The role of environment, local adaptation and past climate fluctuation on the amount and distribution of genetic diversity in the teosinte in Mexico

AbstractWild maize, commonly known as teosinte, has a wide distribution in central Mexico and inhabits a wide range of environmental conditions. According to previous studies, the environment is a determinant factor for the amount and distribution of genetic diversity. In this study, we used a set of neutral markers to explore the influence of contemporary factors and historical environmental shifts on genetic diversity, including present and three historical periods. Using a set of 22 nuclear microsatellite loci, we genotyped 527 individuals from 29 localities. We found highly variable levels of genetic diversity (Z. m. parviglumis HE= 0.3646–0.7699; Z. m. mexicana HE= 0.5885–0.7671) and significant genetic structure among localities (average DEST= 0.4332). Also, we recovered significant values of heterozygote deficiency (average FIS= 0.1796) and variable levels of selfing (sg2=0.0–0.3090). The Bayesian assignment analysis yielded four genetic clusters dividing the sample into subspecies, that in turn, were separated into two clusters. Environmental conditions played a strong influence in the distribution of genetic diversity, as demographic analysis and changes in species range revealed by modeling analyses were consistent. We conclude that current genetic diversity in teosinte is the result of a mixture of local adaptation and genetic isolation along with historical environmental fluctuations.

Download Full-text

Assessment of the Structure and Diversity of Latvian Acer platanoides Populations Using Cross-Species Nuclear Microsatellite Markers

Proceedings of the Latvian Academy of Sciences. Section B. Natural, Exact, and Applied Sciences. ◽

10.2478/prolas-2021-0038 ◽

2021 ◽

Vol 75 (4) ◽

pp. 254-260

Author(s):

Dainis Edgars Ruņģis ◽

Baiba Krivmane

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Genetic Resource ◽

Molecular Data ◽

Initial Assessment ◽

Northern Europe ◽

Acer Platanoides ◽

Norway Maple ◽

Wide Range ◽

Nuclear Microsatellite

Abstract Acer platanoides L. (Norway maple) is the most widespread native maple species in Europe, with a distribution from south and central Europe to northern Europe and Scandinavia. Acer platanoides is widespread throughout the territory of Latvia, and is mainly found in mixed broadleaf and conifer stands. The genetic diversity and differentiation of Latvian A. platanoides populations was analysed. Sampled populations were located throughout the territory of Latvia, and were selected to represent a range of ecological conditions, with differing levels of anthropogenic impact. A total of 496 individuals from 21 populations were analysed with eight microsatellite markers, which were developed from related Acer species. The obtained molecular data revealed a moderate level of polymorphism, and the analysed Latvian A. platanoides populations were moderately differentiated. This study provides an initial assessment of the genetic diversity and differentiation of Latvian A. platanoides populations, and is also one of the first reports of the analysis of A. platanoides populations using microsatellite markers. The results can be utilised to define A. platanoides genetic resource stands to ensure conservation of a wide range of germplasm.

Download Full-text

The role of environment, local adaptation, and past climate fluctuation on the amount and distribution of genetic diversity in two subspecies of Mexican wild Zea mays

American Journal of Botany ◽

10.1002/ajb2.1561 ◽

2020 ◽

Vol 107 (11) ◽

pp. 1542-1554

Author(s):

Jaime Gasca‐Pineda ◽

Yocelyn T. Gutiérrez‐Guerrero ◽

Erika Aguirre‐Planter ◽

Luis E. Eguiarte

Keyword(s):

Genetic Diversity ◽

Zea Mays ◽

Local Adaptation ◽

Past Climate ◽

Climate Fluctuation

Download Full-text

Short Note: Isolation and Characterization of 12 Polymorphic Microsatellite Markers in Engelhardia roxburghiana (Juglandaceae)

Silvae Genetica ◽

10.1515/sg-2014-0014 ◽

2014 ◽

Vol 63 (1-6) ◽

pp. 109-112 ◽

Cited By ~ 2

Author(s):

Dan-Dan Zhang ◽

Pi Luo ◽

Ying Chen ◽

Zheng-Feng Wang ◽

Wan-Hui Ye ◽

...

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Short Note ◽

Screening Method ◽

Wide Distribution ◽

Enriched Library ◽

Isolation And Characterization ◽

Nuclear Microsatellite ◽

Polymorphic Microsatellite

Abstract Engelhardia roxburghiana is a common half evergreen tree with a wide distribution in southeast Asia. Despite its ecological and pharmaceutical values, its genetic diversity is poorly studied. Our objective was to develop nuclear microsatellite markers to investigate the level of genetic diversity within and among populations in the future. Using the microsatellite-enriched library and PCR-based screening method, 12 microsatellite markers were developed and showed polymorphism in a population. The number of alleles per locus for these 12 microsatellites ranged from four to 15. The observed and expected heterozygosities ranged from 0.358 to 0.897 and from 0.369 to 0.886, respectively. The developed microsatellites will be useful for studying genetic diversity and population structure in E. roxburghiana.

Download Full-text

Divergent lineages in the heath mouse (Pseudomys shortridgei) are indicative of major contraction to geographically isolated refugia on the eastern and western sides of Australia during the early Pleistocene

Australian Journal of Zoology ◽

10.1071/zo08097 ◽

2009 ◽

Vol 57 (1) ◽

pp. 41 ◽

Cited By ~ 9

Author(s):

Maria Salinas ◽

Michael Bunce ◽

Damien Cancilla ◽

Deryn L. Alpers ◽

Peter B. S. Spencer

Keyword(s):

Genetic Diversity ◽

Western Australia ◽

Early Pleistocene ◽

Evolutionary Significant Units ◽

Australian Continent ◽

D Loop ◽

Nuclear Microsatellite ◽

Genetic Clusters ◽

Significant Divergence ◽

Nuclear Loci

The heath mouse (Pseudomys shortridgei) is a locally rare species; it was considered extinct in Western Australia until its rediscovery 20 years ago. It is not often detected in faunal surveys and is confined to two ecologically distinct habitats on either side of the Australian continent. An important and immediate conservation question has been to determine the genetic diversity within each of its current habitats and to determine the differences between the geographically separate populations. Measures of genetic differentiation amongst P. shortridgei populations in their eastern (Victoria) and western (Western Australia) distribution were estimated using nuclear (microsatellite loci) and partial sequence of mitochondrial DNA (427 bp Cytochrome b gene and 637 bp of the D-loop). Both markers identified differences between the east- and west-coast populations. MtDNA data showed significant divergence between populations with monophyly within them, and nuclear loci investigated also showed two clear genetic clusters based on Bayesian inference. As a result of these findings, we suggest that the heath mouse comprises two highly divergent (but genetically diverse) lineages and the aridity of the Nullarbor Plain has clearly been a barrier for dispersal since the early Pleistocene (~1.43 million years ago). The populations either side of the Nullarbor Plain are genetically differentiated and should be defined as separate Evolutionary Significant Units (ESUs).

Download Full-text

High gene flow maintains wide-range species cohesion in a Neotropical epiphyte (Tillandsia aeranthos, Bromeliaceae)

Botanical Journal of the Linnean Society ◽

10.1093/botlinnean/boaa040 ◽

2020 ◽

Vol 194 (2) ◽

pp. 239-252

Author(s):

Felipe Aoki-Gonçalves ◽

Marcos Vinicius Dantas De Queiroz ◽

Thais De Beauclair Guimarães ◽

Viviana Solís Neffa ◽

Clarisse Palma-Silva

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Genetic Structure ◽

Breeding System ◽

Ecological Data ◽

Pollination Experiments ◽

Controlled Pollination ◽

Wide Range ◽

Genetic Diversity And Structure ◽

Assignment Analysis

Abstract Studies of patterns of genetic diversity, genetic structure and ecological data across geographical ranges of species allow us to test hypotheses about the evolutionary responses of organisms to fluctuations in habitat connectivity and availability. Here we present a study aiming to assess genetic diversity, population structure and breeding system across the geographical distribution of a subtropical epiphyte, Tillandsia aeranthos (Bromeliaceae), endemic to the Plata River basin (Pampa biome). Seven nuclear microsatellite markers were genotyped in 203 individuals from 13 localities across Brazil and Argentina and 14 plastid regions were sequenced for a subset of the individuals. Additionally, we performed controlled pollination experiments to discuss correlations between breeding system, genetic diversity and structure in the species. Nuclear diversity levels were high (HE = 0.806, HO = 0.745, allelic richness = 5.860) with no haplotype differentiation detected (c. 9 kpb sequenced). Bayesian assignment analysis, supported by principal coordinate analysis and analysis of molecular variance, show low genetic structure across the studied area (FST = 0.031, P < 0.001). Controlled pollination experiments indicated complete self-incompatibility in all localities analysed. Our results show effective gene flow maintaining low genetic structure between localities for T. aeranthos across an extensive area in the Pampa.

Download Full-text

Genetic diversity and population structure of the sweet leaf herb, Stevia rebaudiana B., cultivated and landraces germplasm assessed by EST-SSRs genotyping and steviol glycosides phenotyping

BMC Plant Biology ◽

10.1186/s12870-019-2061-y ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 4

Author(s):

Patrick Cosson ◽

Cécile Hastoy ◽

Luis Ernesto Errazzu ◽

Carlos Jorge Budeguer ◽

Philippe Boutié ◽

...

Keyword(s):

Genetic Diversity ◽

Polymorphic Information Content ◽

Germplasm Collection ◽

Stevia Rebaudiana ◽

Sweet Taste ◽

Genome Project ◽

Steviol Glycosides ◽

Genomic Tools ◽

Wide Range ◽

Genetic Clusters

Abstract Background Stevia rebaudiana (Asteraceae), native from Paraguay, accumulates steviol glycosides (SGs) into its leaves. These compounds exhibit acaloric intense sweet taste which answers to consumer demands for reducing daily sugar intake. Despite the developpement of S. rebaudiana cultivation all over the world, the development of new cultivars is very recent, in particular due to a colossal lack of (1) germplasm collection and breeding, (2) studies on genetic diversity and its structuring, (3) genomic tools. Results In this study, we developped 18 EST-SSR from 150,258 EST from The Compositae Genome Project of UC Davis (http://compgenomics.ucdavis.edu/data/). We genotyped 145 S. rebaudiana individuals, issued from thirty-one cultivars and thirty-one landraces of various origins worldwide. Markers polymorphic information content (PIC) ranged between 0.60 and 0.84. An average of 12 alleles per locus and a high observed heterozygoty of 0.69 could be observed. The landraces revealed twice as many private alleles as cultivars. The genotypes could be clustered into 3 genetic populations. The landraces were grouped in the same cluster in which the oldest cultivars “Eirete” and “MoritaIII” type are also found. The other two clusters only include cultivated genotypes. One of them revealed an original genetic variability. SG phenotypes could not discriminate the three genetic clusters but phenotyping showed a wide range of composition in terms of bitter to sweet SGs. Conclusion This is the first study of genetic diversity in Stevia rebaudiana involving 145 genotypes, including known cultivars as well as landrace populations of different origin. This study pointed out the structuration of S. rebaudiana germplasm and the resource of the landrace populations for genetic improvement, even on the trait of SG’s composition.

Download Full-text

Population genetic structure of Texas horned lizards: implications for reintroduction and captive breeding

PeerJ ◽

10.7717/peerj.7746 ◽

2019 ◽

Vol 7 ◽

pp. e7746 ◽

Cited By ~ 1

Author(s):

Dean A. Williams ◽

Nathan D. Rains ◽

Amanda M. Hale

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Captive Breeding ◽

Suitable Habitat ◽

Fitness Costs ◽

High Genetic Diversity ◽

Horned Lizards ◽

Nuclear Microsatellite ◽

Genetic Clusters ◽

Mitochondrial Clade

The Texas horned lizard (Phrynosoma cornutum) inhabits much of the southern Great Plains of North America. Since the 1950s, this species has been extirpated from much of its eastern range and has suffered declines and local extinctions elsewhere, primarily due to habitat loss. Plans are underway to use captive breeding to produce large numbers of Texas horned lizards for reintroduction into areas that were historically occupied by this species and that currently have suitable habitat. We used mitochondrial markers and nuclear microsatellite markers to determine levels of genetic diversity and population structure in 542 Texas horned lizards sampled from across Texas and some neighboring states to help inform these efforts. Texas horned lizards still retain high genetic diversity in many parts of their current range. We found two highly divergent mitochondrial clades (eastern and western) and three major genetic groupings at nuclear microsatellite loci: a west group corresponding to the western mitochondrial clade and north and south groups within the eastern mitochondrial clade. We also found some evidence for human-mediated movement between these genetic clusters that is probably related to the historical importance of this species in the pet trade and as an iconic symbol of the southwestern United States. We do not know, however, if there are fitness costs associated with admixture (especially for the western and eastern clades) or if there are fitness costs to moving these lizards into habitats that are distinctly different from their ancestral areas. If present, either one or both of these fitness costs would decrease the effectiveness of reintroduction efforts. We therefore recommend that reintroduction efforts should maintain current genetic structure by restricting breeding to be between individuals within their respective genetic clusters, and by reintroducing individuals only into those areas that encompass their respective genetic clusters. This cautionary approach is based on the strong divergence between genetic groupings and their correspondence to different ecoregions.

Download Full-text

Influence of environmental factors on the genetic variation of the aquatic macrophyte Ranunculus subrigidus on the Qinghai-Tibetan Plateau

BMC Evolutionary Biology ◽

10.1186/s12862-019-1559-0 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 2

Author(s):

Zhigang Wu ◽

Xinwei Xu ◽

Juan Zhang ◽

Gerhard Wiegleb ◽

Hongwei Hou

Keyword(s):

Genetic Diversity ◽

Tibetan Plateau ◽

Environmental Factors ◽

Local Adaptation ◽

Aquatic Macrophyte ◽

Spatial Genetic Structure ◽

Long Distance ◽

Elevation Gradients ◽

Mantel Tests ◽

Genetic Patterns

Abstract Background Due to the environmental heterogeneity along elevation gradients, alpine ecosystems are ideal study objects for investigating how ecological variables shape the genetic patterns of natural species. The highest region in the world, the Qinghai-Tibetan Plateau, is a hotspot for the studies of evolutionary processes in plants. Many large rivers spring from the plateau, providing abundant habitats for aquatic and amphibious organisms. In the present study, we examined the genetic diversity of 13 Ranunculus subrigidus populations distributed throughout the plateau in order to elucidate the relative contribution of geographic distance and environmental dissimilarity to the spatial genetic pattern. Results A relatively low level of genetic diversity within populations was found. No spatial genetic structure was suggested by the analyses of molecular variance, Bayesian clustering analysis and Mantel tests. Partial Mantel tests and multiple matrix regression analysis showed a significant influence of the environment on the genetic divergence of the species. Both climatic and water quality variables contribute to the habitat heterogeneity of R. subrigidus populations. Conclusions Our results suggest that historical processes involving long-distance dispersal and local adaptation may account for the genetic patterns of R. subrigidus and current environmental factors play an important role in the genetic differentiation and local adaptation of aquatic plants in alpine landscapes.

Download Full-text

Whole genome-based characterisation of antimicrobial resistance and genetic diversity in Campylobacter jejuni and Campylobacter coli from ruminants

Scientific Reports ◽

10.1038/s41598-021-88318-0 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Medelin Ocejo ◽

Beatriz Oporto ◽

José Luis Lavín ◽

Ana Hurtado

Keyword(s):

Genetic Diversity ◽

Antimicrobial Resistance ◽

Campylobacter Jejuni ◽

Resistance Genes ◽

Campylobacter Coli ◽

Whole Genome ◽

Northern Spain ◽

Sequence Alignments ◽

Phenotypic Data ◽

Wide Range

AbstractCampylobacter, a leading cause of gastroenteritis in humans, asymptomatically colonises the intestinal tract of a wide range of animals.Although antimicrobial treatment is restricted to severe cases, the increase of antimicrobial resistance (AMR) is a concern. Considering the significant contribution of ruminants as reservoirs of resistant Campylobacter, Illumina whole-genome sequencing was used to characterise the mechanisms of AMR in Campylobacter jejuni and Campylobacter coli recovered from beef cattle, dairy cattle, and sheep in northern Spain. Genome analysis showed extensive genetic diversity that clearly separated both species. Resistance genotypes were identified by screening assembled sequences with BLASTn and ABRicate, and additional sequence alignments were performed to search for frameshift mutations and gene modifications. A high correlation was observed between phenotypic resistance to a given antimicrobial and the presence of the corresponding known resistance genes. Detailed sequence analysis allowed us to detect the recently described mosaic tet(O/M/O) gene in one C. coli, describe possible new alleles of blaOXA-61-like genes, and decipher the genetic context of aminoglycoside resistance genes, as well as the plasmid/chromosomal location of the different AMR genes and their implication for resistance spread. Updated resistance gene databases and detailed analysis of the matched open reading frames are needed to avoid errors when using WGS-based analysis pipelines for AMR detection in the absence of phenotypic data.

Download Full-text

Phenotypic Characterisation for Growth and Nut Characteristics Revealed the Extent of Genetic Diversity in Wild Macadamia Germplasm

Agriculture ◽

10.3390/agriculture11070680 ◽

2021 ◽

Vol 11 (7) ◽

pp. 680

Author(s):

Thuy T. P. Mai ◽

Craig M. Hardner ◽

Mobashwer M. Alam ◽

Robert J. Henry ◽

Bruce L. Topp

Keyword(s):

Genetic Diversity ◽

Growth Traits ◽

Principal Component ◽

Conservation Strategies ◽

Wild Germplasm ◽

Phenotypic Characterisation ◽

Wide Range ◽

Genetic And Environmental Factors ◽

Positive Correlations ◽

Wild Accessions

Macadamia is a recently domesticated Australian native nut crop, and a large proportion of its wild germplasm is unexploited. Aiming to explore the existing diversity, 247 wild accessions from four species and inter-specific hybrids were phenotyped. A wide range of variation was found in growth and nut traits. Broad-sense heritability of traits were moderate (0.43–0.64), which suggested that both genetic and environmental factors are equally important for the variability of the traits. Correlations among the growth traits were significantly positive (0.49–0.76). There were significant positive correlations among the nut traits except for kernel recovery. The association between kernel recovery and shell thickness was highly significant and negative. Principal component analysis of the traits separated representative species groups. Accessions from Macadamia integrifolia Maiden and Betche, M. tetraphylla L.A.S. Johnson, and admixtures were clustered into one group and those of M. ternifolia F. Muell were separated into another group. In both M. integrifolia and M. tetraphylla groups, variation within site was greater than across sites, which suggested that the conservation strategies should concentrate on increased sampling within sites to capture wide genetic diversity. This study provides a background on the utilisation of wild germplasm as a genetic resource to be used in breeding programs and the direction for gene pool conservation.

Download Full-text