Do closely related species interact with similar partners? Testing for phylogenetic signal in bipartite interaction networks

Whether interactions between species are conserved on evolutionary time-scales is a central question in ecology and evolution. It has spurred the development of both correlative and model-based approaches for testing phylogenetic signal in interspecific interactions: do closely related species interact with similar sets of partners? Here we test the statistical performances of some of these approaches using simulations. We find that one of the most widely used model-based approach, the Phylogenetic Bipartite Linear Model (PBLM), often detects phylogenetic signal when it should not. Simple Mantel tests investigating the correlation between phylogenetic distances and dissimilarities in sets of interacting partners instead have low type-I error rates and satisfactory statistical power, especially when using weighted interactions and phylogenetic dissimilarity metrics; however, they often artifactually detect anti-phylogenetic signals. Partial Mantel tests, which are used to partial out the phylogenetic signal in the number of partners, actually fail at correcting for this confounding effect, and we instead propose the sequential use of simple Mantel tests. We also explore the ability of simple Mantel tests to analyze clade-specific phylogenetic signal, while current methods only measure an overall signal. We provide general guidelines and an empirical application on an interaction network between orchids and mycorrhizal fungi.

Flavonoids Modulate Bacterial Endophyte Communities of Ginkgo Biloba Leaves

Plant-specialized secondary metabolites have ecological functions in mediating interactions between plants and their entophytes. Here, we aimed to reveal the interaction between flavonoid synthesis and endophytic bacterial communities in wild Ginkgo trees spanning 100-800 years. We found that flavonoids including quercetin, kaempferol and isorhamnetin decreased while the microbial diversity in leaves increased with the age of sampled trees. Older trees had more unique genera and shifted their endophytic bacterial community structure. Also, Mantel tests and correlation analysis indicated a generally significant (p < 0.05) negative correlation between endophytic bacterial communities and flavonoids. Additionally, both deterministic and stochastic processes could play roles in the assembly of endophytic bacterial communities in Ginkgo trees with a progressive increase in stochastic processes as flavonoid concentrations decreased. This study provides a mechanistic understanding of how flavonoids modulate the endophytic microbial community assembly.

Biogeography and Independent Diversification in the Protist Symbiont Community of Heterotermes tenuis

The eukaryotic microbiome of “lower” termites is highly stable and host-specific. This is due to the mutually obligate nature of the symbiosis and the direct inheritance of protists by proctodeal trophallaxis. However, vertical transmission is occasionally imperfect, resulting in daughter colonies that lack one or more of the expected protist species. This phenomenon could conceivably lead to regional differences in protist community composition within a host species. Here, we have characterized the protist symbiont community of Heterotermes tenuis (Hagen) (Blattodea: Rhinotermitidae) from samples spanning South and Central America. Using light microscopy, single cell isolation, and amplicon sequencing, we report eight species-level protist phylotypes belonging to four genera in the phylum Parabasalia. The diversity and distribution of each phylotype’s 18S rRNA amplicon sequence variants (ASVs) mostly did not correlate with geographical or host genetic distances according to Mantel tests, consistent with the lack of correlation we observed between host genetic and geographical distances. However, the ASV distances of Holomastigotoides Ht3 were significantly correlated with geography while those of Holomastigotoides Ht1 were significantly correlated with host phylogeny. These results suggest mechanisms by which termite-associated protist species may diversify independently of each other and of their hosts, shedding light on the coevolutionary dynamics of this important symbiosis.

Influence of Environmental Factors on the Genetic and Chemical Diversity of Brickellia veronicifolia Populations Growing in Fragmented Shrublands from Mexico

Brickellia veronicifolia is a native Asteraceae from Mexico that persists in fragmented habitats. This investigation reports the genetic and chemical diversity of B. veronicifolia. The diversity analysis based on iPBS markers showed an averaged Shannon index (S) of 0.3493, a Nei genetic diversity (h) of 0.2256, and a percentage of polymorphic loci average (P) of 80.7867%. The population structure obtained by AMOVA revealed that the highest variation found within populations was 94.58%. GC-MS profiling of six populations indicated that major volatiles were β–caryophyllene (11.63%), spathulenol (12.85%), caryophyllene oxide (13.98%), α–cadinol (7.04%), cubedol (6.72%) and tau-muurolol (4.81%). Mantel tests suggested a statistically significant relationship between minor volatiles and geographical distance (r = 0.6163; p = 0.0470; p ˂ 0.05). Likewise, major volatiles showed a significant correlation with the soil pH (r = 0.6862; p = 0.0230) and maximum temperature (r = 0.4999; p = 0.0280). Our study suggests that the variation and genetic divergence of B. veronicifolia has no relationship with climatic parameters, whereas the volatiles are probably influenced by environmental factors and not by the genotype per se. Based on the characteristics of B. veronicifolia, this plant could be considered as a candidate for restoring fragmented shrublands in Mexico.

Genetic and Epigenetic Changes during the Upward Expansion of Deyeuxia angustifolia Kom. in the Alpine Tundra of the Changbai Mountains, China

Ecological adaptation plays an important role in the process of plant expansion, and genetics and epigenetics are important in the process of plant adaptation. In this study, genetic and epigenetic analyses and soil properties were performed on D. angustifolia of 17 populations, which were selected in the tundra zone on the western slope of the Changbai Mountains. Our results showed that the levels of genetic and epigenetic diversity of D. angustifolia were relatively low, and the main variation occurred among different populations (amplified fragment length polymorphism (AFLP): 95%, methylation sensitive amplification polymorphism (MSAP): 87%). In addition, DNA methylation levels varied from 23.36% to 35.70%. Principal component analysis (PCA) results showed that soil properties of different populations were heterogeneous. Correlation analyses showed that soil moisture, pH and total nitrogen were significantly correlated with genetic diversity of D. angustifolia, and soil temperature and pH were closely related to epigenetic diversity. Simple Mantel tests and partial Mantel tests showed that genetic variation significantly correlated with habitat or geographical distance. However, the correlation between epigenetic variation and habitat or geographical distance was not significant. Our results showed that, in the case of low genetic variation and genetic diversity, epigenetic variation and DNA methylation may provide a basis for the adaptation of D. angustifolia.

Using Kolmogorov Complexity to Study the Coevolution of Header Files and Source Files of C-alike Programs

In C-alike programs, the source code is separated into header files and source files. During the software evolution process, both these two kinds of files need to adapt to changing requirement and changing environment. This paper studies the coevolution of header files and source files of C-alike programs. Using normalized compression distance that is derived from Kolmogorov complexity, we measure the header file difference and source file difference between versions of an evolving software product. Header files distance and source files distance are compared to understand their difference in pace of evolution. Mantel tests are performed to investigate the correlation of header file evolution and source file evolution. The study is performed on the source code of Apache HTTP web server.

Invariance of edit-distance to tempo in rhythm similarity

Despite the long history of music psychology, rhythm similarity perception remains largely unexplored. Several studies suggest that edit-distance—the minimum number of notational changes required to transform one rhythm into another—predicts similarity judgments. However, the ecological validity of edit-distance remains elusive. We investigated whether the edit-distance model can predict perceptual similarity between rhythms that also differed in a fundamental characteristic of music—tempo. Eighteen participants rated the similarity between a series of rhythms presented in a pairwise fashion. The edit-distance of these rhythms varied from 1 to 4, and tempo was set at either 90 or 150 beats per minute (BPM). A test of congruence among distance matrices (CADM) indicated significant inter-participant reliability of ratings, and non-metric multidimensional scaling (nMDS) visualized that the ratings were clustered based upon both tempo and whether rhythms shared an identical onset pattern, a novel effect we termed rhythm primacy. Finally, Mantel tests revealed significant correlations of edit-distance with similarity ratings on both within- and between-tempo rhythms. Our findings corroborated that the edit-distance predicts rhythm similarity and demonstrated that the edit-distance accounts for similarity of rhythms that are markedly different in tempo. This suggests that rhythmic gestalt is invariant to differences in tempo.

Drivers of molecular and morphometric variation in Triatoma brasiliensis (Hemiptera: Triatominae): the resolution of geometric morphometrics for populational structuring on a microgeographical scale

Background The protozoan Trypanosoma cruzi circulates in semiarid areas of northeastern Brazil in distinct ecotopes (sylvatic, peridomestic and domestic) where Triatoma brasiliensis Neiva, 1911 is the most important Chagas disease vector. In this study, we analyzed microevolutionary and demographic aspects of T. brasiliensis populations at the ecotypic, micro and macro-geographic scales by combining morphometrics and molecular results. Additionally, we aimed to address the resolution of both markers for delimiting populations in distinct scales. Methods We sampled populations of T. brasiliensis from distinct ecotypic and geographic sites in the states Rio Grande do Norte (RN) and Paraíba (PB). The geometric morphometry was carried out with 13 landmarks on the right wings (n = 698) and the genetic structure was assessed by sequencing a region of cytochrome b mitochondrial gene (n = 221). Mahalanobis distance (MD) and coefficient of molecular differentiation (ΦST) were calculated among all pairs of populations. The results of comparisons generated MD and ΦST dendrograms, and graphics of canonical variate analysis (CVA). Results Little structure was observed for both markers for macro-geographic scales. Mantel tests comparing geographic, morphometric and genetic matrices showed low correlation (all R2 < 0.35). The factorial graphics built with the CVA evidenced population delimitation for the morphometric data at micro-geographic scales. Conclusions We believe that T. brasiliensis carries in its genotype a source of information to allow the phenotypical plasticity across its whole distribution for shaping populations, which may have caused a lack of population delimitation for CVAs in morphometric analysis for macro-geographic scale analysis. On the other hand, the pattern of morphometric results in micro-geographic scales showed well-defined groups, highlighting the potential of this tool to inferences on the source for infestation.

Diversity and circulation of Jingmen tick virus in ticks and mammals

Since its initial identification in ticks in 2010, Jingmen tick virus (JMTV) has been described in cattle, rodents, and primates. To better understand the diversity, evolution, and transmission of JMTV, we sampled 215 ticks, 104 cattle bloods, 216 bats, and 119 rodents in Wenzhou city, Zhejiang Province, China as well as 240 bats from Guizhou and Henan Provinces. JMTV was identified in 107 ticks (from two species), 54 bats (eleven species), 8 rodents (three species), and 10 cattle, with prevalence levels of 49.8, 11.8, 6.7, and 9.6 per cent, respectively, suggesting that bats may be a natural reservoir of JMTV. Phylogenetic analyses revealed that all the newly identified JMTVs were closely related to each other and to previously described viruses. Additionally, all tick and mammalian JMTV sampled in Wenzhou shared a consistent genomic structure, suggesting that the virus can cocirculate between ticks and mammals without observable variation in genome organization. All JMTVs sampled globally could be divided into two phylogenetic groups, Mantel tests suggested that geographic isolation, rather than host species, may be the main driver of JMTV diversity. However, the exact geographical origin of JMTV was difficult to determine, suggesting that this virus has a complex evolutionary history.

Drivers of molecular and morphometric variation in Triatoma brasiliensis (Hemiptera: Reduviidae): the resolution of geometric morphometrics for populational structuring in micro-geographic scale

Background The protozoan Trypanosoma cruzi circulates in semiarid areas of the northeastern of Brazil in distinct ecotopes (sylvatic, peridomestic and domestic) where Triatoma brasiliensis is the most important Chagas disease vector.Methods We sampled populations of T. brasiliensis from distinct ecotypic and geographic sites in the Rio Grande do Norte (RN) and Paraíba (PB) States to compare the results of morphometric and genetic variations. The geometric morphometry was carried out with 13 landmarks on the right wings ( N =698) and the genetic structure was assessed by sequencing a region of cytochrome B mitochondrial gene ( N =221). Mahalanobis distance (DM) and molecular differentiation coefficient (Φ ST ) were calculated among all pairs of populations.Results The results of comparisons generated MD and Φ ST dendrograms, and graphics of canonical variate analysis (CVA). Little structure was observed for both markers for macro-geographic scales. Mantel tests comparing geographic, morphometric and genetic matrices showed low correlation (all R 2 <0.35). The factorial graphics built with the CVA evidenced population delimitation for the morphometric data at micro-geographic-scales.Conclusions We believe that T. brasiliensis carries in its genotype a source of information to allow the phenotypical plasticity across its whole distribution for shaping populations, which may have caused a lack of population delimitation for CVAs in morphometric analysis for macro-geographic scale analysis when populations are grouped. On the other hand, the pattern of morphometric results in micro-geographic scales highlights the potential of this tool to infer the source for infestation.