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SUMMARY: Hybridization is a widespread phenomenon in the evolution of plants and exploring its role is crucial to understanding diversification processes of many taxonomic groups. Recently, more attention is focused on the role of ancient hybridization that has repeatedly been shown as triggers of evolutionary radiation, although in some cases, it can prevent further diversification. The causes, frequency, and consequences of ancient hybridization remain to be explored. Here, we present an account of several events of ancient hybridization in turmeric, the economically important plant genus Curcuma (Zingiberaceae), which harbors about 130 known species. We analyzed 1094 targeted low‐copy genes and plastomes obtained by next‐generation sequencing of 37 species of Curcuma, representing the known genetic diversity and spanning the geographical distribution of the genus. Using phylogenetic network analysis, we show that the entire genus Curcuma as well as its most speciose lineage arose via introgression from the genus Pyrgophyllum and one of the extinct lineages, respectively. We also document a single event of ancient hybridization, with C. vamana as a product, that represents an evolutionary dead end. We further discuss distinct circumstances of those hybridization events that deal mainly with (in)congruence in chromosome counts of the parental lineages. Significance Statement: The causes of diversification is one of the main evolutionary questions and ancient hybridization is being studied as one of them, although its circumstances are still poorly understood. We are focusing on economically important tropical genus Curcuma where ancient hybridization happened at least three times during its evolution with various and contrasting consequences. [ABSTRACT FROM AUTHOR]

In the present study, we reconstruct phylogenetic relationships within the chromosomally variable Sorex araneus species group based on 20 nuclear loci and the mitochondrial cyt b gene. In the species tree, Nearctic S. arcticus represents the earliest offshoot of the group followed by Holarctic S. tundrensis and Siberian S. daphaenodon. Five other species distributed mostly in Europe form a well‐supported clade. Coding regions showed stronger phylogenetic signal than introns. The results suggest a high incidence of reticulation in the evolution of the group. The authentic mitochondrial lineage of the Iberian shrew S. granarius was found to be close phylogenetically to S. coronatus, which confirms that some populations of the Iberian shrew S. granarius were introgressed from S. araneus. Footprints of deeper reticulations are revealed for the first time, indicating the potential hybrid origin of the S. arcticus and S. coronatus lineages. Ancient hybridisations are hypothesised to be the source of discordance between molecular‐ and karyotype‐based phylogenetic reconstructions. [ABSTRACT FROM AUTHOR]

Premise: Oceanic islands offer the opportunity to understand evolutionary processes underlying rapid diversification. Along with geographic isolation and ecological shifts, a growing body of genomic evidence has suggested that hybridization can play an important role in island evolution. Here we use genotyping‐by‐sequencing (GBS) to understand the roles of hybridization, ecology, and geographic isolation in the radiation of Canary Island Descurainia (Brassicaceae). Methods: We carried out GBS for multiple individuals of all Canary Island species and two outgroups. Phylogenetic analyses of the GBS data were performed using both supermatrix and gene tree approaches and hybridization events were examined using D‐statistics and Approximate Bayesian Computation. Climatic data were analyzed to examine the relationship between ecology and diversification. Results: Analysis of the supermatrix data set resulted in a fully resolved phylogeny. Species networks suggest a hybridization event has occurred for D. gilva, with these results being supported by Approximate Bayesian Computation analysis. Strong phylogenetic signals for temperature and precipitation indicate one major ecological shift within Canary Island Descurainia. Conclusions: Inter‐island dispersal played a significant role in the diversification of Descurainia, with evidence of only one major shift in climate preferences. Despite weak reproductive barriers and the occurrence of hybrids, hybridization appears to have played only a limited role in the diversification of the group with a single instance detected. The results highlight the need to use phylogenetic network approaches that can simultaneously accommodate incomplete lineage sorting and gene flow when studying groups prone to hybridization; patterns that might otherwise be obscured in species trees. [ABSTRACT FROM AUTHOR]

Social information, acquired through the observation of other individuals, is especially relevant among species belonging to the same guild. The unpredictable and ephemeral nature of carrion implies that social mechanisms may be selected among scavenger species to facilitate carcass location and consumption. Here, we apply a survival-modelling strategy to data obtained through the placement and monitoring of carcasses in the field to analyse possible information transmission cascades within a Neotropical scavenger community. Our study highlights how the use of different senses (smell and sight) within this guild facilitates carcass location through the transmission of social information between species with different carrion foraging efficiencies. Vultures with a highly developed sense of smell play a key role in this process, as they are the first to arrive at the carcasses and their presence seems to serve as a visual cue for other species to locate the resource. Our study supports the local enhancement hypothesis within scavengers, whereby individuals locate carcasses by following foraging heterospecifics, also suggesting the importance of the sense of smell in the maintenance of the community structure. [ABSTRACT FROM AUTHOR]

Aim: Mutualistic interactions between plants and animals are fundamental for the maintenance of natural communities and the ecosystem services they provide. However, particularly in human‐dominated island ecosystems, introduced species may alter mutualistic interactions. Based on an extensive dataset of plant–frugivore interactions, we mapped and analysed a meta‐network across the Caribbean archipelago. Specifically, we searched for subcommunity structure (modularity) and identified the types of species facilitating the integration of introduced species in the Caribbean meta‐network. Location: Caribbean archipelago (Lucayan archipelago, Greater Antilles, Lesser Antilles). Methods: We reviewed published scientific literature, unpublished theses and other nonpeer‐reviewed sources to compile an extensive dataset of plant–frugivore interactions. We visualized spatial patterns and conducted a modularity analysis of the cross‐island meta‐network. We also examined which species were most likely to interact with introduced species: (1) endemic, nonendemic native or introduced species, and (2) generalized or specialized species. Results: We reported 3060 records of interactions between 486 plant and 178 frugivore species. The Caribbean meta‐network was organized in 13 modules, driven by a combination of functional or taxonomic (modules dominated by certain groups of frugivores) and biogeographical (island‐specific modules) mechanisms. Few introduced species or interaction pairs were shared across islands, suggesting little homogenization of the plant–frugivore meta‐network at the regional scale. However, we found evidence of "invader complexes," as introduced frugivores were more likely to interact with introduced plants than expected at random. Moreover, we found generalist species more likely to interact with introduced species than were specialized species. Main conclusions: These results demonstrate that generalist species and "invader complexes" may facilitate the incorporation of introduced species into plant–frugivore communities. Despite the influx of introduced species, the meta‐network was structured into modules related to biogeographical and functional or taxonomic affinities. These findings reveal how introduced species become an integral part of mutualistic systems on tropical islands. [ABSTRACT FROM AUTHOR]

Mixed‐species animal groups (MSGs) are widely acknowledged to increase predator avoidance and foraging efficiency, among other benefits, and thereby increase participants' fitness. Diversity in MSG composition ranges from two to 70 species of very similar or completely different phenotypes. Yet consistency in organization is also observable in that one or a few species usually have disproportionate importance for MSG formation and/or maintenance. We propose a two‐dimensional framework for understanding this diversity and consistency, concentrating on the types of interactions possible between two individuals, usually of different species. One axis represents the similarity of benefit types traded between the individuals, while the second axis expresses asymmetry in the relative amount of benefits/costs accrued. Considering benefit types, one extreme represents the case of single‐species groups wherein all individuals obtain the same supplementary, group‐size‐related benefits, and the other extreme comprises associations of very different, but complementary species (e.g. one partner creates access to food while the other provides vigilance). The relevance of social information and the matching of activities (e.g. speed of movement) are highest for relationships on the supplementary side of this axis, but so is competition; relationships between species will occur at points along this gradient where the benefits outweigh the costs. Considering benefit amounts given or received, extreme asymmetry occurs when one species is exclusively a benefit provider and the other a benefit user. Within this parameter space, some MSG systems are constrained to one kind of interaction, such as shoals of fish of similar species or leader–follower interactions in fish and other taxa. Other MSGs, such as terrestrial bird flocks, can simultaneously include a variety of supplementary and complementary interactions. We review the benefits that species obtain across the diversity of MSG types, and argue that the degree and nature of asymmetry between benefit providers and users should be measured and not just assumed. We then discuss evolutionary shifts in MSG types, focusing on drivers towards similarity in group composition, and selection on benefit providers to enhance the benefits they can receive from other species. Finally, we conclude by considering how individual and collective behaviour in MSGs may influence both the structure and processes of communities. [ABSTRACT FROM AUTHOR]

Abstract Background Hybridization is observed in many eukaryotic lineages and can lead to the formation of polyploid species. The study of hybridization and polyploidization faces challenges both in data generation and in accounting for population-level phenomena such as coalescence processes in phylogenetic analysis. Genus Fragaria is one example of a set of plant taxa in which a range of ploidy levels is observed across species, but phylogenetic origins are unknown. Results Here, using 20 diploid and polyploid Fragaria species, we combine approaches from NGS data analysis and phylogenetics to infer evolutionary origins of polyploid strawberries, taking into account coalescence processes. We generate haplotype sequences for 257 low-copy nuclear markers assembled from Illumina target capture sequence data. We then identify putative hybridization events by analyzing gene tree topologies, and further test predicted hybridizations in a coalescence framework. This approach confirms the allopolyploid ancestry of F. chiloensis and F. virginiana, and provides new allopolyploid ancestry hypotheses for F. iturupensis, F. moschata, and F. orientalis. Evidence of gene flow between diploids F. bucharica and F. vesca is also detected, suggesting that it might be appropriate to consider these groups as conspecifics. Conclusions This study is one of the first in which target capture sequencing followed by computational deconvolution of individual haplotypes is used for tracing origins of polyploid taxa. The study also provides new perspectives on the evolutionary history of Fragaria.

Predicting responses of plankton to variations in essential nutrients is hampered by limited in situ measurements, a poor understanding of community composition, and the lack of reference gene catalogs for key taxa. Iron is a key driver of plankton dynamics and, therefore, of global biogeochemical cycles and climate. To assess the impact of iron availability on plankton communities, we explored the comprehensive bio‐oceanographic and bio‐omics data sets from Tara Oceans in the context of the iron products from two state‐of‐the‐art global scale biogeochemical models. We obtained novel information about adaptation and acclimation toward iron in a range of phytoplankton, including picocyanobacteria and diatoms, and identified whole subcommunities covarying with iron. Many of the observed global patterns were recapitulated in the Marquesas archipelago, where frequent plankton blooms are believed to be caused by natural iron fertilization, although they are not captured in large‐scale biogeochemical models. This work provides a proof of concept that integrative analyses, spanning from genes to ecosystems and viruses to zooplankton, can disentangle the complexity of plankton communities and can lead to more accurate formulations of resource bioavailability in biogeochemical models, thus improving our understanding of plankton resilience in a changing environment. Plain Language Summary: Marine phytoplankton require iron for their growth and proliferation. According to John Martin's iron hypothesis, fertilizing the ocean with iron could dramatically increase photosynthetic activity, thus representing a biological means to counteract global warming. However, while there is a constantly growing knowledge of how iron is distributed in the ocean and about its role in cellular processes in marine photosynthetic groups such as diatoms and cyanobacteria, less is known about how iron availability shapes plankton communities and how they respond to it. In the present work, we exploited recently published Tara Oceans data sets to address these questions. We first defined specific subcommunities of co‐occurring organisms that co‐vary with iron availability in the oceans. We then identified specific patterns of adaptation and acclimation to iron in different groups of phytoplankton. Finally, we validated our global results at local scale, specifically in the Marquesas archipelago, where recurrent phytoplankton blooms are believed to be a result of iron fertilization. By integrating global data with a localized response, we provide a framework for understanding the resilience of plankton ecosystems in a changing environment. Key Points: Coherent assemblages of taxa covarying with iron at global level are identified in plankton communitiesFunctional responses to iron availability involve both changes in copy numbers of iron‐responsive genes and their transcriptional regulationPlankton responses to local variations in iron concentrations recapitulate global patterns [ABSTRACT FROM AUTHOR]

Microbial associations that result in phytoplankton mortality are important for carbon transport in the ocean. This includes parasitism, which in microbial food webs is dominated by the marine alveolate group, Syndiniales. Parasites are expected to contribute to carbon recycling via host lysis; however, knowledge on host dynamics and correlation to carbon export remain unclear and limit the inclusion of parasitism in biogeochemical models. We analyzed a 4-year 18S rRNA gene metabarcoding dataset (2016-19), performing network analysis for 12 discrete depths (1-1000 m) to determine Syndiniales-host associations in the seasonally oligotrophic Sargasso Sea. Analogous water column and sediment trap data were included to define environmental drivers of Syndiniales and their correlation with particulate carbon flux (150 m). Syndiniales accounted for 48-74% of network edges, most often associated with Dinophyceae and Arthropoda (mainly copepods) at the surface and Rhizaria (Polycystinea, Acantharea, and RAD-B) in the aphotic zone. Syndiniales were the only eukaryote group to be significantly (and negatively) correlated with particulate carbon flux, indicating their contribution to flux attenuation via remineralization. Examination of Syndiniales amplicons revealed a range of depth patterns, including specific ecological niches and vertical connection among a subset (19%) of the community, the latter implying sinking of parasites (infected hosts or spores) on particles. Our findings elevate the critical role of Syndiniales in marine microbial systems and reveal their potential use as biomarkers for carbon export., Competing Interests: The authors declare no competing interests., (© The Author(s) 2024. Published by Oxford University Press on behalf of the International Society for Microbial Ecology.)

Background: Hybridization is observed in many eukaryotic lineages and can lead to the formation of polyploid species. The study of hybridization and polyploidization faces challenges both in data generation and in accounting for population-level phenomena such as coalescence processes in phylogenetic analysis. Genus Fragaria is one example of a set of plant taxa in which a range of ploidy levels is observed across species, but phylogenetic origins are unknown. Results: Here, using 20 diploid and polyploid Fragaria species, we combine approaches from NGS data analysis and phylogenetics to infer evolutionary origins of polyploid strawberries, taking into account coalescence processes. We generate haplotype sequences for 257 low-copy nuclear markers assembled from Illumina target capture sequence data. We then identify putative hybridization events by analyzing gene tree topologies, and further test predicted hybridizations in a coalescence framework. This approach confirms the allopolyploid ancestry of F. chiloensis and F. virginiana, and provides new allopolyploid ancestry hypotheses for F. iturupensis, F. moschata, and F. orientalis. Evidence of gene flow between diploids F. bucharica and F. vesca is also detected, suggesting that it might be appropriate to consider these groups as conspecifics. Conclusions: This study is one of the first in which target capture sequencing followed by computational deconvolution of individual haplotypes is used for tracing origins of polyploid taxa. The study also provides new perspectives on the evolutionary history of Fragaria. [ABSTRACT FROM AUTHOR]