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

2020 ◽  
Author(s):  
S Díaz Martínez ◽  
C Boedeker ◽  
Giuseppe Zuccarello
Keyword(s):  
Genetic Diversity ◽  
Lake Baikal ◽  
Species Delimitation ◽  
High Throughput Sequencing ◽  
Algal Species ◽  
Species Flock ◽  
Scoring Method ◽  
Low Genetic Diversity ◽  
Standard Population ◽  
Amplification Rate

© 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.

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

2020 ◽  
Author(s):  
S Díaz Martínez ◽  
C Boedeker ◽  
Giuseppe Zuccarello
Keyword(s):  
Genetic Diversity ◽  
Lake Baikal ◽  
Species Delimitation ◽  
High Throughput Sequencing ◽  
Algal Species ◽  
Species Flock ◽  
Scoring Method ◽  
Low Genetic Diversity ◽  
Standard Population ◽  
Amplification Rate

© 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.

scholarly journals Speciation in the Cladophorales species flock of ancient Lake Baikal

2021 ◽  
Author(s):  
◽  
Sergio Diaz Martinez
Keyword(s):  
Population Genetics ◽  
Genetic Variation ◽  
Reproductive Isolation ◽  
Lake Baikal ◽  
Species Delimitation ◽  
Sympatric Speciation ◽  
Species Flock ◽  
Ancient Lake ◽  
Data Set ◽  
Dispersal Abilities

<p>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.</p>

scholarly journals Speciation in the Cladophorales species flock of ancient Lake Baikal

2021 ◽  
Author(s):  
◽  
Sergio Diaz Martinez
Keyword(s):  
Population Genetics ◽  
Genetic Variation ◽  
Reproductive Isolation ◽  
Lake Baikal ◽  
Species Delimitation ◽  
Sympatric Speciation ◽  
Species Flock ◽  
Ancient Lake ◽  
Data Set ◽  
Dispersal Abilities

<p>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.</p>

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

Phycologia ◽  
2020 ◽  
Vol 59 (4) ◽  
pp. 355-364 ◽  
Author(s):  
Sergio Díaz Martínez ◽  
Christian Boedeker ◽  
Giuseppe C. Zuccarello
Keyword(s):  
Lake Baikal ◽  
Species Delimitation ◽  
Species Flock

scholarly journals Unexpectedly high genetic diversity in a rare and endangered seabird in the Hawaiian Archipelago

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8463 ◽  
Author(s):  
Carmen C. Antaky ◽  
Emily E. Conklin ◽  
Robert J. Toonen ◽  
Ingrid S.S. Knapp ◽  
Melissa R. Price
Keyword(s):  
Genetic Diversity ◽  
High Throughput Sequencing ◽  
Breeding Population ◽  
Small Sample ◽  
Population Declines ◽  
High Genetic Diversity ◽  
Low Genetic Diversity ◽  
Avian Order ◽  
Rare And Endangered ◽  
Small Sample Sizes

Seabirds in the order of Procellariiformes have one of the highest proportions of threatened species of any avian order. Species undergoing recovery may be predicted to have a genetic signature of a bottleneck, low genetic diversity, or higher rates of inbreeding. The Hawaiian Band-rumped Storm Petrel (‘Akē‘akē; Hydrobates castro), a long-lived philopatric seabird, suffered massive population declines resulting in its listing under the Endangered Species Act in 2016 as federally Endangered. We used high-throughput sequencing to assess patterns of genetic diversity and potential for inbreeding in remaining populations in the Hawaiian Islands. We compared a total of 24 individuals, including both historical and modern samples, collected from breeding colonies or downed individuals found on the islands of Kaua‘i, O‘ahu, Maui, and the Big Island of Hawai‘i. Genetic analyses revealed little differentiation between breeding colonies on Kaua‘i and the Big Island colonies. Although small sample sizes limit inferences regarding other island colonies, downed individuals from O‘ahu and Maui did not assign to known breeding colonies, suggesting the existence of an additional distinct breeding population. The maintenance of genetic diversity in future generations is an important consideration for conservation management. This study provides a baseline of population structure for the remaining nesting colonies that could inform potential translocations of the Endangered H. castro.

The Response to Past Climate Perturbations Explains Extremely Low Genetic Diversity in the Genome of an Abundant Ice-Age Remnant, the Alpine Marmot

2018 ◽  
Author(s):  
Toni I. Gossmann​ ◽  
Achchuthan Shanmugasundram​ ◽  
Stefan Börno ◽  
Ludovic Duvaux ◽  
Christophe Lemaire​ ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ice Age ◽  
Past Climate ◽  
Low Genetic Diversity ◽  
Alpine Marmot

Season of birth interacts with measures of inbreeding in multiplex schizophrenia pedigrees: evidence from genetic isolates in Daghestan

Open Medicine ◽  
2006 ◽  
Vol 1 (4) ◽  
pp. 392-398
Author(s):  
Kazima Bulayeva ◽  
John McGrath
Keyword(s):  
Genetic Diversity ◽  
Family History ◽  
Age Of Onset ◽  
Population Genetic Study ◽  
Season Of Birth ◽  
High Genetic Diversity ◽  
Low Genetic Diversity ◽  
High Prevalence ◽  
History Of ◽  
Genetic Isolates

AbstractWhile the season-of-birth effect is one of the most consistent epidemiological features of schizophrenia, there is a lack of consistency with respect to the interaction between season of birth and family history of schizophrenia. Apart from family history, measures related to consanguinity can be used as proxy markers of genomic heterogeneity. Thus, these measures may provide an alternate, indirect index of genetic susceptibility. We had the opportunity to explore the interaction between season of birth and measure of consanguinity in well-described genetic isolates in Daghestan, some of which are known for their relatively high prevalence of schizophrenia. Our previous population-genetic study showed Daghestan has an extremely high genetic diversity between the ethnic populations and a low genetic diversity within them. The isolates selected for this study include some with more than 200 and some with less than 100 generations of demographical history since their founding. Based on pedigrees of multiply-affected families, we found that among individuals with schizophrenia, the measure of consanguinity was significantly higher in the parents of those born in winter/spring compared to those born in summer/autumn. Furthermore, compared to summer/autumn born, winter/spring born individuals with schizophrenia had an earlier age-of-onset, and more prominent auditory hallucinations. Our results suggest that the offspring of consanguineous marriages, and thus those with reduced allelic heterogeneity, may be more susceptible to the environmental factor(s) underpinning the season-of-the effect in schizophrenia.

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