Genetic isolation by distance underlies color pattern divergence in red‐eyed treefrogs ( Agalychnis callidryas )

Investigating the spatial distribution of genetic and phenotypic variation can provide insights into the evolutionary processes that shape diversity in natural systems. We characterized patterns of genetic and phenotypic diversity to learn about drivers of color-pattern diversification in red-eyed treefrogs (Agalychnis callidryas) in Costa Rica. Along the Pacific coast, red-eyed treefrogs have conspicuous leg color patterning that transitions from orange in the north to purple in the south. We measured phenotypic variation of frogs across Pacific sites, with increased sampling at sites where the orange-to-purple transition occurs. At the transition zone, we discovered the co-occurrence of multiple color-pattern morphs. To explore possible causes of this variation, we generated a SNP dataset with RAD sequencing to analyze population genetic structure, measure genetic diversity, and infer the processes that mediate genotype-phenotype dynamics. We investigated how patterns of genetic relatedness correspond with individual measures of color pattern along the coast, including testing for the role of hybridization in geographic regions where orange and purple phenotypic groups co-occur. We found no evidence that color-pattern polymorphism in the transition zone arose through recent hybridization or introgression. Instead, a strong pattern of genetic isolation by distance (IBD) indicates that color-pattern variation was retained through other processes such as ancestral color polymorphisms, ancient secondary contact or generated by novel mutations. We found that color phenotype changes along the Pacific coast more than would be expected from geographic distance alone. Combined, our results suggest the possibility of selective pressures acting on color pattern at a small geographic scale.

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Genetic isolation by distance in the yellowfin goby populations revealed by RAD sequencing

Ichthyological Research ◽

10.1007/s10228-019-00709-6 ◽

2019 ◽

Vol 67 (1) ◽

pp. 98-104 ◽

Cited By ~ 1

Author(s):

Shotaro Hirase ◽

Ayumi Tezuka ◽

Atsushi J. Nagano ◽

Kiyoshi Kikuchi ◽

Wataru Iwasaki

Keyword(s):

Isolation By Distance ◽

Rad Sequencing ◽

Genetic Isolation ◽

Yellowfin Goby

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Genetic population structure constrains local adaptation in sticklebacks

10.1101/2020.01.17.908970 ◽

2020 ◽

Cited By ~ 1

Author(s):

Petri Kemppainen ◽

Zitong Li ◽

Pasi Rastas ◽

Ari Löytynoja ◽

Bohao Fang ◽

...

Keyword(s):

Genetic Variation ◽

Isolation By Distance ◽

Regulatory Element ◽

Morphological Data ◽

Genetic Isolation ◽

Genetic Population ◽

Population Structuring ◽

Different Populations ◽

Trait Locus ◽

Genomic Regions

AbstractRepeated and independent adaptation to specific environmental conditions from standing genetic variation is common. However, if genetic variation is limited, the evolution of similar locally adapted traits may be restricted to genetically different and potentially less optimal solutions, or prevented from happening altogether. Using a quantitative trait locus (QTL) mapping approach, we identified the genomic regions responsible for the repeated pelvic reduction (PR) in three crosses between nine-spined stickleback populations expressing full and reduced pelvic structures. In one cross, PR mapped to linkage group 7 (LG7) containing the gene Pitx1, known to control pelvic reduction also in the three-spined stickleback. In the two other crosses, PR was polygenic and attributed to ten novel QTL, of which 90% were unique to specific crosses. When screening the genomes from 27 different populations for deletions in the Pitx1 regulatory element, these were only found in the population in which PR mapped to LG7, even though the morphological data indicated large effect QTL for PR in several other populations as well. Consistent with the available theory and simulations parameterised on empirical data, we hypothesise that the observed variability in genetic architecture of PR is due to heterogeneity in the spatial distribution of standing genetic variation caused by strong population structuring and genetic isolation by distance in the sea.

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Lack of genetic isolation by distance, similar genetic structuring but different demographic histories in a fig-pollinating wasp mutualism

Molecular Ecology ◽

10.1111/mec.13438 ◽

2015 ◽

Vol 24 (23) ◽

pp. 5976-5991 ◽

Cited By ~ 20

Author(s):

Enwei Tian ◽

John D. Nason ◽

Carlos A. Machado ◽

Linna Zheng ◽

Hui Yu ◽

...

Keyword(s):

Isolation By Distance ◽

Genetic Isolation ◽

Genetic Structuring

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Genetic isolation by distance reveals restricted dispersal across a range of life histories: implications for biodiversity conservation planning across highly variable marine environments

Diversity and Distributions ◽

10.1111/ddi.12302 ◽

2015 ◽

Vol 21 (6) ◽

pp. 698-710 ◽

Cited By ~ 44

Author(s):

Daniel Wright ◽

Jacqueline M. Bishop ◽

Conrad A. Matthee ◽

Sophie von der Heyden

Keyword(s):

Biodiversity Conservation ◽

Conservation Planning ◽

Life Histories ◽

Isolation By Distance ◽

Marine Environments ◽

Genetic Isolation

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Landscape configuration of an Amazonian island-like ecosystem drives population structure and genetic diversity of a habitat-specialist bird

Landscape Ecology ◽

10.1007/s10980-021-01281-z ◽

2021 ◽

Author(s):

Camila D. Ritter ◽

Camila C. Ribas ◽

Juliana Menger ◽

Sergio H. Borges ◽

Christine D. Bacon ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Spatial Distribution ◽

Isolation By Distance ◽

Landscape Configuration ◽

Genetic Isolation ◽

White Sand ◽

Surrounding Matrix ◽

Relative Contribution ◽

Central Amazonia

Abstract Context Amazonian white-sand ecosystems (campinas) are open vegetation patches which form a natural island-like system in a matrix of tropical rainforest. Due to a clear distinction from the surrounding matrix, the spatial characteristics of campina patches may affect the genetic diversity and composition of their specialized organisms, such as the small and endemic passerine Elaenia ruficeps. Objectives To estimate the relative contribution of the current extension, configuration and geographical context of campina patches to the patterns of genetic diversity and population structure of E. ruficeps. Methods We sampled individuals of E. ruficeps from three landscapes in central Amazonia with contrasting campina spatial distribution, from landscapes with large and connected patches to landscapes with small and isolated patches. We estimated population structure, genetic diversity, and contemporary and historical migration within and among the three landscapes and used landscape metrics as predictor variables. Furthermore, we estimated genetic isolation by distance and resistance within landscapes. Results We identified three genetically distinct populations with asymmetrical gene flow among landscapes and a decreasing migration rate with distance. Within each landscape, we found low differentiation without genetic isolation by distance nor by resistance. In contrast, we found differentiation and spatial correlation between landscapes. Conclusions Together with previous studies, the population dynamics of E. ruficeps suggests that both regional context and landscape structure shape the connectivity among populations of campina specialist birds. Also, the spatial distribution of Amazonian landscapes, together with their associated biota, has changed in response to climatic changes in the Late Pleistocene.

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Population level genetic differentiation among temperate Neoconocephalus katydids

10.32469/10355/62323 ◽

2017 ◽

Author(s):

◽

Gideon Ney

Keyword(s):

Genetic Differentiation ◽

Gulf Coast ◽

Isolation By Distance ◽

Population Level ◽

Genetic Isolation ◽

Continental Scale ◽

Pattern Of Variation ◽

Habitat Generalist ◽

Species Specific ◽

The Impact

Recent work indicates that radiation events may play a significant role in shaping species diversity across entire continents. Here we quantify population level genetic differentiation in several species of Neoconocephalus katydids in order to determine the mechanisms of genetic isolation across a continental scale. Patterns of genetic isolation can be generalized into four types: isolation by resistance (IBR), isolation by barrier (IBB), isolation by distance (IBD), and epigenetic incompatibility. N. melanorhinus is a salt marsh specialist restricted to a narrow corridor along the Atlantic and Gulf coasts. IBD was the predominant pattern of variation across their range. In addition, we saw evidence of two possible biogeographic barriers to gene flow (IBB), one at the Atlantic-Gulf divide and the other along the Gulf coast. We investigated the impact of IBR by comparing genetic differentiation between a habitat specialist, N. bivocatus, and a habitat generalist, N. robustus. Similar levels of genetic diversity and genetic differentiation were present within populations of both species. Genetic variation and epigenetic changes can diverge between populations in isolation. We found significant variation in total methylation levels between N. bivocatus and N. robustus. Genetic differentiation did a better job of explaining species-specific phenotypes than epigenetic differentiation. Epigenetic differentiation, although present between species, is likely the result of an interaction between genetic and epigenetic loci.

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Non-linear genetic isolation by distance: implications for dispersal estimation in anadromous and marine fish populations

Marine Ecology Progress Series ◽

10.3354/meps340245 ◽

2007 ◽

Vol 340 ◽

pp. 245-257 ◽

Cited By ~ 65

Author(s):

IR Bradbury ◽

P Bentzen

Keyword(s):

Marine Fish ◽

Isolation By Distance ◽

Fish Populations ◽

Genetic Isolation ◽

Non Linear

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Landscape configuration of an Amazonian island-like ecosystem drives population structure and genetic diversity of a habitat-specialist bird

10.1101/2020.12.25.424395 ◽

2020 ◽

Author(s):

Camila D. Ritter ◽

Camila C. Ribas ◽

Juliana Menger ◽

Sergio H. Borges ◽

Christine D. Bacon ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Isolation By Distance ◽

Landscape Configuration ◽

Genetic Isolation ◽

White Sand ◽

Surrounding Matrix ◽

Relative Contribution ◽

Central Amazonia ◽

Vegetation Patches

AbstractContextAmazonian white-sand ecosystems (campinas) are open vegetation patches which form a natural island-like system in a matrix of tropical rainforest. Due to their clear distinction from the surrounding matrix, the spatial characteristics of campina patches may affect the genetic diversity and composition of their specialized organisms such as the small and endemic passerine Elaenia ruficeps.ObjectivesHere, we estimate the relative contribution of the current extension, configuration and geographical context of campina patches to the patterns of genetic diversity and population structure of E. ruficeps.MethodsWe sampled individuals of E. ruficeps from three landscapes in Central Amazonia with contrasting campina spatial distribution, from landscapes with large and connected patches to landscapes with small and isolated patches. We estimate population structure, genetic diversity, and contemporary and historical migration within and among the three landscapes and used landscape metrics as predictor variables. Furthermore, we estimate genetic isolation by distance and resistance among individuals sampled within landscapes.ResultsWe identified three genetically distinct populations with asymmetrical gene flow among landscapes and a decreasing migration rate with distance. Within each landscape, we found low genetic differentiation without genetic isolation by distance nor by resistance. In contrast, we found differentiation and spatial correlation between landscapes.ConclusionsOur results uncover population dynamics of E. ruficeps through time. Together with previous studies, this suggests that both regional context and landscape structure shape the connectivity among populations of campina specialist birds, and that Amazonian landscapes, together with their associated biota, have responded to recent climatic changes.

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