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Heist, Edward J.; Nicholson, Erica H.; Sipiorski, Justin T.; Keeney, Devon B.

doi:10.1023/a:1015272414957

Cited by 26 publications

(9 citation statements)

References 7 publications

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“…This might be the case of our microsatellite data as all analyzed individuals originated from a pet shop and we could not exclude their relatedness. Except the locus Psp 18 , the estimated ploidy of analyzed loci was in accordance with Heist et al [28] providing confidence for our conclusion based on microsatellite data. Heist et al [28] suggested tetraploidy for the locus Psp 18 , while we did not observe more than two alleles at the locus (Additional file 2, Supplementary Results).…”

Section: Discussionsupporting

confidence: 91%

“…Since paleotetraploid acipenseriform species were considered to be basal group of Acipenseriformes [3], the process of rediploidization probably reaches further than in paleooctaploid species [19]. In light of all these facts, the observation of the duplicated locus Psp-29 in this study and coexistence of diploid and tetraploid allelic band patterns reported by Heist et al [28] at several microsatellite loci of P. spathula supported our observation of partial rediploidization in P. spathula genome from the molecular point of view.…”

Section: Discussionsupporting

confidence: 50%

“…Similarly, P. spathula specific loci (see Additional file 1, Supplementary Methods) had diploid allelic band patterns. An exception to this general pattern was shown at the locus Psp-29 [28] for which more than two alleles were observed (Fig. 4; Additional file 2, Supplementary Results).

Fig.…”

Section: Resultsmentioning

confidence: 93%

“…Microsatellite data (number of alleles) in Polyodon spathula and comparison with sturgeons related to chromosomes numbers and ploidy levels provide evidence of partial genome rediploidization in P. spathula () and sturgeons (●). The figure is based on data from this study and previous studies [18, 28] …”

Section: Resultsmentioning

confidence: 99%

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Molecular cytogenetic differentiation of paralogs of Hox paralogs in duplicated and re-diploidized genome of the North American paddlefish (Polyodon spathula)

et al. 2017

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Background: Acipenseriformes is a basal lineage of ray-finned fishes and comprise 27 extant species of sturgeons and paddlefishes. They are characterized by several specific genomic features as broad ploidy variation, high chromosome numbers, presence of numerous microchromosomes and propensity to interspecific hybridization. The presumed palaeotetraploidy of the American paddlefish was recently validated by molecular phylogeny and Hox genes analyses. A whole genome duplication in the paddlefish lineage was estimated at approximately 42 Mya and was found to be independent from several genome duplications evidenced in its sister lineage, i.e. sturgeons. We tested the ploidy status of available chromosomal markers after the expected rediploidization. Further we tested, whether paralogs of Hox gene clusters originated from this paddlefish specific genome duplication are cytogenetically distinguishable. Results: We found that both paralogs HoxA alpha and beta were distinguishable without any overlapping of the hybridization signal -each on one pair of large metacentric chromosomes. Of the HoxD, only the beta paralog was unequivocally identified, whereas the alpha paralog did not work and yielded only an inconclusive diffuse signal. Chromosomal markers on three diverse ploidy levels reflecting different stages of rediploidization were identified: quadruplets retaining their ancestral tetraploid condition, semi-quadruplets still reflecting the ancestral tetraploidy with clear signs of advanced rediploidization, doublets were diploidized with ancestral tetraploidy already blurred. Also some of the available microsatellite data exhibited diploid allelic band patterns at their loci whereas another locus showed more than two alleles. Conclusions: Our exhaustive staining of paddlefish chromosomes combined with cytogenetic mapping of ribosomal genes and Hox paralogs and with microsatellite data, brings a closer look at results of the process of rediploidization in the course of paddlefish genome evolution. We show a partial rediploidization represented by a complex mosaic structure comparable with segmental paleotetraploidy revealed in sturgeons (Acipenseridae). Sturgeons and paddlefishes with their high propensity for whole genome duplication thus offer suitable animal model systems to further explore evolutionary processes that were shaping the early evolution of all vertebrates.

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Section: Discussionsupporting

confidence: 91%

Section: Discussionsupporting

confidence: 50%

Fig.…”

Section: Resultsmentioning

confidence: 93%

Section: Resultsmentioning

confidence: 99%

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Molecular cytogenetic differentiation of paralogs of Hox paralogs in duplicated and re-diploidized genome of the North American paddlefish (Polyodon spathula)

et al. 2017

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“…According to Neff et al (1999), the rate of sequence divergence at the microsatellite flanking regions may be dependent on the locus itself. However, according to several observations, the slow rate of sequence divergence seems to be the general rule of microsatellite evolution in this ancient fish group, Acipenseriformes: (i) among the 108 loci screened in S. platorynchus, 65%-80% can be successfully amplified on Acipenser species (McQuown et al 2000); (ii) the microsatellite loci originally screened in the American paddlefish P. spathula can be crossamplified on most species of the family Acipenseridae (Heist et al 2002). This apparently easy cross-priming should be the mark of a general slow mutation rate.…”

Section: Flanking Region Evolutionmentioning

confidence: 99%

Evolutionary process of a tetranucleotide microsatellite locus in Acipenseriformes

Shao

Rivals

Zhao

et al. 2011

J Genet

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The evolutionary dynamics of the tetra-nucleotide microsatellite locus Spl-106 were investigated at the repeat and flanking sequences in 137 individuals of 15 Acipenseriform species, giving 93 homologous sequences, which were detected in 11 out of 15 species. Twenty-three haplotypes of flanking sequences and three distinct types of repeats, type I, type II and type III, were found within these 93 sequences. The MS-Align hylogenetic method, newly applied to microsatellite sequences, permitted us to understand the repeat and flanking sequence evolution of Spl-106 locus. The flanking region of locus Spl-106 was highly conserved among the species of genera Acipenser, Huso and Scaphirhynchus, which diverged about 150 million years ago (Mya). The rate of flanking sequence divergence at the microsatellite locus Spl-106 in sturgeons is between 0.011% and 0.079% with an average at 0.028% per million years. Sequence alignment and phylogenetic trees produced by MS-Align showed that both the flanking and repeat regions can cluster the alleles of different species into Pacific and Atlantic lineages. Our results show a synchronous evolutionary pattern between the flanking and repeat regions. Moreover, the coexistence of different repeat types in the same species, even in the same individual, is probably due to two duplication events encompassing the locus Spl-106 that occurred during the divergence of Pacific lineage. The first occured before the diversification of Pacific species (121-96 Mya) and led to repeat types I and II. The second occurred more recently, just before the speciation of A. sinensis and A. dabryanus (69-10 Mya), and led to repeat type III. Sequences in the same species with different repeat types probably corresponds to paralogous loci. This study sheds a new light on the evolutionary mechanisms that shape the complex microsatellite loci involving different repeat types.

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Using fish hard‐part microchemistry and genetics to quantify population impacts of low‐use lock‐and‐dam structures on the Alabama River

et al. 2023

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Objective: We used two approaches, fish hard-part microchemistry and genetics, to quantify effects of low-use lock-and-dam structures on riverine fish movement. Each approach varied in temporal scope, with microchemistry addressing effects within a lifetime and genetics addressing effects across generations. Methods:Water samples and individuals of two species (Paddlefish Polyodon spathula and Smallmouth Buffalo Ictiobus bubalus) were collected from four river sections that were separated by three low-use lock-and-dam structures on the Alabama River. Quarterly water samples were collected from 15 sites during 2017-2018, and concentrations of Sr, Ba, Mn, Mg, and Ca were quantified using mass spectrometry.Result: Water elemental signatures were spatially variable but temporally consistent.The Sr:Ca ratios in fish hard parts differed significantly among river sections for both species. Additionally, discriminant function analyses classified fish to their river capture section with accuracy between 55% and 74% for Paddlefish (errors nearly always assigned individuals to adjacent river sections) and 37-47% for Smallmouth Buffalo.Population genetic analyses included fish from each river section, as well as from Alabama River tributaries and a neighboring watershed. Genotyping-by-sequence techniques identified 1,889 and 3,737 single nucleotide polymorphisms postfiltering in Paddlefish and Smallmouth Buffalo, respectively, which we used to estimate population diversity indices and conduct differentiation analyses. Analysis of molecular variance, discriminant analysis of principal components, Bayesian clustering, and pairwise comparisons of F ST values indicated no strong evidence for genetic divergence in either species among river sections. Conclusion:Within-lifespan results based on hard-part microchemistry suggested a potential for population isolation. However, longer-term genetic effects were not apparent, possibly because the life span of these large and relatively long-lived species means that few generations have passed since dam construction, and there could be sufficient mixing or population connectivity to prevent genetic divergence across river sections, particularly at the most downstream structure.

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Cited by 26 publications

References 7 publications

Molecular cytogenetic differentiation of paralogs of Hox paralogs in duplicated and re-diploidized genome of the North American paddlefish (Polyodon spathula)

Molecular cytogenetic differentiation of paralogs of Hox paralogs in duplicated and re-diploidized genome of the North American paddlefish (Polyodon spathula)

Evolutionary process of a tetranucleotide microsatellite locus in Acipenseriformes

Using fish hard‐part microchemistry and genetics to quantify population impacts of low‐use lock‐and‐dam structures on the Alabama River

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