On applications of landscape genetics

Bowman, Jeff; Greenhorn, Janet E.; Marrotte, Robby R.; McKay, Michelle M.; Morris, Kimberley Y.; Prentice, Melanie B.; Wehtje, Morgan

doi:10.1007/s10592-016-0834-5

Cited by 23 publications

(15 citation statements)

References 35 publications

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“…It is essential to evaluate the geographical patterns of genetic diversity and identify the populations within, and determine areas that display high values of genetic diversity and divergence. However, until now, practitioners have seldom taken into account the relevance of genetics research [58] and few studies on landscape genetics have been applied in practical forest management [59]. From our point of view, landscape genetics can be considered an easy and self-explaining tool to transfer information about spatial distribution of genetic variation into practice.…”

Section: Genetic Diversity Structure and Differentiation Patternsmentioning

confidence: 99%

Population Structure, Genetic Diversity, and Gene Introgression of Two Closely Related Walnuts (Juglans regia and J. sigillata) in Southwestern China Revealed by EST-SSR Markers

Sun

Bai

et al. 2018

Forests

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The common walnut (Juglans regia L.) and iron walnut (J. sigillata Dode) are well-known economically important species cultivated for their edible nuts, high-quality wood, and medicinal properties and display a sympatric distribution in southwestern China. However, detailed research on the genetic diversity and introgression of these two closely related walnut species, especially in southwestern China, are lacking. In this study, we analyzed a total of 506 individuals from 28 populations of J. regia and J. sigillata using 25 EST-SSR markers to determine if their gene introgression was related to sympatric distribution. In addition, we compared the genetic diversity estimates between them. Our results indicated that all J. regia populations possess slightly higher genetic diversity than J. sigillata populations. The Geostatistical IDW technique (HO, PPL, NA and PrA) revealed that northern Yunnan and Guizhou provinces had high genetic diversity for J. regia while the northwestern Yunnan province had high genetic diversity for J. sigillata. AMOVA analysis revealed that significant genetic variation was mainly distributed within population as 73% in J. regia and 76% in J. sigillata. The genetic differentiation (FST) was 0.307 between the two walnut species (p < 0.0001), which was higher than FST values within populations (J. regia FST = 0.265 and J. sigillata FST = 0.236). However, the STRUCTURE analysis of the J. regia and J. sigillata populations revealed two genetic clusters in which gene introgression exists, therefore, the boundary of separation between these two walnut species is not clear. Moreover, these results were validated by NJ and UPGMA analysis with additional conformation from the PCoA. Based on the SSR data, our results indicate that J. sigillata is an ecotype of J. regia. Taken together, these results reveal novel information on population genetics and provide specific geographical regions containing high genetic diversity of the Juglans species sampled, which will assist in future conservation management.

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Section: Genetic Diversity Structure and Differentiation Patternsmentioning

confidence: 99%

Population Structure, Genetic Diversity, and Gene Introgression of Two Closely Related Walnuts (Juglans regia and J. sigillata) in Southwestern China Revealed by EST-SSR Markers

Sun

Bai

et al. 2018

Forests

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“…Understanding the factors underpinning functional connectivity across species is essential to design ecological corridors, identify conservation units, assess population threat status, optimize pathogen and invasive species management, assist planning of natural heritage systems, and restore threatened populations (Bowman et al, 2016;.…”

Section: Introductionmentioning

confidence: 99%

Peer Review #1 of "Everything you always wanted to know about gene flow in tropical landscapes (but were afraid to ask) (v0.2)"

2019

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The bulk of the world's biodiversity is found in tropical regions, which are increasingly threatened by the human-led degradation of natural habitats. Yet, little is known about tropical biodiversity responses to habitat loss and fragmentation. Here we review all available literature assessing landscape effects on gene flow in tropical species, aiming to help unravel the factors underpinning functional connectivity in the tropics. We map and classify studies by focus species, the molecular markers employed, statistical approaches to assess landscape effects on gene flow, and the evaluated landscape and environmental variables. We then compare qualitatively and quantitatively landscape effects on gene flow across species and units of analysis. We found 69 articles assessing landscape effects on gene flow in tropical organisms, most of which were published in the last five years, were concentrated in the Americas, and focused on amphibians or mammals. Most studies employed population-level approaches, microsatellites were the preferred type of markers, and Mantel and partial Mantel tests the most common statistical approaches used. While elevation, land cover and forest cover were the most common gene flow predictors assessed, habitat suitability was found to be a common predictor of gene flow. A third of all surveyed studies explicitly assessed the effect of habitat degradation, but only 14 of these detected a reduced gene flow with increasing habitat loss. Elevation was responsible for most significant microsatellite-based IBR effects and a single study reported significant isolation by non-forested areas in an ant. Our study reveals important knowledge gaps on the study of landscape effects on gene flow in tropical organisms, and provides useful guidelines on how to fill them.PeerJ reviewing PDF |

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“…This knowledge can subsequently inform management efforts at the population level (such as vaccination targeted at key regions, culling), as well as broader decisions relating to the management of the landscape itself, which is a key aim of landscape genetics generally (Manel & Holderegger, ; Segelbacher et al., ). Landscape genetics is being applied by managers at relatively low rates compared to related ecological fields such as landscape ecology, conservation biology and telemetry research (Bowman et al., ). Therefore, studies that contribute to the management of disease agents within populations could increase the practical impacts of landscape genetics significantly.…”

Section: Introductionmentioning

confidence: 99%

Pathogens in space: Advancing understanding of pathogen dynamics and disease ecology through landscape genetics

Kozakiewicz

Burridge

Funk

et al. 2018

Evolutionary Applications

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Landscape genetics has provided many insights into how heterogeneous landscape features drive processes influencing spatial genetic variation in free‐living organisms. This rapidly developing field has focused heavily on vertebrates, and expansion of this scope to the study of infectious diseases holds great potential for landscape geneticists and disease ecologists alike. The potential application of landscape genetics to infectious agents has garnered attention at formative stages in the development of landscape genetics, but systematic examination is lacking. We comprehensively review how landscape genetics is being used to better understand pathogen dynamics. We characterize the field and evaluate the types of questions addressed, approaches used and systems studied. We also review the now established landscape genetic methods and their realized and potential applications to disease ecology. Lastly, we identify emerging frontiers in the landscape genetic study of infectious agents, including recent phylogeographic approaches and frameworks for studying complex multihost and host‐vector systems. Our review emphasizes the expanding utility of landscape genetic methods available for elucidating key pathogen dynamics (particularly transmission and spread) and also how landscape genetic studies of pathogens can provide insight into host population dynamics. Through this review, we convey how increasing awareness of the complementarity of landscape genetics and disease ecology among practitioners of each field promises to drive important cross‐disciplinary advances.

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On applications of landscape genetics

Cited by 23 publications

References 35 publications

Population Structure, Genetic Diversity, and Gene Introgression of Two Closely Related Walnuts (Juglans regia and J. sigillata) in Southwestern China Revealed by EST-SSR Markers

Population Structure, Genetic Diversity, and Gene Introgression of Two Closely Related Walnuts (Juglans regia and J. sigillata) in Southwestern China Revealed by EST-SSR Markers

Peer Review #1 of "Everything you always wanted to know about gene flow in tropical landscapes (but were afraid to ask) (v0.2)"

Pathogens in space: Advancing understanding of pathogen dynamics and disease ecology through landscape genetics

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