The effect of population bottleneck size and selective regime on genetic diversity and evolvability in bacteria

Genome Biology and Evolution ◽

10.1093/gbe/evz243 ◽

2019 ◽

Author(s):

Tanita Wein ◽

Tal Dagan

Keyword(s):

Genetic Diversity ◽

Evolutionary Dynamics ◽

Natural Populations ◽

Population Bottleneck ◽

Population Bottlenecks ◽

High Genetic Diversity ◽

Temperature Regimes ◽

Consequent Reduction ◽

History Of

Abstract Population bottlenecks leading to a drastic reduction of the population size are common in the evolutionary dynamics of natural populations; their occurrence is known to have implications for genome evolution due to genetic drift, the consequent reduction in genetic diversity and the rate of adaptation. Nevertheless, an empirical characterization of the effect of population bottleneck size on evolutionary dynamics of bacteria is currently lacking. Here we show that selective conditions have a stronger effect on the evolutionary history of bacteria in comparison to population bottlenecks. We evolved Escherichia coli populations under three different population bottleneck sizes (small, medium, large) in two temperature regimes (37 °C and 20 °C). We find a high genetic diversity in the large in comparison to the small bottleneck size. Nonetheless, the cold temperature led to reduced genetic diversity regardless the bottleneck size, hence, the temperature has a stronger effect on the genetic diversity in comparison to the bottleneck size. A comparison of the fitness gain among the evolved populations reveals a similar pattern where the temperature has a significant effect on the fitness. Our study demonstrates that population bottlenecks are an important determinant of bacterial evolvability; their consequences depend on the selective conditions and are best understood via their effect on the standing genetic variation.

Download Full-text

The effect of population bottleneck size and selective regime on genetic diversity and evolvability in bacteria

10.1101/726158 ◽

2019 ◽

Author(s):

Tanita Wein ◽

Tal Dagan

Keyword(s):

Genetic Diversity ◽

Genetic Drift ◽

Evolutionary Dynamics ◽

Natural Populations ◽

Population Bottleneck ◽

Population Bottlenecks ◽

High Genetic Diversity ◽

Temperature Regimes ◽

Consequent Reduction ◽

History Of

AbstractPopulation bottlenecks leading to a drastic reduction of the population size are common in the evolutionary dynamics of natural populations; their occurrence is known to have implications for genome evolution due to genetic drift, the consequent reduction in genetic diversity and the rate of adaptation. Nevertheless, an empirical characterization of the effect of population bottleneck size on evolutionary dynamics of bacteria is currently lacking. Here we show that selective conditions have a stronger effect on the evolutionary history of bacteria in comparison to genetic drift following population bottlenecks. We evolved Escherichia coli populations under three different population bottlenecks (small, medium, large) in two temperature regimes (37°C and 20°C). We find a high genetic diversity in the large in comparison to the small bottleneck size. Nonetheless, the cold temperature led to reduced genetic diversity in all bottleneck sizes, hence, the temperature has a stronger effect on the genetic diversity in comparison to the bottleneck size. A comparison of the fitness gain among the evolved populations reveals a similar pattern where the temperature has a significant effect on the fitness. Our study demonstrates that population bottlenecks are an important determinant of the evolvability in bacteria; their consequences depend on the selective conditions and are best understood via their effect on the standing genetic variation.

Download Full-text

Subtype Characterization and Zoonotic Potential of Cryptosporidium felis in Cats in Guangdong and Shanghai, China

Pathogens ◽

10.3390/pathogens10020089 ◽

2021 ◽

Vol 10 (2) ◽

pp. 89

Author(s):

Jiayu Li ◽

Fuxian Yang ◽

Ruobing Liang ◽

Sheng Guo ◽

Yaqiong Guo ◽

...

Keyword(s):

Genetic Diversity ◽

Phylogenetic Analysis ◽

Genetic Characterization ◽

Zoonotic Potential ◽

Common Occurrence ◽

High Genetic Diversity ◽

Gp60 Gene ◽

The Common ◽

Subtyping Tool

Cryptosporidiumfelis is an important cause of feline and human cryptosporidiosis. However, the transmission of this pathogen between humans and cats remains controversial, partially due to a lack of genetic characterization of isolates from cats. The present study was conducted to examine the genetic diversity of C. felis in cats in China and to assess their potential zoonotic transmission. A newly developed subtyping tool based on a sequence analysis of the 60-kDa glycoprotein (gp60) gene was employed to identify the subtypes of 30 cat-derived C. felis isolates from Guangdong and Shanghai. Altogether, 20 C. felis isolates were successfully subtyped. The results of the sequence alignment showed a high genetic diversity, with 13 novel subtypes and 2 known subtypes of the XIXa subtype family being identified. The known subtypes were previously detected in humans, while some of the subtypes formed well-supported subclusters with human-derived subtypes from other countries in a phylogenetic analysis of the gp60 sequences. The results of this study confirmed the high genetic diversity of the XIXa subtype family of C. felis. The common occurrence of this subtype family in both humans and cats suggests that there could be cross-species transmission of C. felis.

Download Full-text

Genetic Diversity of Leuconostoc mesenteroides Isolates from Traditional Montenegrin Brine Cheese

Microorganisms ◽

10.3390/microorganisms9081612 ◽

2021 ◽

Vol 9 (8) ◽

pp. 1612

Author(s):

Werner Ruppitsch ◽

Andjela Nisic ◽

Patrick Hyden ◽

Adriana Cabal ◽

Jasmin Sucher ◽

...

Keyword(s):

Genetic Diversity ◽

Safety Evaluation ◽

Gene Clusters ◽

Northern Region ◽

Genomic Diversity ◽

High Genetic Diversity ◽

Pathogenic Factors ◽

Flavor Development ◽

Genomic Characterization

In many dairy products, Leuconostoc spp. is a natural part of non-starter lactic acid bacteria (NSLAB) accounting for flavor development. However, data on the genomic diversity of Leuconostoc spp. isolates obtained from cheese are still scarce. The focus of this study was the genomic characterization of Leuconostoc spp. obtained from different traditional Montenegrin brine cheeses with the aim to explore their diversity and provide genetic information as a basis for the selection of strains for future cheese production. In 2019, sixteen Leuconostoc spp. isolates were obtained from white brine cheeses from nine different producers located in three municipalities in the northern region of Montenegro. All isolates were identified as Ln. mesenteroides. Classical multilocus sequence tying (MLST) and core genome (cg) MLST revealed a high diversity of the Montenegrin Ln. mesenteroides cheese isolates. All isolates carried genes of the bacteriocin biosynthetic gene clusters, eight out of 16 strains carried the citCDEFG operon, 14 carried butA, and all 16 isolates carried alsS and ilv, genes involved in forming important aromas and flavor compounds. Safety evaluation indicated that isolates carried no pathogenic factors and no virulence factors. In conclusion, Ln. mesenteroides isolates from Montenegrin traditional cheeses displayed a high genetic diversity and were unrelated to strains deposited in GenBank.

Download Full-text

Molecular characterization of echovirus 13 uncovering high genetic diversity and identification of new genotypes in Pakistan

Infection Genetics and Evolution ◽

10.1016/j.meegid.2016.12.017 ◽

2017 ◽

Vol 48 ◽

pp. 102-108

Author(s):

Shahzad Shaukat ◽

Mehar Angez ◽

Tariq Mahmood ◽

Muhammad Masroor Alam ◽

Salmaan Sharif ◽

...

Keyword(s):

Genetic Diversity ◽

Molecular Characterization ◽

High Genetic Diversity

Download Full-text

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

Open Medicine ◽

10.2478/s11536-006-0041-8 ◽

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.

Download Full-text

Global range expansion history of pepper (Capsicum spp.) revealed by over 10,000 genebank accessions

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2104315118 ◽

2021 ◽

Vol 118 (34) ◽

pp. e2104315118

Author(s):

Pasquale Tripodi ◽

Mark Timothy Rabanus-Wallace ◽

Lorenzo Barchi ◽

Sandip Kale ◽

Salvatore Esposito ◽

...

Keyword(s):

Genetic Diversity ◽

Genotyping By Sequencing ◽

Focal Region ◽

Nucleotide Polymorphisms ◽

Trade Routes ◽

Genebank Management ◽

Capsicum Spp ◽

History Of ◽

Cultural Commodity

Genebanks collect and preserve vast collections of plants and detailed passport information, with the aim of preserving genetic diversity for conservation and breeding. Genetic characterization of such collections has the potential to elucidate the genetic histories of important crops, use marker–trait associations to identify loci controlling traits of interest, search for loci undergoing selection, and contribute to genebank management by identifying taxonomic misassignments and duplicates. We conducted a genomic scan with genotyping by sequencing (GBS) derived single nucleotide polymorphisms (SNPs) of 10,038 pepper (Capsicum spp.) accessions from worldwide genebanks and investigated the recent history of this iconic staple. Genomic data detected up to 1,618 duplicate accessions within and between genebanks and showed that taxonomic ambiguity and misclassification often involve interspecific hybrids that are difficult to classify morphologically. We deeply interrogated the genetic diversity of the commonly consumed Capsicum annuum to investigate its history, finding that the kinds of peppers collected in broad regions across the globe overlap considerably. The method ReMIXTURE—using genetic data to quantify the similarity between the complement of peppers from a focal region and those from other regions—was developed to supplement traditional population genetic analyses. The results reflect a vision of pepper as a highly desirable and tradable cultural commodity, spreading rapidly throughout the globe along major maritime and terrestrial trade routes. Marker associations and possible selective sweeps affecting traits such as pungency were observed, and these traits were shown to be distributed nonuniformly across the globe, suggesting that human preferences exerted a primary influence over domesticated pepper genetic structure.

Download Full-text

African buffalo maintain high genetic diversity in the major histocompatibility complex in spite of historically known population bottlenecks

Molecular Ecology ◽

10.1046/j.1365-294x.1998.00463.x ◽

1998 ◽

Vol 7 (10) ◽

pp. 1315-1322 ◽

Cited By ~ 41

Author(s):

P. W. WENINK ◽

A. F. GROEN ◽

M. E. ROELKE‐PARKER ◽

H. H. T. PRINS

Keyword(s):

Genetic Diversity ◽

Major Histocompatibility Complex ◽

African Buffalo ◽

Population Bottlenecks ◽

Major Histocompatibility ◽

High Genetic Diversity ◽

Histocompatibility Complex

Download Full-text

There Is No Evidence of Geographical Patterning among Invasive Kentucky Bluegrass (Poa pratensis) Populations in the Northern Great Plains

Weed Science ◽

10.1614/ws-d-15-00169.1 ◽

2016 ◽

Vol 64 (3) ◽

pp. 409-420 ◽

Cited By ~ 2

Author(s):

Lauren A. Dennhardt ◽

Edward S. DeKeyser ◽

Sarah A. Tennefos ◽

Steven E. Travers

Keyword(s):

Genetic Diversity ◽

Great Plains ◽

Propagule Pressure ◽

Poa Pratensis ◽

Natural Populations ◽

Kentucky Bluegrass ◽

Grass Species ◽

Northern Great Plains ◽

Wild Populations ◽

High Genetic Diversity

The study of colonizing and of dominant grass species is essential for prairie conservation efforts. We sought to answer how naturalized Kentucky bluegrass in the northern Great Plains has become successful in the last 20 yr despite its long history in the northern Great Plains. We tested for evidence of geographical differentiation using flow cytometry and microsatellite markers to ascertain the population genetics of Kentucky bluegrass. Across all tested wild populations, high levels of genetic diversity were detected along with moderate levels of structure. Mantel tests of geographical patterns were not significant. Using clonal assignment, we found two major clones that made up the majority of the tested wild populations. When we compared the wild individuals to pedigree cultivars, we found virtually no genetic overlap across all tests, which did not support our hypothesis of developed cultivars contributing to high genetic diversity in natural populations. Furthermore, DNA content tests indicated a narrow range in ploidy in wild populations compared with lawn cultivars, further supporting a hypothesis of divergence between wild and pedigree cultivars. These results indicate the recent invasion of Kentucky bluegrass in the northern Great Plains is not because of adaptation or propagule pressure, but rather likely an environmental or land use shift.

Download Full-text