Eight papers relating to studies at the population level or population/species interface and using a range of techniques are published in this issue. Here the subject areas involved are summarized and some other relevant recent papers are identified. Finally, the potential of new techniques relating to next-generation sequencing are considered.

Islands have long been seen as natural laboratories for studies of speciation (see Carlquist, 2010, for a review; see García-Verdugo et al., 2010, and Asmussen-Lange, Maunder & Fay, 2010, for specific examples in Olea L. and Hyophorbe Gaertn., respectively) and origins of insular populations (e.g. in Platanthera Rich.; Paverese et al., 2011). In this issue Bone et al. (2012) continue this line of research with a phylogenetic study of the genus Badula Juss. in the Mascarenes. Given the rarity of several of the taxa involved, their study is notable for its near complete sampling of some taxa. The study of Badula in part concerns species delimitation, and studies of species delimitation in problematic groups have also become more tractable as a result of the development of molecular methodologies, but there is still considerable discussion or disagreement in some cases (e.g. Ophrys L.; see Bateman et al., 2011; Vereecken et al., 2011).

Polyploidy is of great significance in plants, and genetic studies have illuminated the relationships between and the origins of polyploid lineages e.g. in Olea (García-Verdugo et al., 2010 and references therein) and Polystachya Hook. (Russell et al., 2011); several systems have been classic examples of this phenomenon. One example that has been studied for several decades is Tragopogon L., in which three introduced European diploids have hybridized to give rise to allotetraploids that are endemic to the USA. Soltis et al. (2012, this issue) document further origins of one of the tetraploids. Studies of wild populations of many plants are still revealing the existence of multiple ploidy levels and or variable chromosome number in sympatry or allopatry (e.g. in Actinidia Lindl., Li et al., 2010; Aster L., Li et al., 2011; Sorbus L., J. Pellicer et al.,; Tacuatiáet al. (2012, this issue) provide a further example of this in Sisyrinchium L. (Iridaceae).

Morphological studies, either alone (e.g. in Brachycorythis Lindl., Pedersen, 2010) or in combination with molecular data (e.g. in Pinus L., Jasińska et al., 2010; Anthoxanthum L., Pimentel, Catalán & Sahuquillo, 2010; Carapa Aubl., Kenfack, 2011) have proved powerful in clarifying species boundaries and in identifying hybrids. As further examples, in this issue, combined morphological and genetic studies on Alyssum L. (Španiel et al., 2012), Daucus L. (Martínez-Flores, Juan & Crespo, 2012), Primula L. (Shao et al., 2012) and Hieracium L. (Frey et al., 2012) are presented.

Consequences of reproductive issues and hybridization can also be investigated genetically. Prentice, Andersson & Månsby (2011) presented, for example, addition data on hybrization in Silene L. across wide geographical scales. Here Sampaio et al. (2012) demonstrate inbreeding depression in Vriesea Lindl.

Despite the wide range of approaches and techniques used in the papers presented in this issue, one notable point is that none of studies uses ‘next-generation’ methods for sequencing, genomics etc. We live in rapidly changing times, at least in terms of the technologies used for genetic studies, and the novel technologies provide huge opportunities for approaching questions in greater depth than previously possible or even for asking questions in ways that the earlier methods did not allow. Much has already been written on this subject elsewhere, and here is not the appropriate place to review the methods or questions in any detail, but I will point the reader towards a few papers relating to plants that have caught my eye. Twyford & Ennos (2011) reviewed the possibilities provided by next generation sequencing in studies of hybridization and introgression, and made suggestions for how emerging techniques could overcome current limitations. The questions to be asked relate to the species/population interface (as in the papers in this issue), and next generation sequencing is seen to allow advances in addressing the questions from both phylogenetic and population genetics perspectives. Using earlier sequencing and marker development methodologies imposes limitations in terms of the parts of the genome (focusing on plastid and nuclear ribosomal DNA) and the number of markers used (due to time and cost implications) when working with non-model plant species. The complexity of plant genomes (summarized by Twyford & Ennos, 2011) exacerbates some of the issues, particularly with species with large genomes (see Pellicer et al., 2010 and references therein) or with polyploids.

One ‘by-product’ of next generation sequencing studies is the easy production of more-or-less complete plastid genomes, and these are available in rapidly increasing numbers. These plastid genomes can be ‘mined’ for microsatellites, allowing the development of far larger numbers of this type of marker than was feasible with Sanger sequencing in all but a few model species (see, e.g., Ebert & Peakall, 2009). As a result, studies such as that in Cephalanthera Rich. by Micheneau et al. (2010) using only three markers will rapidly be followed by studies using tens, if not hundreds, of microsatellites.

Development of nuclear microsatellites using next generation sequencing also provides many more markers than previously possible (e.g. Malausa et al., 2011; Micheneau et al., 2011; Takayama et al., 2011), and this will, for example, help overcome, at least in great part, the limitations associated with the need to have a large number of nuclear markers (and the time and the cost previously involved) to assign individuals to different hybrid classes (see Twyford & Ennos, 2011).

The presence of multiple copies of genes as a result of polyploidy in many plants has also been a major impediment to genetic studies requiring knowledge of the nuclear genome. Again, next generation sequencing may provide solutions to some of the problems, and Griffin, Robin & Hoffman (2011) illustrate this using polyploid species of Poa L.

In conclusion, new techniques are providing exciting new possibilities. I fully expect that papers using next generation sequencing and related methods will begin to appear in the Botanical Journal of the Linnean Society in the very near future.


  1. Top of page
  • Asmussen-Lange CB, Maunder M, Fay MF. 2011. Conservation genetics of the critically endangered Round Island bottle palm, Hyophorbe lagenicaulis (Arecaceae): can cultivated stocks supplement a residual wild population? Botanical Journal of the Linnean Society 167: 301310.
  • Bateman RM, Bradshaw E, Devey DS, Glover BJ, Malmgren S, Sramkó G, Thomas MM, Rudall PJ. 2011. Species arguments: clarifying competing concepts of species delimitation in the pseudo-copulatory orchid genus Ophrys. Botanical Journal of the Linnean Society 165: 336347.
  • Bone RE, Strijk JS, Fritsch PW, Buerki S, Strasberg D, Thébaud C, Hodkinson TR. 2012. Phylogenetic inference of Badula (Primulaceae), a rare and threatened genus endemic to the Mascarene Archipelago. Botanical Journal of the Linnean Society 169: 284296.
  • Carlquist S. 2010. Darwin on island plants. Botanical Journal of the Linnean Society 161: 2025.
  • Ebert D, Peakall R. 2009. A new set of universal de novo sequencing primers for extensive coverage of noncoding chloroplast DNA: new opportunities for phylogenetic studies and cpSSR discovery. Molecular Ecology Resources 9: 7771075.
  • Frey DJ, Haag CR, Kozlowski G, Tison J-M, Mráz P. 2012. High genetic and morphological diversity despite range contraction in the diploid Hieracium eriophorum (Asteraceae) endemic to the coastal sand dunes of south-west France. Botanical Journal of the Linnean Society 169: 365377.
  • García-Verdugo C, Forrest AD, Balaguer L, Fay MF, Vargas P. 2010. Parallel evolution of insular Olea europaea subspecies based on geographical structuring of plastid DNA variation and phenotypic similarity in leaf traits. Botanical Journal of the Linnean Society 162: 5463.
  • Griffin PC, Robin C, Hoffmann AA. 2011. A next-generation sequencing method for overcoming the multiple gene copy problem in polyploid phylogenetics, applied to Poa grasses. BMC Biology 9: 19.
  • Jasińska AK, Wachowiak W, Muchewicz E, Boratyńska K, Montserrat JM, Boratyński A. 2010. Cryptic hybrids between Pinus uncinata and P. sylvestris. Botanical Journal of the Linnean Society 163: 473485.
  • Kenfack D. 2011. Resurrection in Carapa (Meliaceae): a reassessment of morphological variation and species boundaries using multivariate methods in a phylogenetic context. Botanical Journal of the Linnean Society 165: 186221.
  • Li D, Liu Y, Zhong C, Huang H. 2010. Morphological and cytotype variation of wild kiwifruit (Actinidia chinensis complex) along an altitudinal and longitudinal gradient in central-west China. Botanical Journal of the Linnean Society 164: 7283.
  • Li W-P, Tang M, Yin G-S, Yin Y, Yang F-S, Chen S-M. 2011. Extensive chromosome number variation in Aster ageratoides var. pendulus (Asteraceae). Botanical Journal of the Linnean Society 165: 378387.
  • Malausa T, Gilles A, Meglécz E, Blanquart H, Duthoy S, Costedoat C, Dubut V, et al. 2011. High-throughput microsatellite isolation through 454 GS-FLX Titanium pyrosequencing of enriched DNA libraries. Molecular Ecology Resources 11: 638644.
  • Martínez-Flores F, Juan A, Crespo MB. 2012. Molecular and morphological evidence supports the resurrection of a neglected species of Daucus (Apiaceae) from North Africa. Botanical Journal of the Linnean Society 169: 320337.
  • Micheneau C, Duffy KJ, Smith RJ, Stevens LJ, Stout JC, Civeyrel L, Cowan RS, Fay MF. 2010. Plastid microsatellites for the study of genetic variability in the widespread Cephalanthera longifolia, C. damasonium and C. rubra (Neottieae, Orchidaceae), and cross-amplification in other Cephalanthera species. Botanical Journal of the Linnean Society 163: 181193.
  • Micheneau C, Dauby G, Bourland N, Doucet J-L, Hardy OJ. 2011. Development and characterization of microsatellite loci in Pericopsis elata (Fabaceae) using a cost-efficient approach. American Journal of Botany 98: e268e270.
  • Pavarese G, Tranchida-Lombardo V, Cogoni A, Cristaudo A, Cozzolino S. 2011. Where do Sardinian orchids come from: a putative African origin for the insular population of Platanthera bifolia var. kuenkelei? Botanical Journal of the Linnean Society 167: 466475.
  • Pedersen HÆ. 2010. Species delimitation and recognition in the Brachycorythis helferi complex (Orchidaceae) resolved by multivariate morphometric analysis. Botanical Journal of the Linnean Society 162: 6476.
  • Pellicer J, Leitch IJ, Fay MF. 2010. The largest eukaryotic genome of them all? Botanical Journal of the Linnean Society 164: 1015.
  • Pimentel M, Catalán P, Sahuquillo E. 2010. Morphological and molecular taxonomy of the annual diploids Anthoxanthum aristatum and A. ovatum (Poaceae) in the Iberian Peninsula. Evidence of introgression in natural populations. Botanical Journal of the Linnean Society 164: 5371.
  • Prentice HC, Andersson S, Månsby E. 2011. Mosaic variation in allozyme and plastid DNA markers in the European ranges of Silene vulgaris and its partially sympatric relative S. uniflora (Caryophyllaceae). Botanical Journal of the Linnean Society 166: 127148.
  • Russell A, Samuel R, Bogarín D, Fernando S, Wijesundera S, Klejna V, Chase MW. 2011. Genetic variation and phylogenetic relationships of a pantropical species group in Polystachya (Orchidaceae). Botanical Journal of the Linnean Society 165: 235250.
  • Sampaio JAT, Paggi GM, Zanella CM, Bruxel M, Palma-Silva C, Goetze M, Büttow MV, Bered F. 2012. Inbreeding depression in Vriesea gigantea, a perennial bromeliad 1 from southern Brazil. Botanical Journal of the Linnean Society 169: 312319.
  • Shao J-W, Wu Y-F, Kan X-Z, Liang T-J, Zhang X-P. 2012. Reappraisal of Primula ranunculoides (Primulaceae), an endangered species endemic to China, based on morphological, molecular genetic and reproductive characters. Botanical Journal of the Linnean Society 169: 338349.
  • Soltis DE, Mavrodiev EV, Meyers SC, Severns PM, Zhang L, Gitzendanner MA, Ayers T, Chester M, Soltis PS. 2012. Additional origins of Ownbey's Tragopogon mirus. Botanical Journal of the Linnean Society 169: 297311.
  • Španiel S, Marhold K, Thiv M, Zozomová-Lihová J. 2012. A new circumscription of Alyssum montanum subsp. montanum and A. montanum subsp. gmelinii (Brassicaceae) in Central Europe: molecular and morphological evidence. Botanical Journal of the Linnean Society 169: 378402.
  • Tacuatiá LO, Flores AM, Souza-Chies TT, Eggers L, Siljak-Yakovlev S, Kaltchuk-Santos E. 2012. Cytogenetic and molecular characterization of morphologically variable Sisyrinchium micranthum (Iridaceae) in southern Brazil. Botanical Journal of the Linnean Society 169: 350364.
  • Takayama K, López S. P, König C, Kohl G, Novak J, Stuessy TF. 2011. A simple and cost-effective approach for microsatellite isolation in non-model plant species using small-scale 454 pyrosequencing. Taxon 60: 1442-1449.
  • Twyford AD, Ennos RA. 2011. Next-generation hybridization and introgression. Heredity 108: 179-189.
  • Vereecken NJ, Streinzer M, Ayasse M, Spaethe J, Paulus HF, Stökl J, Cortis P, Schiestl FP. 2011. Integrating past and present studies on Ophrys pollination – a comment on Bradshaw et al. Botanical Journal of the Linnean Society 165: 329335.