Coalescent inferences in conservation genetics: should the exception become the rule?

Montano, Valeria

doi:10.1098/rsbl.2016.0211

Cited by 20 publications

(16 citation statements)

References 34 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In addition to quantifying the important decreases in N e due to selection, our results underscored the difficulty in acquiring accurate estimates for this parameter, since estimates based on the same molecular information can be doubled or tripled depending on the evolutionary model considered [70]. It is well-established that better estimates of inbreeding levels and N e are obtained using molecular rather than genealogical information [16], at least when considering more than 10K SNPs [71].…”

Section: Discussionmentioning

confidence: 93%

Genome-wide estimates of genetic diversity, inbreeding and effective size of experimental and commercial rainbow trout lines undergoing selective breeding

et al. 2019

View full text Add to dashboard Cite

Background Selective breeding is a relatively recent practice in aquaculture species compared to terrestrial livestock. Nevertheless, the genetic variability of farmed salmonid lines, which have been selected for several generations, should be assessed. Indeed, a significant decrease in genetic variability due to high selection intensity could have occurred, potentially jeopardizing the long-term genetic progress as well as the adaptive capacities of populations facing change(s) in the environment. Thus, it is important to evaluate the impact of selection practices on genetic diversity to limit future inbreeding. The current study presents an analysis of genetic diversity within and between six French rainbow trout ( Oncorhynchus mykiss ) experimental or commercial lines based on a medium-density single nucleotide polymorphism (SNP) chip and various molecular genetic indicators: fixation index ( F ST ), linkage disequilibrium (LD), effective population size ( N e ) and inbreeding coefficient derived from runs of homozygosity (ROH). Results Our results showed a moderate level of genetic differentiation between selected lines ( F ST ranging from 0.08 to 0.15). LD declined rapidly over the first 100 kb, but then remained quite high at long distances, leading to low estimates of N e in the last generation ranging from 24 to 68 depending on the line and methodology considered. These results were consistent with inbreeding estimates that varied from 10.0% in an unselected experimental line to 19.5% in a commercial line, and which are clearly higher than corresponding estimates in ruminants or pigs. In addition, strong variations in LD and inbreeding were observed along the genome that may be due to differences in local rates of recombination or due to key genes that tended to have fixed favorable alleles for domestication or production. Conclusions This is the first report on ROH for any aquaculture species. Inbreeding appeared to be moderate to high in the six French rainbow trout lines, due to founder effects at the start of the breeding programs, but also likely to sweepstakes reproductive success in addition to selection for the selected lines. Efficient management of inbreeding is a major goal in breeding programs to ensure that populations can adapt to future breeding objectives and SNP information can be used to manage the rate at which inbreeding builds up in the fish genome. Electronic supplementary material The online version of this article (10.1186/s12711-019-0468-4) contains supplementary material, which is available to authorized users.

show abstract

Section: Discussionmentioning

confidence: 93%

Genome-wide estimates of genetic diversity, inbreeding and effective size of experimental and commercial rainbow trout lines undergoing selective breeding

et al. 2019

View full text Add to dashboard Cite

show abstract

“…According to the coalescent theory, the most frequent haplotype is supposed to be the most ancient one [ 76 ]. However, some authors [ 77 ] infirm this for Lepidopteran species. In our case these the modal haplotypes are HT1 (51.4%), HT2 (21.5%), HT13 (10.6%), HT3 (2.5%) (Fig.…”

Section: Discussionmentioning

confidence: 99%

Phylogeographic pattern of the plane leaf miner, Phyllonorycter platani (STAUDINGER, 1870) (Lepidoptera: Gracillariidae) in Europe

Tóth

Lakatos

2018

BMC Evol Biol

View full text Add to dashboard Cite

BackgroundThe plane leaf miner, Phyllonorycter platani is a widely distributed insect species on plane trees and has a well-documented colonisation history in Europe over the last century. However, phylogeographic data of the species are lacking.ResultsWe analysed 284 individuals from 38 populations across Europe, Asia, and North America. A 1242 bp fragment of the mitochondrial COI gene and an 893 bp fragment of the 28S rDNA has been Sanger sequenced. Twenty-four haplotypes were detected on the COI gene, and two alleles were identified on the 28S rDNA. We revealed two distinct clades for both markers reflecting the geographic origins, Asia and Europe. The genetic distance between the two main clades is 2.08% on the COI gene and 0.10% on the nuclear DNA.An overlapping zone of the two clades was found across Eastern Europe and the Anatolian Peninsula. We detected heterozygote individuals of the 28S rDNA gene in Moldavia, Ukraine and in the southern part of Turkey. These suggest that the two clades can hybridise. Furthermore, the presence of European type homozygote individuals has been confirmed in the southern part of Turkey as well.ConclusionsWe have shown that both post-glacial recolonization and recent expansion events influenced the present genetic structure of P. platani. The genetic patterns revealed at least two refugia during the last ice age: one in the Balkan Peninsula and the other in the Caucasus region. Recent expansion was detected in some European and Central Asian populations. The two main clades (Europe/Asia) show definite genetic differences; however, several hybrid individuals were found in the overlapping zone as well (stretching over Eastern Europe and the Anatolian Peninsula). Discrepancies in mitochondrial and nuclear data indicate introgressions in the southern part of the Anatolian Peninsula.Electronic supplementary materialThe online version of this article (10.1186/s12862-018-1240-z) contains supplementary material, which is available to authorized users.

show abstract

“…Overall, our analyses emphasize the importance of accounting for demography and illuminates the serious biases that can arise in the inferred coalescent model if ignored. Such bias can have broad implications on inferred patterns of genetic variation (Eldon and Wakeley 2006;Tellier and Lemaire 2014;Niwa et al 2016), including misguiding conservation efforts (Montano 2016), and obscuring the extent of reproductive skew.…”

Section: Discussionmentioning

confidence: 99%

Coalescent Processes with Skewed Offspring Distributions and Nonequilibrium Demography

et al. 2018

View full text Add to dashboard Cite

Nonequilibrium demography impacts coalescent genealogies leaving detectable, well-studied signatures of variation. However, similar genomic footprints are also expected under models of large reproductive skew, posing a serious problem when trying to make inference. Furthermore, current approaches consider only one of the two processes at a time, neglecting any genomic signal that could arise from their simultaneous effects, preventing the possibility of jointly inferring parameters relating to both offspring distribution and population history. Here, we develop an extended Moran model with exponential population growth, and demonstrate that the underlying ancestral process converges to a time-inhomogeneous psi-coalescent. However, by applying a nonlinear change of time scale-analogous to the Kingman coalescent-we find that the ancestral process can be rescaled to its time-homogeneous analog, allowing the process to be simulated quickly and efficiently. Furthermore, we derive analytical expressions for the expected site-frequency spectrum under the time-inhomogeneous psi-coalescent, and develop an approximate-likelihood framework for the joint estimation of the coalescent and growth parameters. By means of extensive simulation, we demonstrate that both can be estimated accurately from whole-genome data. In addition, not accounting for demography can lead to serious biases in the inferred coalescent model, with broad implications for genomic studies ranging from ecology to conservation biology. Finally, we use our method to analyze sequence data from Japanese sardine populations, and find evidence of high variation in individual reproductive success, but few signs of a recent demographic expansion.

show abstract

Coalescent inferences in conservation genetics: should the exception become the rule?

Cited by 20 publications

References 34 publications

Genome-wide estimates of genetic diversity, inbreeding and effective size of experimental and commercial rainbow trout lines undergoing selective breeding

Genome-wide estimates of genetic diversity, inbreeding and effective size of experimental and commercial rainbow trout lines undergoing selective breeding

Phylogeographic pattern of the plane leaf miner, Phyllonorycter platani (STAUDINGER, 1870) (Lepidoptera: Gracillariidae) in Europe

Coalescent Processes with Skewed Offspring Distributions and Nonequilibrium Demography

Contact Info

Product

Resources

About