Microsatellite markers for hoop‐petticoat daffodils (Narcissus sect. Bulbocodii; Amaryllidaceae)

Könyves, Kálmán; David, J. C.; Culham, Alastair

doi:10.3732/apps.1500127

Cited by 5 publications

(4 citation statements)

References 6 publications

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“…In difficult profiles showing stutters the allele scoring followed the method of the manual routine of Pfeiffer et al (2011) with slight modifications. This approach is considered reliable over automated scoring to reduce noise in difficult loci due to polyploidy (Bhandawat et al 2016;Cărăbuș et al 2015;Könyves et al 2016;Pfeiffer et al 2011). Therefore, depending on their putative quality, the peaks in the chromatograms were considered as alleles.…”

Section: Microsatellite Testingmentioning

confidence: 99%

Microsatellite design for species delimitation and insights into ploidy for the Lake Baikal Cladophoraceae species flock

2020

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Ancient lakes are centres of adaptive radiation and speciation. The Cladophoraceae endemic to ancient Lake Baikal is a morphologically diverse group nested within Rhizoclonium that may represent a case of sympatric speciation. Recent research using ribosomal DNA markers indicates that these taxa form a monophyletic group but was not able to resolve boundaries between all of the investigated morphospecies due to very low genetic diversity. For this reason, a population genetics approach using more variable markers was investigated. In this study, we developed a set of microsatellites (SSRs) using high-throughput sequencing (HTS) data obtained from three morphospecies of Cladophoraceae from Lake Baikal. To increase amplification rate of the microsatellites across taxa, we performed an in silico cross-validation step comparing the microsatellites retrieved from three HTS datasets and tested the most promising loci on 14 of the mostly endemic morphospecies. We obtained 11 SSRs that cross-amplified among morphospecies, eight SSRs in 12 taxa and three in only four taxa. Our results showed that most loci had more than two alleles, but also displayed variation between and within morphospecies. These results indicate that this group may have gone through polyploidisation. Polyploid systems require a different approach from standard population genetic analyses. We produced 'allelic phenotypes' (presence/absence matrices) to analyse genetic diversity. We showed that similarity indices mostly grouped morphospecies, suggesting that this scoring method will be useful in species delimitation, but further work is needed to elucidate the speciation process in this algal species flock in Lake Baikal.

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Section: Microsatellite Testingmentioning

confidence: 99%

Microsatellite design for species delimitation and insights into ploidy for the Lake Baikal Cladophoraceae species flock

2020

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Section: Microsatellite Testingmentioning

confidence: 99%

Microsatellite design for species delimitation and insights into ploidy for the Lake Baikal Cladophoraceae species flock

Martínez¹,

Boedeker²,

Zuccarello³

2020

Preprint

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© 2020 International Phycological Society. Ancient lakes are centres of adaptive radiation and speciation. The Cladophoraceae endemic to ancient Lake Baikal is a morphologically diverse group nested within Rhizoclonium that may represent a case of sympatric speciation. Recent research using ribosomal DNA markers indicates that these taxa form a monophyletic group but was not able to resolve boundaries between all of the investigated morphospecies due to very low genetic diversity. For this reason, a population genetics approach using more variable markers was investigated. In this study, we developed a set of microsatellites (SSRs) using high-throughput sequencing (HTS) data obtained from three morphospecies of Cladophoraceae from Lake Baikal. To increase amplification rate of the microsatellites across taxa, we performed an in silico cross-validation step comparing the microsatellites retrieved from three HTS datasets and tested the most promising loci on 14 of the mostly endemic morphospecies. We obtained 11 SSRs that cross-amplified among morphospecies, eight SSRs in 12 taxa and three in only four taxa. Our results showed that most loci had more than two alleles, but also displayed variation between and within morphospecies. These results indicate that this group may have gone through polyploidisation. Polyploid systems require a different approach from standard population genetic analyses. We produced ‘allelic phenotypes’ (presence/absence matrices) to analyse genetic diversity. We showed that similarity indices mostly grouped morphospecies, suggesting that this scoring method will be useful in species delimitation, but further work is needed to elucidate the speciation process in this algal species flock in Lake Baikal.

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“…In difficult profiles showing stutters the allele scoring followed a similar method to the manual routine of Pfeiffer et al (2011) with slight modifications. This approach is considered reliable over automated scoring to reduce noise in difficult loci due to polyploidy (Pfeiffer et al 2011b, Cărăbuș et al 2015, Bhandawat et al 2016, Könyves et al 2016. Therefore, the peaks in the chromatograms were considered as alleles depending on their putative quality.…”

Section: Microsatellite Testingmentioning

confidence: 99%

Speciation in the Cladophorales species flock of ancient Lake Baikal

Martínez¹

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Understanding speciation is one of the great challenges in evolutionary biology as many of the processes involved in speciation, as well as the forces leading to morphological and genetic differentiation, are not fully understood. Three main modes of speciation have been described: allopatric, parapatric and sympatric. Sympatric speciation is the most enigmatic mode because in the absence of physical barriers, disruptive selection, assortative mating and hybridization play central roles in reproductive isolation. Although it is accepted that sympatric speciation is possible, only a few examples of this process exist to date. Another common method of speciation in plants and algae is via polyploidization. Recently, a promising system to study speciation in sympatry was discovered: the endemic Cladophorales species flock in ancient Lake Baikal, Russia. The flock consists of sixteen taxa grouped in four genera: Chaetocladiella, Chaetomorpha, Cladophora and Gemmiphora. In spite of their morphological diversity, recent molecular analyses have shown that this is a monophyletic group with low genetic variation and nested within the morphologically simple genus Rhizoclonium. Due to their high number of species, endemism and sympatric distribution, many interesting questions have arisen such as what processes are involved in speciation, and whether this group might be a novel example of sympatric speciation. In this study, we analysed the population genetics of the endemic Baikalian Cladophorales to infer the processes shaping the evolution of the group. First, a set of microsatellites was designed using high-throughput sequencing data. Second, species delimitation methods based on genetic clustering were performed. Third, the population genetics of three widely distributed species was analysed looking for evidence of panmixia, a common criteria to support sympatric speciation. A total of 11 microsatellites that mostly cross-amplify between most species were obtained. The genotyping revealed that most loci had more than two alleles per individual indicating polyploidy. As such, the analyses required a different approach which consisted in coding the genotypes as ‘allelic phenotypes’, allowing the use of individuals of different ploidy levels in the same data set. The species delimitation of 15 operative morphotaxa and 727 individuals supported reproductive isolation of five morphotaxa and two hypotheses of conspecificity. However, some morphotaxa showed unclear assignments revealing the need of further research to clarify their reproductive limits. Finally, the population genetics of Chaetomorpha moniliformis, Cladophora compacta and Cl. kursanovii revealed patterns of genetic variation and structure that suggest different reproductive strategies and dispersal abilities. This demonstrates that contrasting biological characteristics may arise in closely related lineages: Chaetomorpha moniliformis with dominant asexual reproduction and long dispersal abilities; Cladophora compacta with high genetic diversity, no population structure and likely to reproduce sexually; Cl. kursanovii with a structure congruent with geographic distribution and more restricted dispersal. The results suggest that polyploidy, rather than speciation with gene flow, is the force driving the reproductive isolation and evolution of this flock. Although many questions remain to be studied, this research provides the first insights into the diversification of this Cladophorales species flock and contributes to the understanding of speciation in freshwater algae.

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Microsatellite markers for hoop‐petticoat daffodils (Narcissus sect. Bulbocodii; Amaryllidaceae)

Cited by 5 publications

References 6 publications

Microsatellite design for species delimitation and insights into ploidy for the Lake Baikal Cladophoraceae species flock

Microsatellite design for species delimitation and insights into ploidy for the Lake Baikal Cladophoraceae species flock

Microsatellite design for species delimitation and insights into ploidy for the Lake Baikal Cladophoraceae species flock

Speciation in the Cladophorales species flock of ancient Lake Baikal

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