scholarly journals Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast

2019 ◽  
Vol 5 (12) ◽  
pp. eaav9963 ◽  
Author(s):  
Hernán E. Morales ◽  
Rui Faria ◽  
Kerstin Johannesson ◽  
Tomas Larsson ◽  
Marina Panova ◽  
...  
Keyword(s):  
Environmental Gradients ◽  
Spatial Scales ◽  
Heterogeneous Environments ◽  
Ecological Divergence ◽  
Chromosomal Inversions ◽  
Balanced Polymorphism ◽  
Whole Genome Resequencing ◽  
Genomic Regions ◽  
Genomic Basis ◽  
Crab Predation

The study of parallel ecological divergence provides important clues to the operation of natural selection. Parallel divergence often occurs in heterogeneous environments with different kinds of environmental gradients in different locations, but the genomic basis underlying this process is unknown. We investigated the genomics of rapid parallel adaptation in the marine snail Littorina saxatilis in response to two independent environmental axes (crab-predation versus wave-action and low-shore versus high-shore). Using pooled whole-genome resequencing, we show that sharing of genomic regions of high differentiation between environments is generally low but increases at smaller spatial scales. We identify different shared genomic regions of divergence for each environmental axis and show that most of these regions overlap with candidate chromosomal inversions. Several inversion regions are divergent and polymorphic across many localities. We argue that chromosomal inversions could store shared variation that fuels rapid parallel adaptation to heterogeneous environments, possibly as balanced polymorphism shared by adaptive gene flow.

scholarly journals Genomic architecture of parallel ecological divergence: beyond a single environmental contrast

2018 ◽  
Author(s):  
Hernán E. Morales ◽  
Rui Faria ◽  
Kerstin Johannesson ◽  
Tomas Larsson ◽  
Marina Panova ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Spatial Scales ◽  
Heterogeneous Environments ◽  
Ecological Divergence ◽  
Balanced Polymorphism ◽  
Standing Variation ◽  
Genomic Architecture ◽  
Whole Genome Resequencing ◽  
Genomic Regions ◽  
Crab Predation

AbstractThe genetic basis of parallel ecological divergence provides important clues to the operation of natural selection and the predictability of evolution. Many examples exist where binary environmental contrasts seem to drive parallel divergence. However, this simplified view can conceal important components of parallel divergence because environmental variation is often more complex. Here, we disentangle the genetic basis of parallel divergence across two axes of environmental differentiation (crab-predation vs. wave-action and low-shore vs. high-shore habitat contrasts) in the marine snail Littorina saxatilis, a well established natural system of parallel ecological divergence. We used whole-genome resequencing across multiple instances of these two environmental axes, at local and regional scales from Spain to Sweden. Overall, sharing of genetic differentiation is generally low but it is highly heterogeneous across the genome and increases at smaller spatial scales. We identified genomic regions, both overlapping and non-overlapping with recently described candidate chromosomal inversions, that are differentially involved in adaptation to each of the environmental axis. Thus, the evolution of parallel divergence in L. saxatilis is largely determined by the joint action of geography, history, genomic architecture and congruence between environmental axes. We argue that the maintenance of standing variation, perhaps as balanced polymorphism, and/or the re-distribution of adaptive variants via gene flow can facilitate parallel divergence in multiple directions as an adaptive response to heterogeneous environments.

scholarly journals Phylogeography of two Andean frogs: Test of vicariance versus elevational gradient models of diversification

2019 ◽  
Author(s):  
Daria Koscinski ◽  
Paul Handford ◽  
Pablo L. Tubaro ◽  
Peiwen Li ◽  
Stephen C. Lougheed
Keyword(s):  
Sequence Data ◽  
Environmental Gradients ◽  
Spatial Scales ◽  
Elevational Gradient ◽  
Northwestern Argentina ◽  
Dna Sequence Data ◽  
The Andes ◽  
Common Causes ◽  
History Of ◽  
Historical Range

ABSTRACTThe tropical and subtropical Andes have among the highest levels of biodiversity in the world. Understanding the forces that underlie speciation and diversification in the Andes is a major focus of research. Here we tested two hypotheses of species origins in the Andes: 1. Vicariance mediated by orogenesis or shifting habitat distribution. 2. Parapatric diversification along elevational environmental gradients. We also sought insights on the factors that impacted the phylogeography of co-distributed taxa, and the influences of divergent species ecology on population genetic structure. We used phylogeographic and coalescent analyses of nuclear and mitochondrial DNA sequence data to compare genetic diversity and evolutionary history of two frog species: Pleurodema borellii (Family: Leiuperidae, 130 individuals; 20 sites), and Hypsiboas riojanus (Family: Hyllidae, 258 individuals; 23 sites) across their shared range in northwestern Argentina. The two showed concordant phylogeographic structuring, and our analyses support the vicariance model over the elevational gradient model. However, Pleurodema borellii exhibited markedly deeper temporal divergence (≥4 Ma) than H. riojanus (1-2 Ma). The three main mtDNA lineages of P. borellii were nearly allopatric and diverged between 4-10 Ma. At similar spatial scales, differentiation was less in the putatively more habitat-specialized H. riojanus than in the more generalist P. borellii. Similar allopatric distributions of major lineages for both species implies common causes of historical range fragmentation and vicariance. However, different divergence times among clades presumably reflect different demographic histories, permeability of different historical barriers at different times, and/or difference in life history attributes and sensitivities to historical environmental change. Our research enriches our understanding of the phylogeography of the Andes in northwestern Argentina.

scholarly journals Evolutionary origins for ecological patterns in space

2020 ◽  
Vol 117 (30) ◽  
pp. 17482-17490 ◽  
Author(s):  
Mark C. Urban ◽  
Sharon Y. Strauss ◽  
Fanie Pelletier ◽  
Eric P. Palkovacs ◽  
Mathew A. Leibold ◽  
...  
Keyword(s):  
Local Adaptation ◽  
Environmental Gradients ◽  
Spatial Scales ◽  
Keystone Species ◽  
Future Research ◽  
Evolutionary Divergence ◽  
Patch Selection ◽  
Fully Integrated ◽  
Evolutionary Origins ◽  
Ecological Patterns

Historically, many biologists assumed that evolution and ecology acted independently because evolution occurred over distances too great to influence most ecological patterns. Today, evidence indicates that evolution can operate over a range of spatial scales, including fine spatial scales. Thus, evolutionary divergence across space might frequently interact with the mechanisms that also determine spatial ecological patterns. Here, we synthesize insights from 500 eco-evolutionary studies and develop a predictive framework that seeks to understand whether and when evolution amplifies, dampens, or creates ecological patterns. We demonstrate that local adaptation can alter everything from spatial variation in population abundances to ecosystem properties. We uncover 14 mechanisms that can mediate the outcome of evolution on spatial ecological patterns. Sometimes, evolution amplifies environmental variation, especially when selection enhances resource uptake or patch selection. The local evolution of foundation or keystone species can create ecological patterns where none existed originally. However, most often, we find that evolution dampens existing environmental gradients, because local adaptation evens out fitness across environments and thus counteracts the variation in associated ecological patterns. Consequently, evolution generally smooths out the underlying heterogeneity in nature, making the world appear less ragged than it would be in the absence of evolution. We end by highlighting the future research needed to inform a fully integrated and predictive biology that accounts for eco-evolutionary interactions in both space and time.

scholarly journals A framework to bridge scales in distribution modeling of soil microbiota

2020 ◽  
Vol 96 (5) ◽  
Author(s):  
Jonas J Lembrechts ◽  
L Broeders ◽  
J De Gruyter ◽  
D Radujković ◽  
I Ramirez-Rojas ◽  
...  
Keyword(s):  
Environmental Gradients ◽  
Spatial Scales ◽  
Biotic Interactions ◽  
Environmental Niche ◽  
Distribution Models ◽  
Soil Microbiota ◽  
Soil Microbial ◽  
Critical Issues ◽  
Multiple Species ◽  
Species Specific

ABSTRACT Creating accurate habitat suitability and distribution models (HSDMs) for soil microbiota is far more challenging than for aboveground organism groups. In this perspective paper, we propose a conceptual framework that addresses several of the critical issues holding back further applications. Most importantly, we tackle the mismatch between the broadscale, long-term averages of environmental variables traditionally used, and the environment as experienced by soil microbiota themselves. We suggest using nested sampling designs across environmental gradients and objectively integrating spatially hierarchic heterogeneity as covariates in HSDMs. Second, to incorporate the crucial role of taxa co-occurrence as driver of soil microbial distributions, we promote the use of joint species distribution models, a class of models that jointly analyze multiple species’ distributions, quantifying both species-specific environmental responses (i.e. the environmental niche) and covariance among species (i.e. biotic interactions). Our approach allows incorporating the environmental niche and its associated distribution across multiple spatial scales. The proposed framework facilitates the inclusion of the true relationships between soil organisms and their abiotic and biotic environments in distribution models, which is crucial to improve predictions of soil microbial redistributions as a result of global change.

scholarly journals Ecotones: Marginal or central areas of transition?

2006 ◽  
Vol 52 (1) ◽  
pp. 29-53 ◽  
Author(s):  
Salit Kark ◽  
Berndt J. van Rensburg
Keyword(s):  
Environmental Gradients ◽  
Spatial Scales ◽  
Small Scale ◽  
Biodiversity Hotspots ◽  
Ecological Communities ◽  
Marginal Populations ◽  
Multiple Spatial Scales ◽  
Scientific Attention

Areas of environmental transition, where ecological communities coincide, are sometimes termed ecotones. These regions often correspond with sharp environmental gradients. Ecotones occur at multiple spatial scales, ranging from transitions between biomes to local small-scale transitions. In recent years ecotones have received increasing scientific attention after being neglected for years, as studies historically often focused on distinct communities. However, it is still debatable whether these transitional regions are speciation and biodiversity hotspots that deserve special conservation interest or are actually areas that hold marginal populations that depend on other parts of the range for the maintenance of their biodiversity and therefore should not deserve primary investment. This paper discusses some of the recent advancements in our understanding of the role of ecotones in ecology, evolution, and conservation.

From continua to patches: examining stream community structure over large environmental gradients

2002 ◽  
Vol 59 (8) ◽  
pp. 1404-1417 ◽  
Author(s):  
Kristopher K Wright ◽  
Judith L Li
Keyword(s):  
Conceptual Framework ◽  
Algal Biomass ◽  
Environmental Gradients ◽  
Spatial Scales ◽  
Habitat Characteristics ◽  
Physical Habitat ◽  
Macroinvertebrate Communities ◽  
Order Stream ◽  
Longitudinal Gradients ◽  
Individual Variables

We present an approach that integrates a conceptual framework with multivariate ordination techniques and traditional parametric analyses to examine biotic and abiotic gradients in stream ecosystems. Ordinations were used to examine multivariate patterns along an environmental gradient, with individual variables used to interpret those patterns across spatial scales. The conceptual framework provides a consistent context to compare community distributions and consequently allows for hypothesis testing using ordinations. To illustrate the approach, we examined the physical template, fish and benthic macroinvertebrate communities, and algal biomass and production along a 1st- through 5th-order stream gradient in eastern Oregon. We hypothesized that longitudinal distributions of physical habitat characteristics, fishes, macroinvertebrates, and periphyton would reflect highly variable, discontinuous gradients. Multivariate patterns were determined by rotating nonparametric ordinations to a common set of variables and comparing them to conceptual models of (i) an ideal continuum, (ii) a random distribution, and (iii) discrete patches. Physical habitat and fishes reflected strong longitudinal gradients, macroinvertebrates were the most patchy, and algal biomass and production were highly variable. Distributions of individual variables from site and stream-order perspectives revealed how different factors, potentially influencing stream communities, may be continuous or patchy depending on spatial scale.

scholarly journals Disentangling the processes driving plant assemblages in mountain grasslands across spatial scales and environmental gradients

2018 ◽  
Vol 107 (1) ◽  
pp. 265-278 ◽  
Author(s):  
Daniel Scherrer ◽  
Heidi K. Mod ◽  
Julien Pottier ◽  
Anne Litsios‐Dubuis ◽  
Loïc Pellissier ◽  
...  
Keyword(s):  
Environmental Gradients ◽  
Spatial Scales ◽  
Mountain Grasslands ◽  
Plant Assemblages

scholarly journals Metacommunity phylogenteic structure along environmental gradients

2017 ◽  
Author(s):  
Diogo Provete
Keyword(s):  
Phylogenetic Trees ◽  
Environmental Gradients ◽  
Spatial Scales ◽  
Canopy Cover ◽  
Freshwater Ecosystems ◽  
Southeastern Brazil ◽  
Quadratic Term ◽  
Lineage Sorting ◽  
Phylogenetic Information ◽  
Phylogenetic Structure

Phylogenetic information has increasingly been included in studies of local communities and also at broad spatial scales. Despite recent criticisms in the last four years, phylogenetic relationships may still provide insights into theorganization and assembly of ecological communities. The objectives of this study were 1) to review the history of the use of phylogenetic information, as well as criticisms and perspectives of its use in community ecology; 2) understand how the size and shape of phylogenetic trees and the phylogenetic structure of metacomunidaes affect the amount of variation accounted for by a eigenvectorbasedmethod used to describe the phylogenetic composition of metacomunidaes (PCPS); 3) to test the effect of diversity of evolutionary history (MNTD and MPD) and species richness as predictors of three variables of freshwater ecosystemfunctioning (productivity, respiration, and decomposition); and finally 4) to test how environmental gradients, especially pond canopy cover, influence the phylogenetic structure of an anuran metacommunity from southeastern Brazil. Ifound that the structure of metacommunities had greater impact on eigenvalues of PCPS than tree shape metrics, such as symmetry and stemminess. In addition, decomposition and respiration were best predicted by MNTD as a linear function, while productivity was affected by the quadratic term of MNTD. Finally, pond canopy cover and floating vegetation strongly affected the phylogenetic structureof the anruan metacommunity, influencing lineage sorting. These findings 1) can help users interpret the results of PCPS; 2) provide better understand of the effectof species loss in multitrophic, freshwater ecosystems; and 3) improve our knowledge about the effect of canopy cover on the lineage composition in anuran metacomunities.

scholarly journals Intercontinental karyotype–environment parallelism supports a role for a chromosomal inversion in local adaptation in a seaweed fly

2018 ◽  
Vol 285 (1881) ◽  
pp. 20180519 ◽  
Author(s):  
Claire Mérot ◽  
Emma L. Berdan ◽  
Charles Babin ◽  
Eric Normandeau ◽  
Maren Wellenreuther ◽  
...  
Keyword(s):  
North America ◽  
Local Adaptation ◽  
Environmental Gradients ◽  
Balancing Selection ◽  
Chromosomal Rearrangements ◽  
Natural Populations ◽  
Inversion Polymorphism ◽  
Life History Strategies ◽  
Heterogeneous Environments ◽  
Adult Size

Large chromosomal rearrangements are thought to facilitate adaptation to heterogeneous environments by limiting genomic recombination. Indeed, inversions have been implicated in adaptation along environmental clines and in ecotype specialization. Here, we combine classical ecological studies and population genetics to investigate an inversion polymorphism previously documented in Europe among natural populations of the seaweed fly Coelopa frigida along a latitudinal cline in North America. We test if the inversion is present in North America and polymorphic, assess which environmental conditions modulate the inversion karyotype frequencies, and document the relationship between inversion karyotype and adult size. We sampled nearly 2000 flies from 20 populations along several environmental gradients to quantify associations of inversion frequencies to heterogeneous environmental variables. Genotyping and phenotyping showed a widespread and conserved inversion polymorphism between Europe and America. Variation in inversion frequency was significantly associated with environmental factors, with parallel patterns between continents, indicating that the inversion may play a role in local adaptation. The three karyotypes of the inversion are differently favoured across micro-habitats and represent life-history strategies likely to be maintained by the collective action of several mechanisms of balancing selection. Our study adds to the mounting evidence that inversions are facilitators of adaptation and enhance within-species diversity.

scholarly journals The evolutionary history and genomics of European blackcap migration

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Kira Delmore ◽  
Juan Carlos Illera ◽  
Javier Pérez-Tris ◽  
Gernot Segelbacher ◽  
Juan S Lugo Ramos ◽  
...  
Keyword(s):  
Seasonal Migration ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Rapid Changes ◽  
Migratory Syndrome ◽  
Enormous Variation ◽  
Whole Genome Resequencing ◽  
Genomic Regions ◽  
Admixture Event ◽  
Shared Variation

Seasonal migration is a taxonomically widespread behaviour that integrates across many traits. The European blackcap exhibits enormous variation in migration and is renowned for research on its evolution and genetic basis. We assembled a reference genome for blackcaps and obtained whole genome resequencing data from individuals across its breeding range. Analyses of population structure and demography suggested divergence began ~30,000 ya, with evidence for one admixture event between migrant and resident continent birds ~5000 ya. The propensity to migrate, orientation and distance of migration all map to a small number of genomic regions that do not overlap with results from other species, suggesting that there are multiple ways to generate variation in migration. Strongly associated single nucleotide polymorphisms (SNPs) were located in regulatory regions of candidate genes that may serve as major regulators of the migratory syndrome. Evidence for selection on shared variation was documented, providing a mechanism by which rapid changes may evolve.

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