Elusive does not always equal rare: genetic assessment of a protected Gila monster (Heloderma suspectum) population in Saguaro National Park, Arizona

2017 ◽  
Vol 38 (1) ◽  
pp. 1-14 ◽  
Author(s):  
Victoria Sophia Farrar ◽  
Taylor Edwards ◽  
Kevin Edward Bonine
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Effective Population Size ◽  
National Parks ◽  
Sonoran Desert ◽  
National Park ◽  
Sequence Data ◽  
Demographic History ◽  
Effective Population ◽  
Heloderma Suspectum

Population genetic baselines for species perceived to be at-risk are crucial for monitoring population trends and making well-informed management decisions. We characterized the genetic status of a population of Gila monsters (Heloderma suspectum), a large venomous lizard native to deserts of the southwestern United States and northern Mexico, by sampling 100 individuals in Sonoran Desert upland habitat at Saguaro National Park, Arizona, USA. We used 18 microsatellite markers, along with 1195 bp of sequence data from the mitochondrial DNA 12S locus, to examine genetic diversity, estimate effective population size, and assess demographic history. Despite suburban development adjacent to the study area, we observed high genetic diversity with uninhibited gene flow within this protected population. We estimated effective population size (Ne) for the total sample area (80 km2) using the linkage disequilibrium method in NeEstimator to be 94 individuals (95% confidence interval: 80.7-111.2). In 2011, we used capture-recapture methods to estimate that 80 adult Gila monsters (95% CI = 37-225) inhabited the area along the 14-km transect that we surveyed most frequently; probability of detecting resident Gila monsters during surveys was <0.01, highlighting the challenges of studying the species. Despite being considered an elusive and thus potentially rare species, these data reveal that in this protected environment the population appears healthy and robust. The results provide an important genetic baseline for future studies and monitoring, and exemplify the success of protective population measures in National Parks and under Arizona state laws.

scholarly journals Modeling the growth and decline of pathogen effective population size provides insight into epidemic dynamics and drivers of antimicrobial resistance

2017 ◽  
Author(s):  
Erik M. Volz ◽  
Xavier Didelot
Keyword(s):  
Growth Rate ◽  
Population Size ◽  
Effective Population Size ◽  
Growth Rates ◽  
Sequence Data ◽  
Demographic History ◽  
Parametric Models ◽  
Effective Population ◽  
Epidemic Dynamics ◽  
Non Parametric

AbstractNon-parametric population genetic modeling provides a simple and flexible approach for studying demographic history and epidemic dynamics using pathogen sequence data. Existing Bayesian approaches are premised on stationary stochastic processes which may provide an unrealistic prior for epidemic histories which feature extended period of exponential growth or decline. We show that non-parametric models defined in terms of the growth rate of the effective population size can provide a more realistic prior for epidemic history. We propose a non-parametric autoregressive model on the growth rate as a prior for effective population size, which corresponds to the dynamics expected under many epidemic situations. We demonstrate the use of this model within a Bayesian phylodynamic inference framework. Our method correctly reconstructs trends of epidemic growth and decline from pathogen genealogies even when genealogical data is sparse and conventional skyline estimators erroneously predict stable population size. We also propose a regression approach for relating growth rates of pathogen effective population size and time-varying variables that may impact the replicative fitness of a pathogen. The model is applied to real data from rabies virus and Staphylococcus aureus epidemics. We find a close correspondence between the estimated growth rates of a lineage of methicillin-resistant S. aureus and population-level prescription rates of β-lactam antibiotics. The new models are implemented in an open source R package called skygrowth which is available at https://mrc-ide.github.io/skygrowth/.

scholarly journals Demography and natural selection have shaped genome-wide variation in the widely distributed conifer Norway Spruce (Picea abies)

2019 ◽  
Author(s):  
Xi Wang ◽  
Carolina Bernhardsson ◽  
Pär K. Ingvarsson
Keyword(s):  
Genetic Diversity ◽  
Natural Selection ◽  
Picea Abies ◽  
Population Size ◽  
Effective Population Size ◽  
Norway Spruce ◽  
Demographic History ◽  
Sequencing Data ◽  
Effective Population ◽  
Genome Wide

AbstractUnder the neutral theory, species with larger effective population sizes are expected to harbour higher genetic diversity. However, across a wide variety of organisms, the range of genetic diversity is orders of magnitude more narrow than the range of effective population size. This observation has become known as Lewontin’s paradox and although aspects of this phenomenon have been extensively studied, the underlying causes for the paradox remain unclear. Norway spruce (Picea abies) is a widely distributed conifer species across the northern hemisphere and it consequently plays a major role in European forestry. Here, we use whole-genome re-sequencing data from 35 individuals to perform population genomic analyses in P. abies in an effort to understand what drives genome-wide patterns of variation in this species. Despite having a very wide geographic distribution and an enormous current population size, our analyses find that genetic diversity of P.abies is low across a number of populations (p=0.005-0.006). To assess the reasons for the low levels of genetic diversity, we infer the demographic history of the species and find that it is characterised by several re-occurring bottlenecks with concomitant decreases in effective population size can, at least partly, provide an explanation for low polymorphism we observe in P. abies. Further analyses suggest that recurrent natural selection, both purifying and positive selection, can also contribute to the loss of genetic diversity in Norway spruce by reducing genetic diversity at linked sites. Finally, the overall low mutation rates seen in conifers can also help explain the low genetic diversity maintained in Norway spruce.

scholarly journals Levels and patterns of genetic diversity differ between two closely related endemicArabidopsisspecies

2016 ◽  
Author(s):  
Julie Jacquemin ◽  
Nora Hohmann ◽  
Matteo Buti ◽  
Alberto Selvaggi ◽  
Thomas Müller ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Effective Population Size ◽  
Endemic Species ◽  
Isolation By Distance ◽  
Demographic History ◽  
Adaptive Potential ◽  
Effective Population ◽  
Distribution Ranges ◽  
Small Effective Population Size

AbstractTheory predicts that a small effective population size leads to slower accumulation of mutations, increased levels of genetic drift and reduction in the efficiency of natural selection. Therefore endemic species should harbor low levels of genetic diversity and exhibit a reduced ability of adaptation to environmental changes.Arabidopsis pedemontanaandArabidopsis cebennensis, two endemic species from Italy and France respectively, provide an excellent model to study the adaptive potential of species with small distribution ranges. To evaluate the genome-wide levels and patterns of genetic variation, effective population size and demographic history of both species, we genotyped 53A. pedemontanaand 28A. cebennensisindividuals across the entire species ranges with Genotyping-by-Sequencing. SNPs data confirmed a low genetic diversity forA. pedemontanaalthough its effective population size is relatively high. Only a weak population structure was observed over the small distribution range ofA. pedemontana, resulting from an isolation-by-distance pattern of gene flow. In contrary,A. cebennensisindividuals clustered in three populations according to their geographic distribution. Despite this and a larger distribution, the overall genetic diversity was even lower forA. cebennensisthan forA. pedemontana.A demographic analysis demonstrated that both endemics have undergone a strong population size decline in the past, without recovery. The more drastic decline observed inA. cebennensispartially explains the very small effective population size observed in the present population. In light of these results, we discuss the adaptive potential of these endemic species in the context of rapid climate change.

scholarly journals Maximum likelihood inference of pathogen population size history from a phylogeny

2021 ◽  
Author(s):  
Xavier Didelot ◽  
Erik M Volz
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Sequence Data ◽  
Demographic History ◽  
Genetic Data ◽  
Parametric Models ◽  
Process Models ◽  
Effective Population ◽  
Latent Process ◽  
Non Parametric

ABSTRACTInference of effective population size from genomic data can provide unique information about demographic history, and when applied to pathogen genetic data can also provide insights into epidemiological dynamics. Non-parametric models for population dynamics combined with molecular clock models which relate genetic data to time have enabled phylodynamic inference based on large sets of time-stamped genetic sequence data. The theory for non-parametric inference of effective population size is well-developed in the Bayesian setting, but here we develop a frequentist approach based on non-parametric latent process models of population size dynamics. We appeal to statistical principles based on out-of-sample prediction accuracy in order to optimize parameters that control shape and smoothness of the population size over time. We demonstrate the flexibility and speed of this approach in a series of simulation experiments and apply the models to genetic data from several pathogen data sets.

scholarly journals Demography and Natural Selection Have Shaped Genetic Variation in the Widely Distributed Conifer Norway Spruce (Picea abies)

2020 ◽  
Vol 12 (2) ◽  
pp. 3803-3817 ◽  
Author(s):  
Xi Wang ◽  
Carolina Bernhardsson ◽  
Pär K Ingvarsson
Keyword(s):  
Genetic Diversity ◽  
Natural Selection ◽  
Picea Abies ◽  
Population Size ◽  
Effective Population Size ◽  
Norway Spruce ◽  
Demographic History ◽  
Neutral Theory ◽  
Effective Population ◽  
Low Genetic Diversity

Abstract Under the neutral theory, species with larger effective population size are expected to harbor higher genetic diversity. However, across a wide variety of organisms, the range of genetic diversity is orders of magnitude more narrow than the range of effective population size. This observation has become known as Lewontin’s paradox and although aspects of this phenomenon have been extensively studied, the underlying causes for the paradox remain unclear. Norway spruce (Picea abies) is a widely distributed conifer species across the northern hemisphere, and it consequently plays a major role in European forestry. Here, we use whole-genome resequencing data from 35 individuals to perform population genomic analyses in P. abies in an effort to understand what drives genome-wide patterns of variation in this species. Despite having a very wide geographic distribution and an corresponding enormous current population size, our analyses find that genetic diversity of P. abies is low across a number of populations (π = 0.0049 in Central-Europe, π = 0.0063 in Sweden-Norway, π = 0.0063 in Finland). To assess the reasons for the low levels of genetic diversity, we infer the demographic history of the species and find that it is characterized by several reoccurring bottlenecks with concomitant decreases in effective population size can, at least partly, provide an explanation for low polymorphism we observe in P. abies. Further analyses suggest that recurrent natural selection, both purifying and positive selection, can also contribute to the loss of genetic diversity in Norway spruce by reducing genetic diversity at linked sites. Finally, the overall low mutation rates seen in conifers can also help explain the low genetic diversity maintained in Norway spruce.

scholarly journals An examination of genetic diversity and effective population size in Atlantic salmon populations

2009 ◽  
Vol 91 (6) ◽  
pp. 395-412 ◽  
Author(s):  
NATACHA NIKOLIC ◽  
JAMES R. A. BUTLER ◽  
JEAN-LUC BAGLINIÈRE ◽  
ROBERT LAUGHTON ◽  
IAIN A. G. McMYN ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Atlantic Salmon ◽  
Population Size ◽  
Effective Population Size ◽  
Demographic History ◽  
Effective Population ◽  
High Genetic Diversity ◽  
Historical Processes ◽  
Wide Range ◽  
Microsatellite Dna Markers

SummaryEffective population size (Ne) is an important parameter in the conservation of genetic diversity. Comparative studies of empirical data that gauge the relative accuracy of Ne methods are limited, and a better understanding of the limitations and potential of Ne estimators is needed. This paper investigates genetic diversity and Ne in four populations of wild anadromous Atlantic salmon (Salmo salar L.) in Europe, from the Rivers Oir and Scorff (France) and Spey and Shin (Scotland). We aimed to understand present diversity and historical processes influencing current population structure. Our results showed high genetic diversity for all populations studied, despite their wide range of current effective sizes. To improve understanding of high genetic diversity observed in the populations with low effective size, we developed a model predicting present diversity as a function of past demographic history. This suggested that high genetic diversity could be explained by a bottleneck occurring within recent centuries rather than by gene flow. Previous studies have demonstrated the efficiency of coalescence models to estimate Ne. Using nine subsets from 37 microsatellite DNA markers from the four salmon populations, we compared three coalescence estimators based on single and dual samples. Comparing Ne estimates confirmed the efficiency of increasing the number and variability of microsatellite markers. This efficiency was more accentuated for the smaller populations. Analysis with low numbers of neutral markers revealed uneven distributions of allelic frequencies and overestimated short-term Ne. In addition, we found evidence of artificial stock enhancement using native and non-native origin. We propose estimates of Ne for the four populations, and their applications for salmon conservation and management are discussed.

scholarly journals Low effective population size and high spatial genetic structure of black poplar populations from the Oder valley in Poland

2021 ◽  
Vol 78 (2) ◽  
Author(s):  
Błażej Wójkiewicz ◽  
Andrzewj Lewandowski ◽  
Weronika B. Żukowska ◽  
Monika Litkowiec ◽  
Witold Wachowiak
Keyword(s):  
Genetic Structure ◽  
Genetic Resources ◽  
Population Size ◽  
Effective Population Size ◽  
Spatial Genetic Structure ◽  
Demographic History ◽  
River Valley ◽  
Ex Situ ◽  
Effective Population ◽  
Black Poplar

Abstract Context Black poplar (Populus nigra L.) is a keystone species of European riparian ecosystems that has been negatively impacted by riverside urbanization for centuries. Consequently, it has become an endangered tree species in many European countries. The establishment of a suitable rescue plan of the remaining black poplar forest stands requires a preliminary knowledge about the distribution of genetic variation among species populations. However, for some parts of the P. nigra distribution in Europe, the genetic resources and demographic history remain poorly recognized. Aims Here, we present the first study on identifying and characterizing the genetic resources of black poplar from the Oder valley in Poland. This study (1) assessed the genetic variability and effective population size of populations and (2) examined whether gene flow is limited by distance or there is a single migrant pool along the studied river system. Methods A total of 582 poplar trees derived from nine black poplar populations were investigated with nuclear microsatellite markers. Results (1) The allelic richness and heterozygosity level were high and comparable between populations. (2) The genetic structure of the studied poplar stands was not homogenous. (3) The signatures of past bottlenecks were detected. Conclusion Our study (1) provides evidence for genetic substructuring of natural black poplar populations from the studied river catchment, which is not a frequent phenomenon reported for this species in Europe, and (2) indicates which poplar stands may serve as new genetic conservation units (GCUs) of this species in Europe. Key message The genetic resources of black poplar in the Oder River valley are still substantial compared to those reported for rivers in Western Europe. On the other hand, clear signals of isolation by distance and genetic erosion reflected in small effective population sizes and high spatial genetic structure of the analyzed populations were detected. Based on these findings, we recommend the in situ and ex situ conservation strategies for conserving and restoring the genetic resources of black poplar populations in this strongly transformed by human river valley ecosystem.

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