Insights Into the Evolutionary History of the Subfamily Orthotrichoideae (Orthotrichaceae, Bryophyta): New and Former Supra-Specific Taxa So Far Obscured by Prevailing Homoplasy.

Mosses of the subfamily Orthotrichoideae represent one of the main components of the cryptogam epiphytic communities in temperate areas. During the last two decades, this taxonomical group has undergone an extensive revision that has led to its rearrangement at the generic level. However, their phylogenetic relationships and inferences on the evolutionary patterns that have driven the present diversity have little advanced. In this study, we present a dated molecular phylogenetic reconstruction at the subfamily level, including 130 samples that represent the 12 genera currently recognized within the subfamily, and the analysis of four molecular markers: ITS2, rps4, trnG, and trnL-F. We also analyze 13 morphological characters of systematic value to infer their origin and diagnostic utility within the subfamily. The phylogenetic reconstruction yields three main clades within the subfamily, two of which correspond to the tribe Zygodonteae, and one to Orthotricheae. Within Zygodonteae, the genus Zygodon results to be a polyphyletic artificial assembly, and we propose to separate a new genus named Australoria. Conversely, our results do not support the separation of Pentastichella and Pleurorthotrichum at the genus level and we therefore propose to include Pleurorthotrichum in Pentastichella. Regarding Orthotricheae, our analyses clearly allow the distinction of two subtribes: Orthotrichinae and Lewinskyinae. Within the latter, Ulota results a polyphyletic entity, and therefore we propose the segregation of a separate new genus named Atlantichella. Dating analyses allow us to conclude that the split of the tribes within Orthotrichoideae dates from the Middle Jurassic, while the diversification of Orthotrichum and Zygodon probably started during the Late Cretaceous. However, most of the extant genera of this subfamily seem to be younger, and apparently its highest diversification burst took place during the Oligocene. Finally, the analysis of the morphological traits reveals that most of the characters previously used to separate genera and here tested are homoplastic, which has hindered the taxonomical and systematic proposals for decades. However, even if there are no exclusive characters, all of the genera can be defined by the combination of a few characters.

The long journey of Orthotrichum shevockii (Orthotrichaceae, Bryopsida): From California to Macaronesia.

Biogeography, systematics and taxonomy are complementary scientific disciplines. To understand a species' origin, migration routes, distribution and evolutionary history, it is first necessary to establish its taxonomic boundaries. Here, we use an integrative approach that takes advantage of complementary disciplines to resolve an intriguing scientific question. Populations of an unknown moss found in the Canary Islands (Tenerife Island) resembled two different Californian endemic species: Orthotrichum shevockii and O. kellmanii. To determine whether this moss belongs to either of these species and, if so, to explain its presence on this distant oceanic island, we combined the evaluation of morphological qualitative characters, statistical morphometric analyses of quantitative traits, and molecular phylogenetic inferences. Our results suggest that the two Californian mosses are conspecific, and that the Canarian populations belong to this putative species, with only one taxon thus involved. Orthotrichum shevockii (the priority name) is therefore recognized as a morphologically variable species that exhibits a transcontinental disjunction between western North America and the Canary Islands. Within its distribution range, the area of occupancy is limited, a notable feature among bryophytes at the intraspecific level. To explain this disjunction, divergence time and ancestral area estimation analyses are carried out and further support the hypothesis of a long-distance dispersal event from California to Tenerife Island.

Resolving Recent Plant Radiations: Power and Robustness of Genotyping-by-Sequencing.

Disentangling species boundaries and phylogenetic relationships within recent evolutionary radiations is a challenge due to the poor morphological differentiation and low genetic divergence between species, frequently accompanied by phenotypic convergence, interspecific gene flow and incomplete lineage sorting. Here we employed a genotyping-by-sequencing (GBS) approach, in combination with morphometric analyses, to investigate a small western Mediterranean clade in the flowering plant genus Linaria that radiated in the Quaternary. After confirming the morphological and genetic distinctness of eight species, we evaluated the relative performances of concatenation and coalescent methods to resolve phylogenetic relationships. Specifically, we focused on assessing the robustness of both approaches to variations in the parameter used to estimate sequence homology (clustering threshold). Concatenation analyses suffered from strong systematic bias, as revealed by the high statistical support for multiple alternative topologies depending on clustering threshold values. By contrast, topologies produced by two coalescent-based methods (NJ$_{\mathrm{st}}$, SVDquartets) were robust to variations in the clustering threshold. Reticulate evolution may partly explain incongruences between NJ$_{\mathrm{st}}$, SVDquartets and concatenated trees. Integration of morphometric and coalescent-based phylogenetic results revealed (i) extensive morphological divergence associated with recent splits between geographically close or sympatric sister species and (ii) morphological convergence in geographically disjunct species. These patterns are particularly true for floral traits related to pollinator specialization, including nectar spur length, tube width and corolla color, suggesting pollinator-driven diversification. Given its relatively simple and inexpensive implementation, GBS is a promising technique for the phylogenetic and systematic study of recent radiations, but care must be taken to evaluate the robustness of results to variation of data assembly parameters.

Comparing three complete mitochondrial genomes of the moss genus Orthotrichum Hedw.

Here, we present a comparative analysis of the mitochondrial genome of three representatives of Orthotrichum Hedw (Bryophyta): two populations of O. diaphanum and one of the related species, namely O. macrocephalum. Their mitochondrial genomes share the same gene content and gene order, and are furthermore structurally identical to those of other arthrodontous mosses. The mitogenome of the allopatric samples of O. diaphanum differ in 0.1% of their sequence, with protein coding genes holding five mutations, including two non-synonymous changes. The divergence between the mitogenomes of the two species, O. diaphanum and O. macrocephalum, is 0.4%. Within a broader sampling of the Orthotrichaceae, patterns of genome divergence are consistent with phylogenetic relationships.

Downscaling pollen-transport networks to the level of individuals.

Most plant-pollinator network studies are conducted at species level, whereas little is known about network patterns at the individual level. In fact, nodes in traditional species-based interaction networks are aggregates of individuals establishing the actual links observed in nature. Thus, emergent properties of interaction networks might be the result of mechanisms acting at the individual level. Pollen loads carried by insect flower visitors from two mountain communities were studied to construct pollen-transport networks. For the first time, these community-wide pollen-transport networks were downscaled from species-species (sp-sp) to individuals-species (i-sp) in order to explore specialization, network patterns and niche variation at both interacting levels. We used a null model approach to account for network size differences inherent to the downscaling process. Specifically, our objectives were (i) to investigate whether network structure changes with downscaling, (ii) to evaluate the incidence and magnitude of individual specialization in pollen use and (iii) to identify potential ecological factors influencing the observed degree of individual specialization. Network downscaling revealed a high specialization of pollinator individuals, which was masked and unexplored in sp-sp networks. The average number of interactions per node, connectance, interaction diversity and degree of nestedness decreased in i-sp networks, because generalized pollinator species were composed of specialized and idiosyncratic conspecific individuals. An analysis with 21 pollinator species representative of two communities showed that mean individual pollen resource niche was only c. 46% of the total species niche. The degree of individual specialization was associated with inter- and intraspecific overlap in pollen use, and it was higher for abundant than for rare species. Such niche heterogeneity depends on individual differences in foraging behaviour and likely has implications for community dynamics and species stability. Our findings highlight the importance of taking interindividual variation into account when studying higher-order structures such as interaction networks. We argue that exploring individual-based networks will improve our understanding of species-based networks and will enhance the link between network analysis, foraging theory and evolutionary biology.