Genetic diversity of butternut (Juglans cinerea) and implications for conservation

2008 ◽  
Vol 38 (4) ◽  
pp. 899-907 ◽  
Author(s):  
Amy Ross-Davis ◽  
Michael Ostry ◽  
Keith E. Woeste
Keyword(s):  
Genetic Diversity ◽  
Population Genetics ◽  
North America ◽  
Endangered Species ◽  
Isolation By Distance ◽  
Eastern North America ◽  
Native Range ◽  
Juglans Cinerea ◽  
Threatened And Endangered Species ◽  
Genetic Diversity And Structure

The management of threatened and endangered species can be improved by understanding their patterns of genetic diversity and structure. This paper presents the results of the first analysis of the population genetics of butternut ( Juglans cinerea L.) using nuclear microsatellites. Butternut once was an economically and ecologically valuable hardwood, but now its numbers are rapidly decreasing throughout its native range in eastern North America. By genotyping butternut trees (n = 157) from five populations at seven highly polymorphic loci, we determined that the remaining genetic diversity for the species is considerably higher than previously estimated (mean HE = 0.75). Populations were nearly genetically homogenous (FST = 0.025), with no evidence of isolation by distance. These results indicate that butternut retains a large amount of genetic diversity, and that it is not too late to implement strategies to conserve local butternut populations.

Geographic patterns of genetic diversity in North American trees: a continent-wide analysis

2021 ◽  
Author(s):  
Andrew V. Gougherty
Keyword(s):  
Genetic Diversity ◽  
Population Genetics ◽  
North America ◽  
North American ◽  
Tree Species ◽  
Geographic Patterns ◽  
Study Characteristics ◽  
Dispersal Traits ◽  
The Last Glacial Maximum ◽  
The Last Glacial

In the northern hemisphere, many species have been reported to have greater genetic diversity in southern populations than northern populations - ostensibly due to migration northward following the last glacial maximum (LGM). The generality of this pattern, while well-established for some taxa, remains unclear for North American trees. To address this issue, I collected published population genetics data for 73 North American tree species, and tested whether genetic diversity was associated with latitude or longitude and whether geographic trends were associated with dispersal traits, range or study characteristics. I found there were no general geographic patterns in genetic diversity, and the strength of the geographic gradients were not associated with any species or study characteristics. Species in the northern and western regions of North America tended to have more species with genetic diversity that declined with latitude, but most species had no significant trend. This work shows that North American trees have complex, individualistic, patterns of genetic diversity that may negate explanation by any particular dispersal trait or range characteristic.

Genetic diversity of the lichen-forming alga, Diplosphaera chodatii, in North America and Europe

2013 ◽  
Vol 45 (6) ◽  
pp. 799-813 ◽  
Author(s):  
Kyle M. FONTAINE ◽  
Elfie STOCKER-WÖRGÖTTER ◽  
Tom BOOTH ◽  
Michele D. PIERCEY-NORMORE
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Flow ◽  
North America ◽  
Isolation By Distance ◽  
Water Level Fluctuations ◽  
Free Living ◽  
Climatic Zones ◽  
Algal Symbiont ◽  
Low Levels

AbstractDermatocarpon luridum is a subaquatic lichen which is distributed within temperate climatic zones around the world. It colonizes rock substrata along the shoreline of lakes and rivers of watersheds that regularly experience water level fluctuations. The mycobiont produces perithecia with small, simple spores that are thought to be wind dispersed. The photobiont, Diplosphaera chodatii, occurs both free-living and lichenized but little is known about its distribution and dispersal. The goal of this study was to compare the population structure of the photobiont from lakes and rivers in central North America with those of Europe. Specimens were collected in Manitoba, Canada and Austria. Population structure of the algal symbiont was assessed using the internal transcribed spacer (ITS) of ribosomal DNA (rDNA) and actin gene sequences. Results showed that genetic diversity and gene flow was high within local populations, but gene flow was low between continental populations. Low levels of gene flow between the most distant populations support the isolation-by-distance theory. The photobiont on both continents is also reported to be the photobiont for other lichen species contributing to photobiont availability for D. luridum.

Genetic diversity and structure of Jatropha curcas L. in its centre of origin

2014 ◽  
Vol 13 (1) ◽  
pp. 9-17 ◽  
Author(s):  
M. Salvador-Figueroa ◽  
J. Magaña-Ramos ◽  
J. A. Vázquez-Ovando ◽  
M. L. Adriano-Anaya ◽  
I. Ovando-Medina
Keyword(s):  
Genetic Diversity ◽  
Jatropha Curcas ◽  
Isolation By Distance ◽  
Random Mating ◽  
Mantel Test ◽  
Reproductive Pattern ◽  
Chain Reactions ◽  
Polymerase Chain Reactions ◽  
Centre Of Origin ◽  
Genetic Diversity And Structure

To investigate the genetic diversity and structure of Jatropha curcas L. oilseed plant, in this study, native populations from Chiapas, Mexico, were evaluated, using microsatellite DNA markers. A total of 93 representative samples were selected from seven sites in two regions in the state of Chiapas grouped by geographical proximity, where leaf samples were collected to isolate the genomic DNA. Individual polymerase chain reactions were carried out with ten pairs of specific oligonucleotides for the microsatellites of J. curcas, separating the products of amplification by acrylamide electrophoresis. Twenty-seven fragments were detected (77% polymorphic) with which heterozygous individuals were distinguished. The most informative microsatellite was Jcps20 (nine alleles, polymorphic index content 0.354). The average polymorphism per population was 58%. The Hardy–Weinberg tests revealed a reproductive pattern of non-random mating. The diversity descriptors and the analysis of molecular variance revealed that the populations were structured and moderately differentiated (FST 0.087) and that this differentiation was not due to isolation by distance, as the Mantel test was not significant (P= 0.137), but rather due to allopatry. Bayesian analysis revealed that the accessions belonged to only four genetic groups and confirmed the differentiation between the regions. Because some loci were in Hardy–Weinberg disequilibrium, it is proposed that differentiation is due to the clonal reproduction of J. curcas practised by farmers in Chiapas, along with the anthropogenic dispersion at regional levels. The results of this study reveal that J. curcas in Chiapas has genetic diversity that is greater than that reported in other parts of the world, which represents a potential germplasm pool for the selection of genotypes.

scholarly journals Crop domestication facilitated rapid geographical expansion of a specialist pollinator, the squash bee Peponapis pruinosa

2016 ◽  
Vol 283 (1833) ◽  
pp. 20160443 ◽  
Author(s):  
Margarita M. López-Uribe ◽  
James H. Cane ◽  
Robert L. Minckley ◽  
Bryan N. Danforth
Keyword(s):  
North America ◽  
Great Basin ◽  
Eastern North America ◽  
Crop Domestication ◽  
Native Range ◽  
Colonization Routes ◽  
Wild Host ◽  
Geographical Expansion ◽  
Founder Events ◽  
Peponapis Pruinosa

Squash was first domesticated in Mexico and is now found throughout North America (NA) along with Peponapis pruinosa , a pollen specialist bee species of the squash genus Cucurbita . The origin and spread of squash cultivation is well-studied archaeologically and phylogenetically; however, no study has documented how cultivation of this or any other crop has influenced species in mutualistic interactions. We used molecular markers to reconstruct the demographic range expansion and colonization routes of P. pruinosa from its native range into temperate NA. Populations east of the Rocky Mountains expanded from the wild host plant's range in Mexico and were established by a series of founder events. Eastern North America was most likely colonized from squash bee populations in the present-day continental Midwest USA and not from routes that followed the Gulf and Atlantic coasts from Mexico. Populations of P. pruinosa west of the Rockies spread north from the warm deserts much more recently, showing two genetically differentiated populations with no admixture: one in California and the other one in eastern Great Basin. These bees have repeatedly endured severe bottlenecks as they colonized NA, following human spread of their Cucurbita pollen hosts during the Holocene.

scholarly journals Genetic Diversity and Population Genetics of Mosquitoes (Diptera: Culicidae:Culexspp.) from the Sonoran Desert of North America

2013 ◽  
Vol 2013 ◽  
pp. 1-11 ◽  
Author(s):  
Edward Pfeiler ◽  
Carlos A. Flores-López ◽  
Jesús Gerardo Mada-Vélez ◽  
Juan Escalante-Verdugo ◽  
Therese A. Markow
Keyword(s):  
Genetic Diversity ◽  
Population Genetics ◽  
North America ◽  
Sonoran Desert ◽  
Phylogenetic Analyses ◽  
Gene Segment ◽  
Population Expansion ◽  
The Other ◽  
Coi Gene ◽  
Unidentified Species

The population genetics and phylogenetic relationships ofCulexmosquitoes inhabiting the Sonoran Desert region of North America were studied using mitochondrial DNA and microsatellite molecular markers. Phylogenetic analyses of mitochondrial cytochromecoxidase subunit I (COI) from mosquitoes collected over a wide geographic area, including the Baja California peninsula, and mainland localities in southern Arizona, USA and Sonora, Mexico, showed several well-supported partitions corresponding toCx. quinquefasciatus, Cx. tarsalis,and two unidentified species,Culexsp. 1 and sp. 2.Culex quinquefasciatuswas found at all localities and was the most abundant species collected.Culex tarsaliswas collected only at Tucson, Arizona and Guaymas, Sonora. The two unidentified species ofCulexwere most abundant at Navojoa in southern Sonora. Haplotype and nucleotide diversities in the COI gene segment were substantially lower inCx. quinquefasciatuscompared with the other three species. Analysis of molecular variance revealed little structure among seven populations ofCx. quinquefasciatus, whereas significant structure was found between the two populations ofCx. tarsalis. Evidence for an historical population expansion beginning in the Pleistocene was found forCx. tarsalis. Possible explanations for the large differences in genetic diversity betweenCx. quinquefasciatusand the other species ofCulexare presented.

scholarly journals Does silvoagropecuary landscape fragmentation affect the genetic diversity of the sigmodontine rodent Oligoryzomys longicaudatus?

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3842 ◽  
Author(s):  
Daniela Lazo-Cancino ◽  
Selim S. Musleh ◽  
Cristian E. Hernandez ◽  
Eduardo Palma ◽  
Enrique Rodriguez-Serrano
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Isolation By Distance ◽  
Landscape Fragmentation ◽  
Native Forest ◽  
Least Cost Path ◽  
Natural Habitats ◽  
Forest Patches ◽  
Genetic Diversity And Structure ◽  
Oligoryzomys Longicaudatus

Background Fragmentation of native forests is a highly visible result of human land-use throughout the world. In this study, we evaluated the effects of landscape fragmentation and matrix features on the genetic diversity and structure of Oligoryzomys longicaudatus, the natural reservoir of Hantavirus in southern South America. We focused our work in the Valdivian Rainforest where human activities have produced strong change of natural habitats, with an important number of human cases of Hantavirus. Methods We sampled specimens of O. longicaudatus from five native forest patches surrounded by silvoagropecuary matrix from Panguipulli, Los Rios Region, Chile. Using the hypervariable domain I (mtDNA), we characterized the genetic diversity and evaluated the effect of fragmentation and landscape matrix on the genetic structure of O. longicaudatus. For the latter, we used three approaches: (i) Isolation by Distance (IBD) as null model, (ii) Least-cost Path (LCP) where genetic distances between patch pairs increase with cost-weighted distances, and (iii) Isolation by Resistance (IBR) where the resistance distance is the average number of steps that is needed to commute between the patches during a random walk. Results We found low values of nucleotide diversity (π) for the five patches surveyed, ranging from 0.012 to 0.015, revealing that the 73 sampled specimens of this study belong to two populations but with low values of genetic distance (γST) ranging from 0.022 to 0.099. Likewise, we found that there are no significant associations between genetic distance and geographic distance for IBD and IBR. However, we found for the LCP approach, a significant positive relationship (r = 0.737, p = 0.05), with shortest least-cost paths traced through native forest and arborescent shrublands. Discussion In this work we found that, at this reduced geographical scale, Oligoryzomys longicaudatus shows genetic signs of fragmentation. In addition, we found that connectivity between full growth native forest remnants is mediated by the presence of dense shrublands and native forest corridors. In this sense, our results are important because they show how native forest patches and associated routes act as source of vector species in silvoagropecuary landscape, increasing the infection risk on human population. This study is the first approach to understand the epidemiological spatial context of silvoagropecuary risk of Hantavirus emergence. Further studies are needed to elucidate the effects of landscape fragmentation in order to generate new predictive models based on vector intrinsic attributes and landscape features.

scholarly journals De novo assembly and transcriptome characterization of an endemic species of Vietnam, Panax vietnamensis Ha et Grushv., including the development of EST-SSR markers for population genetics

2020 ◽  
Author(s):  
Duy Dinh Vu ◽  
Syed Noor Muhammad Shah ◽  
Mai Phuong Pham ◽  
Van Thang Bui ◽  
Minh Tam Nguyen ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Endangered Species ◽  
De Novo ◽  
Average Length ◽  
Species Conservation ◽  
Illumina Hiseq ◽  
Bottleneck Analysis ◽  
Genetic Diversity And Structure ◽  
Geographical Distances ◽  
High Level

Abstract Background: Understanding the genetic diversity in endangered species that occur in forest remnants is necessary to establish efficient strategies for the species conservation, restoration and management. Panax vietnamensis Ha et Grushv. is medicinally important, endemic and endangered species of Vietnam. However, genetic diversity and structure of population are unknown due to lack of efficient molecular markers. Results: In this study, we employed Illumina HiSeqTM 4000 sequencing to analyze the transcriptomes of P. vietnamensis (roots, leaves and stems). Raw reads total of 23,741,783 was obtained and then assembled, from which the generated unigenes were 89,271 (average length = 598.3191 nt). The 31,686 unigenes were annotated in different databases i.e. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, Nucleotide Collection (NR/NT) and Swiss-Prot for functional annotation. Further, 11,343 EST-SSRs were detected. From 7,774 primer pairs, 101 were selected for polymorphism validation, in which; 20 primer pairs were successfully amplified to DNA fragments and significant amounts of polymorphism was observed within population. The nine polymorphic microsatellite loci were used for population structure and diversity analyses. The obtained results revealed high levels of genetic diversity in populations, the average observed and expected heterozygosity were HO = 0.422 and HE = 0.479, respectively. During the Bottleneck analysis using TPM and SMM models (p < 0.01) shows that targeted population is significantly heterozygote deficient. This suggests sign of the bottleneck in all populations. Genetic differentiation between populations was moderate (FST = 0.133) and indicating slightly high level of gene flow (Nm = 1.63). Analysis of molecular variance (AMOVA) showed 63.17% of variation within individuals and 12.45% among populations. Our results shows two genetic clusters related to geographical distances. Conclusion: Our study will assist conservators in future conservation management, breeding, production and habitats restoration of the species.

The population genetic structure and diversification of Aristolochia delavayi (Aristolochiaceae), an endangered species of the dry hot valleys of the Jinsha River, southwestern China

Botany ◽  
2014 ◽  
Vol 92 (8) ◽  
pp. 579-587 ◽  
Author(s):  
Zhi-Yun Yang ◽  
Ting-Shuang Yi ◽  
Liang-Qin Zeng ◽  
Xun Gong
Keyword(s):  
Genetic Diversity ◽  
Endangered Species ◽  
Population Size ◽  
Gene Diversity ◽  
Issr Markers ◽  
Habitat Destruction ◽  
Ex Situ ◽  
Southwestern China ◽  
Jinsha River ◽  
Genetic Diversity And Structure

Aristolochia delavayi Franch. is an endangered species of the dry hot valleys of the Jinsha River, southwestern China. The genetic diversity and structure of the species and the occurrence of gene flow were investigated with eight inter-simple sequence repeat (ISSR) markers and four plastid loci (matK, trnL-trnT, rps4-trnT, and trnC-rpoB). The analysis of ISSR markers indicated that the genetic diversity of the species is relatively high (PPB = 84.71%). Similarly, a high gene diversity of HT = 0.833 was found based on the four plastid loci. It is possible that this species previously maintained a large effective population size and that the current relict distribution of the species is a result of large-scale fragmentation and habitat destruction. The origin of the species at approximately 3.407 million years ago and the ensuing intraspecific divergence are generally consistent with the history of two major glaciations in this region. Conservation measures are urgently needed to increase the genetic diversity and population size of this species through both in- and ex-situ action.

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