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Background Widespread sympatry between sibling species can be limited if they are ecologically too close, potentially leading to the formation of narrow zones of secondary contact. While the ecological niche is commonly estimated using abiotic factors, the potential differentiation in gut microbial communities as a proxy for biotic niche differentiation is less well studied. We address this gap in research, focusing on two Alpine butterfly species of the genus Erebia that form a stable and very narrow contact zone. Results Using a metabarcoding approach to sequence the adult gut microbial communities of our two focal species as well as capturing the microbial diversity found on three nectar plant species, we found that the microbial community i) significantly differed between species but not between sexes, that ii) the abundance of the heritable endosymbiont Wolbachia differed between species, where its high abundance resulted in the detection of fewer other microbial taxa, and that iii) microbes found on flowers largely but not completely overlapped with the ones found in the butterfly hosts, suggesting that intestinal environmental filtering occurs only to some degree. Conclusions Consistent with biotic niche differentiation, we uncovered species specific differences in the gut microbial communities, further highlighting the complex interactions between host biology and environmental factors in shaping the gut microbiota. The observed microbial differences could reflect local adaptation to different resources or microhabitats. Overall, our study highlights the utility of gut microbial metabarcoding to study ecological niche differentiation, also during secondary contact.

In Rubiaceae phylogenetics, the number of markers often proved a limitation with authors failing to provide well-supported trees at tribal and generic levels. A robust phylogeny is a prerequisite to study the evolutionary patterns of traits at different taxonomic levels. Advances in next-generation sequencing technologies have revolutionized biology by providing, at reduced cost, huge amounts of data for an increased number of species. Due to their highly conserved structure, generally recombination-free, and mostly uniparental inheritance, chloroplast DNA sequences have long been used as choice markers for plant phylogeny reconstruction. The main objectives of this study are: 1) to gain insight in chloroplast genome evolution in the Rubiaceae (Ixoroideae) through efficient methodology for de novo assembly of plastid genomes; and, 2) to test the efficiency of mining SNPs in the nuclear genome of Ixoroideae based on the use of a coffee reference genome to produce well-supported nuclear trees. We assembled whole chloroplast genome sequences for 27 species of the Rubiaceae subfamily Ixoroideae using next-generation sequences. Analysis of the plastid genome structure reveals a relatively good conservation of gene content and order. Generally, low variation was observed between taxa in the boundary regions with the exception of the inverted repeat at both the large and short single copy junctions for some taxa. An average of 79% of the SNP determined in the Coffea genus are transferable to Ixoroideae, with variation ranging from 35% to 96%. In general, the plastid and the nuclear genome phylogenies are congruent with each other. They are well-resolved with well-supported branches. Generally, the tribes form well-identified clades but the tribe Sherbournieae is shown to be polyphyletic. The results are discussed relative to the methodology used and the chloroplast genome features in Rubiaceae and compared to previous Rubiaceae phylogenies.

Understanding the factors underlying the co-occurrence of multiple species remains a challenge in ecology. Biotic interactions, environmental filtering and neutral processes are among the main mechanisms evoked to explain species co-occurrence. However, they are most often studied separately or even considered as mutually exclusive. This likely hampers a more global understanding of species assembly. Here, we investigate the general hypothesis that the structure of co-occurrence networks results from multiple assembly rules and its potential implications for grassland ecosystems. We surveyed orthopteran and plant communities in 48 permanent grasslands of the French Jura Mountains and gathered functional and phylogenetic data for all species. We constructed a network of plant and orthopteran species co-occurrences and verified whether its structure was modular or nested. We investigated the role of all species in the structure of the network (modularity and nestedness). We also investigated the assembly rules driving the structure of the plant-orthopteran co-occurrence network by using null models on species functional traits, phylogenetic relatedness and environmental conditions. We finally compared our results to abundance-based approaches. We found that the plant-orthopteran co-occurrence network had a modular organization. Community assembly rules differed among modules for plants while interactions with plants best explained the distribution of orthopterans into modules. Few species had a disproportionately high positive contribution to this modular organization and are likely to have a key importance to modulate future changes. The impact of agricultural practices was restricted to some modules (3 out of 5) suggesting that shifts in agricultural practices might not impact the entire plant-orthopteran co-occurrence network. These findings support our hypothesis that multiple assembly rules drive the modular structure of the plant-orthopteran network. This modular structure is likely to play a key role in the response of grassland ecosystems to future changes by limiting the impact of changes in agricultural practices such as intensification to some modules leaving species from other modules poorly impacted. The next step is to understand the importance of this modular structure for the long-term maintenance of grassland ecosystem structure and functions as well as to develop tools to integrate network structure into models to improve their capacity to predict future changes.

The diversification of ecological roles and related adaptations in closely related species within a lineage is one of the most important processes linking plant evolution and ecology. Plant architecture offers a robust framework to study these processes as it can highlight how plant structure influences plant diversification and ecological strategies. We investigated a case of gradual evolution of branching architecture in spp. (Rubiaceae), forming a monophyletic group in New Caledonia that has diversified rapidly, predominantly in rainforest understory habitats. We used a transdisciplinary approach to depict architectural variations and revealed multiple evolutionary transitions from a branched (Stone's architectural model) to a monocaulous habit (Corner's architectural model), which involved the functional reduction of branches into inflorescences. We propose an integrative functional index that assesses branching incidence on functional traits influencing both assimilation and exploration functions. We showed that architectural transitions correlate with ecologically important functional traits. Variation in ecologically important traits among closely relatives, as supported by the architectural analysis, is suggestive of intense competition that favored divergence among locally coexisting species. We propose that Pleistocene climatic fluctuations causing expansion and contraction of rainforest could also have offered ecological opportunities for colonizers in addition to the process of divergent evolution.

Background The Philippine archipelago is globally one of the most important model island systems for studying evolutionary processes. However, most plant species on this archipelago have not yet been studied in sufficient detail. The main aim of this study is to unravel the evolutionary history and biogeographic relationships of the Philippine members of the pantropical genus Ixora . Results The complex plastid and nuclear divergence patterns in Philippine Ixora , documented using tree and network approaches, reveal a highly dynamic evolution in Ixora , involving several phases of radiation and recolonization. Philippine Ixora comprises at least five lineages, of which one is most closely related to species from Wallacea, and the remaining four to species from Asia. Conclusions Our study highlights the importance of Philippine species for understanding phytogeographic patterns in the Indomalayan-Australasian eco-region. The overall genetic differentiation, as well as the incongruence between genealogies based on the biparentally inherited nucleome and the maternally inherited plastome in Ixora , reflect the complex tectonic history of the Philippine archipelago. The Ixora lineage related to Wallacean species supports the delimitation of different ecozones along Huxley’s line, because it is absent from Palawan. The remaining four lineages are all allied with Asian taxa, reflecting several waves of colonization. Close relationships between some widespread Philippine species and locally adapted narrow endemics suggest that the widespread, genetically diverse species act as pools for the formation of new species in a process of ongoing speciation. Our results suggest that the species concepts of some of the more widespread taxa need to be revised.

Background and aims – New Caledonia is a hotspot of biodiversity in the world. Among the most diverse New Caledonian plant families is Rubiaceae, which consist of 30 genera containing 220 species, with a level of endemism of 93%. The tribe Gardenieae is represented by four genera, Gardenia (8 species), Aidia (2 species), Randia (7 species), and Atractocarpus (10 species). As Randia has now been restricted to the Neotropics, the New Caledonian Randia species remain unplaced within the tribe. Atractocarpus is a Pacific genus, easily characterized by long imbricated stipules, a feature also present in the Randia species and in several Gardenia species in New Caledonia. The aims of the present study are to test the monophyly of Atractocarpus and to assess the phylogenetic placement of the Randia and Gardenia species with long imbricated stipules within Gardenieae and specifically their relationships with taxa of the Porterandia group to which Atractocarpus belongs.Material and methods – We investigated 63 species of Pacific Gardenieae, with a focus on the Porterandia group, in a Bayesian phylogenetic reconstruction (cpDNA: trnTF and rpl32, and nrDNA: ITS).Key results – Our study provides a mostly supported consensus tree topology of the Porterandia group. Five Gardenia and seven Randia species fall within a clade that comprises the New Caledonian Atractocarpus species, rendering both Atractocarpus and Gardenia polyphyletic.Conclusion – We enlarge the delimitation of Atractocarpus to include 12 New Caledonian Randia and Gardenia species. New Caledonia is consequently confirmed as the centre of diversity for Atractocarpus with 31 species. According to our study, three genera of Gardenieae occur in the archipelago: Aidia, Gardenia, and Atractocarpus.

In the past, the circumscription of the large genus Psychotria (Rubiaceae) was difficult, until molecular phylogenetic studies revealed its considerable paraphyly, enabling the delimitation of its major lineages and the grouping of related genera, and most notably the separation of Psychotria and its relatives (former Psychotrieae) into two tribes: Psychotrieae and Palicoureeae. The genus Margaritopsis, which is included in Palicoureeae, encompasses 27 Neotropical species, and in previous studies these have been shown to be close relatives of a group of eight Psychotria species that occur over a large region extending from South-East Asia to tropical South Pacific through Malesia (= the AMP region, defined as including South-East Asia, Malesia, tropical Australia, Melanesia, Micronesia, New Caledonia and Polynesia). A molecular phylogenetic study, using one nuclear DNA region (ITS) and four plastid DNA regions (ndhF, rps16, trnH-psbA, trnT-F), is undertaken in order to test the placement of 17 AMP Psychotria species within Palicoureeae. The phylogenetic results show that they form a monophyletic clade (= clade G), which also includes the monotypic Fijian genus Readea and Hodgkinsonia frutescens from Australia. Clade G is embedded in a well-supported grade with five Neotropical representatives of Margaritopsis. A morphological survey based on twenty characters, with the potential to circumscribe generic entities, shows that the monophyly of clade G is supported by a character combination that is similar to species of Neotropical Margaritopsis, confirming their inclusion in this genus. Taxonomic and nomenclatural work on these species is required to formalize nomenclatural implications. Based on the same set of morphological characters, but in absence of molecular data, 28 other Psychotria species from the AMP region were detected as likely candidates for inclusion in Margaritopsis, allowing the estimation of species richness of clade G to be a minimum of 47 species. Within clade G, five well-supported subclades and a Readea lineage are delimited and each of these is generally supported by unique morphological features. Phylogenetic topologies reveal biogeographical patterns, including a main route of dispersal from western to eastern parts of the AMP region, with subsequent dispersals between archipelagos in the region.

Understanding how land‐use changes affect different facets of plant biodiversity in seminatural European grasslands is of particular importance for biodiversity conservation. As conclusions of previous experimental or synchronic observational studies did not converge toward a general agreement, assessing the recent trends in vegetation change in various grassland systems using a diachronic approach is needed. In this resurvey study, we investigated the recent changes in grassland vegetation of the French Jura Mountains, a region with a long tradition of pastoralism. We compared the floristic composition of 150 grassland plots recorded between 1990 and 2000 with new relevés made in 2012 on the same plots. We considered taxonomic, phylogenetic and functional diversity as well as ecological characteristics of the plant communities derived from ecological indicator values and life strategies of the species. PCA of the floristic composition revealed a significant general trend linked to the sampling year. Wilcoxon paired tests showed that contemporary communities were generally more dominated by grass species and presented a higher tolerance to defoliation, a higher pastoral value, and a higher nutrient indicator value. Comparisons revealed a decrease in phylogenetic and functional diversity. By contrast, local species richness has slightly increased. The intensity of change in species composition, measured by Hellinger distance between pairs of relevés, was dependent on neither the time lag between the two surveys, the author of the first relevé nor its location or elevation. The most important changes were observed in grasslands that previously presented low pastoral value, low grass cover, low tolerance to defoliation, and high proportion of stress‐tolerant species. This trend was likely linked to the intensification of grassland management reported in the region, with a parallel increase in mowing frequency, grazing pressure, and fertilization level. More restrictive specifications should be applied to agricultural practices to avoid overexploitation of mountain species‐rich grasslands and its negative consequences on their biodiversity and resilience. This diachronic study analyzed recent changes in grassland vegetation of the French Jura Mountains, a region with a long tradition of pastoralism. The floristic composition of 150 grasslands recorded between 1990 and 2000 was compared with new relevés made in 2012 at the same plots. Comparisons revealed a decrease in phylogenetic and functional diversity, and an increase in nutrient and disturbance indicator values, independent on elevation.

In this study we investigate the large and diverse Rubiaceae-Gardenieae and closely related tribes Bertiereae, Coffeeae, Cremasporeae, Octotropideae, and Pavetteae. Some of the tribes or groups have been shown to be monophyletic and strongly supported, but the phylogeny of this large complex is still far from being satisfactorily elucidated particularly for Gardenieae, both in terms of intertribal relationships as well as tribal delimitations. We reconstruct the phylogeny of the complex using an extensive sampling of 108 genera and five plastid DNA regions. Phylogenetic relationships demonstrate that Gardenieae sensu Andreasen & Bremer is polyphyletic, asBurchellia, Didymosalpinx, Monosalpinx, andMantalaniaa re closer to Octot ropideae -Cremasporeae. In addition, Pavetteae and the investigated members of Aulacocalyceae are nested in a supported but partially unresolved Gardenieae-Pavetteae clade. Within this clade, several strongly supported groups are resolved: anAidiagroup, anAlibertiagroup, aGardeniagroup, Pavetteae includingPelagodendron, aPorterandiagroup, aRandiagroup, aRothmanniagroup (includingAulacocalyxandHeinsenia), aSherbourniagroup, and the two isolated generaMassulariaandSchumanniophyton. The latter genus presented a high rate of genetic substitutions, which resulted in perturbations of the phylogenetic reconstruction. A revised tribal circumscription is given for Gardenieae, theAlibertiagroup is recognized at tribal level as an emended Cordiereae, and a new tribe, Sherbournieae, is described to accommodate the members of theSherbourniagroup.

Background and AimsPrevious work on the pantropical genus Ixora has revealed an Afro-Madagascan clade, but as yet no study has focused in detail on the evolutionary history and morphological trends in this group. Here the evolutionary history of Afro-Madagascan Ixora spp. (a clade of approx. 80 taxa) is investigated and the phylogenetic trees compared with several key morphological traits in taxa occurring in Madagascar.MethodsPhylogenetic relationships of Afro-Madagascan Ixora are assessed using sequence data from four plastid regions (petD, rps16, rpoB-trnC and trnL-trnF) and nuclear ribosomal external transcribed spacer (ETS) and internal transcribed spacer (ITS) regions. The phylogenetic distribution of key morphological characters is assessed. Bayesian inference (implemented in BEAST) is used to estimate the temporal origin of Ixora based on fossil evidence.Key ResultsTwo separate lineages of Madagascan taxa are recovered, one of which is nested in a group of East African taxa. Divergence in Ixora is estimated to have commenced during the mid Miocene, with extensive cladogenesis occurring in the Afro-Madagascan clade during the Pliocene onwards.ConclusionsBoth lineages of Madagascan Ixora exhibit morphological innovations that are rare throughout the rest of the genus, including a trend towards pauciflorous inflorescences and a trend towards extreme corolla tube length, suggesting that the same ecological and selective pressures are acting upon taxa from both Madagascan lineages. Novel ecological opportunities resulting from climate-induced habitat fragmentation and corolla tube length diversification are likely to have facilitated species radiation on Madagascar.