The intraspecific genetic variability of siliceous and calcareous Gentiana species is shaped by contrasting demographic and re-colonization processes

Christe, Camille; Caetano, S.; Aeschimann, David; Kropf, Matthias; Diadema, Katia; Naciri, Yamama

doi:10.1016/j.ympev.2013.09.022

Cited by 39 publications

(31 citation statements)

References 101 publications

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“…Similar results have been reported in many phylogeographic studies of closely related plant taxa. The distributions of chloroplast haplotypes frequently reveal geographic structure, and this geographic pattern may be incongruent with the current taxonomy (Rautenberg et al, 2010; Christe et al, 2014). …”

Section: Discussionmentioning

confidence: 99%

Population Genetic Structure and Phylogeography of Camellia flavida (Theaceae) Based on Chloroplast and Nuclear DNA Sequences

Wei

et al. 2017

Front. Plant Sci.

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Camellia flavida is an endangered species of yellow camellia growing in limestone mountains in southwest China. The current classification of C. flavida into two varieties, var. flavida and var. patens, is controversial. We conducted a genetic analysis of C. flavida to determine its taxonomic structure. A total of 188 individual plants from 20 populations across the entire distribution range in southwest China were analyzed using two DNA fragments: a chloroplast DNA fragment from the small single copy region and a single-copy nuclear gene called phenylalanine ammonia-lyase (PAL). Sequences from both chloroplast and nuclear DNA were highly diverse; with high levels of genetic differentiation and restricted gene flow. This result can be attributed to the high habitat heterogeneity in limestone karst, which isolates C. flavida populations from each other. Our nuclear DNA results demonstrate that there are three differentiated groups within C. flavida: var. flavida 1, var. flavida 2, and var. patens. These genetic groupings are consistent with the morphological characteristics of the plants. We suggest that the samples included in this study constitute three taxa and the var. flavida 2 group is the genuine C. flavida. The three groups should be recognized as three management units for conservation concerns.

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Section: Discussionmentioning

confidence: 99%

Population Genetic Structure and Phylogeography of Camellia flavida (Theaceae) Based on Chloroplast and Nuclear DNA Sequences

Wei

et al. 2017

Front. Plant Sci.

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“…& Chopinet (Diadema et al 2005, Christe et al 2014. Indeed, a molecular study suggested that the genetic structure of G. ligustica is the result of isolation and genetic drift occurred during glaciation (Diadema et al 2005).…”

Section: Historical Factorsmentioning

confidence: 99%

The plant endemism in the Maritime and Ligurian Alps

Casazza¹,

Barberis²,

Guerrina³

et al. 2016

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SUMMARYThe Maritime and Ligurian Alps have a flora characterised by a very high number of endemic species in relation to their small geographical extension. This area is considered one of the most important centres of diversification of the Alps and a Mediterranean hotspot of biodiversity. In the last years many studies were performed in order to describe the distribution and phylogeographical patterns of endemism. Despite these studies, Maritime and Ligurian Alps still lack in a broad view about the evolution of endemisms in this area. In this review, we examine the knowledge about the distribution patterns of endemic plant species living in the Maritime and Ligurian Alps in order to identify the evolutionary and biogeographical mechanisms operating on them. INTRODUCTIONThe Mediterranean Basin is one of the world's terrestrial biodiversity hotspots (Quézel 1995, Médail andMyers 2004). This area hosts most of the biodiversity of Europe, but its species richness is threatened by human pressure and climate change (EEA 2010). In particular, habitat fragmentation and global warming have caused changes in the ecosystems structure leaving the ecosystems more vulnerable to invasion by alien species (EEA 2006). For these reasons, there is an urgency to conserve this richness (Blondel and Médail 2009).The great biodiversity of the Mediterranean Basin is primarily due to particular climate conditions, to habitat heterogeneity as a result of paleogeographical and historical factors, and to different origins of the elements of its flora (Quézel 1985, 1995, Nieto Feliner 2014. Insular, mountain and isolated edaphic systems (i.e., ultrabasic and serpentine rocks) generally appear to be major endemic centres (Quézel 1985, Stevanović 2003, Bacchetta et al. 2013, Sciandrello et al. 2015. Circum-Mediterranean vascular flora owes its taxonomic richness (Médail and Quézel 1997) to its relatively high degree of endemism, varying from 50% (Quézel 1985) to 59% (Greuter 1991) in relation to the taxonomic interpretations of authors.

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“…In the past, the effect of invalid assumptions at the species level was obscured by the use of few specimens per species (often a single one) and by the analysis of sequence data from only one genome or even only one locus. Recently, population genetics, applied at the species level to phylogeography (Jaramillo-Correa & al., 2009;Pandey & Rajora, 2012;Christe & al., 2014a) and barcoding (CBOL Plant Working Group, 2009;Ashfaq & al., 2013;Feng & al., 2013), led to concern about the consequences of these inappropriate assumptions at the species level or above.…”

Section: Introductionmentioning

confidence: 99%

“…Ciminalis (Adans) Dumort. chloroplast haplotype sharing was found in four species, despite interspecific discrimination by the nuclear ribosomal ITS marker and an obvious morphological divergence (Christe & al., 2014a). Similar chloroplast sharing was seen among closely related species of Solidago subsect.…”

Section: Introductionmentioning

confidence: 99%

Species delimitation and relationships: The dance of the seven veils

Naciri

Linder

2015

TAXON

162

137

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An increasing number of studies using genetic data at the generic and species levels reveal complex patterns of relationships among populations and species. Incomplete lineage sorting and reticulation are, for instance, commonly observed in low-rank phylogenies. These two processes falsify the simplifying assumptions often used when reconstructing phylogenetic relationships or when assigning specimens to species using barcodes, i.e., the absence of ancestral polymorphism or the obligate dichotomous relationship among species. We recognize seven processes that act as veils to obscure species boundaries and relationships and lead to erroneous interpretations if not diagnosed and analysed properly. These processes include the transfer of genetic material from plastids or mitochondria to the nuclear genome (NuPt, NuMt), hybridization, the stochasticity of lineage sorting within and among species, genome organization, species demography, selection, genetic and geographic structure. Most of these processes have a direct impact on species effective population sizes, a central parameter to be considered. Failure to take the seven processes into account can affect the accuracy of barcode-based identification, in particular between closely related species. It can also bias the delimitation of species, result in inaccurate estimations of species relationships and lead to incorrect estimation of species ages. We suggest that these problems can be identified and, to some extent, mitigated by ensuring that the full spatial and genetic ranges of the species are sampled, and by the use of information from all genomes of the species. By analysing numerous loci, each as a separate entity in a coalescence framework, it is possible to take into account stochasticity as well as variation in genome effective population sizes. Such a critical approach would allow the use of genetic data to make realistic assessments of species delimitation, affinities and ages, and should promote a more biologically realistic view of species and speciation.

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The intraspecific genetic variability of siliceous and calcareous Gentiana species is shaped by contrasting demographic and re-colonization processes

Cited by 39 publications

References 101 publications

Population Genetic Structure and Phylogeography of Camellia flavida (Theaceae) Based on Chloroplast and Nuclear DNA Sequences

Population Genetic Structure and Phylogeography of Camellia flavida (Theaceae) Based on Chloroplast and Nuclear DNA Sequences

The plant endemism in the Maritime and Ligurian Alps

Species delimitation and relationships: The dance of the seven veils

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