Ploidy Levels and Genome Sizes of Berberis L. and Mahonia Nutt. Species, Hybrids, and Cultivars

Rounsaville, Todd J.; Ranney, Thomas G.

doi:10.21273/hortsci.45.7.1029

Cited by 40 publications

(37 citation statements)

References 21 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Based on data from related species, the sampled Berberis species have an expected genome size between 0.50 and 1.83 Gbp (Rounsaville & Ranney, 2010), while the range is from 9 to 10 Gbp for the Juniperus species (Zonneveld, 2012). For both taxa, ddRAD libraries were prepared using modified versions of protocols by Parchman et al (2012) and Peterson, Weber, Kay, Fisher, and Hoekstra (2012).…”

Section: Molecular Methodsmentioning

confidence: 99%

Long‐term in situ persistence of biodiversity in tropical sky islands revealed by landscape genomics

et al. 2018

View full text Add to dashboard Cite

Tropical mountains are areas of high species richness and endemism. Two historical phenomena may have contributed to this: (i) fragmentation and isolation of habitats may have promoted the genetic differentiation of populations and increased the possibility of allopatric divergence and speciation and (ii) the mountain areas may have allowed long-term population persistence during global climate fluctuations. These two phenomena have been studied using either species occurrence data or estimating species divergence times. However, only few studies have used intraspecific genetic data to analyse the mechanisms by which endemism may emerge at the microevolutionary scale. Here, we use landscape analysis of genomic SNP data sampled from two high-elevation plant species from an archipelago of tropical sky islands (the Trans-Mexican Volcanic Belt) to test for population genetic differentiation, synchronous demographic changes and habitat persistence. We show that genetic differentiation can be explained by the degree of glacial habitat connectivity among mountains and that mountains have facilitated the persistence of populations throughout glacial/interglacial cycles. Our results support the ongoing role of tropical mountains as cradles for biodiversity by uncovering cryptic differentiation and limits to gene flow.

show abstract

Section: Molecular Methodsmentioning

confidence: 99%

Long‐term in situ persistence of biodiversity in tropical sky islands revealed by landscape genomics

et al. 2018

View full text Add to dashboard Cite

show abstract

“…The focal species is Berberis alpina (Zamudio 2009), a diploid plant with a probable genome size of between 0.5 and 1.83 Gbp, based on values of related species (Rounsaville & Ranney 2010). Berberis alpina inhabits the Transmexican Volcanic Belt (TMVB), a biodiversity hot spot for temperate forest plant species (Myers et al 2000) where the species is restricted to a few mountain tops ( Fig.…”

Section: Study System and Samplingmentioning

confidence: 99%

Restriction site‐associated DNA sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference

Mastretta‐Yanes

Arrigo

Álvarez

et al. 2014

Molecular Ecology Resources

362

435

View full text Add to dashboard Cite

Restriction site-associated DNA sequencing (RADseq) provides researchers with the ability to record genetic polymorphism across thousands of loci for nonmodel organisms, potentially revolutionizing the field of molecular ecology. However, as with other genotyping methods, RADseq is prone to a number of sources of error that may have consequential effects for population genetic inferences, and these have received only limited attention in terms of the estimation and reporting of genotyping error rates. Here we use individual sample replicates, under the expectation of identical genotypes, to quantify genotyping error in the absence of a reference genome. We then use sample replicates to (i) optimize de novo assembly parameters within the program Stacks, by minimizing error and maximizing the retrieval of informative loci; and (ii) quantify error rates for loci, alleles and single-nucleotide polymorphisms. As an empirical example, we use a double-digest RAD data set of a nonmodel plant species, Berberis alpina, collected from high-altitude mountains in Mexico.

show abstract

“…However, despite their popularity and importance both economically and scientifically, the question of whether Mahonia should be recognized as a distinct genus separated from "simple-leaved" Berberis (Berberis s.str.) has been debated intermittently for almost two centuries (Fedde, 1901;Takeda, 1917;Shen, 1954;Ahrendt, 1961;Meacham, 1980;McCain & Hennen, 1982;Moran, 1982;Terabayashi, 1985a, b;Loconte & Estes, 1989;Laferrière, 1997;Marroquín & Laferrière, 1997;Whittemore, 1997;Kim & al., 2004a;Harms, 2007;Zamudio, 2009;Rounsaville & Ranney, 2010;Ying & al., 2011;Holmgren & Holmgren, 2012;Jeelani & al., 2014;Adhikari & al., 2015). Supporters of a broadly defined Berberis (Berberis s.l.)…”

Section: Introductionmentioning

confidence: 99%

Why Mahonia? Molecular recircumscription of Berberis s.l., with the description of two new genera, Alloberberis and Moranothamnus

Chung

2017

TAXON

View full text Add to dashboard Cite

Whether Mahonia should be recognized as a distinct genus or subsumed under Berberis has long been debated since its publication in 1818. Although recent molecular phylogenetic studies showed the paraphyly of Mahonia and some advocated a broadly defined Berberis to include Mahonia, the acceptance of Berberis s.l. is far from universal. Due to insufficient sampling and analytical issues of outgroup rooting, taxon misidentification, and the inclusion of a problematic GenBank DNA sequence, we argue that the phylogenetic status of Mahonia and consequently the circumscription of Berberis s.l. remains problematic. In particular, Berberis claireae and Mahonia sect. Horridae, taxa both inhabiting xeric habitats and characterized by a transitional morphology between Berberis s.str. and typical Mahonia (core Mahonia), have not been adequately sampled and well‐positioned phylogenetically. With the inclusion of these key species and an expanded sampling of core Mahonia, we re‐examine the phylogenetic relationships of Berberis s.l. using the internal transcribed spacer (ITS) of nrDNA, and three coding regions (accD, ndhF, rbcL) and one non‐coding region (psbA‐trnH) of the chloroplast genome. Our analyses reveal four clades within Berberis s.l., corresponding to Berberis s.str., B. claireae, core Mahonia, and Mahonia sect. Horridae, with the latter three (all compound‐leaved) forming a paraphyletic grade sister to simple‐leaved Berberis. Because of morphological and ecological distinctness of these four clades and their deep stem divergences equivalent to other genera of Berberidaceae, we propose a new classification of Berberis s.l. by applying a strict definition of Berberis (≡ Berberis s.str.), reinstating Mahonia (≡ core Mahonia), and proposing the two new genera Alloberberis nom. & stat. nov. (≡ Mahonia sect. Horridae) and Moranothamnus gen. nov. (≡ B. claireae). This revised classification is consistent with the traditional perception of Berberis and results in a monophyletic Mahonia, maintaining the stable usage of these two household names in both academic and non‐academic communities.

show abstract

Ploidy Levels and Genome Sizes of Berberis L. and Mahonia Nutt. Species, Hybrids, and Cultivars

Cited by 40 publications

References 21 publications

Long‐term in situ persistence of biodiversity in tropical sky islands revealed by landscape genomics

Long‐term in situ persistence of biodiversity in tropical sky islands revealed by landscape genomics

Restriction site‐associated DNA sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference

Why Mahonia? Molecular recircumscription of Berberis s.l., with the description of two new genera, Alloberberis and Moranothamnus

Contact Info

Product

Resources

About