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.

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.

scholarly journals High-Throughput Sequencing Reveals Further Diversity of Little Cherry Virus 1 with Implications for Diagnostics

Viruses ◽  
2018 ◽  
Vol 10 (7) ◽  
pp. 385 ◽  
Author(s):  
Asimina Katsiani ◽  
Varvara Maliogka ◽  
Nikolaos Katis ◽  
Laurence Svanella-Dumas ◽  
Antonio Olmos ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Sour Cherry ◽  
Prunus Species ◽  
Cherry Tree ◽  
High Genetic Diversity ◽  
Viral Genomes ◽  
Virus Diversity ◽  
First Time

Little cherry virus 1 (LChV1, Velarivirus, Closteroviridae) is a widespread pathogen of sweet or sour cherry and other Prunus species, which exhibits high genetic diversity and lacks a putative efficient transmission vector. Thus far, four distinct phylogenetic clusters of LChV1 have been described, including isolates from different Prunus species. The recent application of high throughput sequencing (HTS) technologies in fruit tree virology has facilitated the acquisition of new viral genomes and the study of virus diversity. In the present work, several new LChV1 isolates from different countries were fully sequenced using different HTS approaches. Our results reveal the presence of further genetic diversity within the LChV1 species. Interestingly, mixed infections of the same sweet cherry tree with different LChV1 variants were identified for the first time. Taken together, the high intra-host and intra-species diversities of LChV1 might affect its pathogenicity and have clear implications for its accurate diagnostics.

Comparative genetic diversity of Cryptosporidium species causing human infections

Parasitology ◽  
2020 ◽  
Vol 147 (13) ◽  
pp. 1532-1537 ◽  
Author(s):  
Juan C. Garcia-R ◽  
Murray P. Cox ◽  
David T. S. Hayman
Keyword(s):  
Genetic Diversity ◽  
Population Expansion ◽  
Recent Population Expansion ◽  
Cryptosporidium Hominis ◽  
High Genetic Diversity ◽  
Genetic Changes ◽  
Low Genetic Diversity ◽  
Human Infections ◽  
Host Parasite ◽  
Founder Events

AbstractParasites sometimes expand their host range and cause new disease aetiologies. Genetic changes can then occur due to host-specific adaptive alterations, particularly when parasites cross between evolutionarily distant hosts. Characterizing genetic variation in Cryptosporidium from humans and other animals may have important implications for understanding disease dynamics and transmission. We analyse sequences from four loci (gp60, HSP-70, COWP and actin) representing multiple Cryptosporidium species reported in humans. We predicted low genetic diversity in species that present unusual human infections due to founder events and bottlenecks. High genetic diversity was observed in isolates from humans of Cryptosporidium meleagridis, Cryptosporidium cuniculus, Cryptosporidium hominis and Cryptosporidium parvum. A deviation of expected values of neutrality using Tajima's D was observed in C. cuniculus and C. meleagridis. The high genetic diversity in C. meleagridis and C. cuniculus did not match our expectations but deviations from neutrality indicate a recent decrease in genetic variability through a population bottleneck after an expansion event. Cryptosporidium hominis was also found with a significant Tajima's D positive value likely caused by recent population expansion of unusual genotypes in humans. These insights indicate that changes in genetic diversity can help us to understand host-parasite adaptation and evolution.

High genetic diversity in a rare and endangered sunflower as compared to a common congener

2006 ◽  
Vol 15 (9) ◽  
pp. 2345-2355 ◽  
Author(s):  
J. R. ELLIS ◽  
C. H. PASHLEY ◽  
J. M. BURKE ◽  
D. E. McCAULEY
Keyword(s):  
Genetic Diversity ◽  
High Genetic Diversity ◽  
Rare And Endangered

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 Genetic variability of Indonesian Oryctes rhinoceros nudivirus (OrNV) as genus of Alphanudivirus

2020 ◽  
Vol 21 (5) ◽  
Author(s):  
Sat Rahayuwati ◽  
Yayi Munara Kusumah ◽  
Sudharto Prawirosukarto ◽  
Dadang ◽  
Teguh Santoso
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Biological Control Agent ◽  
Classical Biological Control ◽  
Control Agent ◽  
Nucleotide Level ◽  
High Genetic Diversity ◽  
Oryctes Rhinoceros ◽  
Low Genetic Diversity ◽  
Plantation Development

Abstract. Rahayuwati S, Kusumah YM, Prawirosukarto S, Dadang, Santoso T. 2020. Genetic variability of Indonesian Oryctes rhinoceros nudivirus (OrNV) as genus of Alphanudivirus. Biodiversitas 21: 2047-2055. Oryctes rhinoceros nudivirus (OrNV) is known as a successful classical biological control agent. Recent reports have revealed differences in pathogenicity among OrNV isolates, with correlation suspected between virus virulence and genetic variability. The aim of the research is to study the genetic variability of OrNV isolates based on the DNA polymerase (DNA pol) gene and their phylogenetic relationship with Genus Alphanudivirus. Oryctes rhinoceros (Coleoptera: Scarabaeidae) as an OrNV host were collected from Sumatra, Belitung, Java, Kalimantan, and Sulawesi. Primers were designed to amplify complete gene of DNA pol. Sequencing, phylogenetic, and investigate genetic diversity scores were used to determine variability at nucleotide level. Five primers successfully amplified the entire DNA pol gene. Genetic variability of OrNV was high, from nine isolates found eight genetically different. Isolates could be divided into two groups of genetic diversity: high and low. High genetic diversity of OrNV supposed as an old population that occupied Sundaland and Wallacean paleogeography at first appearance in Miocene Era until early Pliocene 5 Mya. New population of OrNV had low genetic diversity were travel cross-island that supposed to correlate with oil palm plantation development and the genetic drift. The benefit information of the OrNV genetic variability is as preliminary guideline for virulence test. OrNV is a member of Nudiviridae family, Genus Alphanudivirus, and at recent moment they consist of eight species. Alphanudivirus infect Coleoptera, Diptera, Hemiptera and Orthoptera order that soil as immature niche may explain their closely related taxa.

scholarly journals Is genetic diversity of Plasmodium falciparum suggestive of malaria endemic zone in West Africa? An attempt to respond by a cross-sectional comparative study between Senegal and Nigeria

2020 ◽  
Author(s):  
Mary Aigbiremo Oboh ◽  
Tolla Ndiaye ◽  
Khadim Diongue ◽  
Yaye D Ndiaye ◽  
Mouhamad Sy ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Plasmodium Falciparum ◽  
Holistic Approach ◽  
Control Measures ◽  
Allelic Polymorphism ◽  
African Countries ◽  
High Genetic Diversity ◽  
Cross Sectional ◽  
Low Genetic Diversity ◽  
Infection Types

Background: Characterization of malaria parasite populations in different endemic settings (from low to high) could be helpful for ascertaining the progress of malaria interventions in endemic settings. The present study aims to compare Plasmodium falciparum parasite population structure between two West African countries with very different level of endemicity using P. falciparum allelic polymorphic markers: msp1 and msp2. Methods: Parasite genomic DNA was extracted from 187 dried blood spot collected from confirmed uncomplicated P. falciparum malaria infected patients in Senegal (94) being at the pre-elimination stage in most part of the country and Nigeria (93) which is still at the control stage. Allelic polymorphism of msp1 and msp2 genes were assessed by nested PCR. Results: In Senegal as well as in Nigeria, K1 and IC3D7 allelic families were the most represented for msp1 and msp2 genes respectively. A higher multiplicity of infection (MOI) was found in both study sites in Senegal (Thies:1.51/2.53; Kedougou:2.2/2.0 for msp 1/2) than from sites in Nigeria (Gbagada: 1.39/1.96; Oredo: 1.35/1.75]). The heterozygosity of msp 1 gene was higher in P. falciparum isolates from Senegal (Thies: 0.62; Kedougou: 0.53) than isolates from Nigeria (Gbagada: 0.55; Oredo: 0.50). In Senegal, K1 alleles were associated with heavy (28) than with moderate (18) infections, in Nigeria however, equal proportions of K1 were observed in both infection types. The IC3D7 subtype allele of the msp 2 family showed high occurrence in heavily infected individuals from both countries (Senegal- 32; Nigeria- 26) than in the moderately infected participants. Conclusion: With the unusual high genetic diversity obtained in low endemic setting in Senegal and low genetic diversity in a high endemic Nigerian setting, multiple holistic approach should be employed in evaluating the actual transmission of a place in order to effectively direct control measures.

scholarly journals Deep sampling of Hawaiian Caenorhabditis elegans reveals high genetic diversity and admixture with global populations

2019 ◽  
Author(s):  
Timothy A. Crombie ◽  
Stefan Zdraljevic ◽  
Daniel E. Cook ◽  
Robyn E. Tanny ◽  
Shannon C. Brady ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Caenorhabditis Elegans ◽  
Model Organism ◽  
Population Admixture ◽  
Selective Sweeps ◽  
High Genetic Diversity ◽  
C Elegans ◽  
Low Genetic Diversity ◽  
High Elevations ◽  
Global Population

AbstractRecent efforts to understand the natural niche of the keystone model organism Caenorhabditis elegans have suggested that this species is cosmopolitan and associated with rotting vegetation and fruits. However, most of the strains isolated from nature have low genetic diversity likely because recent chromosome-scale selective sweeps contain alleles that increase fitness in human-associated habitats. Strains from the Hawaii Islands are highly divergent from non-Hawaiian strains. This result suggests that Hawaiian strains might contain ancestral genetic diversity that was purged from most non-Hawaiian strains by the selective sweeps. To characterize the genetic diversity and niche of Hawaiian C. elegans, we sampled across the Hawaiian Islands and isolated 100 new C. elegans strains. We found that C. elegans strains are not associated with any one substrate but are found in cooler climates at high elevations. These Hawaiian strains are highly diverged compared to the rest of the global population. Admixture analysis identified 11 global populations, four of which are from Hawaii. Surprisingly, one of the Hawaiian populations shares recent ancestry with non-Hawaiian populations, including portions of globally swept haplotypes. This discovery provides the first evidence of gene flow between Hawaiian and non-Hawaiian populations. Most importantly, the high levels of diversity observed in Hawaiian strains might represent the complex patterns of ancestral genetic diversity in the C. elegans species before human influence.

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