RDA) should be preferred to detect factors that affect phylogeographic patterns in the Amazon, instead of linear multiple regressions (e.g. Mantel tests). Given the high level of cryptic diversity detected within this and other Amazonian species, we caution against hypothesis tests based solely on the distribution of nominal taxa, which can provide a rather incomplete view of the processes behind Amazonian diversity.

    more » « less