Genetic consequences of tropical second-growth forest regeneration

Secondary forests are more extensive than old-growth forests in many tropical regions, yet the genetic composition of colonizing populations is poorly understood. We analyzed the parentage of a founder population of 130 individuals of the canopy palm Iriartea deltoidea in a 24-year-old second-growth forest in lowland Costa Rica. Among 66 trees in adjacent old-growth forest, only two individuals contributed 56% of the genes in founders. Second-growth trees had lower genetic diversity and larger patches of similar genotypes than old-growth trees. Recovery of genetic diversity of populations in tropical second-growth forests may take many generations and will require continued dispersal from genetically diverse source populations

The Douglas-Fir Genome Sequence Reveals Specialization of the Photosynthetic Apparatus in Pinaceae.

A reference genome sequence for Pseudotsuga menziesii var. menziesii (Mirb.) Franco (Coastal Douglas-fir) is reported, thus providing a reference sequence for a third genus of the family Pinaceae. The contiguity and quality of the genome assembly far exceeds that of other conifer reference genome sequences (contig N50 = 44,136 bp and scaffold N50 = 340,704 bp). Incremental improvements in sequencing and assembly technologies are in part responsible for the higher quality reference genome, but it may also be due to a slightly lower exact repeat content in Douglas-fir vs. pine and spruce. Comparative genome annotation with angiosperm species reveals gene-family expansion and contraction in Douglas-fir and other conifers which may account for some of the major morphological and physiological differences between the two major plant groups. Notable differences in the size of the NDH-complex gene family and genes underlying the functional basis of shade tolerance/intolerance were observed. This reference genome sequence not only provides an important resource for Douglas-fir breeders and geneticists but also sheds additional light on the evolutionary processes that have led to the divergence of modern angiosperms from the more ancient gymnosperms

The Evolution of an Invasive Plant, Sorghum halepense L. (Johnsongrass).

From noble beginnings as a prospective forage, polyploid Sorghum halepense (Johnsongrass) is both an invasive species and one of the worlds worst agricultural weeds. Formed by S. bicolor x S. propinquum hybridization, we show S. halepense to have S. bicolor-enriched allele composition and striking mutations in 5,957 genes that differentiate it from representatives of its progenitor species and an outgroup. The spread of S. halepense may have been facilitated by introgression from closely-related cultivated sorghum near genetic loci affecting rhizome development, seed size, and levels of lutein, a photochemical protectant and abscisic acid precursor. Rhizomes, subterranean stems that store carbohydrates and spawn clonal propagules, have growth correlated with reproductive rather than other vegetative tissues, and increase survival of both temperate cold seasons and tropical dry seasons. Rhizomes of S. halepense are more extensive than those of its rhizomatous progenitor S. propinquum, with gene expression including many alleles from its non-rhizomatous S. bicolor progenitor. The first surviving polyploid in its lineage in ∼96 million years, its post-Columbian spread across six continents carried rich genetic diversity that in the United States has facilitated transition from agricultural to non-agricultural niches. Projected to spread another 200-600 km northward in the coming century, despite its drawbacks S. halepense may offer novel alleles and traits of value to improvement of sorghum

Parentage analysis of a regenerating canopy palm population in a tropical second-growth forest

Tropical secondary forests cover an estimated 500 million ha globally encompassing more land area than old-growth forests in many countries. Secondary forests will form the genetic template of future forests, and therefore require scientific attention. I studied dispersal and parentage of three generations of the abundant, animal-dispersed Neotropical canopy palm Iriartea deltoidea in a 24-yr old second-growth forest in northeastern Costa Rica. The founding generation revealed an extreme case of reproductive dominance, where more than half were produced as a result of mating events between only two of the 66 potential parent trees located in the adjacent old-growth forest. Spatial genetic analysis of trees in both forests demonstrated significantly lower genetic diversity among second-growth trees compared to the adjacent old-growth forest population. Inbreeding among founding trees within 400 m of the border with old-growth forest produced a cascading effect in the first generation of seedlings, further depressing genetic diversity. In contrast, seedlings and saplings in the old-growth and the distant portion (400-800 m) of second-growth forest showed high genetic diversity among all size classes. Seed dispersal and pollination distances obtained from the parentage analysis indicate a very large genetic neighborhood in this palm. Detailed analysis of parentage in five seedling patches surrounding reproductive trees revealed that few to none of the seedlings were produced by respective focal trees. At first sight, what appear to be seedling shadows of individual reproductive trees are, in fact, clusters of recruited seedlings from mixed genetic sources. Targeted deposition of seeds by toucans renders inverse models inaccurate for prediction of seed dispersal, as these models assume that the nearest reproductive tree is the genetic parent. Further, seedlings were to a large extent full or half-siblings originating from dozens of parents spread over large areas. Long-term genetic recovery of this species is possible, provided that diverse forests with intact animal dispersers remain in the surrounding landscape. At least for vertebrate-dispersed tree species with high rates of long-distance dispersal, second-growth forests can mitigate biodiversity loss following deforestation.

Parentage analysis of a regenerating canopy palm population in a tropical second-growth forest

Tropical secondary forests cover an estimated 500 million ha globally encompassing more land area than old-growth forests in many countries. Secondary forests will form the genetic template of future forests, and therefore require scientific attention. I studied dispersal and parentage of three generations of the abundant, animal-dispersed Neotropical canopy palm Iriartea deltoidea in a 24-yr old second-growth forest in northeastern Costa Rica. The founding generation revealed an extreme case of reproductive dominance, where more than half were produced as a result of mating events between only two of the 66 potential parent trees located in the adjacent old-growth forest. Spatial genetic analysis of trees in both forests demonstrated significantly lower genetic diversity among second-growth trees compared to the adjacent old-growth forest population. Inbreeding among founding trees within 400 m of the border with old-growth forest produced a cascading effect in the first generation of seedlings, further depressing genetic diversity. In contrast, seedlings and saplings in the old-growth and the distant portion (400-800 m) of second-growth forest showed high genetic diversity among all size classes. Seed dispersal and pollination distances obtained from the parentage analysis indicate a very large genetic neighborhood in this palm. Detailed analysis of parentage in five seedling patches surrounding reproductive trees revealed that few to none of the seedlings were produced by respective focal trees. At first sight, what appear to be seedling shadows of individual reproductive trees are, in fact, clusters of recruited seedlings from mixed genetic sources. Targeted deposition of seeds by toucans renders inverse models inaccurate for prediction of seed dispersal, as these models assume that the nearest reproductive tree is the genetic parent. Further, seedlings were to a large extent full or half-siblings originating from dozens of parents spread over large areas. Long-term genetic recovery of this species is possible, provided that diverse forests with intact animal dispersers remain in the surrounding landscape. At least for vertebrate-dispersed tree species with high rates of long-distance dispersal, second-growth forests can mitigate biodiversity loss following deforestation.

Data from: Reconstructing changes in the genotype, phenotype, and climatic niche of an introduced species

An introduced species must contend with enormous environmental variation in its introduced range. In this study, we use niche models and ordination analyses to reconstruct changes in genotype, phenotype, and climatic niche of Johnsongrass (Sorghum halepense), which is regarded as one of the world's most threatening invasive plants. In the United States, Johnsongrass has rapidly evolved within- and among-population genetic diversity; our results show that genetic differentiation in expanding Johnsongrass populations has resulted in phenotypic variation that is consistent with habitat and climatic variation encountered during its expansion. Moreover, Johnsongrass expanded from agricultural to non-agricultural habitat, and now, despite occupying overlapping ranges, extant agricultural and non-agricultural populations are genetically and phenotypically distinct and manifest different plastic responses when encountering environmental variation. Non-agricultural accessions are broadly distributed in climatic and geographic space and their fitness traits demonstrate plastic responses to common garden conditions that are consistent with local specialization. In contrast, agricultural accessions demonstrate “general purpose” plastic responses and have more restricted climatic niches and geographic distributions. They also grow much larger than non-agricultural accessions. If these differences are adaptive, our results suggest that adaptation to local habitat variation plays a crucial role in the ecology of this invader. Further, its success relates to its ability to succeed on dual fronts, by responding simultaneously to habitat and climate variability and by capitalizing on differential responses to these factors during its range expansion

Comparative transcriptomics of tropical woody plants supports fast and furious strategy along the leaf economics spectrum in lianas

Lianas, climbing woody plants, influence the structure and function of tropical forests. Climbing traits have evolved multiple times, including ancestral groups such as gymnosperms and pteridophytes, but the genetic basis of the liana strategy is largely unknown. Here, we use a comparative transcriptomic approach for 47 tropical plant species, including ten lianas of diverse taxonomic origins, to identify genes that are consistently expressed or downregulated only in lianas. Our comparative analysis of full-length transcripts enabled the identification of a core interactomic network common to lianas. Sets of transcripts identified from our analysis reveal features related to functional traits pertinent to leaf economics spectrum in lianas, include upregulation of genes controlling epidermal cuticular properties, cell wall remodeling, carbon concentrating mechanism, cell cycle progression, DNA repair and a large suit of downregulated transcription factors and enzymes involved in ABA-mediated stress response as well as lignin and suberin synthesis. All together, these genes are known to be significant in shaping plant morphologies through responses such as gravitropism, phyllotaxy and shade avoidance