Phylogeny and classification of Odonata using targeted genomics

A molecular phylogeny of the Petaluridae (Odonata: Anisoptera): A 160-Million-Year-Old story of drift and extinction

Petaluridae (Odonata: Anisoptera) is a relict dragonfly family, having diverged from its sister family in the Jurassic, of eleven species that are notable among odonates (dragonflies and damselflies) for their exclusive use of fen and bog habitats, their burrowing behavior as nymphs, large body size as adults, and extended lifespans. To date, several nodes within this family remain unresolved, limiting the study of the evolution of this peculiar family. Using an anchored hybrid enrichment dataset of over 900 loci we reconstructed the species tree of Petaluridae. To estimate the temporal origin of the genera within this family, we used a set of well-vetted fossils and a relaxed molecular clock model in a divergence time estimation analysis. We estimate that Petaluridae originated in the early Cretaceous and confirm the existence of monophyletic Gondwanan and Laurasian clades within the family. Our relaxed molecular clock analysis estimated that these clades diverged from their MRCA approximately 160 mya. Extant lineages within this family were identified to have persisted from 6 (Uropetala) to 120 million years (Phenes). Our biogeographical analyses focusing on a set of key regions suggest that divergence within Petaluridae is largely correlated with continental drift, the exposure of land bridges, and the development of mountain ranges. Our results support the hypothesis that species within Petaluridae have persisted for tens of millions of years, with little fossil evidence to suggest widespread extinction in the family, despite optimal conditions for the fossilization of nymphs. Petaluridae appear to be a rare example of habitat specialists that have persisted for tens of millions of years.

Museomics help resolving the phylogeny of snowfinches (Aves, Passeridae, Montifringilla and allies)

Historical specimens from museum collections provide a valuable source of material also from remote areas or regions of conflict that are not easily accessible to scientists today. With this study, we are providing a taxon-complete phylogeny of snowfinches using historical DNA from whole skins of an endemic species from Afghanistan, the Afghan snowfinch, Pyrgilauda theresae. To resolve the strong conflict between previous phylogenetic hypotheses, we generated novel mitogenome sequences for selected taxa and genome-wide SNP data using ddRAD sequencing for all extant snowfinch species endemic to the Qinghai-Tibet Plateau (QTP) and for an extended intraspecific sampling of the sole Central and Western Palearctic snowfinch species (Montifringilla nivalis). Our phylogenetic reconstructions unanimously refuted the previously suggested paraphyly of genus Pyrgilauda. Misplacement of one species-level taxon (Onychostruthus tazcanowskii) in previous snowfinch phylogenies was undoubtedly inferred from chimeric mitogenomes that included heterospecific sequence information. Furthermore, comparison of novel and previously generated sequence data showed that the presumed sister-group relationship between M. nivalis and the QTP endemic M. henrici was suggested based on flawed taxonomy. Our phylogenetic reconstructions based on genome-wide SNP data and on mitogenomes were largely congruent and supported reciprocal monophyly of genera Montifringilla and Pyrgilauda with monotypic Onychostruthus being sister to the latter. The Afghan endemic P. theresae likely originated from a rather ancient Pliocene out-of-Tibet dispersal probably from a common ancestor with P. ruficollis. Our extended trans-Palearctic sampling for the white-winged snowfinch, M. nivalis, confirmed strong lineage divergence between an Asian and a European clade dated to 1.5 - 2.7 million years ago (mya). Genome-wide SNP data suggested subtle divergence among European samples from the Alps and from the Cantabrian mountains.

Structures and genetic information of control region in mitogenomes of Odonata

Mitogenome data of Odonata is accumulating and widely used in phylogenetic analysis. However, noncoding regions, especially control region, were usually omitted from the phylogenetic reconstruction. In an effort to uncover the phylogenetic insights offered by the control region, we have amassed 65 Odonata mitogenomes and conducted an examination of their control regions. Our analysis discovered that species belonging to Anisoptera and Anisozygoptera exhibited a stem-loop structure, which was formed by a conserved polyC-polyG stretch located near the rrns gene (encoding 12S rRNA). Conversely, the polyC-polyG region was not a conserved fragment in Zygoptera. The length and number of repetitions within the control region were identified as the primary determinants of its overall length. Further, sibling species within Odonata, particularly those in the genus Euphaea, displayed similar patterns of repetition in their control region. Collectively, our research delineates the structural variations within the control region of Odonata and suggests the potential utility of this region in elucidating phylogenetic relationships among closely related species.

Tropical Origin, Global Diversification, and Dispersal in the Pond Damselflies (Coenagrionoidea) Revealed by a New Molecular Phylogeny

The processes responsible for the formation of Earth's most conspicuous diversity pattern, the latitudinal diversity gradient (LDG), remain unexplored for many clades in the Tree of Life. Here, we present a densely sampled and dated molecular phylogeny for the most speciose clade of damselflies worldwide (Odonata: Coenagrionoidea) and investigate the role of time, macroevolutionary processes, and biome-shift dynamics in shaping the LDG in this ancient insect superfamily. We used process-based biogeographic models to jointly infer ancestral ranges and speciation times and to characterize within-biome dispersal and biome-shift dynamics across the cosmopolitan distribution of Coenagrionoidea. We also investigated temporal and biome-dependent variation in diversification rates. Our results uncover a tropical origin of pond damselflies and featherlegs ~105 Ma, while highlighting the uncertainty of ancestral ranges within the tropics in deep time. Even though diversification rates have declined since the origin of this clade, global climate change and biome-shifts have slowly increased diversity in warm- and cold-temperate areas, where lineage turnover rates have been relatively higher. This study underscores the importance of biogeographic origin and time to diversify as important drivers of the LDG in pond damselflies and their relatives, while diversification dynamics have instead resulted in the formation of ephemeral species in temperate regions. Biome-shifts, although limited by tropical niche conservatism, have been the main factor reducing the steepness of the LDG in the last 30 Myr. With ongoing climate change and increasing northward range expansions of many damselfly taxa, the LDG may become less pronounced. Our results support recent calls to unify biogeographic and macroevolutionary approaches to improve our understanding of how latitudinal diversity gradients are formed and why they vary across time and among taxa.

Diversity and complexity of arthropod references in haiku

Haiku are short poems, each composed of about 10 words, that typically describe moments in nature. People have written haiku since at least the 17th century, and the medium continues to be popular with poets, amateurs, educators, and students. Collectively, these poems represent an opportunity to understand which aspects of nature-e.g., which taxa and biological traits-resonate with humans and whether there are temporal trends in their representation or the emotions associated with these moments. We tested this potential using a mix of linguistic and biological methods, in analyses of nearly 4,000 haiku that reference arthropods. We documented the taxa and the life history traits represented in these poems and how they changed over time. We also analyzed the poems for emotion and tone. Our results reveal a mix of predictable trends and compelling surprises, each of which stand to potentially inform engagement strategies. At least 99 families of arthropods, in 28 orders, are represented in these haiku. The eight most commonly referenced taxa, from highest to lowest number of references, include: Lepidoptera, Hymenoptera, Diptera, Coleoptera, Araneae, Orthoptera, Hemiptera, and Odonata. Several common, conspicuous orders were never referenced, including Trichoptera, Plecoptera, and Megaloptera. The most commonly referenced traits relate to ecology (especially habitat, phenology, time of day), behavior (especially sound production), phenotype (especially color), and locomotion (especially flight). The least common traits in haiku relate to arthropod reproduction and physiology. Our analyses revealed few obvious temporal trends in the representations of taxa, biological traits, or emotion and tone. The broader implications of these results and possible future directions are discussed.

Diversity of an Odonata assemblage from a tropical dry forest in San Buenaventura, Jalisco, Mexico (Insecta, Odonata)

Background

The patterns of richness, diversity, and abundance of an odonate assemblage from San Buenaventura, Jalisco are presented here. A total of 1087 specimens from seven families, 35 genera and 66 species were obtained through monthly samplings of five days each during a period of one year. Libellulidae was the most diverse family (28 species), followed by Coenagrionidae (21), Gomphidae (7), Aeshnidae (6), Calopterygidae (2), Lestidae (1) and Platystictidae (1). Argia was the most speciose genus. The highest species richness and Shannon diversity were found during August and September, whereas the highest abundance was observed in June and the highest Simpson diversity was recorded in September - all of which were associated with the rainy season. The highest values of phylogenetic diversity were found from June to October. The different diversity facets of this assemblage were positively correlated with precipitation and minimum temperature, whereas maximum temperature showed no influence. In addition, we found that this odonate diversity was higher than most Mexican localities with tropical dry forest (TDF) studied.

New information

We continue our efforts to describe the patterns of richness, diversity and abundance of some insect groups associated with the tropical dry forest ecosystem in Mexico, following a latitudinal gradient of the distribution of this ecosystem in the country. Our emphasis here was to evaluate the spatial and temporal patterns of richness and diversity of an Odonata assemblage from Jalisco, Mexico.

Little bits of dragonfly history repeating exemplified by a new Pennsylvanian family

During its 320 Myr evolution, dragon- and damselfly (Odonata) wing morphology underwent intense modifications. The resulting diversity prompted comparative analyses focusing on phylogeny. However, homoplasy proved to plague wing-related characters. Concurrently, limited benefits were obtained from considering fossil taxa, similarly impacted. Herein, we investigate two aspects particularly affected by convergence, namely the acquisition of vein-like structuring elements derived from regular cross-venation, termed conamina; and the evolution of butter knife wing shape. Conamen implementation is found to be consistently linked with vein curvature sharpening, itself generating potential breaking points. Conamina therefore likely evolved to address wing integrity issues during ever-more-demanding flight performance. Moreover, an existing conamen is likely to trigger the acquisition of further, associated conamina. As for butter knife shape, previously documented in the extinct Archizygoptera and among damselflies, we report a new, 315 Ma occurrence with the rare species Haidilaozhen cuiae gen. et sp. nov. (family Haidilaozhenidae fam. nov.), from the Xiaheyan locality (China). The repeated acquisition of butter knife-shaped wing can be related to slow speed flight and, in turn, predator avoidance. In both cases of iterated regularities, the unique 'network-and-membrane' wing design proper to insects is found to compose a strong, constraining factor.

Evolution of Odonata: genomic insights

Odonata is an order of insects that comprises ∼6500 species. They are among the earliest flying insects, and one of the first diverging lineages in the Pterygota. Odonate evolution has been a topic of research for over 100 years, with studies focusing primarily on their flight behavior, color, vision, and aquatic juvenile lifestyles. Recent genomics studies have provided new interpretations about the evolution of these traits. In this paper, we look at how high-throughput sequence data (i.e. subgenomic and genomic data) have been used to answer long-standing questions in Odonata ranging from evolutionary relationships to vision evolution to flight behavior. Additionally, we evaluate these data at multiple taxonomic levels (i.e. ordinal, familial, generic, and population) and provide comparative analysis of genomes across Odonata, identifying features of these new data. Last, we discuss the next two years of Odonata genomic study, with context about what questions are currently being tackled.

A new species of Dimeragrion Calvert, 1913 (Odonata: Zygoptera: Heteragrionidae) from Northwestern Brazil

Dimeragrion Calvert, 1913 is a genus with five species, restricted to the Pantepui region. Here, we describe Dimeragrion baniwa sp. nov. (Holotype. ♂ (LABECO, N° 12276), BRAZIL, Amazonas, São Gabriel da Cachoeira, (0.017, -66.891, 81 m a.s.l.), first-order stream inside Terra Firme Forest, in lateral swamps: 29.xi.2021, C. C. Mendoza-Penagos & M. Gonçalves, leg.), the sixth species of the genus from 13 males and 3 females collected in the municipality of São Gabriel da Cachoeira in the Brazilian Amazon, located at the southern extreme of the Pantepui region. Additionally, we provide photographs of the diagnostic characters of the male and female, photographs of live specimens as well as information on their biology. Finally, identification keys are provided, as well as a distribution map of the species of the genus.

Reference genome for the American rubyspot damselfly, Hetaerina americana

Damselflies and dragonflies (Order: Odonata) play important roles in both aquatic and terrestrial food webs and can serve as sentinels of ecosystem health and predictors of population trends in other taxa. The habitat requirements and limited dispersal of lotic damselflies make them especially sensitive to habitat loss and fragmentation. As such, landscape genomic studies of these taxa can help focus conservation efforts on watersheds with high levels of genetic diversity, local adaptation, and even cryptic endemism. Here, as part of the California Conservation Genomics Project (CCGP), we report the first reference genome for the American rubyspot damselfly, Hetaerina americana, a species associated with springs, streams and rivers throughout California. Following the CCGP assembly pipeline, we produced two de novo genome assemblies. The primary assembly includes 1,630,044,487 base pairs, with a contig N50 of 5.4 Mb, a scaffold N50 of 86.2 Mb, and a BUSCO completeness score of 97.6%. This is the seventh Odonata genome to be made publicly available and the first for the subfamily Hetaerininae. This reference genome fills an important phylogenetic gap in our understanding of Odonata genome evolution, and provides a genomic resource for a host of interesting ecological, evolutionary, and conservation questions for which the rubyspot damselfly genus Hetaerina is an important model system.

Amazonian Odonata Trait Bank

Discussion regarding the gaps of knowledge on Odonata is common in the literature. Such gaps are even greater when dealing with basic biological data for biodiverse environments like the Amazon Rainforest. Therefore, studies that address, classify, and standardize functional traits allow the elaboration of a wide range of ecological and evolutionary hypotheses. Moreover, such endeavors aid conservation and management planning by providing a better understanding of which functional traits are filtered or favored under environmental changes. Here, our main goal was to produce a database with 68 functional traits of 218 Odonata species that occur in the Brazilian Amazon. We extracted data on behavior, habit/habitat (larvae and adults), thermoregulation, and geographic distribution from 419 literature sources classified into different research areas. Moreover, we measured 22 morphological traits of approximately 2500 adults and categorized species distributions based on approximately 40,000 geographic records for the Americas. As a result, we provided a functional matrix and identified different functional patterns for the Odonata suborders, as well as a strong relationship between the different trait categories. For this reason, we recommend the selection of key traits that represent a set of functional variables, reducing the sampling effort. In conclusion, we detect and discuss gaps in the literature and suggest research to be developed with the present Amazonian Odonata Trait Bank (AMO-TB).

The damselfly genus Furagrion Petrulevičius et al. (Odonata, Zygoptera) from the early Eocene Fur Formation of Denmark and the dysagrionoid grade

The earliest Eocene odonate genus Furagrion Petrulevičius et al. from the Danish Fur Formation is revised based on eighteen specimens, two of which apparently have been lost since their publication. The holotype of Phenacolestes jutlandicus Henriksen, type species of Furagrion, is incomplete and lacks the characters currently used to differentiate species, genera and higher taxa in Odonata. We, therefore, propose that the holotype is set aside and a recently discovered nearly complete Fur Formation fossil is designated as neotype. Furagrion possesses all of the nine wing character states currently used along with head shape for diagnosing the Dysagrionidae; however, Furagrion has a characteristically zygopteran head, not the distinctive head shape of the suborder Cephalozygoptera. We, therefore, treat it as a zygopteran unassigned to family. These nine wing character states appear in different combinations not only in various Zygoptera and Cephalozygoptera, but also in the Frenguelliidae, an Eocene family of Argentina that may represent an unnamed suborder. We recognise these taxa as constituting a dysagrionoid grade, in which these character states appear either convergently or as symplesiomorphies. Furagrion morsi Zessin is synonymized with Phenacolestes jutlandicus Henriksen, syn. nov. and Morsagrion Zessin with Furagrion Petrulevičius, Wappler, Wedmann, Rust, and Nel, syn. nov.

Species diversity, hotspot congruence, and conservation of North American damselflies (Odonata: Zygoptera)

The rapid extinction of species is of considerable concern for biodiversity conservation. Identifying the drivers of species diversity and hotspots is beneficial for developing conservation strategies. Studies on insects have mainly focused on terrestrial species and rarely on semiaquatic species. Using 135,208 georeferenced occurrence records of 296 damselflies across North America, their species richness and endemism (represented by weighted endemism) patterns were mapped in a 100 × 100-km grid size, and the effects of environmental variables on species richness and endemism were investigated using generalized linear models and hierarchical partitioning. Subsequently, the top 5% grids with species richness and weighted endemism were separately selected as hotspots and their congruence was evaluated. Finally, species diversity hotspots were identified by integrating two types of hotspot grids, and gap analysis was performed to evaluate their conservation status. Temperature conditions and water availability had the strongest influence on species richness and endemism, respectively. Low congruence among species richness and endemism hotspots was observed. Moreover, four species diversity hotspots were identified, namely, region of the eastern United States and southeastern Canada, southwestern United States, central Mexico, and southernmost North America. Approximately 69.31% of the hotspot grids are not a part of the existing protected areas, presenting a significant conservation gap. The habitats of taxonomic groups should be considered while identifying the most common driving mechanisms of endemism. Strengthening the establishment of protected areas in regions with conservation gaps is urgently needed to promote the conservation of damselflies in North America.

A Bibliometric Analysis of the Global Research in Odonata: Trends and Gaps

Insects of the order Odonata have been used as indicators of environmental quality in different aquatic systems around the world. In this context, we conducted a bibliometric analysis to understand the general patterns of research on Odonata published in the past decade (2012–2021). We extracted literature from the Web of Science (WoS) in the advanced search option and used search terms related to Odonata plus search strings for each term. A total of 2764 Odonata publications were identified. The journals with the most published articles on Odonata were Zootaxa, International Journal of Odonatology and Odonatologica. The countries with the most Odonata publications were the USA, Brazil and China. Most studies were conducted on streams, ponds and rivers. Ecology, taxonomy and behavior were the main study topics. Of the total articles on Odonata, 982 involved Zygoptera and 946 Anisoptera. Another 756 studies were focused on both suborders. The increase in ecological and taxonomic studies of Odonata reflects the dynamic characteristics of this order, and its relatively well-defined systematics, especially in the case of adults. Despite the recent increase in the number of publications, there are still many gaps related to topics such as biogeography, parasitism, competition within and between species, evolutionary and phylogenetic relationships, as well as studies of the eggs (e.g., their development) and larval exuviae (e.g., their morphological features).

Predictors of sequence capture in a large-scale anchored phylogenomics project

Next-generation sequencing (NGS) technologies have revolutionized phylogenomics by decreasing the cost and time required to generate sequence data from multiple markers or whole genomes. Further, the fragmented DNA of biological specimens collected decades ago can be sequenced with NGS, reducing the need for collecting fresh specimens. Sequence capture, also known as anchored hybrid enrichment, is a method to produce reduced representation libraries for NGS sequencing. The technique uses single-stranded oligonucleotide probes that hybridize with pre-selected regions of the genome that are sequenced via NGS, culminating in a dataset of numerous orthologous loci from multiple taxa. Phylogenetic analyses using these sequences have the potential to resolve deep and shallow phylogenetic relationships. Identifying the factors that affect sequence capture success could save time, money, and valuable specimens that might be destructively sampled despite low likelihood of sequencing success. We investigated the impacts of specimen age, preservation method, and DNA concentration on sequence capture (number of captured sequences and sequence quality) while accounting for taxonomy and extracted tissue type in a large-scale butterfly phylogenomics project. This project used two probe sets to extract 391 loci or a subset of 13 loci from over 6,000 butterfly specimens. We found that sequence capture is a resilient method capable of amplifying loci in samples of varying age (0–111 years), preservation method (alcohol, papered, pinned), and DNA concentration (0.020 ng/μl - 316 ng/ul). Regression analyses demonstrate that sequence capture is positively correlated with DNA concentration. However, sequence capture and DNA concentration are negatively correlated with sample age and preservation method. Our findings suggest that sequence capture projects should prioritize the use of alcohol-preserved samples younger than 20 years old when available. In the absence of such specimens, dried samples of any age can yield sequence data, albeit with returns that diminish with increasing age.

Taxonomic note on the species status of Epiophlebiadiana (Insecta, Odonata, Epiophlebiidae), including remarks on biogeography and possible species distribution

The species included in the genus Epiophlebia Calvert, 1903 represent an exception within Recent lineages - they do not belong to either dragonflies (Anisoptera) nor damselflies (Zygoptera). Nowadays, the genus is solely known from the Asian continent. Due to their stenoecious lifestyle, representatives of Epiophlebia are found in often very small relict populations in Nepal, Bhutan, India, Vietnam, China, North Korea, and Japan. We here present a taxonomic re-evaluation on the species status of Epiophlebiadiana Carle, 2012, known from the Sichuan province in China, supplemented with a morphological character mapping on a genetic tree to highlight synapomorphies of E.diana and E.laidlawi Tillyard, 1921. We conclude that E.diana is a junior synonym of E.laidlawi. Furthermore, we discuss the Recent distribution of the group, allowing for predictions of new habitats of representatives of this group.

Detecting Darwinian Shortfalls in the Amazonian Odonata

Among the oldest winged insects, odonates are a monophyletic order that have become important models for ecological studies because of their highly diverse reproductive behaviors and their role as top predators and bioindicators. However, knowledge on evolutionary relationships within the order is still scarce compared to other taxa, and this situation is even more complicated in areas with high biodiversity, such as in the Amazon. Here, we sought to identify knowledge gaps on Amazonian Odonata regarding three main aspects: (i) how the inclusion of Amazonian taxa affects our interpretation of the evolutionary relationships of Zygoptera and Anisoptera; (ii) the position of Amazonian taxa in the existing supertree of the Odonata; (iii) dating evolutionary divergence between nodes using fossil records; (iv) assessing whether more species-rich basins (e.g., Amazon basin) have a larger phylogenetic gap when compared to basins with lower richness in South and Central America; and (v) in the light of our knowledge, we discuss diversification patterns found in the most predominant clades of Amazonian taxa. We built a supertree from currently available phylogenetic information of Odonata. The results show that there is no genetic information for 85% (n: 503) of the Amazonian species and that family level relationships are unknown for 17 genera. After compiling the data, we observed that clades belonging to Neotropical lineages are the most poorly resolved, with large polytomies. This problem was identified in many Anisoptera genera, such as Macrothemis, Dasythemis, Elasmothemis, and Erythrodiplax. Our results also suggest that not always the richest basins have the greatest phylogenetic gaps. As expected, we found important gaps in the existing Odonata phylogenies, especially in clades that include Amazonian representatives, that are also those less known from ecological and conservation perspectives.

Evolutionary history and divergence times of Odonata (dragonflies and damselflies) revealed through transcriptomics

Dragonflies and damselflies are among the earliest flying insects with extant representatives. However, unraveling details of their long evolutionary history, such as egg laying (oviposition) strategies, is impeded by unresolved phylogenetic relationships, particularly in damselflies. Here we present a transcriptome-based phylogenetic reconstruction of Odonata, analyzing 2,980 protein-coding genes in 105 species representing nearly all the order's families. All damselfly and most dragonfly families are recovered as monophyletic. Our data suggest a sister relationship between dragonfly families of Gomphidae and Petaluridae. According to our divergence time estimates, both crown-Zygoptera and -Anisoptera arose during the late Triassic. Egg-laying with a reduced ovipositor apparently evolved in dragonflies during the late Jurassic/early Cretaceous. Lastly, we also test the impact of fossil choice and placement, particularly, of the extinct fossil species, †Triassolestodes asiaticus, and †Proterogomphus renateae on divergence time estimates. We find placement of †Proterogomphus renateae to be much more impactful than †Triassolestodes asiaticus.