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Genome size variation is a crucial aspect of plant evolution, influenced by a complex interplay of factors. Repetitive elements, which are fundamental components of genomic architecture, often play a role in genome expansion by selectively amplifying specific repeat motifs. This study focuses on Amomum, a genus in the ginger family (Zingiberaceae), known for its 4.4-fold variation in genome size. Using a robust methodology involving PhyloNet reconstruction, RepeatExplorer clustering, and repeat similarity-based phylogenetic network construction, we investigated the repeatome composition, analyzed repeat dynamics, and identified potential hybridization events within the genus. Our analysis confirmed the presence of four major infrageneric clades (A-D) within Amomum, with clades A-C exclusively comprising diploid species (2n = 48) and clade D encompassing both diploid and tetraploid species (2n = 48 and 96). We observed an increase in the repeat content within the genus, ranging from 84% to 89%, compared to outgroup species with 75% of the repeatome. The SIRE lineage of the Ty1-Copia repeat superfamily was prevalent in most analyzed ingroup genomes. We identified significant difference in repeatome structure between the basal Amomum clades (A, B, C) and the most diverged clade D. Our investigation revealed evidence of ancient hybridization events within Amomum, coinciding with a substantial proliferation of multiple repeat groups. This finding supports the hypothesis that ancient hybridization is a driving force in the genomic evolution of Amomum. Furthermore, we contextualize our findings within the broader context of genome size variations and repeatome dynamics observed across major monocot lineages. This study enhances our understanding of evolutionary processes within monocots by highlighting the crucial roles of repetitive elements in shaping genome size and suggesting the mechanisms that drive these changes. [ABSTRACT FROM AUTHOR]

European larch (Larix decidua Mill.) is an important tree species commonly used in managed forests of central Europe. However, its genetic structure, post-glacial range dynamics, and consequent nativity status are poorly understood. Here we provide the fi rst study focusing on the genetic structure of in situ larch populations in the north-eastern Czech Republic using molecular genetics. Most of the studied area is traditionally considered to be a part of the autochthonous native range of the Jeseníky lineage of larch and some of the included populations are protected as belonging to this type. We confi rm a common presence of the Jeseníky type and its close evolutionary relation with larch populations from both the Carpathians and Poland. However, we also found important levels of admixture of genetic material from the Alps in all of the analyzed populations. Th e highest amount of Alpine admixture was found in the populations of intensively managed forests, the proportion of non-native material in the protected areas was relatively lower but still signifi cant. Our results show the importance of populationgenetic research for practical conservation of local populations and lineages even for common species. [ABSTRACT FROM AUTHOR]

Ochagavia (four species) and Fascicularia (one species) form a well-supported clade of the early-diverging Bromelioideae. The two genera are morphologically similar, but they can be easily discerned on the basis of generative characters. Besides the species distributed on the Chilean mainland, the group includes O. elegans , endemic to the Robinson Crusoe Island of the Juan Fernández Islands. In previous molecular phylogenetic studies, O. elegans formed a sister clade to the remainder of Fascicularia and Ochagavia. A phylogenomic approach, including nearly complete and, in five cases, full plastomes (c. 160 kbp) and the nuclear rDNA cistron (c. 6 kbp), and scanning electron microscope (SEM) images of pollen were used to analyse relationships in the Fascicularia-Ochagavia group. Plastome and nuclear trees were largely congruent and supported previous phylogenetic analyses of O. elegans being sister to the remainder of the group. A divergent phylogenetic position was suggested for O. carnea using different organellar trees. SEM analysis of pollen supported the division of Fascicularia and Ochagavia. Evolutionary and taxonomic implications of our results are discussed. [ABSTRACT FROM AUTHOR]

Changes in growth forms frequently accompany plant adaptive radiations, including páramo-a high-elevation treeless habitat type of the northern Andes. We tested whether diverse group of Senecio inhabiting montane forests and páramo represented such growth form changes. We also investigated the role of Andean geography and environment in structuring genetic variation of this group. We sampled 108 populations and 28 species of Senecio (focusing on species from former genera Lasiocephalus and Culcitium) and analyzed their genetic relationships and patterns of intraspecific variation using DNA fingerprinting (AFLPs) and nuclear DNA sequences (ITS). We partitioned genetic variation into environmental and geographical components. ITS-based phylogeny supported monophyly of a Lasiocephalus- Culcitium clade. A grade of herbaceous alpine Senecio species subtended the Lasiocephalus- Culcitium clade suggesting a change from the herbaceous to the woody growth form. Both ITS sequences and the AFLPs separated a group composed of the majority of páramo subshrubs from other group(s) comprising both forest and páramo species of various growth forms. These morphologically variable group(s) further split into clades encompassing both the páramo subshrubs and forest lianas, indicating independent switches among the growth forms and habitats. The finest AFLP genetic structure corresponded to morphologically delimited species except in two independent cases in which patterns of genetic variation instead reflected geography. Several morphologically variable species were genetically admixed, which suggests possible hybrid origins. Latitude and longitude accounted for 5%-8% of genetic variation in each of three AFLP groups, while the proportion of variation attributed to environment varied between 8% and 31% among them. A change from the herbaceous to the woody growth form is suggested for species of high-elevation Andean Senecio. Independent switches between habitats and growth forms likely occurred within the group. Hybridization likely played an important role in species diversification. [ABSTRACT FROM AUTHOR]

Identification of postglacial migration patterns and localization of possible glacial refugia are the main tasks of phylogeographical studies. Analyses of AFLPs in the European temperate shrub Rosa pendulina L. provided an insight into this issue. Similarly to a previous study of chloroplast DNA (cp DNA) haplotype variation in this species, we detected two widely distributed groups of AFLP genotypes that probably contributed to the postglacial colonization of Central Europe. The first group comprises populations from most of the Alps, the Balkans, and the Apennines. The second group includes populations from the Carpathians, the Bohemian Massif, and part of the Alps. However, geographical delimitation of the contact zone between these two lineages was situated slightly southward from the zone defined by cp DNA haplotypes. This might reflect different dispersal abilities of seeds and pollen. Populations from the Iberian Peninsula represent a separate genetic subgroup within the Alpine-Balkan group that apparently did not contribute to the most recent postglacial expansion of the species. Indications for glacial survival (defined by higher-than-average frequency-down-weighted marker values) were identified in the Balkan Peninsula and in the Southern Alps. However, one population at the northern edge of the Alps and one in the Western Carpathians also possessed very high values. This finding might be an indication of full-glacial survival in these regions and points out the importance of the Carpathians for the historical distributional changes of R. pendulina. [ABSTRACT FROM AUTHOR]

The role of glacial oscillations in shaping plant diversity has been only rarely addressed in endemics of formerly glaciated areas. The Galium pusillum group represents a rare example of an ecologically diverse and ploidy-variable species complex that exhibits substantial diversity in deglaciated northern Europe. Using AFLP and plastid and nuclear DNA sequences of 67 populations from northern, central, and western Europe with known ecological preferences, we elucidate the evolutionary history of lineages restricted to deglaciated areas and identify the eco-geographic partitioning of their genetic variation. We reveal three distinct endemic northern lineages: (i) diploids from southern Sweden + the British Isles, (ii) tetraploids from southern Scandinavia and the British Isles that show signs of ancient hybridization between the first lineage and populations from unglaciated central Europe, and (iii) tetraploids from Iceland + central Norway. Available evidence supports a stepwise differentiation of these three lineages that started at least before the last glacial maximum by processes of genome duplication, interlineage hybridization and/or allopatric evolution in distinct periglacial refugia. We reject the hypothesis of more recent postglacial speciation. Ecological characteristics of the populations under study only partly reflect genetic variation and suggest broad niches of postglacial colonizers. Despite their largely allopatric modern distributions, the north-European lineages of the G. pusillum group do not show signs of rapid postglacial divergence, in contrast to most other northern endemics. Our study suggests that plants inhabiting deglaciated areas outside the Arctic may exhibit very different evolutionary histories compared with their more thoroughly investigated high-arctic counterparts. [ABSTRACT FROM AUTHOR]

Despite the extensive use of phylogenetic methods in comparative plant biology, there is little information on how traits and their plastic responses can be affected by phylogenetic constraints (i.e. limitations in phenotypic expression resulting from the phylogenetic history of a lineage), particularly in plant radiations that may have occurred over a relatively short time period. In this study, we examined phylogenetic constraints in a monophyletic group of species of Descurainia ( Brassicaceae) endemic to the Canary Islands. We measured growth and reproductive traits in a glasshouse experiment representing 17 populations of eight taxa previously analysed in a phylogenetic context. Two water availability treatments were used to assess the plasticity of the examined traits. Most of the traits did not show strong phylogenetic signal; only weak evidence for phylogenetic constraint was found in traits related to reproduction (total number of flowers, onset of flowering) and biomass allocation to roots. Substantial levels of plasticity were observed in all the examined traits, but plasticity showed little interaction between treatment and taxon, suggesting little divergence among taxa. Our study provides evidence that phylogenetic constraints in these quantitative traits, including their plastic expression, have not played a significant role in the pattern of phenotypic diversification of this island plant group. Phenotypic plasticity may thus have favoured adjustment to the habitats occupied by each species during the radiation process. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 174, 384-398. [ABSTRACT FROM AUTHOR]

• Premise: Studies of hybridizing species are facilitated by the availability of species-specific molecular markers for identifying early- and later-generation hybrids. Cattails are a dominant feature of wetland communities, and a better understanding of the prevalence of hybrids is needed to assess the ecological and evolutionary effects of hybridization. Hybridization between Typha angustifolia and T. latifolia produce long-lived clones, known as Typha x glauca, which are considered to be invasive. Although morphological variation in cattails makes it difficult to recognize early- and later-generation hybrids, several dominant, species-specific RAPD markers are available. Our goal was to find codominant, species-specific markers with greater polymorphism than RAPDs, to identify later-generation hybrids more efficiently. • Methods: We screened nine SSR (simple sequence repeat) loci that were described from populations in Ukraine, and we surveyed 31 cattail populations from the upper Midwest and eastern USA. • Key results: Seven SSR loci distinguished the parent taxa and were consistent with known species-specific RAPD markers. allowing easier detection of backcrossing. We used linear discriminant analysis to show that F~ hybrid phenotypes were intermediate between the parent taxa, while those of backcrossed plants overlapped with the hybrids and their parents. Log(leaf length/leaf width), spike gap length, spike length, and stem diameter explained much of the variation among groups. • Conclusions: We provide the first documentation of backcrossed plants in hybridizing cattail populations in Michigan. The diagnostic SSR loci we identified should be extremely useful for examining the evolutionary and ecology interactions of hybridizing cattails in North America. [ABSTRACT FROM AUTHOR]

The phylogeographical structure amongst 39 populations of the temperate forest plant Carex pilosa in Europe was studied using amplified fragment length polymorphism (AFLP), polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), and sequencing of non-coding regions of plastid DNA. No plastid DNA polymorphisms were found within almost the entire 14 000 bp investigated, and it seems that chloroplast sequence analysis is not appropriate for studying the migration history of this species. The AFLP data also showed no clear genetic pattern. Marginal separation of central and north-eastern European populations did not allow for the detection of glacial refugia in this species. Rare AFLP fragments showed no association with geography and led to speculations regarding the possibility of glacial survival of C. pilosa in microenvironmentally suitable patches in central Europe. This is in accordance with recent palaeopalynological and macrofossil evidence. © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society, 2008, 158, 115–130. [ABSTRACT FROM AUTHOR]