Proportional sampling strategy often captures more genetic diversity when population sizes vary

Rosenberger, Kaylee; Schumacher, Emily; Brown, Alissa J.; Hoban, Sean

doi:10.1016/j.biocon.2021.109261

Cited by 10 publications

(5 citation statements)

References 89 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This may be attributed to the varying amounts of weedy rice in each region. The results demonstrate that the selection of a high number of samples from diverse populations throughout a particular area provides an accurate estimate of genetic diversity within the weedy rice population (Hobas et al 2013; Nazareno et al 2017; Rosenberger et al 2021).…”

Section: Resultsmentioning

confidence: 92%

“…Nonetheless, the limited geographic coverage in previous studies makes comparison of population structures difficult, as sample sizes per se are critical in evolutionary studies (Hobas et al 2013; Nazareno et al 2017). The high number of samples and diverse populations selected in certain areas represent accurate estimates of genetic diversity within weedy rice populations (Rosenberger et al 2021). The aim of this study, therefore, is to determine the genetic diversity and population structure of weedy rice throughout northeast Thailand.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

The genetic diversity and population structure of weedy rice in northeast Thailand accessed by SSR markers

Ponsen,

Loasatit,

Monkham

et al. 2023

Weed Sci

View full text Add to dashboard Cite

Thailand’s northeast (NE) region is an area of high-quality cultivated rice (Oryza sativa L.) production. However, an outbreak of weedy rice has recently spread throughout the region. Weedy rice is phenotypically and morphologically similar to cultivated rice, making identification difficult. The prospective management of weedy rice in the future will involve the study of its genetic diversity and population structure in this region. This study assesses the genetic diversity and population structure of 380 weedy rice samples in the northeast of Thailand through simple sequence repeat (SSR) markers. Thirty-one SSR markers generated 213 alleles with an average of 6.87 per locus and an overall gene diversity of 0.723. Based on its geographical origin, weedy rice in the Southern NE showed greater gene diversity than that in the Central NE and Northern NE areas. The out-crossing rate in all regions was relatively high, with the highest being in the Southern NE at 9.769%. According to genetic distance analysis, the clustering of weedy rice samples in Northeast Thailand was not associated with the geographical region. Neighbor-joining and principal coordinate analysis revealed that the 380 weedy rice samples fell into two major clusters. Cluster I contained three weedy rice samples and four wild. In Cluster II, 377 weedy rice samples were closely related to the four cultivated rice cultivars as well as brownbeard rice (Oryza rufipogon Griffiths) wild species. The results suggest that weedy rice in Northeast Thailand may have originated as a cross between cultivated and wild rice, as seen in the closely related species, O. rufipogon. Overall, the findings of this study demonstrate the high genetic diversity of weedy rice in this region. Notably, some samples adapted, performing more like cultivated rice, which may be problematic for the future production of high-quality rice in this region. The prevention of weedy rice should, therefore, be given greater consideration in future studies.

show abstract

Section: Resultsmentioning

confidence: 92%

Section: Introductionmentioning

confidence: 99%

The genetic diversity and population structure of weedy rice in northeast Thailand accessed by SSR markers

Ponsen,

Loasatit,

Monkham

et al. 2023

Weed Sci

View full text Add to dashboard Cite

show abstract

“…In comparison, a population genetic study on the eastern North American A. ludovicana , recovered higher genetic variation ( H O = 0.36–0.54) and similar inbreeding coefficients ( F IS = 0.01–0.13) (Figure 2 , Table 1 , Smallwood et al., 2018 ). The differences in genetic diversity could be explained by data collection method (ddRADseq vs. microsatellites) (Hodel et al., 2017 ; Sunde et al., 2020 ), sampling collection bias (Hale et al., 2012 ; Rosenberger et al., 2021 ), population sizes, or a result of being more distantly related to the western Amsonia species. By contrast, the inbreeding coefficients across populations of all four taxa ( A. ludovicana and A. tharpii , A. fugatei , and A. longiflora ) were low and consistent with a self‐incompatible breeding system, which is known in the Apocynaceae (Gibbs, 2014 ; Lipow & Wyatt, 1999 ; Shuttleworth & Johnson, 2006 ).…”

Section: Discussionmentioning

confidence: 99%

Conservation genomics assessment of Tharp's bluestar (Amsonia tharpii) with comparisons to widespread (A. longilora) and narrowly endemic (A. fugatei) congeners

Cohen,

Fant,

Skogen

2024

Evolutionary Applications

View full text Add to dashboard Cite

Land‐use change and habitat fragmentation are threats to biodiversity. The decrease in available habitat, increase in isolation, and mating within populations can lead to elevated inbreeding, lower genetic diversity, and poor fitness. Here we investigate the genetics of two rare and threatened plant species, Amsonia tharpii and A. fugatei, and we compare them to a widespread congener A. longiflora. We also report the first phylogenetic study of the genus Amsonia (Apocynaceae), including 10 of the 17 taxa and multiple sampling locations, to understand species relationships. We used a double digest restriction‐site associated DNA sequencing (ddRADseq) approach to investigate the genetic diversity and gene flow of each species and to create a maximum likelihood phylogeny. The ddRADseq data was mapped to a reference genome to separate out the chloroplast and nuclear markers for population genetic analysis. Our results show that genetic diversity and inbreeding were low across all three species. The chloroplast and nuclear dataset in A. tharpii were highly structured, whereas they showed no structure for A. fugatei, while A. longiflora lacked structure for nuclear data but not chloroplast. Phylogenetic results revealed that A. tharpii is distinct and sister to A. fugatei, and together they are distantly related to A. longiflora. Our results demonstrated that evolutionary history and contemporary ecological processes largely influences genetic diversity within Amsonia. Interestingly, we show that in A. tharpii there was significant structure despite being pollinated by large, bodied hawkmoths that are known to be able to carry pollen long distances, suggesting that other factors are contributing to the structure observed among A. tharpii populations. Conservation efforts should focus on protecting all of the A. tharpii populations, as they contain unique genetic diversity, and a protection plan for A. fugatei needs to be established due to its limited distribution.

show abstract

“…When collecting, producing, and using seeds or plugs for restoration, care must be taken to capture the genetic diversity present at a source site while avoiding steps that may narrow diversity reintroduced (Basey et al, 2015). Large populations, especially where plants are distributed over a wide range of microhabitats, should harbor higher genetic diversity, while small populations (especially those that are fragmented) are more likely to have lower diversity as well as greater risk of being inbred (McGlaughlin et al, 2002;Rosenberger et al, 2021; question G1, Table 1). For longer-term persistence, genetic diversity helps populations survive local disturbances and adapt to future climate changes (Lau et al, 2019).…”

Section: Diversitymentioning

confidence: 99%

Why are some plant species missing from restorations? A diagnostic tool for temperate grassland ecosystems

Vitis

Havens

Barak

et al. 2022

Front. Conserv. Sci.

View full text Add to dashboard Cite

The U.N. Decade on Ecosystem Restoration aims to accelerate actions to prevent, halt, and reverse the degradation of ecosystems, and re-establish ecosystem functioning and species diversity. The practice of ecological restoration has made great progress in recent decades, as has recognition of the importance of species diversity to maintaining the long-term stability and functioning of restored ecosystems. Restorations may also focus on specific species to fulfill needed functions, such as supporting dependent wildlife or mitigating extinction risk. Yet even in the most carefully planned and managed restoration, target species may fail to germinate, establish, or persist. To support the successful reintroduction of ecologically and culturally important plant species with an emphasis on temperate grasslands, we developed a tool to diagnose common causes of missing species, focusing on four major categories of filters, or factors: genetic, biotic, abiotic, and planning & land management. Through a review of the scientific literature, we propose a series of diagnostic tests to identify potential causes of failure to restore target species, and treatments that could improve future outcomes. This practical diagnostic tool is meant to strengthen collaboration between restoration practitioners and researchers on diagnosing and treating causes of missing species in order to effectively restore them.

show abstract

Proportional sampling strategy often captures more genetic diversity when population sizes vary

Cited by 10 publications

References 89 publications

The genetic diversity and population structure of weedy rice in northeast Thailand accessed by SSR markers

The genetic diversity and population structure of weedy rice in northeast Thailand accessed by SSR markers

Conservation genomics assessment of Tharp's bluestar (Amsonia tharpii) with comparisons to widespread (A. longilora) and narrowly endemic (A. fugatei) congeners

Why are some plant species missing from restorations? A diagnostic tool for temperate grassland ecosystems

Contact Info

Product

Resources

About