Genetic relationships and variation in reproductive strategies in four closely related bromeliads adapted to neotropical ‘inselbergs': Alcantarea glaziouana, A. regina, A. geniculata and A. imperialis (Bromeliaceae)

Background and Aims Bromeliads (Bromeliaceae) adapted to rock outcrops or ‘inselbergs' in neotropical rain forests have been identified as suitable plant models for studying population divergence and speciation during continental plant radiations. Little is known about genetic relationships and variation in reproductive strategies within and among inselberg-adapted species, yet knowledge of these parameters is important for understanding divergence processes and for conservation planning. Methods Nuclear microsatellites were used to assess the role of clonal reproduction, estimate genetic diversity and explore genetic relationships and variation in reproductive strategies for a total of 15 populations of four closely related Alcantarea inselberg species in south-eastern Brazil: A. glaziouana, A. regina, A. geniculata and A. imperialis. Key Results Clonal propagation is frequent in coastal populations of A. glaziouana and A. regina, but absent in the high-altitude species A. geniculata and A. imperialis. Considerable variation in clonal diversity, gene diversity (He), allelic richness, and Wright's inbreeding coefficient (FIS) exists within and between species of Alcantarea. A Bayesian analysis of coastal inselberg species indicated pronounced genetic structure. A neighbor-joining analysis grouped populations of each species together with moderate bootstrap support, except for the high altitude species A. imperialis. Conclusions The coastal inselberg species A. glaziouana and A. regina tend to propagate asexually via vegetative clonal growth, and both reproductive strategies and breeding systems vary greatly between populations and species of Alcantarea. The microsatellite data indicate a history of hybridization and reticulation involving the high-altitude species A. geniculata and A. imperialis in areas of co-occurrence. The results highlight the need to understand similarities and differences in reproductive strategies both within and between related species for conservation planning and as a basis for understanding evolutionary processes in tropical radiation

Gene flow and diversification in a species complex of Alcantarea inselberg bromeliads

Inselberg-adapted species of bromeliads (Bromeliaceae) have been suggested as model systems for understanding the evolutionary genetics of species complexes and radiations in terrestrial, island-like environments. Bromeliads are particularly suitable for addressing the potential roles of interspecific gene exchange during plant speciation and radiation. We have studied populations of five narrowly endemic Alcantarea species adapted to high-elevation inselbergs of the Atlantic Rainforest of Brazil with nuclear and plastid DNA markers, estimated outcrossing rates in the giant bromeliad A. imperialis using progeny arrays and carried out a pilot study on the use of next generation sequencing-based genotyping in this group. Our results suggest widespread and asymmetric interspecific gene flow in the studied species complex, which visibly affects patterns of genetic diversity in the phenotypically variable mixed outcrosser A. imperialis. Our data support the hypothesis that gene flow has contributed to the origin of phenotypic forms in the A. imperialis s.l. species complex. We discuss potential conflicts between our neutral marker data and previous taxonomic work and suggest how these might be resolved. We close with a brief outlook on the potential of genomic tools to uncover the hidden links between genotypes, phenotypes and niches in bromeliads and other plant radiations

Recombinant hybrids retain heterozygosity at many loci: new insights into the genomics of reproductive isolation in Populus

The maintenance of species barriers in the face of gene flow is often thought to result from strong selection against intermediate genotypes, thereby preserving genetic differentiation. Most speciation genomic studies thus aim to identify exceptionally divergent loci between populations, but divergence will be affected by many processes other than reproductive isolation (RI) and speciation. Through genomic studies of recombinant hybrids sampled in the wild, genetic variation associated with RI can be observed in situ, because selection against incompatible genotypes will leave detectable patterns of variation in the hybrid genomes. To better understand the mechanisms directly involved in RI, we investigated three natural ‘replicate’ hybrid zones between two divergent Populus species via locus-specific patterns of ancestry across recombinant hybrid genomes. As expected, genomic patterns in hybrids and their parental species were consistent with the presence of underdominant selection at several genomic regions. Surprisingly, many loci displayed greatly increased between-species heterozygosity in recombinant hybrids despite striking genetic differentiation between the parental genomes, the opposite of what would be expected with selection against intermediate genotypes. Only a limited, reproducible set of genotypic combinations was present in hybrid genomes across localities. In the absence of clearly delimited ‘hybrid habitats’, our results suggest that complex epistatic interactions within genomes play an important role in advanced stages of RI between these ecologically divergent forest trees. This calls for more genomic studies that test for unusual patterns of genomic ancestry in hybridizing species

Patterns of genetic diversity and differentiation in resistance gene clusters of two hybridizing European Populus species

Resistance genes (R-genes) are essential for long-lived organisms such as forest trees, which are exposed to diverse herbivores and pathogens. In short-lived model species, R-genes have been shown to be involved in species isolation. Here, we studied more than 400 trees from two natural hybrid zones of the European Populus species Populus alba and Populus tremula for microsatellite markers located in three R-gene clusters, including one cluster situated in the incipient sex chromosome region. The results indicate that all three R-gene clusters present extensive linkage disequilibrium (LD). Outlier tests suggest balancing selection as a potential driver of R-gene diversity, but divergent selection was also detected. Nucleotide-binding site leucine-rich repeat (NBS-LRR) type R-gene clusters exhibit low species differentiation and appear to be affected by shared selection pressures between species, recurrent interspecific gene flow, or both. Our results are consistent with a role for R-gene clusters in the evolution of chromosome XIX, recently put forward as an incipient sex chromosome in Populus

Range-wide patterns of nuclear and chloroplast DNA diversity in Vriesea gigantea (Bromeliaceae), a neotropical forest species

The processes that have shaped the extraordinary species diversity in neotropical rainforests are poorly understood, and knowledge about the patterns of genetic diversity across species' ranges is scarce, in contrast to other regions of the globe. We have conducted a range-wide study of genetic diversity in a plant endemic to the Brazilian Atlantic Rainforest, Vriesea gigantea (Bromeliaceae), based on a combined data set of nuclear microsatellites and chloroplast (cp) DNA markers typed in 429 plants from 13 populations. The results indicate a strong negative correlation between genetic diversity and population latitude, consistent with historical forest expansion from the northern half of the present distribution range. A deep phylogeographic split exists between the Brazilian states of São Paulo and Rio de Janeiro at ca. 23 °S latitude, probably reflecting past population isolation within more than one glacial refuge during the climatic changes of the Pleistocene. A comparison of genetic structures at cpDNA and nuclear markers revealed a pollen/seed flow ratio of more than 3:1, thus indicating an important role of the pollinating animals (that is, bats) in shaping the population genetic structure of this species. Diversity was reduced for cpDNA markers in the island populations off the coast, and reduced diversity and increased differentiation were observed for both nuclear and cpDNA at the edges of the species' range. The link between patterns of genetic and species diversity supports the hypothesis that both were shaped by the same biogeographic processes, triggered by the climatic oscillations of the Pleistocene

Molecular phylogenetics of the Brazilian giant bromeliads (Alcantarea, Bromeliaceae): implications for morphological evolution and biogeography

The genus Alcantarea comprises near 30 species endemic to rocky outcrops from eastern Brazil. Most species are ornamental and several are threatened due to habitat loss and over collection. In this paper we examine the phylogenetics of Alcantarea and its relationship with the Brazilian members of Vriesea, a genus of which Alcantarea has been treated as a subgenus. We discuss the morphological evolution of the stamen position and its implication for pollination and the occurrence of Alcantarea in the Espinhaço mountain range rocky savanna-like habitat vegetation. DNA sequence data derived from two plastid markers (trnK-rps16, trnC-petN) and from a low copy nuclear gene (Floricaula/Leafy) together with 20 nuclear microsatellite loci were the data source to perform analyses and construct phylogenetic and Neighbor Joining trees for the genus. Alcantarea is well supported as monophyletic in both Bayesian and parsimony analyses, but sections of Vriesea, represented by the eastern Brazilian species, appear paraphyletic. Microsatellites delimit geographically isolated species groups. Nevertheless individuals belonging to a single species may appear related to distinct clusters of species, suggesting that hybridization and/or homoplasy and/or incomplete lineage sorting are also influencing the analysis based on such markers and may be the reasons for some unexpected results. Alcantarea brasiliana is hypothesized as putative hybrid between A. imperialis and A. geniculata. Spreading stamens, a morphological floral characteristic assumed to be related to Chiropterophily, apparently evolved multiple times within the genus, and invasion of rocky savanna-like habitat vegetation by Atlantic rainforest ancestors seems to have occurred multiple times as well

Sympatric bromeliad species (Pitcairnia spp.) facilitate tests of mechanisms involved in species cohesion and reproductive isolation in Neotropical inselbergs

The roles of intra- and interspecific gene flow in speciation and species evolution are topics of great current interest in molecular ecology and evolutionary biology. Recent modelling studies call for new empirical data to test hypotheses arising from the recent shift from a ‘whole-genome reproductive isolation’ view to a ‘genic’ view of species and speciation. Particularly scarce (and thus of particular interest) are molecular genetic data on recently radiated, naturally hybridizing species in strongly structured and species-rich environments. Here, we studied four sympatric plant species (Pitcairnia spp.; Bromeliaceae) adapted to Neotropical inselbergs (isolated outcrops resembling habitat ‘islands’ in tropical rainforests) using nuclear and plastid DNA. Patterns of plastid DNA haplotype sharing and nuclear genomic admixture suggest the presence of both, incomplete lineage sorting and interspecific gene flow over extended periods of time. Integrity and cohesion of inselberg species of Pitcairnia are maintained despite introgression and in the face of extremely low within-species migration rates (Nem < 1 migrant per generation). Cross-evaluation of our genetic data against published pollination experiments indicate that species integrity is maintained by the simultaneous action of multiple prezygotic barriers, including flowering phenology, pollinator isolation and divergent mating systems. Postzygotic Bateson–Dobzhansky–Muller incompatibilities appear to contribute to isolation, as suggested by asymmetric introgression rates of single loci. Our results suggest that incomplete lineage sorting, hybridization and introgression form integral aspects of adaptive radiation in Neotropical inselberg ‘archipelagos’. Inselbergs with multiple closely related co-occurring species should be of special interest to students of speciation in mountain systems, and to ongoing conservation programmes in the Atlantic Rainforest biodiversity hotspot

Gene flow and diversification in a species complex of Alcantarea inselberg bromeliads

Inselberg-adapted species of bromeliads (Bromeliaceae) have been suggested as model systems for understanding the evolutionary genetics of species complexes and radiations in terrestrial, island-like environments. Bromeliads are particularly suitable for addressing the potential roles of interspecific gene exchange during plant speciation and radiation. We have studied populations of five narrowly endemic Alcantarea species adapted to high-elevation inselbergs of the Atlantic Rainforest of Brazil with nuclear and plastid DNA markers, estimated outcrossing rates in the giant bromeliad A. imperialis using progeny arrays and carried out a pilot study on the use of next generation sequencing-based genotyping in this group. Our results suggest widespread and asymmetric interspecific gene flow in the studied species complex, which visibly affects patterns of genetic diversity in the phenotypically variable mixed outcrosser A. imperialis. Our data support the hypothesis that gene flow has contributed to the origin of phenotypic forms in the A. imperialis s.l. species complex. We discuss potential conflicts between our neutral marker data and previous taxonomic work and suggest how these might be resolved. We close with a brief outlook on the potential of genomic tools to uncover the hidden links between genotypes, phenotypes and niches in bromeliads and other plant radiations

Genetic relationships and variation in reproductive strategies in four closely related bromeliads adapted to neotropical ‘inselbergs’: Alcantarea glaziouana, A. regina, A. geniculata and A. imperialis (Bromeliaceae)

Background and Aims: Bromeliads (Bromeliaceae) adapted to rock outcrops or ‘inselbergs’ in neotropical rain forests have been identified as suitable plant models for studying population divergence and speciation during continental plant radiations. Little is known about genetic relationships and variation in reproductive strategies within and among inselberg-adapted species, yet knowledge of these parameters is important for understanding divergence processes and for conservation planning.Methods: Nuclear microsatellites were used to assess the role of clonal reproduction, estimate genetic diversity and explore genetic relationships and variation in reproductive strategies for a total of 15 populations of four closely related Alcantarea inselberg species in south-eastern Brazil: A. glaziouana, A. regina, A. geniculata and A. imperialis.Key Results: Clonal propagation is frequent in coastal populations of A. glaziouana and A. regina, but absent in the high-altitude species A. geniculata and A. imperialis. Considerable variation in clonal diversity, gene diversity (He), allelic richness, and Wright's inbreeding coefficient (FIS) exists within and between species of Alcantarea. A Bayesian analysis of coastal inselberg species indicated pronounced genetic structure. A neighbor-joining analysis grouped populations of each species together with moderate bootstrap support, except for the high altitude species A. imperialis.Conclusions: The coastal inselberg species A. glaziouana and A. regina tend to propagate asexually via vegetative clonal growth, and both reproductive strategies and breeding systems vary greatly between populations and species of Alcantarea. The microsatellite data indicate a history of hybridization and reticulation involving the high-altitude species A. geniculata and A. imperialis in areas of co-occurrence. The results highlight the need to understand similarities and differences in reproductive strategies both within and between related species for conservation planning and as a basis for understanding evolutionary processes in tropical radiations