The evolutionary assembly of forest communities along environmental gradients: recent diversification or sorting of pre-adapted clades?

Historical biogeographic events such as mountain orogeny are associated with the creation of environmental gradients, giving rise to the assembly of communities of species observed today. However, key gaps remain in our understanding of the relative importance of different eco-evolutionary processes acting as drivers of community assembly across environmental gradients. In this study, we test two non-exclusive hypotheses of the eco-evolutionary processes that shape tree communities across the Central Andean elevational gradient: Communities are assembled via 1) immigration and ecological sorting of pre-adapted clades, and 2) recent adaptive diversification along the elevational gradient. We used species surveys in the Bolivian and Peruvian Andes and a novel phylogenetic framework to test the relative importance of these hypotheses. Although adaptive diversification has previously been observed in specific clades, immigration and sorting of clades pre-adapted to montane habitats is the primary mechanism shaping communities across elevations.

Ecological niche partitioning in a fragmented landscape between two highly specialized avian flush-pursuit foragers in the Andean zone of sympatry

In the Andes, pairs of ecologically similar species are often separated by narrow elevational sympatry zones but the mechanisms mediating sympatry are not fully understood. Here, we describe niche partitioning within a sympatry zone in a fragmented Andean landscape between two closely related flush-pursue species: a high-elevation montane forest dweller, (Myioborus melanocephalus), and a mid-elevation montane forest dweller, (M. miniatus). As all flush-pursuers use very similar hunting techniques involving visual displays to flush and pursue insects in air, and benefit from being the “rare predators”, ecological sorting between species in sympatry zones should allow their co-existence. We found that both species occupied vegetation resembling their typical allopatric habitats: a mosaic of pastures, clearings, and shrubs with small proportion of high trees for M. melanocephalus, and dense high forests with high proportion of trees, lower irradiance and higher humidity for M. miniatus. M. melanocephalus often foraged in bushes and at lower heights, whereas M. miniatus often foraged in tree crowns. The two species differed relatively little in their foraging technique. These results demonstrate how ecological sorting permits species of divergent elevational distributions and habitats to successfully coexist in sympatric zones where habitat diversity allows both species to find their preferred habitat.

Whole genome data reveal the complex history of a diverse ecological community

How widespread ecological communities assemble remains a key question in ecology. Trophic interactions between widespread species may reflect a shared population history, or ecological sorting of local pools of species with very different population histories. Which scenario applies is central to the stability of trophic associations, and the potential for coevolution between species. Here we show how alternative community assembly hypotheses can be discriminated using whole genome data for component species, and provide a novel likelihood framework that overcomes current limitations in formal comparison of multispecies histories. We illustrate our approach by inferring the assembly history of a Western Palaearctic community of insect herbivores and parasitoid natural enemies, trophic groups that together comprise 50% of terrestrial species. We reject models of co-dispersal from a shared origin, and of delayed enemy pursuit of their herbivore hosts, arguing against herbivore attainment of ‘enemy-free space’. The community-wide distribution of species expansion times is also incompatible with a random, neutral model of assembly. Instead, we reveal a complex assembly history of single- and multi-species range expansions through the Pleistocene from different directions and over a range of timescales. Our results suggest substantial turnover in species associations, and argue against tight coevolution in this system. The approach we illustrate is widely applicable to natural communities of non-model species, and makes it possible to reveal the historical backdrop against which selection acts.

Functional stabilisation and partner selection during repeated co-culivation in a methanotrophic interactome

Background Biological oxidation of methane (CH4) is an essential ecosystem function. Accumulating evidence indicated that this function is mediated by associations of methanotrophic bacteria (MOB) with non-methanotrophic partners; together referred to as a methanotrophic interactome. Given the potency of CH4 as a greenhouse gas, a thorough understanding of how these interactomes exert an effect on methane oxidation is of special interest. Furthermore, MOB - non-MOB associations could be exploited for sustainable biotechnological applications in light of the renewed interest in MOB as natural and cost-efficient biocatalysts. The selectivity of MOB for non-MOB partners, as well as the stimulation of MOB activity (CH4 oxidation rate, MOR) with increasing non-MOB richness have both been recently described for a single batch incubation period. Therefore, we hypothesized that during repeated co-cultivation of MOB with non-MOB, ecological sorting would guide the methanotrophic interactome towards its optimal composition, which could additionally boost functionality (MOR). Methods Co-cultures of 8 non-MOB partners with a single alpha- or a single gammaproteobacterial MOB were repeatedly sub-cultivated. In every cycle, the headspace CH4 concentration was measured to over time to determine the MOR, while headspace CO2 concentrations and total protein in the culture were determined to track the fate of CH4-derived carbon (catabolism and assimilation respectively). Finally, the relative abundance of each co-culture partner was assessed using a 16S rRNA gene-targeted denaturing gradient gel electrophoresis (DGGE). Results and Discussion While no significant improvement of functionality was observed, the biological variability of MOR was stabilized by co-cultivation with non-MOB partners. Overall, higher biomass yields were obtained when MOB were co-cultivated with non-MOB partners and the alphaproteobacterial MOB appeared to be able to support more non-MOB biomass than the gammaproteobacterial MOB, which could be linked to the proposed life-strategies of these clades. A clear partner selection was observed as only 4 out of 8 initial partners were found to persist during repeated cycles of co-cultivation. While 2 of the persisting partners could coexist with either MOB type, the other two were more restricted to a specific MOB. Differential metabolic potential of non-MOB was resolved by genome mining publicly available genomes; our attempt to find clues for the partner selectivity did not reveal a clear link with the potential for C1-compound metabolism. However, genes for sugar metabolism (fructose, mannose, sucrose) were restricted to the persisting partners while genes encoding an ATP-dependent vitamin B12 importer were restricted to the non-persisting partners, underlining the importance of metabolic exchange in the methanotrophic interactome.

Functional stabilisation and partner selection during repeated co-culivation in a methanotrophic interactome

Background Biological oxidation of methane (CH4) is an essential ecosystem function. Accumulating evidence indicated that this function is mediated by associations of methanotrophic bacteria (MOB) with non-methanotrophic partners; together referred to as a methanotrophic interactome. Given the potency of CH4 as a greenhouse gas, a thorough understanding of how these interactomes exert an effect on methane oxidation is of special interest. Furthermore, MOB - non-MOB associations could be exploited for sustainable biotechnological applications in light of the renewed interest in MOB as natural and cost-efficient biocatalysts. The selectivity of MOB for non-MOB partners, as well as the stimulation of MOB activity (CH4 oxidation rate, MOR) with increasing non-MOB richness have both been recently described for a single batch incubation period. Therefore, we hypothesized that during repeated co-cultivation of MOB with non-MOB, ecological sorting would guide the methanotrophic interactome towards its optimal composition, which could additionally boost functionality (MOR). Methods Co-cultures of 8 non-MOB partners with a single alpha- or a single gammaproteobacterial MOB were repeatedly sub-cultivated. In every cycle, the headspace CH4 concentration was measured to over time to determine the MOR, while headspace CO2 concentrations and total protein in the culture were determined to track the fate of CH4-derived carbon (catabolism and assimilation respectively). Finally, the relative abundance of each co-culture partner was assessed using a 16S rRNA gene-targeted denaturing gradient gel electrophoresis (DGGE). Results and Discussion While no significant improvement of functionality was observed, the biological variability of MOR was stabilized by co-cultivation with non-MOB partners. Overall, higher biomass yields were obtained when MOB were co-cultivated with non-MOB partners and the alphaproteobacterial MOB appeared to be able to support more non-MOB biomass than the gammaproteobacterial MOB, which could be linked to the proposed life-strategies of these clades. A clear partner selection was observed as only 4 out of 8 initial partners were found to persist during repeated cycles of co-cultivation. While 2 of the persisting partners could coexist with either MOB type, the other two were more restricted to a specific MOB. Differential metabolic potential of non-MOB was resolved by genome mining publicly available genomes; our attempt to find clues for the partner selectivity did not reveal a clear link with the potential for C1-compound metabolism. However, genes for sugar metabolism (fructose, mannose, sucrose) were restricted to the persisting partners while genes encoding an ATP-dependent vitamin B12 importer were restricted to the non-persisting partners, underlining the importance of metabolic exchange in the methanotrophic interactome.

Plant trait - environmental linkages among contrasting landscapes and climate regimes in temperate eucalypt woodlands

Ecological sorting of species along climate and landscape gradients is a fundamental global pattern. However, the extent to which functional traits reflect floristic turnover in response to interactions between climate and landscape gradients is rarely assessed. We tested whether floristic variation among sites within a bioregion was more strongly correlated with soil fertility or climate. We then examined the relationship between floristic composition, environment and the co-variation of selected vegetative and regenerative functional traits. This allowed us to assess the ecological sorting of species along soil fertility and rainfall gradients and to detect any resource compensation effects via interactions between these factors. Floristic differences were equally associated with soil fertility and climate contrasts but species’ trait patterns were more strongly associated with soil fertility than rainfall. No interactive effects, which would suggest resource compensation, were detected. Instead, more fertile sites consistently had more forbs, annuals and grasses in comparison with less fertile sites which were dominated by woody species and had a higher abundance of graminoids. Three broad mechanisms for sorting of species based on trait patterns are proposed (1) differences in the fundamental regenerative and growth niche, (2) resource competition during establishment and (3) disturbance-mediated sorting.

Mortality and recruitment in a lowland tropical rain forest of French Guiana: effects of soil type and species guild

A variety of processes have been identified as playing a key role in maintenance of hyper-rich tropical forest, among which ecological sorting caused by niche partitioning challenges stochastic dispersal processes. However, demographic responses to spatio-temporal resource variation that could result in biased species distributions are still little studied. In this paper we investigate from two censuses, c. 15 y apart, of a 12-ha permanent forest sample in French Guiana, how tree recruitment and mortality rates vary among hydrological soil types known to affect species habitat preferences and among ecological guilds related to species light requirement. The results indicate that both recruitment and mortality vary significantly with respect to these factors. While the mean instantaneous mortality and recruitment rates are estimated to 0.98 and 0.81%, respectively, pioneer species, canopy trees and hydromorphic bottomland soils depart significantly from these values. In particular, the pioneers, regenerating either from the soil seed bank or from post-opening seed rain, show faster dynamics than other species. These two guilds harbour probabilities of mortality elevated by a factor of 1.9 and 3.2, respectively, and probabilities of recruitment elevated by a factor of 4.9 and 3.1, respectively. Conversely, canopy trees show slower dynamics, with probabilities of mortality and recruitment lowered by a mean factor of about 0.5 with respect to other species. We also observe that trees growing in hydromorphic bottomlands prove to have significantly higher mortality and recruitment probabilities, by a factor of about 2 with respect to those growing in terra firme.