scholarly journals Dioecy Is Associated with High Genetic Diversity and Adaptation Rates in the Plant Genus Silene

2020 ◽  
Author(s):  
Aline Muyle ◽  
Hélène Martin ◽  
Niklaus Zemp ◽  
Maéva Mollion ◽  
Sophie Gallina ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Genomics ◽  
Extinction Risk ◽  
Population Level ◽  
High Genetic Diversity ◽  
Geographic Ranges ◽  
Sexual Systems ◽  
Dead End ◽  
The Dead ◽  
Genus Silene

Abstract About 15,000 angiosperm species (∼6%) have separate sexes, a phenomenon known as dioecy. Why dioecious taxa are so rare is still an open question. Early work reported lower species richness in dioecious compared with nondioecious sister clades, raising the hypothesis that dioecy may be an evolutionary dead-end. This hypothesis has been recently challenged by macroevolutionary analyses that detected no or even positive effect of dioecy on diversification. However, the possible genetic consequences of dioecy at the population level, which could drive the long-term fate of dioecious lineages, have not been tested so far. Here, we used a population genomics approach in the Silene genus to look for possible effects of dioecy, especially for potential evidence of evolutionary handicaps of dioecy underlying the dead-end hypothesis. We collected individual-based RNA-seq data from several populations in 13 closely related species with different sexual systems: seven dioecious, three hermaphroditic, and three gynodioecious species. We show that dioecy is associated with increased genetic diversity, as well as higher selection efficacy both against deleterious mutations and for beneficial mutations. The results hold after controlling for phylogenetic inertia, differences in species census population sizes and geographic ranges. We conclude that dioecious Silene species neither show signs of increased mutational load nor genetic evidence for extinction risk. We discuss these observations in the light of the possible demographic differences between dioecious and self-compatible hermaphroditic species and how this could be related to alternatives to the dead-end hypothesis to explain the rarity of dioecy.

scholarly journals Range reduction of the Oblong Rocksnail, Leptoxis compacta, shapes riverscape genetic patterns

2020 ◽  
Author(s):  
Aaliyah D. Wright ◽  
Nicole L. Garrison ◽  
Ashantye’ S. Williams ◽  
Paul D. Johnson ◽  
Nathan V. Whelan
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Human Impacts ◽  
Isolation By Distance ◽  
Extinction Risk ◽  
River System ◽  
High Genetic Diversity ◽  
Range Contraction ◽  
Genetic Patterns ◽  
Cahaba River

AbstractMany freshwater gastropod species face extinction, including 79% of species in the family Pleuroceridae. The Oblong Rocksnail, Leptoxis compacta, is a narrow range endemic pleurocerid from the Cahaba River basin in central Alabama that has seen rapid range contraction in the last 100 years. Such a decline is expected to negatively affect genetic diversity in the species. However, precise patterns of genetic variation and gene flow across the restricted range of L. compacta are unknown. This lack of information limits our understanding of human impacts on the Cahaba River system and Pleuroceridae. Here, we show that L. compacta has likely seen a species-wide decline in genetic diversity, but remaining populations have relatively high genetic diversity. We also report a contemporary range extension compared to the last published survey. Leptoxis compacta does not display an isolation by distance pattern, contrasting patterns seen in many riverine taxa. Our findings also indicate that historical range contraction has resulted in the absence of common genetic patterns seen in many riverine taxa like isolation by distance as the small distribution of L. compacta allows for relatively unrestricted gene flow across its remaining range despite limited dispersal abilities. Two collection sites had higher genetic diversity than others, and broodstock sites for future captive propagation and reintroduction efforts should utilize sites identified here as having the highest genetic diversity. Broadly, our results support the hypothesis that range contraction will result in the reduction of species-wide genetic diversity, and common riverscape genetic patterns cannot be assumed to be present in species facing extinction risk.

scholarly journals Range reduction of Oblong Rocksnail, Leptoxis compacta, shapes riverscape genetic patterns

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9789
Author(s):  
Aaliyah D. Wright ◽  
Nicole L. Garrison ◽  
Ashantye’ S. Williams ◽  
Paul D. Johnson ◽  
Nathan V. Whelan
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Human Impacts ◽  
Isolation By Distance ◽  
Extinction Risk ◽  
River System ◽  
High Genetic Diversity ◽  
Range Contraction ◽  
Genetic Patterns ◽  
Cahaba River

Many freshwater gastropod species face extinction, including 79% of species in the family Pleuroceridae. The Oblong Rocksnail, Leptoxis compacta, is a narrow range endemic pleurocerid from the Cahaba River basin in central Alabama that has seen rapid range contraction in the last 100 years. Such a decline is expected to negatively affect genetic diversity in the species. However, precise patterns of genetic variation and gene flow across the restricted range of L. compacta are unknown. This lack of information limits our understanding of human impacts on the Cahaba River system and Pleuroceridae. Here, we show that L. compacta has likely seen a species-wide decline in genetic diversity, but remaining populations have relatively high genetic diversity. We also report a contemporary range extension compared to the last published survey. Our findings indicate that historical range contraction has resulted in the absence of common genetic patterns seen in many riverine taxa like isolation by distance as the small distribution of L. compacta allows for relatively unrestricted gene flow across its remaining range despite limited dispersal abilities. Two collection sites had higher genetic diversity than others, and broodstock sites for future captive propagation and reintroduction efforts should utilize sites identified here as having the highest genetic diversity. Broadly, our results support the hypothesis that range contraction will result in the reduction of species-wide genetic diversity, and common riverscape genetic patterns cannot be assumed to be present in species facing extinction risk.

scholarly journals Pollen-mediated gene flow ensures connectivity among spatially discrete sub-populations of Phalaenopsis pulcherrima, a tropical food-deceptive orchid

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Zhe Zhang ◽  
Stephan W. Gale ◽  
Ji-Hong Li ◽  
Gunter A. Fischer ◽  
Ming-Xun Ren ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Polynomial Regression ◽  
Genetic Erosion ◽  
Population Level ◽  
Hainan Island ◽  
Paternity Analysis ◽  
Genetic Structuring ◽  
Long Distance ◽  
High Genetic Diversity

Abstract Background Gene flow in plants via pollen and seeds is asymmetrical at different geographic scales. Orchid seeds are adapted to long-distance wind dispersal but pollinium transfer is often influenced by pollinator behavior. We combined field studies with an analysis of genetic diversity among 155 physically mapped adults and 1105 F1 seedlings to evaluate the relative contribution of pollen and seed dispersal to overall gene flow among three sub-populations of the food-deceptive orchid Phalaenopsis pulcherrima on Hainan Island, China. Results Phalaenopsis pulcherrima is self-sterile and predominantly outcrossing, resulting in high population-level genetic diversity, but plants are clumped and exhibit fine-scale genetic structuring. Even so, we detected low differentiation among sub-populations, with polynomial regression analysis suggesting gene flow via seed to be more restricted than that via pollen. Paternity analysis confirmed capsules of P. pulcherrima to each be sired by a single pollen donor, probably in part facilitated by post-pollination stigma obfuscation, with a mean pollen flow distance of 272.7 m. Despite limited sampling, we detected no loss of genetic diversity from one generation to the next. Conclusions Outcrossing mediated by deceptive pollination and self-sterility promote high genetic diversity in P. pulcherrima. Long-range pollinia transfer ensures connectivity among sub-populations, offsetting the risk of genetic erosion at local scales.

scholarly journals Genetic characterization of Cycas panzhihuaensis (Cycadaceae): crisis lurks behind a seemingly bright prospect

2018 ◽  
Author(s):  
Siyue Xiao ◽  
Yunheng Ji ◽  
Jian Liu ◽  
Xun Gong
Keyword(s):  
Genetic Diversity ◽  
Genetic Characterization ◽  
Extinction Risk ◽  
Demographic History ◽  
Single Copy ◽  
Jinsha River ◽  
High Genetic Diversity ◽  
Natural Reserve ◽  
Endangered Status

Background Cycas panzhihuaensis L. Zhou & S. Y. Yang (Cycadaceae) is an endangered gymnosperm species endemic in the dry-hot valley of Jinsha River basin from southwest China. Although the wild C. panzhihuaensis population from Panzhihua Cycad Natural Reserve is well protected, other known populations that fall outside the natural reserve may preserve specific genetic resources while face with larger extinction risk because of lacking essential monitoring. Methods In this study, we analyzed the genetic diversity, phylogeographical structure and demographic history of C. panzhihuaensis from seven known locations so far by sequencing three chloroplastic DNA regions (psbA-trnH, psbM-trnD, and trnS-trnG), four single-copy nuclear genes (PHYP, AC5, HSP70, and AAT) from 61 individuals, and eleven microsatellite loci (SSR) from 102 individuals. Results and Discussion We found relative high genetic diversity within populations and high genetic differentiation among the populations of C. panzhihuaensis, which is similar with the other Asian inland cycads. Despite no significant phylogeographical structure was detected, small and unprotected populations possess higher genetic diversity and more unique haplotypes, which deserve due attention. Results of demographic dynamics suggest that human activity is the key factor that leads C. panzhihuaensis to endangered status. Basing on the genetic characterization of C. panzhihuaensis, we proposed several practical guidelines for the conservation of this species, especially for its small populations.

Allozyme variation and population structure of Carex humilis var. nana (Cyperaceae) in Korea

2001 ◽  
Vol 79 (4) ◽  
pp. 457-463 ◽  
Author(s):  
Man Kyu Huh
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
North American ◽  
Population Level ◽  
Allozyme Variation ◽  
Population Divergence ◽  
Geographic Ranges ◽  
The Mean ◽  
Allozyme Loci

Genetic diversity and population structure of 22 Carex humilis var. nana Ohwi (Cyperaceae) populations in Korea were determined using genetic variation at 23 allozyme loci. This is a long-lived herbaceous species with a widespread distribution in eastern Asia. The 12 enzymes revealed 23 putative loci, of which 11 were polymorphic (47.8%). Genetic diversity at the varietal level and at the population level was 0.131 and 0.118, respectively. Total genetic diversity (HT = 0.274) and within population genetic diversity (HS = 0.256) were high, whereas the extent of the population divergence was relatively low (GST = 0.068). An indirect estimate of the number of migrants per generation (Nm = 3.42) indicated that gene flow was high among Korean populations. Wide geographic ranges, perennial herbaceous nature, and the persistence of multiple generations are associated with the high level of genetic variation. A distinct difference between Asian and North American Carex is shown in the proportion of genetic variation (GST) (p < 0.001). The mean GST of Asian Carex was estimated as 0.056; thus, only 5.6% of genetic variability was distributed among populations, whereas the mean GST of North American Carex was estimated as 19.5% (3.5 times higher). It is probable that the geographical distance between population pairs and presence or absence of glacial history may play roles in the substantial difference between both groups.Key words: Carex humilis var. nana, genetic diversity, population structure.

scholarly journals Genetic diversity of Picea likiangensis natural population at different altitudes revealed by EST-SSR markers

2014 ◽  
Vol 63 (1-6) ◽  
pp. 191-197 ◽  
Author(s):  
X. Cheng ◽  
Y. Jiang ◽  
T. Tang ◽  
G. Fan ◽  
Xiaoxia Huang
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Ssr Markers ◽  
Gene Diversity ◽  
Population Level ◽  
High Elevation ◽  
Species Level ◽  
High Genetic Diversity ◽  
Elevation Gradients ◽  
Different Altitudes

AbstractAltitude is thought to have greatly influenced current species distribution and their genetic diversity. However, it is unclear how different altitudes have affected the distribution and genetic diversity of Picea likiangensis, a dominant forestry species in the Qinghai-Tibetan Plateau region (QTP). In this study, we investigated the genetic diversity of Picea likiangensis populations which distributed in different altitudes of QTP using EST-SSR markers. The results suggested that this species has high genetic diversity at species level, with 100% of loci being polymorphic and an average Nei’s gene diversity (He) of 0.7186 and Shannon’s information index (I) of 1.5415. While the genetic diversity of Picea likiangensis at population level was lower than that at species level, with He and I being 0.6562 and 1.3742, respectively. The variation in genetic diversity of all four studied populations indicated a low-high-low pattern along the elevation gradients. The mid-elevation population (3050 m) was more genetically diverse than both low-elevation (2900 m) and high-elevation populations (3200 m and 3350 m). Nei’s genetic diversity (Fst= 0.0809) and AMOVA analysis (Phist = 0.1135) indicated that a low level of genetic differentiation among populations. Gene flow among populations was 2.8384, suggesting that high gene flow is a main factor leading to high levels of the genetic diversity among populations.

scholarly journals The population genomics of transposable element activation in the highly repressive genome of an agricultural pathogen

2020 ◽  
Author(s):  
Danilo Pereira ◽  
Ursula Oggenfuss ◽  
Bruce A. McDonald ◽  
Daniel Croll
Keyword(s):  
Genetic Diversity ◽  
Transposable Elements ◽  
Evolutionary Dynamics ◽  
Population Genomics ◽  
Sequence Data ◽  
Demographic History ◽  
Purifying Selection ◽  
Population Level ◽  
Wide Range ◽  
Genome Analyses

AbstractThe activity of transposable elements (TEs) can be an important driver of genetic diversity with TE-mediated mutations having a wide range of fitness consequences. To avoid deleterious effects of TE activity, some fungi evolved highly sophisticated genomic defences to reduce TE proliferation across the genome. Repeat-induced point (RIP) mutations is a fungal-specific TE defence mechanism efficiently targeting duplicated sequences. The rapid accumulation of RIP mutations is expected to deactivate TEs over the course of a few generations. The evolutionary dynamics of TEs at the population level in a species with highly repressive genome defences is poorly understood. Here, we analyze 366 whole-genome sequences of Parastagonospora nodorum, a fungal pathogen of wheat with efficient RIP. A global population genomics analysis revealed high levels of genetic diversity and signs of frequent sexual recombination. Contrary to expectations for a species with RIP, we identified recent TE activity in multiple populations. The TE composition and copy numbers showed little divergence among global populations regardless of the demographic history. Miniature inverted-repeat transposable elements (MITEs) and terminal repeat retrotransposons in miniature (TRIMs) were largely underlying recent intra-species TE expansions. We inferred RIP footprints in individual TE families and found that recently active, high-copy TEs have possibly evaded genomic defences. We find no evidence that recent positive selection acted on TE-mediated mutations rather that purifying selection maintained new TE insertions at low insertion frequencies in populations. Our findings highlight the complex evolutionary equilibria established by the joint action of TE activity, selection and genomic repression.Data SummaryAll Illumina sequence data is available from the NCBI SRA BioProject numbers PRJNA606320, PRJNA398070 and PRJNA476481 (https://www.ncbi.nlm.nih.gov/bioproject). The Methods and Supplementary Figures S1-S11 and Supplementary Tables S1-S4 provide all information on strain locations and outcomes of genome analyses.

scholarly journals Genetic characterization of Cycas panzhihuaensis (Cycadaceae): crisis lurks behind a seemingly bright prospect

2018 ◽  
Author(s):  
Siyue Xiao ◽  
Yunheng Ji ◽  
Jian Liu ◽  
Xun Gong
Keyword(s):  
Genetic Diversity ◽  
Genetic Characterization ◽  
Extinction Risk ◽  
Demographic History ◽  
Single Copy ◽  
Jinsha River ◽  
High Genetic Diversity ◽  
Natural Reserve ◽  
Endangered Status

Background Cycas panzhihuaensis L. Zhou & S. Y. Yang (Cycadaceae) is an endangered gymnosperm species endemic in the dry-hot valley of Jinsha River basin from southwest China. Although the wild C. panzhihuaensis population from Panzhihua Cycad Natural Reserve is well protected, other known populations that fall outside the natural reserve may preserve specific genetic resources while face with larger extinction risk because of lacking essential monitoring. Methods In this study, we analyzed the genetic diversity, phylogeographical structure and demographic history of C. panzhihuaensis from seven known locations so far by sequencing three chloroplastic DNA regions (psbA-trnH, psbM-trnD, and trnS-trnG), four single-copy nuclear genes (PHYP, AC5, HSP70, and AAT) from 61 individuals, and eleven microsatellite loci (SSR) from 102 individuals. Results and Discussion We found relative high genetic diversity within populations and high genetic differentiation among the populations of C. panzhihuaensis, which is similar with the other Asian inland cycads. Despite no significant phylogeographical structure was detected, small and unprotected populations possess higher genetic diversity and more unique haplotypes, which deserve due attention. Results of demographic dynamics suggest that human activity is the key factor that leads C. panzhihuaensis to endangered status. Basing on the genetic characterization of C. panzhihuaensis, we proposed several practical guidelines for the conservation of this species, especially for its small populations.

scholarly journals Genetic diversity and relationships among populations of Camellia japonica, an endangered species in China

2021 ◽  
Author(s):  
Kai Yang ◽  
Yingkun Sun ◽  
Wei Li ◽  
Xiao Guo ◽  
Qinghua Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Natural Population ◽  
Rank Order ◽  
Natural Populations ◽  
Population Level ◽  
Botanical Garden ◽  
High Genetic Diversity ◽  
Camellia Japonica ◽  
Information Index ◽  
Cultivated Populations

Camellia japonica, an evergreen ornamental plant in the Theaceae, its natural range is now shrinking. This is evidenced by the fact that the species is on the verge of extinction in Laoshan Mountain (Qingdao), the northernmost area of China for natural population of C. japonica. Little is known about the genetic diversity and relationships among cultivated and wild C. japonica populations. 180 samples of six C. japonica populations were tested for genetic diversity with SSR markers; these included three cultivated populations, two natural populations in Qingdao, and one natural population in Daqingshan. The average values of polymorphism information content (PIC), expected heterozygosity (He), and Shannon’s information index (I) were 0.5849, 0.6385 and 1.3170, respectively, indicating that C. japonica has a high genetic diversity. The genetic diversities of the six populations in rank order were as follows: Daqingshan > Zhongshan Park > Changmenyan Island > Daguan Island > Botanical Garden > May Fourth Square. The geographical isolation of the islands had no significant influence on the genetic diversity of C. japonica. Clustering results showed that the six C. japonica populations could be grouped into three categories, and most populations were clustered according to their geographical origin and genetic background. These results also reconfirmed that the C. japonica (Naidong) population in Qingdao originated from Changmenyan Island. Genetic variation was highest within populations (89%), indicating that C. japonica can be protected at the population level. These findings will prove useful for the genetic analysis, protection, and horticultural use of C. japonica.

scholarly journals Diversity and Genetic Structure of Dioon holmgrenii (Cycadales: Zamiaceae) in the Mexican Pacific Coast Biogeographic Province: Implications for Conservation

Plants ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 2250
Author(s):  
Mario Valerio Velasco-García ◽  
Carlos Ramírez-Herrera ◽  
Javier López-Upton ◽  
Juan Ignacio Valdez-Hernández ◽  
Higinio López-Sánchez ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Pacific Coast ◽  
Population Level ◽  
Fixation Index ◽  
High Genetic Diversity ◽  
Mexican Pacific ◽  
Biogeographic Province ◽  
Multiple Factors ◽  
F Statistics

Dioon holmgrenii De Luca, Sabato et Vázq.Torres is an endangered species; it is endemic and its distribution is restricted to the biogeographic province of the Mexican Pacific Coast. The aim of this work was to determine the diversity and genetic structure of nine populations. The genetic diversity parameters and Wright’s F statistics were determined with six microsatellite loci. The genetic structure was determined by using the Structure software and by a discriminant analysis. The genetic diversity of the populations was high. The proportion of polymorphic loci was 0.89, the observed heterogeneity was higher (Ho = 0.62 to 0.98) than expected (He = 0.48 to 0.78), and the fixation index was negative (IF = −0.091 to −0.601). Heterozygous deficiency (FIT = 0.071) was found at the species level and heterozygotes excess (FIS = −0.287) at the population level. The genetic differentiation between populations was high (FST = 0.287), with the number of migrants less than one. Three groups of populations were differentiated, and the variation within populations, between populations, and between groups was: 65.5, 26.3, and 8.2%, respectively. Multiple factors explain the high genetic diversity, while the genetic structure is due to geographic barriers. Community reserves are urgent in at least one most diverse population of each group.

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