Comparative ITS and AFLP Analysis of Diploid Cardamine (Brassicaceae) Taxa from Closely Related Polyploid Complexes

Marhold, Karol; Lihová, Judita; Perný, Marián; Bleeker, Walter

doi:10.1093/aob/mch073

Cited by 41 publications

(42 citation statements)

References 30 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…A systematic revision of P. crinita is therefore advisable. The presence of different ribotypes in the same genome has been frequently interpreted as an outcome of past reticulation events between divergent lineages either at the polyploid (Campbell & al., 1997;Vargas & al., 1999;Hodkinson & al., 2002;Yonemori & al., 2002) or diploid level (Wichman & al., 2002;Fuertes Aguilar & Nieto Feliner, 2003;Marhold & al., 2004). There is evidence suggesting that polymorphisms in Phlomis might be acquired by hybridization in our study.…”

Section: Discussionmentioning

confidence: 99%

Contrasting nuclear‐plastidial phylogenetic patterns in the recently diverged IberianPhlomis crinitaandP. lychnitislineages (Lamiaceae)

Albaladejo

Aguilar

Aparicio

et al. 2005

TAXON

View full text Add to dashboard Cite

Systematic and evolutionary relationships within the diploid Western Mediterranean Phlomis crinita/lychnitis complex remain controversial apparently due to hybridization and introgression. This study examines patterns of sequence variation in the nuclear ribosomal DNA (ITS region) and three non‐coding plastid DNA regions (trnH‐psbA, trnT‐trnL and atpB‐rbcL) in this complex in an aim to clarify whether hybridization, introgression or lineage sorting resulting from recent diversification is mainly responsible for poorly understood relationships. Information recovered from nuclear and chloroplast markers was found to be strongly incongruent. Phylogenetic analysis of inferred nuclear ITS ribotypes is consistent with previous morphometric and taxonomic results in distinguishing two sister lineages, P. crinita s.l. and P. lychnitis. In addition, the high number of additive polymorphisms detected in ITS sequences suggests the sharing of ancestral variability and local patterns of gene flow within the complex. In contrast, the pattern of chloroplast haplotype variation is geographic rather than taxonomic, which might be caused by low mutation rates combined with frequent instances of interspecific hybridization. To integrate the apparently discordant plastid and nuclear evidence, we suggest that both lineage sorting and horizontal transfer have been involved. Even though pinpointing cases due to either phenomenon is difficult, the available data provide evidence of two sister lineages where hybridization events can be identified despite the inheritance of ancestral polymorphisms.

show abstract

Section: Discussionmentioning

confidence: 99%

Contrasting nuclear‐plastidial phylogenetic patterns in the recently diverged IberianPhlomis crinitaandP. lychnitislineages (Lamiaceae)

Albaladejo

Aguilar

Aparicio

et al. 2005

TAXON

View full text Add to dashboard Cite

show abstract

“…More problematic is the delimitation of taxa the evolutionary history of which involved extensive polyploidy, hybridization, and apomixis. Polyploidy and hybridization have been well documented in Draba (Brochmann 1992;Brochmann et al 1992 and references therein; Widmer and Baltisberger 1999a, b;Koch and Al-Shehbaz 2002;Scheen et al 2002;Beilstein and Windham 2003;Grundt et al 2004), Cardamine (Neuffer and Janche 1997;Urbanska et al 1997;Franzke et al 1998;Franzke and Mummenhoff 1999;Franzke and Hurka 2000;Lihova´et al 2000;Bleeker et al 2002a;Marhold et al 2002aMarhold et al , 2002bMarhold et al , 2004, and Lepidium (Lee et al 2002;Mummenhoff et al 2001a, 2004 andreferences therein). It is likely that these two phenomena influenced the evolution of all major genera of the family.…”

Section: Problematic Groupsmentioning

confidence: 98%

Systematics and phylogeny of the Brassicaceae (Cruciferae): an overview

2006

View full text Add to dashboard Cite

Abstract. A critical review of characters used in the systematics of the Brassicaceae is given, and aspects of the origin, classification, and generic delimitation of the family discussed. Molecular phylogenetic studies of the family were reviewed, and major clades identified. Based on molecular studies, especially from the ndhF chloroplast gene, and careful evaluation of morphology and generic circumscriptions, a new tribal alignment of the Brassicaceae is proposed. In all, 25 tribes are recognized, of which seven (Aethionemeae, Boechereae, Descurainieae, Eutremeae, Halimolobeae, Noccaeeae, and Smelowskieae) are described as new. For each tribe, the center(s) of distribution, morphology, and number of taxa are given. Of the 338 genera currently recognized in the Brassicaceae, about 260 genera (or about 77%) were either assigned or tentatively assigned to the 25 tribes. Some problems relating to various genera and tribes are discussed, and future research developments are briefly covered.

show abstract

“…Of particular interest in this study is the use of AFLP to generate data for phylogenetic studies. Although some researchers have suggested that AFLP data are inappropriate for phylogenetic applications (Hollingsworth and Ennos, 2004;Kosman and Leonard, 2005), several empirical studies have revealed tree-like properties in AFLP data sets, and AFLP data are increasingly being used to estimate phylogenies, including for very shallow radiations (e.g., Marhold et al, 2004;Sullivan et al, 2004;Koopman, 2005;Mendelson and Shaw, 2005;Spooner et al, 2005a;Albach, 2007;Kilian et al, 2007). Meudt and Clarke (2007) reviewed several conditions in which the AFLP technique can be ideal.…”

mentioning

confidence: 99%

“…ing the phylogeny of organisms such as plants for which other nuclear and organellar markers are often lacking, insufficiently variable, or even inappropriate (Després et al, 2003;Pelser et al, 2003;Marhold et al, 2004;Bensch andÅkesson, 2005;Tremetsberger et al, 2006;Pellmyr et al, 2007). AFLPs can also complement other marker systems (such as DNA sequencing markers) in a phylogenetic study by, for example, providing resolution in different parts of the tree (Després et al, 2003;Pelser et al, 2003;Marhold et al, 2004;Koopman, 2005;Spooner et al, 2005b).…”

mentioning

confidence: 99%

“…AFLPs can also complement other marker systems (such as DNA sequencing markers) in a phylogenetic study by, for example, providing resolution in different parts of the tree (Després et al, 2003;Pelser et al, 2003;Marhold et al, 2004;Koopman, 2005;Spooner et al, 2005b). AFLPs may not be able to provide an accurate estimate of the species phylogeny when genetic divergence is too high (although precisely where this cut-off is has been the subject of debate; see Meudt and Clarke (2007) and references therein), or when frequent hybridization and reticulation have obscured the phylogenetic signal throughout the phylogeny, but these shortcomings are not unique to AFLP data.…”

mentioning

confidence: 99%

See 1 more Smart Citation

Optimizing Automated AFLP Scoring Parameters to Improve Phylogenetic Resolution

2008

View full text Add to dashboard Cite

The amplified fragment length polymorphism (AFLP) technique is an increasingly popular component of the phylogenetic toolbox, particularly for plant species. Technological advances in capillary electrophoresis now allow very precise estimates of DNA fragment mobility and amplitude, and current AFLP software allows greater control of data scoring and the production of the binary character matrix. However, for AFLP to become a useful modern tool for large data sets, improvements to automated scoring are required. We design a procedure that can be used to optimize AFLP scoring parameters to improve phylogenetic resolution and demonstrate it for two AFLP scoring programs (GeneMapper and GeneMarker). In general, we found that there was a trade-off between getting more characters of lower quality and fewer characters of high quality. Conservative settings that gave the least error did not give the best phylogenetic resolution, as too many useful characters were discarded. For example, in GeneMapper, we found that bin width was a crucial parameter, and that although reducing bin width from 1.0 to 0.5 base pairs increased the error rate, it nevertheless improved resolution due to the increased number of informative characters. For our 30-taxon data sets, moving from default to optimized parameter settings gave between 3 and 11 extra internal edges with >50% bootstrap support, in the best case increasing the number of resolved edges from 14 to 25 out of a possible 27. Nevertheless, improvements to current AFLP software packages are needed to (1) make use of replicate profiles to calibrate the data and perform error calculations and (2) perform tests to optimize scoring parameters in a rigorous and automated way. This is true not only when AFLP data are used for phylogenetics, but also for other applications, including linkage mapping and population genetics.

show abstract

Comparative ITS and AFLP Analysis of Diploid Cardamine (Brassicaceae) Taxa from Closely Related Polyploid Complexes

Cited by 41 publications

References 30 publications

Contrasting nuclear‐plastidial phylogenetic patterns in the recently diverged IberianPhlomis crinitaandP. lychnitislineages (Lamiaceae)

Contrasting nuclear‐plastidial phylogenetic patterns in the recently diverged IberianPhlomis crinitaandP. lychnitislineages (Lamiaceae)

Systematics and phylogeny of the Brassicaceae (Cruciferae): an overview

Optimizing Automated AFLP Scoring Parameters to Improve Phylogenetic Resolution

Contact Info

Product

Resources

About