Figure - available from: Botany
This content is subject to copyright. Terms and conditions apply.
Source publication
Low-copy nuclear genes have been suggested as a promising source of independent phylogeographic markers in plants. However, the available studies at the intraspecific level have revealed that extracting information from them is frequently hampered by paralogy and lack of coalescence of alleles. It is thus relevant to test their utility with plants...
Citations
... (Jolley et al., 2001) demonstrated the lowest rate of type I and type II errors (cf. Piñeiro et al., 2009). Therefore, we adopted it in this study. ...
Potamogeton is a cosmopolitan genus of aquatic plants comprising ca. 72 species and 99 hybrids. Hybridization and polyploidization events are characteristic of its evolutionary history, thus molecular approach is desirable for confirmation of species and hybrids determinations. In this study, we tested the suitability of low-copy nuclear gene PHYB as a barcoding marker, as this gene was shown to have sufficient level of variability in Potamogeton in preceding studies. We cloned and sequenced part of gene PHYB exon 1 for 19 samples of 8 Potamogeton species. Our sampling took place in East Europe, Siberia, Russian Far East and NE North America. The obtained sequences were used to construct a genetic network. We report some features of PHYB which hamper its application as a barcode in Potamogeton. Most of the tetraploid species provided two sets of dissimilar PHYB sequences, which probably stand for two paralogs. PCR-derived errors, such as recombination and random substitutions, shifted the position of some sequences in the network. In addition, one haplotype was shared between two closely related species, breaking the species-specificity of PHYB barcode. Even though it may provide higher resolution for hybrid identification than ITS or 5S-NTS, using it as a marker for standard barcoding in this genus is not the best option.
Full-text available on request.
... Various phenomena can be responsible for the presence of APS in diploid H. nobilis and for appearance of those APS in tetraploid H. transsilvanica which are apparently not related to the hybrid status of species. These can result from gene flow between populations, incomplete sorting of ancestral polymorphism or paralogy (due to independent duplication events of the gene in certain populations) (Piñeiro et al., 2009). Discerning the relative contribution of these phenomena to the intra-individual polymorphism of At103 gene in selected taxa of the genus Hepatica was beyond the scopes of this study. ...
... Whatever the reason behind the above findings, the pattern of At103 variation would be worth exploring in a phylogeographic context. Piñeiro et al. (2009) Table 2) ...
Allopolyploidy (hybridisation followed by genome doubling) has been recognised as a major force driving plant speciation. The genus Hepatica includes both diploid and polyploid species where the origin of polyploids has not been fully established, yet. In particular, the origin of Romanian endemic, tetraploid Hepatica transsilvanica Fuss. remained challenging because a previous study found its incongruent placement between plastid and nuclear phylogenies (suggestive of its hybrid origin). In this study a more direct method was applied in order to shed lights on the hybrid origin of species. A fragment of nuclear At103 gene was sequenced in H. transsilvanica and in both of its putative diploid progenitors, the European distributed H. nobilis Schreb. (var. nobilis) and the Central Asian endemic Hepatica falconeri Thomson. Direct At103 sequence of H. transsilvanica clearly showed an additive pattern between the parental sequence types, supporting the allopolyploid origin of species. A few additional additive polymorphic sites (i.e. superimposed peaks) neither supporting, nor contradicting the hybrid origin were also found in the sequence of H. transsilvanica but these were not shared by all samples analysed. Origin of this 'inconclusive sequence variation' can be explained by various phenomena, like random sorting of ancestral polymorphism or paralogy. In this study a new platform is provided on which the auto-vs. allopolyploid origin of the rest of tetraploid Hepatica taxa can be tested.
... Inheritance of plastid DNA is predominantly uniparental and maternal in plants, whereas nuclear DNA is biparentally inherited, although due to conversion nrDNA can become uniparental. Processes like incomplete lineage sorting, hybridization, coalescence times longer than species ages, and introgression may complicate interpretation of results (Piñeiro & al., 2009; Willyard & al., 2009). More difficulties arise when polyploid taxa or multi-copy nuclear genes and gene families are investigated (e.g., Sang & al., 2004). ...
The monocot family Bromeliaceae comprises approximately 3,140 species distributed in tropical and subtropical regions of the New World from the southern United States to southern Argentina. The family is subdivided into eight subfamilies; the most species-rich are Tillandsioideae and Bromelioideae. Taxonomic concepts within Bromeliaceae are highly problematic, since discriminating morphological characters have been shown to be homoplastic or plesiomorphic. The present study aims to provide a robust phylogenetic framework for Bromeliaceae, especially for the most diverse and complicated subfamilies Bromelioideae and Tillandsioideae. Resulting phylogenies provide a basis to estimate the usefulness of morphological characters and to propose or strengthen hypotheses concerning evolutionary traits, biogeography, age and origins of bromeliads.
The main questions raised are:
(1) Do additional sequence data from the plastid genome and a wider sampling within Bromeliaceae provide a better resolved, robust phylogenetic framework? What are the reasons for the low DNA sequence divergence observed up to now?
(2) Can nuclear DNA sequences be successfully implemented for phylogenetic reconstruction? What are the challenges to optimize nuclear markers and do they perform better than plastid loci?
(3) Can the resulting phylogeny based on plastid and nuclear DNA sequences together with the re-evaluated morphological characters provide a reasonable, stable classification?
To provide a more robust phylogenetic hypothesis for the classification of Bromeliaceae, eight rapidly evolving plastid DNA markers (atpB-rbcL, matK, ndhF, psbA-trnH, rpl32-trnL, rps16, trnL intron, and trnL-trnF) and 90 bromeliad species were included in the current study and analysed using maximum-parsimony, maximum-likelihood, and Bayesian approaches. Results support the formerly proposed eight-subfamily classification based on the single plastid gene ndhF. Support values for five of the subfamilies increase, but that for Lindmanioideae, Puyoideae, and Bromelioideae decrease as a result of expanded taxon sampling, including several more divergent species. The initially proposed monophyletic origin of Puyoideae cannot be unambiguously confirmed. Calibration of the resulting phylogeny against time and biogeographic analysis reveals that Bromeliaceae originated in the Guayana Shield about 100 million years ago (Ma) and spread radially into adjacent areas ca. 16—13 Ma. Extant lineages arose between 20 and 5 Ma. Andean uplift facilitated diversification of core Tillandsioideae about 14.2 Ma and Bromelioideae 10.1 Ma, the latter having their greatest diversity in the Brazilian Shield due to dispersal from the Andes. The most species-rich genera did not appear before 8.7 My with a high diversification between 5 and 4 Ma, which is most likely the reason for the comparatively low sequence divergence.
To test the usefulness of nuclear regions for phylogenetic reconstruction in Bromelioideae, DNA sequences of part of the low-copy nuclear gene phosphoribulokinase (PRK) and five plastid loci (matK, 3'trnK intron, trnL intron, trnL-trnF, and atpB-rbcL) were investigated. Phylogenetic trees obtained from analyses of the PRK sequences do not contradict trees obtained from plastid markers. The PRK matrix shows a significantly higher number of potentially PICs (phylogenetically informative characters) than the plastid dataset (16.9% vs. 3.1%), which improves resolution and support in the resulting trees. Although PRK is not able to resolve relationships completely, the combined analysis with plastid markers yields good support for several uncertain relationships observed previously. The early diverging lineages can be identified (“basal bromelioids”) and the remainder of the subfamily clustered into a highly supported clade (“eu-bromelioids”). Results indicate that taxonomic circumscriptions within “core bromeliads” are still insufficient, and relationships complex and difficult to solve. Several genera appear polyphyletic, and Aechmea as well as Quesnelia remain the most complicated genera of the subfamily. Most-parsimonious character state reconstructions for two evolutionary traits (tank habit, sepal symmetry) indicate that both characters have undergone few transitions within the subfamily and thus are not as homoplasious as previously assumed. The comparative study of nuclear DNA sequences within Tillandsioideae shows that some nuclear markers are able to provide more information and a higher degree of resolution in phylogenetic trees than plastid markers. However, their utility does not depend only on sequence variability, but also on methodological challenges in using traditional Sanger-sequencing. The internal transcribed spacer of nuclear ribosomal DNA (ITS nrDNA) is not recommended as a suitable marker for phylogenetic investigations of Bromeliaceae due to the presence of strong secondary structures which create problems in amplification and sequencing as well as its low number of PICs for resolving deeper nodes. Amplified fragments of the genes malate synthase (MS) and RNA polymerase II, beta subunit (RPB2) are not helpful due to their small size and limited number of PICs. Glucose-6-phosphate isomerase (PGIC), nitrate reductase (NIA), and xanthine dehydrogenase (XDH) need to be further investigated. Phosphoribulokinase (PRK) and phytochrome C (PHYC) are useful nuclear markers and able to provide considerable resolution in phylogenetic trees, but some relationships are poorly supported.
The combined analysis of nuclear DNA sequence data (PRK, PHYC) with the already existing plastid DNA sequence data (atpB-rbcL, matK, rbcL, partial rbcL-accD, rps16 intron, partial trnK intron, trnL intron and trnL-trnF) shows a significant increase of resolution within phylogenetic trees of Tillandsioideae. Nine accepted genera can be re-circumscribed and three new genera are described taxonomically based on morphology. For morphologically distinct species groups within Racinaea and Tillandsia, two new subgenera are erected. Viridantha has been downgraded to subgeneric rank. Poor sampling within the Cipuropsis-Mezobromelia clade and missing support for clades within Tillandsia prevent the recognition of further taxonomic groups.
... The use of plastid markers is highly suitable for assessing the genetic effects of colonization due to maternal inheritance and low effective population size (Clegg et al., 1994) of the haploid chloroplast genome, which make it more sensitive to genetic drift than the nuclear genome. In agreement with this prediction, patterns of variation of the low-copy nuclear gene GapC in A. pungens were shown to be partially blurred by incomplete lineage sorting (Piñ eiro et al., 2009). The use of ITS sequences in phylogeography is less straightforward, given that the concerted evolution of different ITS copies usually results in low levels of variation within reproductive groups (Baldwin et al., 1995). ...
The coastal shrub Armeria pungens has a disjunct Atlantic-Mediterranean distribution. The historic range expansion underlying this distribution was investigated using the nuclear internal transcribed spacer region, three plastid regions (namely trnL-F, trnS-fM and matK) and morphometric data. A highly diverse ancestral lineage was identified in southwest Portugal. More recently, two areas have been colonized: (1) Corsica and Sardinia, where disjunct Mediterranean populations have been established as a result of the long-distance dispersal of Portuguese genotypes, and (2) the southern part of the Atlantic range, Gulf of Cadiz, where a distinct lineage showing no genetic differentiation among populations occurs. Genetic consequences of colonization seem to have been more severe in the Gulf of Cadiz than in Corsica-Sardinia. Although significant genetic divergence is associated with low plastid diversity in the Gulf of Cadiz, in Corsica-Sardinia, the loss of plastid haplotypes was not accompanied by divergence from disjunct Portuguese source populations. In addition, in its northernmost and southernmost populations, A. pungens exhibited evidence for ancient or ongoing introgression from sympatric congeners. Introgression might have created novel genotypes able to expand beyond the latitudinal margins of the species or, alternatively, these genotypes may be the result of surfing of alleles from other species in demographic equilibrium into peripheral populations of A. pungens. Our results highlight the evolutionary significance of genetic drift following the colonization of new areas and the key role of introgression in range expansion.
... Genetic data provide a tool for dissecting the evolutionary relationships of recently derived taxa, independent of morphology and geography. Studies that employ multiple data types (Schaal et al., 1998;Schaal and Olsen, 2000;Gamble et al., 2008;Pineiro et al., 2009) are particularly suited to understanding the complexities of population-level evolutionary processes and relationships that are indicative of both historical and contemporary diversification. However, conflict among data types, particularly DNA sequence data from different genomes, has been widely documented (e.g. ...
The Hawaiian silversword alliance (Asteraceae) is one the best examples of a plant adaptive radiation, exhibiting extensive morphological and ecological diversity. No research within this group has addressed the role of geographical isolation, independent of ecological adaptation, in contributing to taxonomic diversity. The aims of this study were to examine genetic differentiation among subspecies of Dubautia laxa (Asteraceae) to determine if allopatric or sympatric populations and subspecies form distinct genetic clusters to understand better the role of geography in diversification within the alliance.
Dubautia laxa is a widespread member of the Hawaiian silversword alliance, occurring on four of the five major islands of the Hawaiian archipelago, with four subspecies recognized on the basis of morphological, ecological and geographical variation. Nuclear microsatellites and plastid DNA sequence data were examined. Data were analysed using maximum-likelihood and Bayesian phylogenetic methodologies to identify unique evolutionary lineages.
Plastid DNA sequence data resolved two highly divergent lineages, recognized as the Laxa and Hirsuta groups, that are more similar to other members of the Hawaiian silversword alliance than they are to each other. The Laxa group is basal to the young island species of Dubautia, whereas the Hirsuta group forms a clade with the old island lineages of Dubautia and with Argyroxiphium. The divergence between the plastid groups is supported by Bayesian microsatellite clustering analyses, but the degree of nuclear differentiation is not as great. Clear genetic differentiation is only observed between allopatric populations, both within and among islands.
These results indicate that geographical separation has aided diversification in D. laxa, whereas ecologically associated morphological differences are not associated with neutral genetic differentiation. This suggests that, despite the stunning ecological adaptation observed, geography has also played an important role in the Hawaiian silversword alliance plant adaptive radiation.
The genetic diversity and possible geographic structure of the Madeiran endemic Armeria maderensis have been assessed with AFLP. Its scarce distribution (less than 3km between the two most distant localities) and restricted
habitat (vertical pastures on the highest elevations of Madeira), at least in part due to grazing by goats, suggest an assessment
of its conservation status. Diversity estimates obtained for A. maderensis were evaluated through comparison with reference values of AFLP diversity for outcrossing plants and, in order to correct
for phylogenetic constraints, with a widespread congener analyzed with the same AFLP markers. Our results reveal that low
levels of genetic diversity and a weak intraspecific genetic structure underlie the restricted distribution of A. maderensis.
Coastal plants are ideal models for studying the colonization routes of species because of the simple linear distributions of these species. Carex extensa occurs mainly in salt marshes along the Mediterranean and European coasts. Variation in cpDNA sequences, amplified fragment length polymorphisms (AFLPs) and simple sequence repeats (SSRs) of 24 populations were analysed to reconstruct its colonization history. Phylogenetic relationships indicate that C. extensa together with the South American Carex vixdentata and the southern African Carex ecklonii form a monophyletic group of halophilic species. Analyses of divergence times suggest that early lineage diversification may have occurred between the late Miocene and the late Pliocene (Messinian crisis). Phylogenetic and network analyses of cpDNA variation revealed the monophyly of the species and an ancestral haplotype contained in populations of the eastern Mediterranean. The AFLP and SSR analyses support a pattern of variation compatible with these two lineages. These analyses also show higher levels of genetic diversity and differentiation in the eastern population group, which underwent an east-to-west Mediterranean colonization. Quaternary climatic oscillations appear to have been responsible for the split between these two lineages. Secondary contacts may have taken place in areas near the Ligurian Sea in agreement with the gene flow detected in Corsican populations. The AFLP and SSR data accord with the 'tabula rasa' hypothesis in which a recent and rapid colonization of northern Europe took place from the western Mediterranean after the Last Glacial Maximum. The unbalanced west-east vs. west-north colonization may be as a result of 'high density blocking' effect.
