Influence of phenological barriers and habitat differentiation on the population genetic structure of the balearic endemic Rhamnus ludovici-salvatoris Chodat and R. alaternus L

[EN] Rhamnus ludovici-salvatoris, endemic to the Gymnesian Islands, coexists with the related and widespread R. alaternus in Mallorca and Menorca. In both species, the population genetic structure using RAPD, and flowering during a 3-year period to check for possible phenological barriers, were analyzed. Rhamnus ludovici-salvatoris showed lower genetic diversity and stronger population structure than R. alaternus, the Cabrera population being less diverse and the most differentiated. Rhamnus ludovici-salvatoris flowered one month later, although flowering of both species coincided sporadically. These congeners seem to have diverged through isolation by time and differentiation in habitat. The population genetic structure of R. ludovici-salvatoris could mainly be due to the existence of small populations on the one hand, and a gene flow caused by rare hybridization events on the other, which may also explain the presence of morphologically intermediate individuals in Menorca. The conservation of R. ludovici-salvatoris populations may include population reinforcements and other in situ interventions.Ferriol Molina, M.; Llorens García, L.; Gil, L.; Boira Tortajada, H. (2009). Influence of phenological barriers and habitat differentiation on the population genetic structure of the balearic endemic Rhamnus ludovici-salvatoris Chodat and R. alaternus L. Plant Systematics and Evolution. 277(1-2):105-116. doi:10.1007/s00606-008-0110-3S1051162771-2Affre L, Thompson JD, Debussche M (1997) Genetic structure of continental and island populations of the Mediterranean endemic Cyclamen balearicum (Primulaceae). Amer J Bot 84(4): 437–451BOIB (2005) Decreto 75/2005. BOIB 106: 29–32Bolmgren K, Oxelman B (2004) Generic limits in Rhamnus L. s.l. (Rhamnaceae) inferred from nuclear and chloroplast DNA sequence phylogenies. Taxon 53(2):383–390Bolòs O, Molinier R (1958) Recherches phytosociologiques dans l’île de Majorque. Collectanea Botanica 34:699–865Cardona MA (1979) Consideracions sobre l’endemisme i l’origen de la flora de las Illes Balears. Butlletí del Institut Catalá de Historia Natural 44 (Sec. Bot. 3):7–15Cardona MA, Contandriopoulos J (1979) Endemism and evolution in the islands of the Western Mediterranean. In: Bramwell D (ed) Plants and islands. Academic Press, London, pp 133–169Chodat L (1924) Contributions à la Géo-Botanique de Majorque. PhD Thesis, Université de Genève—Institut de Botanique, SwitzerlandCollins D, Mill RR, Moller M (2003) Species separation of Taxus baccata, T. canadensis, and T. cuspidata (Taxaceae) and origins of their reputed hybrids inferred from RAPD and cpDNA data. Amer J Bot 90(2):175–182Cronk QCB (1997) Islands: stability, diversity, conservation. Biodivers Conserv 6(3):477–493Doyle JJ, Doyle JL (1990) Isolation of plant DNA from fresh tissue. Focus 12:13–15Ducarme V, Wesselingh RA (2005) Detecting hybridization in mixed populations of Rhinanthus minor and Rhinanthus angustifolius. Folia Geobot 40(2/3):151–161Englishloeb GM, Karban R (1992) Consequences of variation in flowering phenology for seed head herbivory and reproductive success in Erigeron glaucus (Compositae). Oecologia 89:588–595Gautier F, Caluzon G, Suk JP, Violanti D (1994) Age et durée de la crise de salinité Messinienne. Comptes Rendus de l’Académie des Sciences de Paris 318:1103–1109Gerard PR, Fernandez-Manjarres JF, Frascaria-Lacoste N (2006) Temporal cline in a hybrid zone population between Fraxinus excelsior L. and Fraxinus angustifolia Vahl. Molec Ecol 15:3655–3667Gil L, Llorens L, Tébar FJ, Costa M (1995) La vegetación de la isla de Cabrera. In: Guía de la excursión geobotánica de las XV Jornadas de Fitosociología. Datos sobre la vegetación de Cabrera. Palma de Mallorca: Universitat de les Illes Balears, pp 51–77Gulías J, Flexas J, Abadía A, Medrano H (2002) Photosynthetic responses to water deficit in six Mediterranean sclerophyll species: possible factors explaining the declining distribution of Rhamnus ludovici-salvatoris, and endemic Balearic species. Tree Physiol 22:687–697Gulías J, Traveset A, Riera N, Mus M (2004) Critical stages in the recruitment process of Rhamnus alaternus L. Ann Bot 93:723–731Gustafsson S, Sjögren-Gulve P (2002) Genetic diversity in the rare orchid, Gymnadenia odoratissima and a comparison with the more common congener, G. conopsea. Conserv Genet 3:225–234Gustafsson S (2003) Population genetic analyses in the orchid genus Gymnadenia—a conservation genetic perspective. PhD Thesis, Uppsala University, SwedenGustafsson S, Lönn M (2003) Genetic differentiation and habitat preference of flowering-time variants within Gymnadenia conopsea. Heredity 91:284–292Harris W (1996) Genecological aspects of flowering patterns of populations of Kunzea ericoides and K. sinclairii (Myrtaceae). New Zealand J Bot 34:333–354Hendry AP, Dray T (2005) Population structure attributable to reproductive time: isolation by time and adaptation by time. Molec Ecol 14:901–916Hosokawa K, Minami M, Kawahara K, Nakamura I, Shibata T (2000) Discrimination among three species of medicinal Scutellaria plants using RAPD markers. Pl Med 66:270–272Huang Z, Liu L, Zhou T, Ju B (2005) Effects of environmental factors on the population genetic structure in chukar partridge (Alectoris chukar). J Arid Environ 62:427–434Juan A, Crespo MB, Cowan RS, Lexer C, Fay F (2004) Patterns of variability and gene flow in Medicago citrina, an endangered endemic of islands in the western Mediterranean, as revealed by amplified fragment length polymorphism (AFLP). Molec Ecol 13:2679–2690Krijgsman W, Hilgen FJ, Raffi I, Sierro FJ, Wilson DS (1999) Chronology, causes and progression of the Messinian salinity crisis. Nature 400:652–655Lamont BB, He T, Enright NJ, Krauss SL, Miller BP (2003) Anthropogenic disturbance promotes hybridization between Banksia species by altering their biology. J Evol Biol 16:551–557Lennartsson T (1997) Seasonal differentiation—a conservative reproductive barrier in two grassland Gentianella (Gentianaceae) species. Pl Syst Evol 208:45–69Martinez-Solis I, Iranzo J, Estrelles E, Ibars AM (1993) Leaf domatia in the section Alaternus (Miller) DC. of the genus Rhamnus (Rhamnaceae). Bot J Linn Soc 112:311–318McIntosh ME (2002) Flowering phenology and reproductive output in two sister species of Ferocactus (Cactaceae). Pl Ecol 159:1–13Nei M (1973) Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci USA 70:3321–3323Nei M (1978) Estimation of average heterozigosity and genetic distance from a small number of individuals. Genetics 89:583–590Nei M, Li W (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci USA 79:5269–5273Nybom H, Bartish IV (2000) Effects of life history traits and sampling strategies on genetic diversity estimates obtained with RAPD markers in plants. Perspect Pl Ecol Evol Syst 3(2):93–114Oostermeijer JGB, Luijten SH, Ellis-Adam AC, den Nijs JCM (2002) Future prospects for the rare, late-flowering Gentianella germanica and Gentianopsis ciliata in Dutch nutrient-poor calcareous grasslands. Biol Conserv 104:339–350Pease CM, Lande R, Bull JJ (1989) A model of population growth, dispersal and evolution in a changing environment. Ecology 70(6):1657–1664Perron M, Gordon AG, Bousquet J (1995) Species-specific RAPD fingerprints for the closely related Picea mariana and P. rubens. Theor Appl Genet 91:142–149Pierce S, Ceriani RM, Villa M, Cerabolini B (2006) Quantifying relative extinction risks and targeting intervention for the orchid flora of a natural park in the European prealps. Conserv Biol 20(6):1804–1810Richardson JE, Fay MF, Cronk QCB, Bowman D, Chase MW (2000) A phylogenetic analysis of Rhamnaceae using rbcL and trnL-F plastid DNA sequences. Amer J Bot 87(9):1309–1324Roselló JA, Sáez L (2000) Index Balearicum: an annotated check-list of the vascular plants described from the Balearic Islands. Collect Bot 25(1):3–203Roselló JA, Cebrián MC, Mayol M (2002) Testing taxonomic and biogeographical relationships in a narrow mediterranean endemic complex (Hippocrepis balearica) using RAPD markers. Ann Bot 89:321–327Sales E, Nebauer SG, Mus M, Segura J (2001) Population genetic study in the Balearic plant species Digitalis minor (Scrophulariaceae) using RAPD markers. Amer J Bot 88(10):1750–1759Sherwin WB, Moritz C (2000) Managing and monitoring genetic erosion. In: Young AG, Clarke GM (eds) Genetics, demography and viability of fragmented populations. Cambridge University Press, Cambridge, pp 9–34Sneath PHA, Sokal RR (1973) Numerical taxonomy. Freeman and Co., San FranciscoTraveset A, Gulías J, Riera N, Mus M (2003) Transition probabilities from pollination to establishment in a rare dioecious shrub species (Rhamnus ludovici-salvatoris) in two habitats. J Ecol 91:427–437Tutin TG, Heywood VH, Burges NA, Valentine DH, Walters SM, Webb DA (eds) (2001) Flora Europaea, vol 2. Rosaceae to Umbelliferae. Cambridge University Press, CambridgeWright S (1931) Evolution in Mendelian populations. Genetics 16:97–159Zimmerman M (1980a) Reproduction in Polemonium: pre-dispersal seed predation. Ecology 61:502–506Zimmerman M (1980b) Reproduction in Polemonium: competition for pollinators. Ecology 61:497–50

Deconstruction of the (Paleo)Polyploid Grapevine Genome Based on the Analysis of Transposition Events Involving NBS Resistance Genes

Plants have followed a reticulate type of evolution and taxa have frequently merged via allopolyploidization. A polyploid structure of sequenced genomes has often been proposed, but the chromosomes belonging to putative component genomes are difficult to identify. The 19 grapevine chromosomes are evolutionary stable structures: their homologous triplets have strongly conserved gene order, interrupted by rare translocations. The aim of this study is to examine how the grapevine nucleotide-binding site (NBS)-encoding resistance (NBS-R) genes have evolved in the genomic context and to understand mechanisms for the genome evolution. We show that, in grapevine, i) helitrons have significantly contributed to transposition of NBS-R genes, and ii) NBS-R gene cluster similarity indicates the existence of two groups of chromosomes (named as Va and Vc) that may have evolved independently. Chromosome triplets consist of two Va and one Vc chromosomes, as expected from the tetraploid and diploid conditions of the two component genomes. The hexaploid state could have been derived from either allopolyploidy or the separation of the Va and Vc component genomes in the same nucleus before fusion, as known for Rosaceae species. Time estimation indicates that grapevine component genomes may have fused about 60 mya, having had at least 40–60 mya to evolve independently. Chromosome number variation in the Vitaceae and related families, and the gap between the time of eudicot radiation and the age of Vitaceae fossils, are accounted for by our hypothesis

Patterns of Polymorphism and Demographic History in Natural Populations of Arabidopsis lyrata

Many of the processes affecting genetic diversity act on local populations. However, studies of plant nucleotide diversity have largely ignored local sampling, making it difficult to infer the demographic history of populations and to assess the importance of local adaptation. Arabidopsis lyrata, a self-incompatible, perennial species with a circumpolar distribution, is an excellent model system in which to study the roles of demographic history and local adaptation in patterning genetic variation.We studied nucleotide diversity in six natural populations of Arabidopsis lyrata, using 77 loci sampled from 140 chromosomes. The six populations were highly differentiated, with a median FST of 0.52, and structure analysis revealed no evidence of admixed individuals. Average within-population diversity varied among populations, with the highest diversity found in a German population; this population harbors 3-fold higher levels of silent diversity than worldwide samples of A. thaliana. All A. lyrata populations also yielded positive values of Tajima's D. We estimated a demographic model for these populations, finding evidence of population divergence over the past 19,000 to 47,000 years involving non-equilibrium demographic events that reduced the effective size of most populations. Finally, we used the inferred demographic model to perform an initial test for local adaptation and identified several genes, including the flowering time gene FCA and a disease resistance locus, as candidates for local adaptation events.Our results underscore the importance of population-specific, non-equilibrium demographic processes in patterning diversity within A. lyrata. Moreover, our extensive dataset provides an important resource for future molecular population genetic studies of local adaptation in A. lyrata

Life history, climate and biogeography interactively affect worldwide genetic diversity of plant and animal populations.

Understanding how biological and environmental factors interactively shape the global distribution of plant and animal genetic diversity is fundamental to biodiversity conservation. Genetic diversity measured in local populations (GDP) is correspondingly assumed representative for population fitness and eco-evolutionary dynamics. For 8356 populations across the globe, we report that plants systematically display much lower GDP than animals, and that life history traits shape GDP patterns both directly (animal longevity and size), and indirectly by mediating core-periphery patterns (animal fecundity and plant dispersal). Particularly in some plant groups, peripheral populations can sustain similar GDP as core populations, emphasizing their potential conservation value. We further find surprisingly weak support for general latitudinal GDP trends. Finally, contemporary rather than past climate contributes to the spatial distribution of GDP, suggesting that contemporary environmental changes affect global patterns of GDP. Our findings generate new perspectives for the conservation of genetic resources at worldwide and taxonomic-wide scales