Genetic Evidence for Polygamy as a Mating Strategy in Caiman crocodilus

Oliveira, Deyla Paula de; Marioni, Boris; Farias, Izeni Pires; Hrbek, Tomas

doi:10.1093/jhered/esu020

Cited by 23 publications

(26 citation statements)

References 28 publications

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“…An ant dataset (Hammond, Bourke, & Bruford, 2001), a spectacled caiman dataset (Oliveira, Marioni, Farias, & Hrbek, 2014), and a sockeye salmon dataset (Hauser, Baird, Hilborn, Seeb, & Seeb, 2011) were reanalysed for pedigree reconstruction, erroneous genotype identification and genotyping error rate estimation by the method described above. Details of the three datasets are in Supporting Information.…”

Section: Three Empirical Datasetsmentioning

confidence: 99%

Estimating genotyping errors from genotype and reconstructed pedigree data

Wang

2017

Methods Ecol Evol

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Abstract1. Genotyping errors are rules rather than exceptions in reality, and are found in virtually all but very small datasets. These errors, even when occurring at an extremely low rate, can derail many genetic analyses such as parentage/sibship assignments and linkage/association studies.2. Nonetheless, few robust and accurate methods are available for estimating the rate of occurrence of genotyping errors and for identifying individual erroneous genotypes at a locus. Methods based on duplicate genotyping are expensive, and estimate genotype inconsistency rather than error rate at a locus. Methods based on Hardy-Weinberg equilibrium tests have low robustness and low power, and apply only to those particular errors that cause excessive homozygosity. Methods based on pedigrees are powerful, robust and accurate. However, they rely on known and complete pedigrees that are unfortunately rarely available from natural populations in the wild.3. I proposed a maximum likelihood method to reconstruct pedigrees from genotype data with errors occurring at a roughly estimated (presumed) rate. In this paper, I describe how to use the method and inferred pedigree in estimating allelic dropout (or null allele) rate and false allele rate jointly at each marker locus, in identifying the erroneous genotypes, and in inferring the most likely genotypes at each locus of each individual. I examine the power, accuracy and robustness of the method by extensive simulations, and demonstrate the usefulness of the method by analysing three empirical datasets.4. It is concluded that, both pedigrees and the rates of genotyping errors at each locus can be reliably estimated from the same genotype data by the same likelihood method, when marker information is sufficient and some sampled individuals are first-degree relatives. The erroneous genotypes are however inferred conservatively, and are reliably detected only when they occur in large families and/or at highly polymorphic loci. Estimation of genotyping error rates per locus and identification of erroneous genotypes of each individual at each locus should be routinely conducted to assess and improve data quality, to highlight markers for optimization of genotyping protocols or for replacement, and to enable the integration of genotyping errors in a robust statistical analysis. K E Y W O R D Sallelic dropouts, false alleles, markers, mistyping rates, null alleles, parentage, pedigree, sibling

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Section: Three Empirical Datasetsmentioning

confidence: 99%

Estimating genotyping errors from genotype and reconstructed pedigree data

Wang

2017

Methods Ecol Evol

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“…Crocodilians, which have widely varying population densities and degrees of male territoriality, provide an excellent system to explore the evolutionary and ecological drivers that underlie the observed variation in the frequency of multiple paternity (Amavet, Rosso, Markariani, & Piña, 2008;Budd, Spotila, & Mauger, 2015;Davis, Glenn, Elsey, Dessauer, & Sawyer, 2001;Lance et al, 2009;Lewis, FitzSimmons, Jamerlan, Buchan, & Grigg, 2013;Mcvay et al, 2008;Muniz et al, 2011;Ojeda, Amavet, Rueda, Siroski, & Larriera, 2017;Oliveira, Marioni, Farias, & Hrbek, 2014;Lafferriere et al, 2016;Wu & Hu, 2010). The frequency of multiple paternity observed across crocodilian taxa ranges from 32% in the Chinese alligator (Alligator sinensis) to 100% in black caiman (Melanosuchus niger) (Muniz et al, 2011;Wu & Hu, 2010).…”

Section: Introductionmentioning

confidence: 99%

“…The frequency of multiple paternity observed across crocodilian taxa ranges from 32% in the Chinese alligator (Alligator sinensis) to 100% in black caiman (Melanosuchus niger) (Muniz et al, 2011;Wu & Hu, 2010). Among crocodilians, it is not clear if the frequency of multiple paternity is driven by population density and/or mate encounter rate (Amavet et al, 2008;Budd et al, 2015;Davis et al, 2001;Lance et al, 2009;Lewis et al, 2013;McVay et al, 2008;Muniz et al, 2011;Oliveira et al, 2014;Lafferriere et al, 2016;Wu & Hu, 2010) though both have been suggested (Budd et al, 2015;Lafferriere et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Mating dynamics and multiple paternity in a long‐lived vertebrate

Zajdel

Lance

Rainwater

et al. 2019

Ecology and Evolution

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Multiple paternity is relatively common across diverse taxa; however, the drivers and implications related to paternal and maternal fitness are not well understood. Several hypotheses have been offered to explain the occurrence and frequency of multiple paternity. One set of hypotheses seeks to explain multiple paternity through direct and indirect benefits including increased genetic diversity or enhanced offspring fitness, whereas another set of hypotheses explains multiple paternity as a by‐product of sexual conflict and population‐specific parameters such as density. Here, we investigate mating system dynamics in a historically studied population of the American alligator (Alligator mississippiensis) in coastal South Carolina. We examine parentage in 151 nests across 6 years and find that 43% of nests were sired by multiple males and that male reproductive success is strongly influenced by male size. Whereas clutch size and hatchling size did not differ between singly sired and multiply sired nests, fertility rates were observed to be lower in multiply sired clutches. Our findings suggest that multiple paternity may exert cost in regard to female fitness, and raise the possibility that sexual conflict might influence the frequency of multiple paternity in wild alligator populations.

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“…; Oliveira et al . ). Genes involved in regulating cellular senescence are good targets for MAB development, with cell cycle regulators such as CDKN2A (GenBank GeneID 1029, also known as p16, INK4a, p16INK4b, ARF) providing a good example.…”

Section: Ageing and Molecular Changementioning

confidence: 97%

“…Dysfunctional telomere shortening can lead to immortalization of cancerous cells because they do not senesce or undergo programmed cell death through apoptosis or autophagy, which in healthy calls is triggered by telomere shortening (Günes & Rudolph ; Oliveira et al . ).…”

Section: Ageing and Molecular Changementioning

confidence: 97%

Molecular biomarkers for chronological age in animal ecology

et al. 2015

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The chronological age of an individual animal predicts many of its biological characteristics, and these in turn influence population-level ecological processes. Animal age information can therefore be valuable in ecological research, but many species have no external features that allow age to be reliably determined. Molecular age biomarkers provide a potential solution to this problem. Research in this area of molecular ecology has so far focused on a limited range of age biomarkers. The most commonly tested molecular age biomarker is change in average telomere length, which predicts age well in a small number of species and tissues, but performs poorly in many other situations. Epigenetic regulation of gene expression has recently been shown to cause agerelated modifications to DNA and to cause changes in abundance of several RNA types throughout animal lifespans. Age biomarkers based on these epigenetic changes, and other new DNA-based assays, have already been applied to model organisms, humans and a limited number of wild animals. There is clear potential to apply these marker types more widely in ecological studies. For many species, these new approaches will produce age estimates where this was previously impractical. They will also enable age information to be gathered in cross-sectional studies and expand the range of demographic characteristics that can be quantified with molecular methods. We describe the range of molecular age biomarkers that have been investigated to date and suggest approaches for developing the newer marker types as age assays in nonmodel animal species.

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Genetic Evidence for Polygamy as a Mating Strategy in Caiman crocodilus

Cited by 23 publications

References 28 publications

Estimating genotyping errors from genotype and reconstructed pedigree data

Estimating genotyping errors from genotype and reconstructed pedigree data

Mating dynamics and multiple paternity in a long‐lived vertebrate

Molecular biomarkers for chronological age in animal ecology

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