Beta diversity at multiple hierarchical levels: explaining the high diversity of scarab beetles in tropical montane forests

Aim: High gamma diversity in tropical montane forests may be ascribed to high geographical turnover of community composition, resulting from population isolation that leads to speciation. We studied the evolutionary processes responsible for diversity and turnover in assemblages of tropical scarab beetles (Scarabaeidae) by assessing DNA sequence variation at multiple hierarchical levels. Location: A 300-km transect across six montane forests (900–1100 m) in Costa Rica. Methods: Assemblages of Scarabaeidae (subfamilies Dynastinae, Rutelinae, Melolonthinae) including 118 morphospecies and > 500 individuals were sequenced for the cox1 gene to establish species limits with a mixed Yule–coalescent method. A species-level phylogenetic tree was constructed from cox1 and rrnL genes. Total diversity and turnover among assemblages were then assessed at three hierarchical levels: haplotypes, species and higher clades. Results: DNA-based analyses showed high turnover among communities at all hierarchical levels. Turnover was highest at the haplotype level (community similarity 0.02–0.12) and decreased with each step of the hierarchy (species: 0.21–0.46; clades: 0.41–0.43). Both compositional and phylogenetic similarities of communities were geographically structured, but turnover was not correlated with distance among forests. When three major clades were investigated separately, communities of Dynastinae showed consistently higher alpha diversity, larger species ranges and lower turnover than Rutelinae and Melolonthinae. Main conclusions: Scarab communities of montane forests show evidence of evolutionary persistence of communities in relative isolation, presumably tracking suitable habitats elevationally to accommodate climatic changes. Patterns of diversity on all hierarchical levels seem to be determined by restricted dispersal, and differences in Dynastinae could be explained by their greater dispersal ability. Community-wide DNA sequencing across multiple lineages and hierarchical levels reveals the evolutionary processes that led to high beta diversity in tropical montane forests through time.

Molecular Techniques (2015-2016). Lesson 8

Powerpoint slides for Lesson 8.

Sequencing and functional analysis of the genome of a nematode egg-parasitic fungus, Pochonia chlamydosporia

Pochonia chlamydosporia is a worldwide-distributed soil fungus with a great capacity to infect and destroy the eggs and kill females of plant-parasitic nematodes. Additionally, it has the ability to colonize endophytically roots of economically-important crop plants, thereby promoting their growth and eliciting plant defenses. This multitrophic behavior makes P. chlamydosporia a potentially useful tool for sustainable agriculture approaches. We sequenced and assembled ∼41 Mb of P. chlamydosporia genomic DNA and predicted 12,122 gene models, of which many were homologous to genes of fungal pathogens of invertebrates and fungal plant pathogens. Predicted genes (65%) were functionally annotated according to Gene Ontology, and 16% of them found to share homology with genes in the Pathogen Host Interactions (PHI) database. The genome of this fungus is highly enriched in genes encoding hydrolytic enzymes, such as proteases, glycoside hydrolases and carbohydrate esterases. We used RNA-Seq technology in order to identify the genes expressed during endophytic behavior of P. chlamydosporia when colonizing barley roots. Functional annotation of these genes showed that hydrolytic enzymes and transporters are expressed during endophytism. This structural and functional analysis of the P. chlamydosporia genome provides a starting point for understanding the molecular mechanisms involved in the multitrophic lifestyle of this fungus. The genomic information provided here should also prove useful for enhancing the capabilities of this fungus as a biocontrol agent of plant-parasitic nematodes and as a plant growth-promoting organism.