Using Genomic Data to Infer Historic Population Dynamics of Nonmodel Organisms

2018 ◽  
Vol 49 (1) ◽  
pp. 433-456 ◽  
Author(s):  
Annabel C. Beichman ◽  
Emilia Huerta-Sanchez ◽  
Kirk E. Lohmueller
Keyword(s):  
Population Dynamics ◽  
Statistical Inference ◽  
Statistical Methods ◽  
Genome Sequence ◽  
Sequence Data ◽  
Demographic History ◽  
Genomic Data ◽  
Underlying Theory ◽  
History Of ◽  
Pros And Cons

Genome sequence data are now being routinely obtained from many nonmodel organisms. These data contain a wealth of information about the demographic history of the populations from which they originate. Many sophisticated statistical inference procedures have been developed to infer the demographic history of populations from this type of genomic data. In this review, we discuss the different statistical methods available for inference of demography, providing an overview of the underlying theory and logic behind each approach. We also discuss the types of data required and the pros and cons of each method. We then discuss how these methods have been applied to a variety of nonmodel organisms. We conclude by presenting some recommendations for researchers looking to use genomic data to infer demographic history.

scholarly journals Rapid statistical methods for inferring intra- and inter-hospital transmission of nosocomial pathogens from whole genome sequence data

2018 ◽  
Author(s):  
Marianne Aspbury ◽  
James Sciberras ◽  
Jukka Corander ◽  
Sion C. Bayliss ◽  
Tjibbe Donker ◽  
...  
Keyword(s):  
Statistical Methods ◽  
Genome Sequence ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Bacterial Pathogens ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Transmission Networks ◽  
Genome Sequence Data ◽  
Hospital Transmission

AbstractWhole genome sequence (WGS) data for bacterial pathogens can provide evidence as to the source of nosocomial infection, and more specifically the ability to distinguish between intra- and inter-hospital transmission. This is currently achieved either through using SNP thresholds, which can lack statistical robustness, or by constructing phylogenetic trees, which can be computationally expensive and difficult to interpret. Here we compare two alternative statistical approaches using 1022 genomes of methicillin resistantStaphylococcus aureus(MRSA) clone ST22. In 71% of cases both methods predict the same hospital origin, which is also supported by the ML tree. Robust assignments are divided approximately equally between intra-hospital transmission and inter-hospital transmission. Our approaches are rapid and produce intuitive output that could inform on immediate infection control priorities, as well as providing long-term data on inter-hospital transmission networks. We discuss the strengths and weakness of our methods, and the generalisability of this approach.One Sentence SummaryWe present rapid statistical methods for distinguishing intra- versus inter-hospital transmission of bacterial pathogens using whole genome sequence data; these methods do not require the use of SNP thresholds or the generation and interpretation of phylogenetic trees.

scholarly journals Inferring the Joint Demographic History of Multiple Populations: Beyond the Diffusion Approximation

2017 ◽  
Author(s):  
Julien Jouganous ◽  
Will Long ◽  
Simon Gravel
Keyword(s):  
Diffusion Approximation ◽  
Sequence Data ◽  
Demographic History ◽  
Allele Frequencies ◽  
Human Sequence ◽  
Medical Study ◽  
Joint Frequency ◽  
Classical Models ◽  
History Of ◽  
Demographic Inference

AbstractUnderstanding variation in allele frequencies across populations is a central goal of population genetics. Classical models for the distribution of allele frequencies, using forward simulation, coalescent theory, or the diffusion approximation, have been applied extensively for demographic inference, medical study design, and evolutionary studies. Here we propose a tractable model of ordinary differential equations for the evolution of allele frequencies that is closely related to the diffusion approximation but avoids many of its limitations and approximations. We show that the approach is typically faster, more numerically stable, and more easily generalizable than the state-of-the-art software implementation of the diffusion approximation. We present a number of applications to human sequence data, including demographic inference with a five-population joint frequency spectrum and a discussion of the transferability of demographic histories across populations.

scholarly journals Genetic structure of the grey side-gilled sea slug (Pleurobranchaea maculata) in coastal waters of New Zealand

2017 ◽  
Author(s):  
Yeşerin Yıldırım ◽  
Marti J. Anderson ◽  
Selina Patel ◽  
Craig D. Millar ◽  
Paul B. Rainey
Keyword(s):  
New Zealand ◽  
Genetic Structure ◽  
Sequence Data ◽  
Demographic History ◽  
Population Expansion ◽  
Haplotype Network ◽  
Founding Population ◽  
Mtdna Sequence ◽  
Expansion Time ◽  
History Of

AbstractPleurobranchaea maculatais a rarely studied species of the Heterobranchia found throughout the south and western Pacific – and recently recorded in Argentina – whose population genetic structure is unknown. Interest in the species was sparked in New Zealand following a series of dog deaths caused by ingestions of slugs containing high levels of the neurotoxin tetrodotoxin. Here we describe the genetic structure and demographic history ofP. maculatapopulations from five principle locations in New Zealand based on extensive analyses of 12 microsatellite loci and theCOIandCytBregions of mitochondrial DNA (mtDNA). Microsatellite data showed significant differentiation between northern and southern populations with population structure being associated with previously described regional variations in tetrodotoxin concentrations. However, mtDNA sequence data did not support such structure, revealing a star-shaped haplotype network with estimates of expansion time suggesting a population expansion in the Pleistocene era. Inclusion of publicly available mtDNA sequence from Argentinian sea slugs did not alter the star-shaped network. We interpret our data as indicative of a single founding population that fragmented following geographical changes that brought about the present day north-south divide in New Zealand waters. Lack of evidence of cryptic species supports data indicating that differences in toxicity of individuals among regions are a consequence of differences in diet.

scholarly journals Complex patterns of sex-biased demography in canines

2019 ◽  
Vol 286 (1903) ◽  
pp. 20181976 ◽  
Author(s):  
Tanya N. Phung ◽  
Robert K. Wayne ◽  
Melissa A. Wilson ◽  
Kirk E. Lohmueller
Keyword(s):  
Sequence Data ◽  
Demographic History ◽  
Multiple Paternity ◽  
Whole Genome Sequence ◽  
Evolutionary Time ◽  
Genetic Studies ◽  
History Of ◽  
Males And Females ◽  
Dog Domestication ◽  
Number Of Males

The demographic history of dogs is complex, involving multiple bottlenecks, admixture events and artificial selection. However, existing genetic studies have not explored variance in the number of reproducing males and females, and whether it has changed across evolutionary time. While male-biased mating practices, such as male-biased migration and multiple paternity, have been observed in wolves, recent breeding practices could have led to female-biased mating patterns in breed dogs. For example, breed dogs are thought to have experienced a popular sire effect, where a small number of males father many offspring with a large number of females. Here we use genetic variation data to test how widespread sex-biased mating practices in canines are during different evolutionary time points. Using whole-genome sequence data from 33 dogs and wolves, we show that patterns of diversity on the X chromosome and autosomes are consistent with a higher number of reproducing males than females over ancient evolutionary history in both dogs and wolves, suggesting that mating practices did not change during early dog domestication. By contrast, since breed formation, we found evidence for a larger number of reproducing females than males in breed dogs, consistent with the popular sire effect. Our results confirm that canine demography has been complex, with opposing sex-biased processes occurring throughout their history. The signatures observed in genetic data are consistent with documented sex-biased mating practices in both the wild and domesticated populations, suggesting that these mating practices are pervasive.

Widespread Gene Flow Model Explains the Genetic–Morphological Variation in a Giant Water Bug Species Under Fine-Scale Spatial Sampling

2019 ◽  
Vol 113 (3) ◽  
pp. 160-170
Author(s):  
Fabiano Stefanello ◽  
Rodolpho S T Menezes ◽  
José Ricardo I Ribeiro ◽  
Eduardo A B Almeida
Keyword(s):  
Population Dynamics ◽  
Gene Flow ◽  
Morphological Variation ◽  
Flow Model ◽  
Demographic History ◽  
Spatial Sampling ◽  
Fine Scale ◽  
Freshwater Organisms ◽  
History Of ◽  
The Last Glacial

Abstract The population dynamics of freshwater organisms are expected to be related to the connectivity among comparable streams, ponds, or rivers in a patchy habitat. Here, we investigated the population dynamics of the giant water bug, Belostoma angustum Lauck 1964 (Hemiptera: Belostomatidae), in a fine-scale spatial sampling, and evaluated which gene flow model previously described for freshwater organisms could explain the genetic–morphological variation in this species. For these purposes, we evaluated genetic and morphological variations, as well as the demographic history of this freshwater insect. Our genetic analyses showed a lack of geographical structure within B. angustum populations across the evaluated range, concordant with widespread gene flow model. Our findings of the demographic history of B. angustum suggest recent and rapid expansion beginning during the late Pleistocene after the Last Glacial Maximum. Likewise, we did not find geographically structured morphological variation in B. angustum, except for body size. The lack of structure of genetic–morphological variation in B. angustum could be explained by a stepping ponds system resulting in the widespread gene flow detected among populations of this species. The warmer and wetter climatic conditions after the last glacial period may have favored the demographic expansion of B. angustum populations due to the increasing of potential freshwater habitats and food resources. This favorable habitat probably allowed the stepping ponds dispersal mode resulting in the verified geographically unstructured genetic–morphological variation.

scholarly journals Diverse demographic histories in a guild of hymenopteran parasitoids

2019 ◽  
Author(s):  
William Walton ◽  
Graham N Stone ◽  
Konrad Lohse
Keyword(s):  
Population Size ◽  
Sequence Data ◽  
Demographic History ◽  
Whole Genome Sequence ◽  
Parasitoid Wasps ◽  
Effective Population ◽  
Glacial Cycles ◽  
Genome Wide ◽  
History Of ◽  
Hymenopteran Parasitoids

AbstractSignatures of changes in population size have been detected in genome-wide variation in many species. However, the causes of such changes and the extent to which they are shared across co-distributed species remain poorly understood. During Pleistocene glacial maxima, many temperate European species were confined to southern refugia. While vicariance and range expansion processes associated with glacial cycles have been widely studied, little is known about the demographic history of refugial populations, and the extent and causes of demographic variation among codistributed species. We used whole genome sequence data to reconstruct and compare demographic histories during the Quaternary for Iberian refuge populations in a single ecological guild (seven species of chalcid parasitoid wasps associated with oak cynipid galls). We find support for large changes in effective population size (Ne) through the Pleistocene that coincide with major climate change events. However, there is little evidence that the timing, direction and magnitude of demographic change are shared across species, suggesting that demographic histories are largely idiosyncratic. Our results are compatible with the idea that specialist parasitoids attacking a narrow range of hosts experience greater fluctuations in Ne than generalists.

scholarly journals Ancient DNA and human history

2016 ◽  
Vol 113 (23) ◽  
pp. 6380-6387 ◽  
Author(s):  
Montgomery Slatkin ◽  
Fernando Racimo
Keyword(s):  
Early Modern ◽  
Ancient Dna ◽  
Demographic History ◽  
Genomic Data ◽  
The Arctic ◽  
The Past ◽  
Early Modern Humans ◽  
History Of ◽  
Demographic Patterns ◽  
Rich History

We review studies of genomic data obtained by sequencing hominin fossils with particular emphasis on the unique information that ancient DNA (aDNA) can provide about the demographic history of humans and our closest relatives. We concentrate on nuclear genomic sequences that have been published in the past few years. In many cases, particularly in the Arctic, the Americas, and Europe, aDNA has revealed historical demographic patterns in a way that could not be resolved by analyzing present-day genomes alone. Ancient DNA from archaic hominins has revealed a rich history of admixture between early modern humans, Neanderthals, and Denisovans, and has allowed us to disentangle complex selective processes. Information from aDNA studies is nowhere near saturation, and we believe that future aDNA sequences will continue to change our understanding of hominin history.

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