Jeffrey A. Joseph

Barrier to gene flow between two ecologically divergent Populus species, P. alba (white poplar) and P. tremula (European aspen): the role of ecology and life history in gene introgression

The renewed interest in the use of hybrid zones for studying speciation calls for the identification and study of hybrid zones across a wide range of organisms, especially in long‐lived taxa for which it is often difficult to generate interpopulation variation through controlled crosses. Here, we report on the extent and direction of introgression between two members of the ‘model tree’ genus Populus: Populus alba (white poplar) and Populus tremula (European aspen), across a large zone of sympatry located in the Danube valley. We genotyped 93 hybrid morphotypes and samples from four parental reference populations from within and outside the zone of sympatry for a genome‐wide set of 20 nuclear microsatellites and eight plastid DNA restriction site polymorphisms. Our results indicate that introgression occurs preferentially from P. tremula to P. alba via P. tremula pollen. This unidirectional pattern is facilitated by high levels of pollen vs. seed dispersal in P. tremula (pollen/seed flow = 23.9) and by great ecological opportunity in the lowland floodplain forest in proximity to P. alba seed parents, which maintains gene flow in the direction of P. alba despite smaller effective population sizes (Ne) in this species (P. alba Nec. 500–550; P. tremula Nec. 550–700). Our results indicate that hybrid zones will be valuable tools for studying the genetic architecture of the barrier to gene flow between these two ecologically divergent Populus species.

Absence of phylogenetic signal in the niche structure of meadow plant communities

A significant proportion of the global diversity of flowering plants has evolved in recent geological time, probably through adaptive radiation into new niches. However, rapid evolution is at odds with recent research which has suggested that plant ecological traits, including the β- (or habitat) niche, evolve only slowly. We have quantified traits that determine within-habitat α diversity (α niches) in two communities in which species segregate on hydrological gradients. Molecular phylogenetic analysis of these data shows practically no evidence of a correlation between the ecological and evolutionary distances separating species, indicating that hydrological α niches are evolutionarily labile. We propose that contrasting patterns of evolutionary conservatism for α- and β-niches is a general phenomenon necessitated by the hierarchical filtering of species during community assembly. This determines that species must have similar β niches in order to occupy the same habitat, but different α niches in order to coexist.

Admixture in European Populus hybrid zones makes feasible the mapping of loci that contribute to reproductive isolation and trait differences

The use of admixed human populations to scan the genome for chromosomal segments affecting complex phenotypic traits has proved a powerful analytical tool. However, its potential in other organisms has not yet been evaluated. Here, we use DNA microsatellites to assess the feasibility of this approach in hybrid zones between two members of the ‘model tree’ genus Populus: Populus alba (white poplar) and Populus tremula (European aspen). We analyzed samples of both species and a Central European hybrid zone (N=544 chromosomes) for a genome-wide set of 19 polymorphic DNA microsatellites. Our results indicate that allele frequency differentials between the two species are substantial (mean δ=0.619±0.067). Background linkage disequilibrium (LD) in samples of the parental gene pools is moderate and should respond to sampling schemes that minimize drift and account for rare alleles. LD in hybrids decays with increasing number of backcross generations as expected from theory and approaches background levels of the parental gene pools in advanced generation backcrosses. Introgression from P. tremula into P. alba varies strongly across marker loci. For several markers, alleles from P. tremula are slightly over-represented relative to neutral expectations, whereas a single locus exhibits evidence of selection against P. tremula genotypes. We interpret our results in terms of the potential for admixture mapping in these two ecologically divergent Populus species, and we validate a modified approach of studying genotypic clines in ‘mosaic’ hybrid zones.

Admixture facilitates adaptation from standing variation in the European aspen (Populus tremula L.), a widespread forest tree

Adaptation to new environments can start from new mutations or from standing variation already present in natural populations. Whether admixture constrains or facilitates adaptation from standing variation is largely unknown, especially in ecological keystone or foundation species. We examined patterns of neutral and adaptive population divergence in Populus tremula L., a widespread forest tree, using mapped molecular genetic markers. We detected the genetic signature of postglacial admixture between a Western and an Eastern lineage of P. tremula in Scandinavia, an area suspected to represent a zone of postglacial contact for many species of animals and plants. Stringent divergence‐based neutrality tests provided clear indications for locally varying selection at the European scale. Six of 12 polymorphisms under selection were located less than 1 kb away from the nearest gene predicted by the Populus trichocarpa genome sequence. Few of these loci exhibited a signature of ‘selective sweeps’ in diversity‐based tests, which is to be expected if adaptation occurs primarily from standing variation. In Scandinavia, admixture explained genomic patterns of ancestry and the nature of clinal variation and strength of selection for bud set, a phenological trait of great adaptive significance in temperate trees, measured in a common garden trial. Our data provide a hitherto missing direct link between past range shifts because of climatic oscillations, and levels of standing variation currently available for selection and adaptation in a terrestrial foundation species.

Genomic Admixture Analysis in European Populus spp. Reveals Unexpected Patterns of Reproductive Isolation and Mating

Admixture between genetically divergent populations facilitates genomic studies of the mechanisms involved in adaptation, reproductive isolation, and speciation, including mapping of the loci involved in these phenomena. Little is known about how pre- and postzygotic barriers will affect the prospects of “admixture mapping” in wild species. We have studied 93 mapped genetic markers (microsatellites, indels, and sequence polymorphisms, ∼60,000 data points) to address this topic in hybrid zones of Populus alba and P. tremula, two widespread, ecologically important forest trees. Using genotype and linkage information and recently developed analytical tools we show that (1) reproductive isolation between these species is much stronger than previously assumed but this cannot prevent the introgression of neutral or advantageous alleles, (2) unexpected genotypic gaps exist between recombinant hybrids and their parental taxa, (3) these conspicuous genotypic patterns are due to assortative mating and strong postzygotic barriers, rather than recent population history. We discuss possible evolutionary trajectories of hybrid lineages between these species and outline strategies for admixture mapping in hybrid zones between highly divergent populations. Datasets such as this one are still rare in studies of natural hybrid zones but should soon become more common as high throughput genotyping and resequencing become feasible in nonmodel species.

Genetic analysis of post-mating reproductive barriers in hybridizing European Populus species

Molecular genetic analyses of experimental crosses provide important information on the strength and nature of post-mating barriers to gene exchange between divergent populations, which are topics of great interest to evolutionary geneticists and breeders. Although not a trivial task in long-lived organisms such as trees, experimental interspecific recombinants can sometimes be created through controlled crosses involving natural F1s. Here, we used this approach to understand the genetics of post-mating isolation and barriers to introgression in Populus alba and Populus tremula, two ecologically divergent, hybridizing forest trees. We studied 86 interspecific backcross (BC1) progeny and >350 individuals from natural populations of these species for up to 98 nuclear genetic markers, including microsatellites, indels and single nucleotide polymorphisms, and inferred the origin of the cytoplasm of the cross with plastid DNA. Genetic analysis of the BC1 revealed extensive segregation distortions on six chromosomes, and >90% of these (12 out of 13) favored P. tremula donor alleles in the heterospecific genomic background. Since selection was documented during early diploid stages of the progeny, this surprising result was attributed to epistasis, cyto-nuclear coadaptation, heterozygote advantage at nuclear loci experiencing introgression or a combination of these. Our results indicate that gene flow across ‘porous’ species barriers affects these poplars and aspens beyond neutral, Mendelian expectations and suggests the mechanisms responsible. Contrary to expectations, the Populus sex determination region is not protected from introgression. Understanding the population dynamics of the Populus sex determination region will require tests based on natural interspecific hybrid zones.

A set of novel DNA polymorphisms within candidate genes potentially involved in ecological divergence between Populus alba and P. tremula, two hybridizing European forest trees

We have identified 53 DNA (single nucleotide, microsatellite, and insertion‐deletion) polymorphisms within 12 candidate genes potentially involved in ecological differences between Populus alba and P. tremula, two hybridizing European forest trees. The genes represent candidates for functional roles associated with abiotic or biotic stress response, cross‐talk, phenology, and leaf development. Distributions within sequences, intraspecific levels of diversity, and genetic divergence (FST) between species are reported for each polymorphism, as are haplotype frequencies for each gene. The markers will be used for population genomic studies of the barrier to gene flow between these two ecologically divergent forest trees.

A PHYLOGENETIC ANALYSIS OF ALYXIEAE (APOCYNACEAE) BASED ON RBCL, MATK, TRNL INTRON, TRNL-F SPACER SEQUENCES, AND MORPHOLOGICAL CHARACTERS1

Abstract Within Rauvolfioideae (Apocynaceae), genera have long been assigned to tribes based mainly on only one or two superficial fruit and seed characters. Taxa with drupaceous fruits were included in Alyxieae. To elucidate relationships within Alyxieae, we analyzed phylogenetically a data set of sequences from four plastid DNA regions (RbcL, matK, TrnL intron, and TrnL-F intergenic spacer) and a morphological data set for 33 genera of Apocynaceae, including representatives of all genera previously included in Alyxieae and two non-Apocynaceae species. Results of parsimony analysis indicate that Alyxieae as previously delimited are polyphyletic, with most genera falling into two main clades. The Alyxia clade includes seven genera: Alyxia Banks ex R. Br., Lepinia Decne., Lepiniopsis Valeton, Pteralyxia K. Schum., and Condylocarpon Desf. together with Plectaneia Thouars. (earlier included in Plumerieae) and Chilocarpus Blume (earlier included in Chilocarpeae). The Vinca clade includes eight genera: Cabucala Pichon, Petchia Livera, Rauvolfia L., Catharanthus G. Don, Vinca L., Neisosperma Raf., Ochrosia Juss., and Kopsia Blume. Vallesia Ruiz & Pav. and Anechites Griseb. are not related to either clade and come out as sister to Aspidosperma Mart. & Zucc. (Aspidospermeae) and Thevetia L. (Plumerieae), respectively. The fruit and seed characters previously used to demarcate Alyxieae are homoplasious, as are other morphological characters such as style head structure and syncarpy versus apocarpy. Conversely, pollen morphology, which has not previously played much of a role in tribal delimitation, was shown to be the most useful morphological character for delimiting Alyxieae from other tribes of Rauvolfioideae.

Chromosome behavior at the base of the angiosperm radiation: Karyology of Trithuria submersa (Hydatellaceae, Nymphaeales)

UNLABELLED • PREMISE OF THE STUDY Hydatellaceae are minute annual herbs with potential as a model system for studying early angiosperm evolution, but their karyology and ploidy levels are almost unknown. We investigated these aspects of Trithuria submersa, a widespread species that we show to be amenable to extended vegetative propagation.• METHODS We cultivated plants of T. submersa in vitro after developing and optimizing culture conditions. We estimated genome size using flow cytometry, counted chromosome numbers using root-meristem squashes after Feulgen staining, and examined meiotic chromosome behavior using microsporocytes.• KEY RESULTS We developed methods to reliably germinate seeds of T. submersa and to propagate them vegetatively in critical thermo- and photoperiod regimes on 1/2 Murashige-Skoog (MS) medium with vitamins and 2% sucrose solidified with 0.7% agar-agar. Seedling growth requires the medium be supplemented with activated charcoal. The mean nuclear DNA content of T. submersa sporophytes is 2C = 2.74 pg (∼2.68 Gbp). The sporophytic chromosome number is 2n = 56 with a bimodal complement, which may suggest an allopolyploid origin. Some of the largest chromosomes lack a recognizable constriction, which relates to a highly unusual and irregular chromosome behavior. Microsporocytes undergo reduced and asynchronous meioses that show a modified intermediate cell division with a nucleus division by fractional postreduction, indicating partially inverted microsporogenesis.• CONCLUSIONS In vitro cultivation and karyological assessment of T. submersa open new opportunities for investigating early-divergent angiosperms. The remarkably different meiotic behavior exhibits new insights into a potentially ancestral microsporogenesis.

Beyond the EDGE with EDAM: Prioritising British Plant Species According to Evolutionary Distinctiveness, and Accuracy and Magnitude of Decline.

Conservation biologists have only finite resources, and so must prioritise some species over others. The EDGE-listing approach ranks species according to their combined evolutionary distinctiveness and degree of threat, but ignores the uncertainty surrounding both threat and evolutionary distinctiveness. We develop a new family of measures for species, which we name EDAM, that incorporates evolutionary distinctiveness, the magnitude of decline, and the accuracy with which decline can be predicted. Further, we show how the method can be extended to explore phyogenetic uncertainty. Using the vascular plants of Britain as a case study, we find that the various EDAM measures emphasise different species and parts of Britain, and that phylogenetic uncertainty can strongly affect the prioritisation scores of some species.