scholarly journals Conservation genetics of the threatened plant species Physaria filiformis (Missouri bladderpod) reveals strong genetic structure and a possible cryptic species

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0247586
Author(s):  
Christine E. Edwards ◽  
Brooke C. Tessier ◽  
Joel F. Swift ◽  
Burgund Bassüner ◽  
Alexander G. Linan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Structure ◽  
Plant Species ◽  
Genetic Drift ◽  
Rare Species ◽  
Ex Situ ◽  
Ouachita Mountains ◽  
Genetic Diversity And Structure ◽  
Genetic Clusters

Understanding genetic diversity and structure in a rare species is critical for prioritizing both in situ and ex situ conservation efforts. One such rare species is Physaria filiformis (Brassicaceae), a threatened, winter annual plant species. The species has a naturally fragmented distribution, occupying three different soil types spread across four disjunct geographical locations in Missouri and Arkansas. The goals of this study were to understand: (1) whether factors associated with fragmentation and small population size (i.e., inbreeding, genetic drift or genetic bottlenecks) have reduced levels of genetic diversity, (2) how genetic variation is structured and which factors have influenced genetic structure, and (3) how much extant genetic variation of P. filiformis is currently publicly protected and the implications for the development of conservation strategies to protect its genetic diversity. Using 16 microsatellite markers, we genotyped individuals from 20 populations of P. filiformis from across its geographical range and one population of Physaria gracilis for comparison and analyzed genetic diversity and structure. Populations of P. filiformis showed comparable levels of genetic diversity to its congener, except a single population in northwest Arkansas showed evidence of a genetic bottleneck and two populations in the Ouachita Mountains of Arkansas showed lower genetic variation, consistent with genetic drift. Populations showed isolation by distance, indicating that migration is geographically limited, and analyses of genetic structure grouped individuals into seven geographically structured genetic clusters, with geographic location/spatial separation showing a strong influence on genetic structure. At least one population is protected for all genetic clusters except one in north-central Arkansas, which should therefore be prioritized for protection. Populations in the Ouachita Mountains were genetically divergent from the rest of P. filiformis; future morphological analyses are needed to identify whether it merits recognition as a new, extremely rare species.

scholarly journals Seedling Selection Using Molecular Approach for Ex Situ Conservation of Critically Endangered Tree Species (Vatica bantamensis (Hassk.) Benth. & Hook. ex Miq.) in Java, Indonesia

2019 ◽  
Vol 12 ◽  
pp. 194008291984950 ◽  
Author(s):  
Yayan Wahyu C. Kusuma ◽  
Siti R. Ariati ◽  
Rosniati A. Risna ◽  
Chika Mitsuyuki ◽  
Yoshihisa Suyama ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Plant Species ◽  
Ex Situ Conservation ◽  
Critically Endangered ◽  
Ex Situ ◽  
Genetic Diversity And Structure ◽  
In The Wild ◽  
Genetic Clusters ◽  
Ex Situ Collection

Ex situ conservation is an important complementary strategy for in situ to conserve endangered plant species. However, the limited areas designated for ex situ conservation such as in botanic gardens have become a great challenge for conservation practitioners and scientists attempting to optimally conserve the genetic diversity of targeted plant species. Our study aimed to assess genetic diversity and structure of wild seedlings of Vatica bantamensis, an endemic and critically endangered dipterocarp from Java (Indonesia). We also estimated genetic differentiation between the wild seedlings and existing ex situ collection and evaluated the genetic diversity preserved in the ex situ collection. Our analysis, using 730 single-nucleotide polymorphisms loci, showed that wild seedlings exhibited higher genetic diversity than the ex situ collection (nucleotide diversity, µ = 0.26 and 0.16, respectively). Significant genetic differentiation was also detected ( FST = 0.32) between wild seedlings and ex situ collection. Furthermore, we found high kinship within the ex situ collection suggesting low genetic diversity since the founding collection. We also detected three distinct genetic clusters from all samples combined (analysis of molecular variance, ϕ = 0.48, p < .001), with two clusters present in the wild seedlings that were not represented in the ex situ collection. We recommend that supplementary collections from the two newly identified genetic clusters in the wild seedlings should be incorporated to increase genetic diversity in the ex situ collection. Furthermore, our study demonstrated that understanding the population genetics of targeted endangered species provides better results for ex situ conservation strategies.

scholarly journals Genetic diversity and structure of Astrocaryum jauari (Mart.) palm in two Amazon river basins

2014 ◽  
Vol 14 (3) ◽  
pp. 166-173 ◽  
Author(s):  
Liliane D. Santos Oliveira ◽  
Santiago L. Ferreyra Ramos ◽  
Maria T. Gomes Lopes ◽  
Gabriel Dequigiovanni ◽  
Elizabeth Ann Veasey ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Structure ◽  
Microsatellite Loci ◽  
Plant Material ◽  
Spatial Genetic Structure ◽  
River Basins ◽  
Genetic Analyses ◽  
Main River ◽  
Genetic Diversity And Structure

Astrocaryum jauari is a non-domesticated palm that is exploited by poachers. Our objective was to investigate the organization of the geneticdiversity and structure of three A. jauari populations. The study was carried out in the state of Amazonas, between the municipalities of Coari and Manaus. Nine microsatellite loci were used for the genetic analyses. High genetic variation was found, with a mean number of alleles per locus varying from 3.9 to 4.4. The average observed heterozygosity, varying from 0.71 to 0.78, was higher than expected. No spatial genetic structure was detected, since only one cluster was observed. Our results indicate a possible dispersion strategy and suggest that conservation measures of this species should focus mainly on the populations found at the end of the main river (Solimões) where most of the plant material originating from the headwaters of the tributaries of this river is concentrated.

scholarly journals Genetic diversity and population structure of the endangered basal angiospermBrasenia schreberi(Cabombaceae) in China

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5296 ◽  
Author(s):  
Zhi-Zhong Li ◽  
Andrew W. Gichira ◽  
Qing-Feng Wang ◽  
Jin-Ming Chen
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Habitat Fragmentation ◽  
Glacial Refugia ◽  
Mantel Test ◽  
Ex Situ ◽  
Brasenia Schreberi ◽  
Genetic Diversity And Structure ◽  
Rare And Endangered

Brasenia schreberiJ.F. Gmelin (Cabombaceae), an aquatic herb that occurs in fragmented locations in China, is rare and endangered. Understanding its genetic diversity and structure is crucial for its conservation and management. In this study, 12 microsatellite markers were used to estimate the genetic diversity and variation in 21 populations ofB. schreberiin China. A total of 61 alleles were found; assessment of allelic richness (Ar = 1.92) and observed and expected heterozygosity (HO= 0.200,HE= 0.256) suggest lower genetic diversity compared to some endangered species, and higher variation was observed within populations (58.68%) rather than among populations (41.32%). No significant correlation between geographical and genetic distance among populations was detected (Mantel test,r= 0.0694;P= 0.7985), which may have likely resulted from barriers to gene flow (Nm = 0.361) that were produced by habitat fragmentation. However, Bayesian and neighbor-joining cluster analyses suggest a population genetic structure consisting of two clusters (I and II) or four subclusters (I-1, 2 and II-1, 2). The genetic structure and distribution ofB. schreberiin China may have involved glacial refugia that underwent range expansions, introgression, and habitat fragmentation. The findings of the present study emphasize the importance for both in situ and ex situ conservation efforts.

scholarly journals Genetic diversity and population structure of Amorphophallus albus, a plant species with extremely small populations (PSESP) endemic to dry-hot valley of Jinsha River

2020 ◽  
Author(s):  
Rong Tang ◽  
Erxi Liu ◽  
Yazhou Zhang ◽  
Johann Schinnerl ◽  
Weibang Sun ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Plant Species ◽  
Ex Situ ◽  
Small Populations ◽  
Wild Populations ◽  
Jinsha River ◽  
High Genetic Diversity ◽  
Cultivated Populations

Abstract Background: Amorphophallus albus P. Y. Liu & J. F. Chen (Araceae) is a plant species with extremely small populations (PSESP) and an important economic crop endemic to dry-hot valleys along the Jinsha River. In order to gain information for sustaining the development and conservation of A. albus, we studied the genetic diversity and population structure of this species using microsatellite markers (SSR). In this study, we analysed 364 individuals belonging to 24 populations, including four wild populations and three ex-situ cultivated populations, collected in the provinces Yunnan, Sichuan and Hubei. Results: The population genetic analyses indicated that A. albus possesses moderate genetic diversity with the percentage of polymorphic loci (PPL) from 69.23% to 100%, an expected heterozygosity (He) of 0.504 and an average Shannon's Information Index (I) 0.912. Analysis of molecular variance (AMOVA) indicated that most of the variance (71%) resided within populations and the estimated gene flow (Nm) was 0.61. The results of UPGMA cluster tree, STRUCTURE analyses together with the Mantel test (R2 = 0.352, P < 0.01) indicated that geographically closely located populations are clustered together with some exceptions. Conclusions: Our results showed that A. albus still possesses moderate genetic variation in most of the studied populations, and for now, most cultivated populations were naturally distributed but still some reintroduction exists. For sustaining the present genetic variation, some protections measures are necessary for the wild populations and also for the cultivated ones with high genetic diversity.

scholarly journals Genetic variation among 481 diverse soybean accessions, inferred from genomic re-sequencing

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Babu Valliyodan ◽  
Anne V. Brown ◽  
Juexin Wang ◽  
Gunvant Patil ◽  
Yang Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Glycine Max ◽  
Linkage Disequilibrium ◽  
Genetic Structure ◽  
Glycine Soja ◽  
Geographic Location ◽  
High Similarity ◽  
Genetic Diversity And Structure ◽  
Selection Of

AbstractWe report characteristics of soybean genetic diversity and structure from the resequencing of 481 diverse soybean accessions, comprising 52 wild (Glycine soja) selections and 429 cultivated (Glycine max) varieties (landraces and elites). This data was used to identify 7.8 million SNPs, to predict SNP effects relative to genic regions, and to identify the genetic structure, relationships, and linkage disequilibrium. We found evidence of distinct, mostly independent selection of lineages by particular geographic location. Among cultivated varieties, we identified numerous highly conserved regions, suggesting selection during domestication. Comparisons of these accessions against the whole U.S. germplasm genotyped with the SoySNP50K iSelect BeadChip revealed that over 95% of the re-sequenced accessions have a high similarity to their SoySNP50K counterparts. Probable errors in seed source or genotype tracking were also identified in approximately 5% of the accessions.

scholarly journals Genetic diversity and population structure of Amorphophallus albus, a plant species with extremely small populations (PSESP) endemic to dry-hot valley of Jinsha River

2019 ◽  
Author(s):  
Rong Tang ◽  
Erxi Liu ◽  
Yazhou Zhang ◽  
Johann Schinnerl ◽  
Weibang Sun ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Plant Species ◽  
Ex Situ ◽  
Small Populations ◽  
Wild Populations ◽  
Jinsha River ◽  
High Genetic Diversity ◽  
Cultivated Populations

Abstract Background Amorphophallus albus P. Y. Liu & J. F. Chen (Araceae) is a plant species with extremely small populations (PSESP) and important economic crop endemic to dry-hot valleys along the Jinsha River. In order to gain information for sustaining the development and conservation of A. albus , we studied the genetic diversity and population structure of this species using microsatellite markers (SSR). In this study, we analyzed 364 individuals belonging to 24 populations, including four wild populations and three ex-situ cultivated populations, collected in the provinces Yunnan, Sichuan and Hubei.Results The population genetic analyses indicated that A. albus possesses moderate genetic diversity with the percentage of polymorphic loci ( PPL ) from 69.23% to 100%, an expected heterozygosity ( He ) of 0.504 and an average Shannon's Information Index ( I ) 0.912. Analysis of molecular variance (AMOVA) indicated that most of the variance (71%) resided within populations and the estimated gene flow ( Nm ) was 0.61. The results of UPGMA cluster tree, STRUCTURE analyses together with the Mantel test (R 2 = 0.352, P < 0.01) indicated that geographically closely located populations are cluster together with some exceptions.Conclusions Our results showed that A. albus still possesses moderate genetic variation in most of the studied populations, and for now, most cultivated populations were naturally distributed but still some reintroduction exists. For sustaining the present genetic variation, some protections measures are necessary for the wild populations and also for the cultivated ones with high genetic diversity.

scholarly journals Genetic diversity and structure of one of the most endangered freshwater fish species in Mexico: Tlaloc hildebrandi (Miller, 1950) and recognition of its evolutionarily significant units

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11952
Author(s):  
Rosa G. Beltrán-López ◽  
Alfonso A. González-Díaz ◽  
Miriam Soria-Barreto ◽  
Marco Antonio Garduño-Sánchez ◽  
Carmela Xochitla-Castrejón ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Freshwater Fish ◽  
Fish Species ◽  
Ex Situ ◽  
Freshwater Species ◽  
Freshwater Fish Species ◽  
Evolutionarily Significant Units ◽  
Las Casas ◽  
Genetic Diversity And Structure ◽  
Genetic Clusters

The endangered Chiapas killifish Tlaloc hildebrandi is an endemic freshwater species that lives in four subbasins of the Grijalva and Usumacinta basins, and one of the most geographically restricted species of the Produndulidae family. The species was originally described as endemic to springs in the high limestone plateau in San Cristóbal de Las Casas in the Río Amarillo subbasin (upper Grijalva basin). However, it was recently recorded in the Jataté and Tzaconejá subbasins in the upper Usumacinta basin, thereby expanding its known distribution range. The discovery of these populations is relevant not only for the conservation of the species but also for a better understanding of its evolutionary history. Currently, the scarce populations of T. hildebrandi, found in only a few localities in the Grijalva and Usumacinta basins, are fragmented and living under unfavorable conditions. Here, we analyzed three mitochondrial (mt-atp8&6 and mt-nd2) and one nuclear (nuc-s7) marker in order to assess the genetic diversity and population structure of T. hildebrandi. We found that, in comparison with other endangered freshwater fish species from Mexico, T. hildebrandi showed a lower level of genetic diversity (mt-nd2: h = 0.469, π = 0.0009; mt-atp8&6: h = 0.398, π = 0.001; and nuc-S7: h = 0.433, π = 0.001). Moreover, the analyzed populations exhibited a strong genetic structure in accordance with their geographic distribution, and can be placed into three genetic clusters: (1) Amarillo plus Chenhaló in the upper Grijalva basin, (2) Jataté, and (3) Tzaconejá, both in the upper Usumacinta basin. On the basis of our results, we propose the recognition of at least three evolutionarily significant units (ESUs) for the species and the urgent implementation of ex situ and in situ conservation and management efforts that consider the genetic background of the species.

scholarly journals Genetic diversity and population structure of Amorphophallus albus, a plant species with extremely small populations (PSESP) endemic to dry-hot valley of Jinsha River

BMC Genetics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Rong Tang ◽  
Erxi Liu ◽  
Yazhou Zhang ◽  
Johann Schinnerl ◽  
Weibang Sun ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Plant Species ◽  
Ex Situ ◽  
Small Populations ◽  
Wild Populations ◽  
Jinsha River ◽  
High Genetic Diversity ◽  
Cultivated Populations

Abstract Background Amorphophallus albus P. Y. Liu & J. F. Chen (Araceae) is a plant species with extremely small populations (PSESP) and an important economic crop endemic to dry-hot valleys along the Jinsha River. In order to gain information for sustaining the development and conservation of A. albus, we studied the genetic diversity and population structure of this species using microsatellite markers (SSR). In this study, we analysed 364 individuals belonging to 24 populations, including four wild populations and three ex-situ cultivated populations, collected in the provinces Yunnan, Sichuan and Hubei. Results The population genetic analyses indicated that A. albus possesses moderate genetic diversity with the percentage of polymorphic loci (PPL) from 69.23 to 100%, an expected heterozygosity (He) of 0.504 and an average Shannon’s Information Index (I) 0.912. Analysis of molecular variance (AMOVA) indicated that most of the variance (71%) resided within populations and the estimated gene flow (Nm) was 0.61. The results of UPGMA cluster tree, STRUCTURE analyses together with the Mantel test (R2 = 0.352, P < 0.01) indicated that geographically closely located populations are clustered together with some exceptions. Conclusions Our results showed that A. albus still possesses moderate genetic variation in most of the studied populations, and for now, most cultivated populations were naturally distributed but still some reintroduction exists. For sustaining the present genetic variation, some protections measures are necessary for the wild populations and also for the cultivated ones with high genetic diversity.

scholarly journals Genetic diversity of native and cultivated Ugandan Robusta coffee (Coffea canephora Pierre ex A. Froehner): Climate influences, breeding potential and diversity conservation

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0245965
Author(s):  
Catherine Kiwuka ◽  
Eva Goudsmit ◽  
Rémi Tournebize ◽  
Sinara Oliveira de Aquino ◽  
Jacob C. Douma ◽  
...  
Keyword(s):  
Climate Change ◽  
Genetic Diversity ◽  
Allelic Variation ◽  
Coffea Canephora ◽  
Ex Situ ◽  
Negative Effects ◽  
Robusta Coffee ◽  
Genetic Diversity And Structure ◽  
Adaptive Diversity ◽  
Southern Central

Wild genetic resources and their ability to adapt to environmental change are critically important in light of the projected climate change, while constituting the foundation of agricultural sustainability. To address the expected negative effects of climate change on Robusta coffee trees (Coffea canephora), collecting missions were conducted to explore its current native distribution in Uganda over a broad climatic range. Wild material from seven forests could thus be collected. We used 19 microsatellite (SSR) markers to assess genetic diversity and structure of this material as well as material from two ex-situ collections and a feral population. The Ugandan C. canephora diversity was then positioned relative to the species’ global diversity structure. Twenty-two climatic variables were used to explore variations in climatic zones across the sampled forests. Overall, Uganda’s native C. canephora diversity differs from other known genetic groups of this species. In northwestern (NW) Uganda, four distinct genetic clusters were distinguished being from Zoka, Budongo, Itwara and Kibale forests A large southern-central (SC) cluster included Malabigambo, Mabira, and Kalangala forest accessions, as well as feral and cultivated accessions, suggesting similarity in genetic origin and strong gene flow between wild and cultivated compartments. We also confirmed the introduction of Congolese varieties into the SC region where most Robusta coffee production takes place. Identified populations occurred in divergent environmental conditions and 12 environmental variables significantly explained 16.3% of the total allelic variation across populations. The substantial genetic variation within and between Ugandan populations with different climatic envelopes might contain adaptive diversity to cope with climate change. The accessions that we collected have substantially enriched the diversity hosted in the Ugandan collections and thus contribute to ex situ conservation of this vital genetic resource. However, there is an urgent need to develop strategies to enhance complementary in-situ conservation of Coffea canephora in native forests in northwestern Uganda.

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