Inheritance of microsatellite loci in the polyploid lake sturgeon (Acipenser fulvescens)

Conservation Genetics of Lake Sturgeon (Acipenser fulvescens): Nuclear Phylogeography Drives Contemporary Patterns of Genetic Structure and Diversity

Sustainable management of exploited and endangered species is facilitated by knowledge of their geographic genetic structure. Lake sturgeon (Acipenser fulvescens) epitomizes both categories, but genetic information has largely been limited to the Laurentian Great Lakes basin. We assessed the hierarchical geographic genetic structure of lake sturgeon across their Canadian range using a variation at 14 microsatellite loci. Observed patterns showed evidence of two ancestral groups which originated from Mississippian and Missourian glacial refugia. Coalescent analysis indicates the two lineages most recently shared common ancestry during the late Pleistocene and were likely isolated by the late Wisconsinan ice advance, with subsequent interpopulation divergences within each lineage reflecting their reciprocal isolation as glacial meltwaters receded. Hierarchical patterns of genetic relationships among contemporary populations largely reflect colonization histories and connections within primary and secondary watersheds. Populations in western Canada showed strong similarities based on their shared Missourian origins and colonization from glacial Lake Agassiz. By contrast, populations in the Great Lakes–St. Lawrence River drainage were largely founded from a Mississippian source. Sturgeon populations in northern parts of Ontario and Quebec showed evidence of mixed ancestry from secondary contact between the two refugial groups through Holocene meltwater lakes. Within major watersheds, the strong similarity among geographically separate populations reflects their shared ancestry during postglacial colonization. The general lack of structure within major river systems highlights historically continuous habitat (connectivity) and gene flow rather than contemporary barriers (dams). These data highlight the importance of Quaternary and prehistoric events on patterns of genetic diversity and divergence within and among contemporary populations, as well as the importance of these populations for conserving the species’ evolutionary legacy.

Flow cytometry for assessing the efficacy of interspecific gynogenesis induction in sturgeon

The efficacy of ploidy analysis for separating progeny of Siberian sturgeon Acipenser baerii after induced gynogenesis was demonstrated using sperm of a paternal species differing in ploidy level from the maternal species. Gynogenesis was induced in tetraploid A. baerii with UV-C irradiated sperm from the diploid sterlet Acipenser ruthenus and vice-versa. The success of sperm UV irradiation and diploidy restoration by heat-shock was estimated based on the ploidy level of progeny, confirmed by microsatellite parentage assignment. Hatching rates of interspecific gynogenotes were comparable with rates reported for gynogenesis induction using sperm and eggs of the same species. Juvenile mortality was similar to that observed in the control hybrids. The efficiency and reliability of this method may foster its use for production of gynogenotes in aquaculture, potentially allowing interspecific gynogenesis to replace intraspecific.

Parentage and sibship inference from markers in polyploids

Many plants and some animal species are polyploids. Nondisomically inherited markers (e.g. microsatellites) in such species cannot be analysed directly by standard population genetics methods developed for diploid species. One solution is to transform the polyploid codominant genotypes to pseudodiploid-dominant genotypes, which can then be analysed by standard methods for various purposes such as spatial genetic structure, individual relatedness and relationship. Although this data transformation approach has been used repeatedly in the literature, no systematic study has been conducted to investigate how efficient it is, how much marker information is lost and thus how much analysis accuracy is reduced. More specifically, it is unknown whether or not the transformed data can be used to infer parentage and sibship jointly, and how different sampling schemes (number and polymorphism of markers, number of individuals) and ploidy level affect the inference accuracy. This study analyses both simulated and empirical data to examine the effects of polyploid levels, actual pedigree structures and marker number and polymorphism on the accuracy of joint parentage and sibship assignments in polyploid species. We show that sibship, parentage and selfing rates in polyploids can be inferred accurately from a typical set of microsatellite loci. We also show that inferences can be substantially improved by allowing for a small genotyping error rate to accommodate the distortion in assumed Mendelian inheritance of the converted markers when large sibship groups are involved. The results are discussed in the context of polyploid data analysis in molecular ecology.

Genome evolution trend of common carp (Cyprinus carpio L.) as revealed by the analysis of microsatellite loci in a gynogentic family

Genome evolution arises from two main ways of duplication and reduction. Fish specific genome duplication (FSGD) may have occurred before the radiation of the teleosts. Common carp (Cyprinus carpio L.) has been considered to be a tetraploid species, because of its chromosome numbers (2n=100) and its high DNA content. Using 69 microsatellite primer pairs, the variations were studied to better understand the genome evolution (genome duplication and diploidization) of common carp from a gynogenetic family. About 48% of primer pairs were estimated to amplify duplicates based on the number of PCR amplification per individual. Segregation patterns in the family suggested a partially duplicated genome structure and disomic inheritance. This indicates that the common carp is tetraploid and polyploidy occurred by allotetraploidy. Two primer pairs (HLJ021 and HLJ332) were estimated to amplify reduction based on the number of PCR amplification per individual. One allele in HLJ002 locus and HLJ332 locus was clearly lost in the gynogenetic family and the same as in six wild populations. Segregation patterns in the family suggested a partially diplodization genome structure. A hypothesis transition (dynamic) and equilibrium (static) were proposed to explain the common carp genome evolution between genome duplication and diploidization.

Inheritance of microsatellite loci in the white sturgeon (Acipenser transmontanus)

Nine tetramer motif (GATA)n microsatellite systems were developed for use in the white sturgeon, Acipenser transmontanus. We report inheritance patterns for these nine systems, which range from one possible disomic system to tetrasomy and octosomy, with some systems containing null alleles. Because of the complex modes of inheritance underlying these systems and the highly duplicated nature of the genome, we propose each allele be scored as its own dominant marker, similar to AFLPs or RAPDs. The utility of this method is validated by the observation that individual alleles within a microsatellite system generally fit the expectation for independent transmission and fit the expected transmission frequency for single copy nuclear markers.

Genome duplication events and functional reduction of ploidy levels in sturgeon (Acipenser, Huso and Scaphirhynchus)

Sturgeon (order Acipenserformes) provide an ideal taxonomic context for examination of genome duplication events. Multiple levels of ploidy exist among these fish. In a novel microsatellite approach, data from 962 fish from 20 sturgeon species were used for analysis of ploidy in sturgeon. Allele numbers in a sample of individuals were assessed at six microsatellite loci. Species with approximately 120 chromosomes are classified as functional diploid species, species with approximately 250 chromosomes as functional tetraploid species, and with approximately 500 chromosomes as functional octaploids. A molecular phylogeny of the sturgeon was determined on the basis of sequences of the entire mitochondrial cytochrome b gene. By mapping the estimated levels of ploidy on this proposed phylogeny we demonstrate that (I) polyploidization events independently occurred in the acipenseriform radiation; (II) the process of functional genome reduction is nearly finished in species with approximately 120 chromosomes and more active in species with approximately 250 chromosomes and approximately 500 chromosomes; and (III) species with approximately 250 and approximately 500 chromosomes arose more recently than those with approximately 120 chromosomes. These results suggest that gene silencing, chromosomal rearrangements, and transposition events played an important role in the acipenseriform genome formation. Furthermore, this phylogeny is broadly consistent with previous hypotheses but reveals a highly supported oceanic (Atlantic-Pacific) subdivision within the Acipenser/Huso complex.