The competitive exclusion-tolerance rule explains habitat partitioning among co-occurring species of burying beetles

Habitat partitioning among co-occurring, ecologically similar species is widespread in nature and thought to be an important mechanism for coexistence. The factors that cause habitat partitioning, however, are unknown for most species. We experimentally tested among three alternative hypotheses to explain habitat partitioning among two species of co-occurring burying beetle (Nicrophorus) that occupy forest (Nicrophorus orbicollis) and wetland (Nicrophorus hebes) habitats. Captive experiments revealed that the larger N. orbicollis (forest) was consistently dominant to N. hebes (wetland) in competitive interactions for carcasses that they require for reproduction. Transplant enclosure experiments in nature revealed that N. hebes had poor reproductive success whenever the dominant N. orbicollis was present. In the absence of N. orbicollis, N. hebes performed as well, or better, in forest versus its typical wetland habitat. In contrast, N. orbicollis performed poorly in wetlands regardless of the presence of N. hebes. These results support the competitive exclusion-tolerance rule where the competitively dominant N. orbicollis excludes the subordinate N. hebes from otherwise suitable or preferable forest habitat, while the subordinate N. hebes is uniquely able to tolerate the challenges of breeding in wetlands. Transplant experiments further showed that carcass burial depth-an important trait thought to enhance the competitive ability of the dominant N. orbicollis-is costly in wetland habitats. In the presence of N. hebes, N. orbicollis buried carcasses deeper; deeper burial is thought to provide a competitive advantage in forests but further compromised the reproductive success of N. orbicollis in wetlands. Overall, results provide evidence that the competitive exclusion-tolerance rule underlies habitat partitioning among ecologically similar species and that the traits important for competitive dominance in relatively benign environments are costly in more challenging environments, consistent with a trade-off.

Genomic divergence between two sister Medicago species triggered by the Quaternary climatic oscillations in the Qinghai-Tibet Plateau and northern China

Speciation is a central topic in evolutionary biology. However, it remains poorly understood of how genomic divergence originated and accumulatedin the face of gene flow during ecological adaptation. Closely related species that have adapted to distinct environments but inhabit some overlapping ranges provide an ideal system to evaluate this issue.Here, we combine population genomics and species distribution models (SDMs) to examine genomic divergences between two sister species, Medicago ruthenicaand M. archiducis-nicolai, that occur in northern China and the northeast Qinghai-Tibet Plateau (QTP), respectively, with overlapping distribution in the border of the two regions.Medicago ruthenicaand M. archiducis-nicolai are well-delimited based on population genomic data, although hybrids exist in sympatric sampling locations. Coalescent simulations and SDMs suggest that the two species diverged from each other in the Quaternary but have been in continuous contact with gene flow occurring between the two species ever since. We also discovered positive selection signatures associated with genes both outside and within genomic islands in both species that are likely involved in adaptations to arid and high-altitude environments. Our findings provide insights into how natural selection and climatic changes in the Quaternary initiated and maintained interspecific divergence of the two sister species.

Extensive Adaptive Variation in Gene Expression within and between Closely Related Horseshoe Bats (Chiroptera, Rhinolophus) Revealed by Three Organs

In the process of species differentiation and adaption, the relative influence of natural selection on gene expression variation often remains unclear (especially its impact on phenotypic divergence). In this study, we used differentially expressed genes from brain, cochlea, and liver samples collected from two species of bats to determine the gene expression variation forced by natural selection when comparing at the interspecific (Rhinolophus siamensis and R. episcopus episcopus) and the intraspecific (R. e. episcopus and R. episcopus spp.) levels. In both cases, gene expression variation was extensively adaptive (>66.0%) and mainly governed by directional selection, followed by stabilizing selection, and finally balancing selection. The expression variation related to acoustic signals (resting frequency, RF) and body size (forearm length, FA) was also widely governed by natural selection (>69.1%). Different functional patterns of RF- or FA-related adaptive expression variation were found between the two comparisons, which manifested as abundant immune-related regulations between subspecies (indicating a relationship between immune response and phenotypic adaption). Our study verifies the extensive adaptive expression variation between both species and subspecies and provides insight into the effects of natural selection on species differentiation and adaptation as well as phenotypic divergence at the expression level.

Patterns of leaf trait variation underlie ecological differences among sympatric tree species of Damburneya in a tropical rainforest

PREMISE

Although ecological differentiation driven by altitude and soil is hypothesized to promote coexistence of sympatric tree species of Damburneya (Lauraceae), the mechanistic role of leaf functional variation on ecological differentiation among co-occurring species remains unexplored. We aimed to determine whether the patterns of leaf trait variation reflect ecological differences among sympatric Damburneya species. We tested whether trait correlations underlying functional strategies and average species traits vary in response to local soil heterogeneity along an altitudinal gradient, potentially affecting species distributions.

METHODS

At two contrasting altitudes (100, 1100 m a.s.l.) in a Mexican tropical rainforest, we characterized soil chemical and physical properties and sampled four Damburneya species to quantify five leaf functional traits. We used linear models to analyze paired and multivariate trait correlations, spatial and interspecific effects on trait variation, and trait response to local soil heterogeneity. Relative contributions of intra- and interspecific variation to local trait variability were quantified with an ANOVA.

RESULTS

Soil nutrient availability was higher at low altitude, but all species had a high leaf N:P ratio across altitudes suggesting a limited P supply for plants. Species distribution differed altitudinally, with some species constrained to low or high altitude, potentially reflecting soil nutrient availability. Leaf traits responded to altitude and local soil properties, suggesting interspecific differences in functional strategies according to the leaf economics spectrum (conservative vs. acquisitive).

CONCLUSIONS

The interspecific divergence in functional strategies in response to local environmental conditions suggests that trait variation could underlie ecological differentiation among Damburneya sympatric species.

Killing two bugs with one stone: a perspective for targeting multiple pest species by incorporating reproductive interference into sterile insect technique

The sterile insect technique is an environmentally friendly method to control and even eradicate agricultural and veterinary insect pests without using chemical pesticides in excess. However, the continuous production and release of sterile insects is economically costly and eradication programs using sterile insects have not always been successful owing to the incomplete mating ability of the sterile insects. Here we focus on the theory and empirical findings of interspecific negative mating interaction, known as reproductive interference, to develop a more cost-effective and value-added pest management program. We suggest that sterile insects can be used for simultaneous control of both wild-type conspecifics and closely related pest species by taking advantage of the fact that, when species recognition abilities are incomplete, courtship and mating are often misdirected toward heterospecies. This new approach might help mitigate economic damage and human health crises caused by pest insects. © 2018 Society of Chemical Industry.

Patterns of temporal and enemy niche use by a community of leaf cone moths (Caloptilia) coexisting on maples (Acer) as revealed by metabarcoding

The diversity of herbivorous insects is often considered a function of host plant diversity. However, recent research has uncovered many examples of closely related herbivores using the same host plant(s), suggesting that partitioning of host plants is not the only mechanism generating diversity. Herbivores sharing hosts may utilize different parts of the same plant, but such resource partitioning is often not apparent; hence, the factors that allow closely related herbivores to coexist are still largely undetermined. We examined whether partitioning of phenology or natural enemies may explain the coexistence of leaf cone moths (Caloptilia; Gracillariidae) associated with maples (Acer; Sapindaceae). Larval activity of 10 sympatric Caloptilia species found on nine maple species was monitored every 2-3 weeks for a total of 13 sampling events, and an exhaustive search for internal parasitoid wasps was conducted using high-throughput sequencing. Blocking primers were used to facilitate the detection of wasp larvae inside moth tissue. We found considerable phenological overlap among Caloptilia species, with two clear peaks in July and September-October. Coexisting Caloptilia species also had largely overlapping parasitoid communities; a total of 13 chalcid and ichneumon wasp species attacked Caloptilia in a nonspecific fashion at an overall parasitism rate of 46.4%. Although coexistence may be facilitated by factors not accounted for in this study, it appears that niche partitioning is not necessary for closely related herbivores to stably coexist on shared hosts. Co-occurrence without resource partitioning may provide an additional axis along which herbivorous insects attain increased species richness.

Accurate genome relative abundance estimation for closely related species in a metagenomic sample

BACKGROUND

Metagenomics has a great potential to discover previously unattainable information about microbial communities. An important prerequisite for such discoveries is to accurately estimate the composition of microbial communities. Most of prevalent homology-based approaches utilize solely the results of an alignment tool such as BLAST, limiting their estimation accuracy to high ranks of the taxonomy tree.

RESULTS

We developed a new homology-based approach called Taxonomic Analysis by Elimination and Correction (TAEC), which utilizes the similarity in the genomic sequence in addition to the result of an alignment tool. The proposed method is comprehensively tested on various simulated benchmark datasets of diverse complexity of microbial structure. Compared with other available methods designed for estimating taxonomic composition at a relatively low taxonomic rank, TAEC demonstrates greater accuracy in quantification of genomes in a given microbial sample. We also applied TAEC on two real metagenomic datasets, oral cavity dataset and Crohn's disease dataset. Our results, while agreeing with previous findings at higher ranks of the taxonomy tree, provide accurate estimation of taxonomic compositions at the species/strain level, narrowing down which species/strains need more attention in the study of oral cavity and the Crohn's disease.

CONCLUSIONS

By taking account of the similarity in the genomic sequence TAEC outperforms other available tools in estimating taxonomic composition at a very low rank, especially when closely related species/strains exist in a metagenomic sample.

Incorporating trnH-psbA to the core DNA barcodes improves significantly species discrimination within southern African Combretaceae

Recent studies indicate that the discriminatory power of the core DNA barcodes (rbcLa + matK) for land plants may have been overestimated since their performance have been tested only on few closely related species. In this study we focused mainly on how the addition of complementary barcodes (nrITS and trnH-psbA) to the core barcodes will affect the performance of the core barcodes in discriminating closely related species from family to section levels. In general, we found that the core barcodes performed poorly compared to the various combinations tested. Using multiple criteria, we finally advocated for the use of the core + trnH-psbA as potential DNA barcode for the family Combretaceae at least in southern Africa. Our results also indicate that the success of DNA barcoding in discriminating closely related species may be related to evolutionary and possibly the biogeographic histories of the taxonomic group tested.