Allelic resolution of insect and spider silk genes reveals hidden genetic diversity.

Arthropod silk is vital to the evolutionary success of hundreds of thousands of species. The primary proteins in silks are often encoded by long, repetitive gene sequences. Until recently, sequencing and assembling these complex gene sequences has proven intractable given their repetitive structure. Here, using high-quality long-read sequencing, we show that there is extensive variation-both in terms of length and repeat motif order-between alleles of silk genes within individual arthropods. Further, this variation exists across two deep, independent origins of silk which diverged more than 500 Mya: the insect clade containing caddisflies and butterflies and spiders. This remarkable convergence in previously overlooked patterns of allelic variation across multiple origins of silk suggests common mechanisms for the generation and maintenance of structural protein-coding genes. Future genomic efforts to connect genotypes to phenotypes should account for such allelic variation.

Phylogenomics recovers multiple origins of portable case making in caddisflies (Insecta: Trichoptera), nature's underwater architects.

Caddisflies (Trichoptera) are among the most diverse groups of freshwater animals with more than 16 000 described species. They play a fundamental role in freshwater ecology and environmental engineering in streams, rivers and lakes. Because of this, they are frequently used as indicator organisms in biomonitoring programmes. Despite their importance, key questions concerning the evolutionary history of caddisflies, such as the timing and origin of larval case making, remain unanswered owing to the lack of a well-resolved phylogeny. Here, we estimated a phylogenetic tree using a combination of transcriptomes and targeted enrichment data for 207 species, representing 48 of 52 extant families and 174 genera. We calibrated and dated the tree with 33 carefully selected fossils. The first caddisflies originated approximately 295 million years ago in the Permian, and major suborders began to diversify in the Triassic. Furthermore, we show that portable case making evolved in three separate lineages, and shifts in diversification occurred in concert with key evolutionary innovations beyond case making.

Revision and phylogeny of the caddisfly subfamily Protoptilinae (Trichoptera: Glossosomatidae) inferred from adult morphology and mitochondrial DNA.

Protoptilinae Ross, 1956, is the most diverse subfamily belonging to the saddle- or tortoise-case-making caddisfly family Glossosomatidae Wallengren, 1891. The subfamily has a disjunct distribution: 5 genera are known from the East Palae-arctic and Oriental regions; the remaining 13 are restricted to the Nearctic and Neotropical regions. Monophyly of Pro-toptilinae and each of 17 genera was tested using 80 taxa, 99 morphological characters, and mitochondrial DNA (COI). Additionally, homologies of morphological characters were assessed across genera and a standardized terminology for those structures was established. Mitochondrial DNA data were unavailable for 55 of the 80 taxa included in this study. To test the effects of the missing molecular data, 5 different datasets were analyzed using both parsimony and Bayesian methods. There was incongruence between the COI and morphological data, but results suggest the inclusion of COI data in a combined analysis, although incomplete, improved the overall phylogenetic signal. Bayesian and parsimony analyses of all 5 datasets strongly supported the monophyly of Protoptilinae. Monophyly of the following genera was also support-ed: Canoptila Mosely, 1939; Culoptila Mosely, 1954; Itauara Müller, 1888; Mastigoptila Flint, 1967; Mortoniella Ulmer, 1906; Protoptila Banks, 1904; and Tolhuaca Schmid, 1964. Several taxonomic changes were necessary for classification to reflect phylogeny accurately. Accordingly, Matrioptila Ross, 1938; Poeciloptila Schmid, 1991; Temburongpsyche Malicky, 1992; and Nepaloptila Kimmins, 1964, are designated new junior synonyms of Padunia Martynov, 1910. Addition-ally, the endemic Caribbean genera Campsiophora Flint, 1964, and Cubanoptila Sykora, 1973, are designated new junior synonyms of Cariboptila Flint, 1964. Diagnoses and a key to the subfamilies of Glossosomatidae and world genera of Protoptilinae incorporating these taxonomic changes are provided.

A preliminary molecular phylogeny of the family Hydroptilidae (Trichoptera): an exploration of combined targeted enrichment data and legacy sequence data.

Hydroptilidae is an extremely diverse family within Trichoptera, containing over 2,600 known species, that displays a wide array of ecological, morphological, and habitat diversity. However, exploration into the evolutionary history of microcaddisflies based on current phylogenetic methods is mostly lacking. The purpose of this study is to provide a proof-of-concept that the use of molecular data, particularly targeted enrichment data, and statistically supported methods of analysis can result in the construction of a stable phylogenetic framework for the microcaddisflies. Here, a preliminary exploration of the hydroptilid phylogeny is presented using a combination of targeted enrichment data for ca. 300 nuclear protein-coding genes and legacy (Sanger-based) sequence data for the mitochondrial COI gene and partial sequence from the 28S rRNA gene.

A new genus and new species of Ecuadorian Philopotamidae (Trichoptera).

A new genus and species of Philopotamidae (Trichoptera), Sumacodellaelongata, is described from the southern slope of Volcán Sumaco in Ecuador. This new genus differs from other philopotamid genera by having very elongate, narrow anterolateral apodemes on segment IX and the inferior appendages, a very elongate and narrow tergum X, and a very elongate, tubular phallus. In addition, two new species of Wormaldia are also described and illustrated from Sumaco as well as three new Chimarra (Chimarra), one new Chimarra (Curgia), and one new Chimarra (Otarrha) from the eastern and western slopes of the Ecuadorian Andes.

Elevational biodiversity gradients in the Neotropics: Perspectives from freshwater caddisflies (Insecta: Trichoptera).

Aquatic insects in the order Trichoptera are extremely diverse in number of species and their trophic roles. However, their distribution and diversity patterns are poorly known in the Neotropics, including the species restricted to tropical mountain ecosystems. Recent studies in tropical mountains have shown high levels of endemism of aquatic insects and changes in the composition of communities over short distances. Still, the incidence of environmental filters that explain such patterns has not been addressed quantitatively. Given the relevance of understanding Trichoptera spatial diversity patterns to prioritize conservation areas for freshwaters, as well as to obtain baseline information to predict changes in aquatic communities facing global environmental changes, we assessed the species distribution and assemblages of caddisflies along an elevational gradient from 600 to 3,600 m a.s.l. on the equatorial Andes. In this area, we had long-term continuous climate data with hourly resolution. We collected adult caddisflies in seven localities along this gradient using light traps. We sampled each locality for two hours after sunset for three consecutive days. All specimens collected were identified to species or morphospecies. Our results showed an increase in species and genera numbers with decreasing altitude, albeit no significant. Minimum air temperature is the main environmental variable explaining Trichoptera community assemblages. ß-diversity (taxon turnover among sites), as opposed to species richness, increased with altitude and showed a bimodal distribution along the elevation gradient for both genera and species assemblages, which resulted in a significant shift in community composition of species and genera at 2,000 m a.s.l. Our null-models confirm the observed patterns of B-diversity are non-random and suggest a strong environmental filtering of tropical caddisflies community assemblies and turnover. Geographic distance coupled with changes in environmental conditions along the elevation gradient explained a high percentage of community variance, as documented for other taxa (e.g., vascular plants), suggesting the importance of securing habitat connectivity along the altitudinal gradient to protect aquatic insect diversity effectively.

De Novo Genome Assembly and Annotation of an Andean Caddisfly, Atopsyche davidsoni Sykora, 1991, a Model for Genome Research of High-Elevation Adaptations.

We sequence, assemble, and annotate the genome of Atopsyche davidsoni Sykora, 1991, the first whole-genome assembly for the caddisfly family Hydrobiosidae. This free-living and predatory caddisfly inhabits streams in the high-elevation Andes and is separated by more than 200 Myr of evolutionary history from the most closely related caddisfly species with genome assemblies available. We demonstrate the promise of PacBio HiFi reads by assembling the most contiguous caddisfly genome assembly to date with a contig N50 of 14 Mb, which is more than 6× more contiguous than the current most contiguous assembly for a caddisfly (Hydropsyche tenuis). We recover 98.8% of insect BUSCO genes indicating a high level of gene completeness. We also provide a genome annotation of 12,232 annotated proteins. This new genome assembly provides an important new resource for studying genomic adaptation of aquatic insects to harsh, high-altitude environments.

Checklist of the caddisflies (Insecta, Trichoptera) of the Upper Midwest region of the United States.

Five hundred and fifty-two caddisfly species are reported from the Upper Midwest region of the United States, an area that includes 13 states and ~ 2 million km2. Of these, 62 species are reported for the first time from the state of Iowa, 25 from Wisconsin, 18 from South Dakota, 12 from Illinois, five from Indiana, four from North Dakota, four from Minnesota, and one from Nebraska. The Upper Midwest fauna contains nearly 40% of all species known from the United States and Canada, as well as 22 species endemic to the region. Overall species richness was highest in Michigan (319 species), Kentucky (296), Minnesota (292), and Wisconsin (284). Differences in state species assemblages within the region largely followed a geographic pattern, with species richness declining in the western prairie states. There are almost certainly further species remaining to be found in this large region.

Draft Genome Assemblies and Annotations of Agrypnia vestita Walker, and Hesperophylax magnus Banks Reveal Substantial Repetitive Element Expansion in Tube Case-Making Caddisflies (Insecta: Trichoptera).

Trichoptera (caddisflies) play an essential role in freshwater ecosystems; for instance, larvae process organic material from the water and are food for a variety of predators. Knowledge on the genomic diversity of caddisflies can facilitate comparative and phylogenetic studies thereby allowing scientists to better understand the evolutionary history of caddisflies. Although Trichoptera are the most diverse aquatic insect order, they remain poorly represented in terms of genomic resources. To date, all long-read based genomes have been sequenced from individuals in the retreat-making suborder, Annulipalpia, leaving ∼275 Ma of evolution without high-quality genomic resources. Here, we report the first long-read based de novo genome assemblies of two tube case-making Trichoptera from the suborder Integripalpia, Agrypnia vestita Walker and Hesperophylax magnus Banks. We find that these tube case-making caddisflies have genome sizes that are at least 3-fold larger than those of currently sequenced annulipalpian genomes and that this pattern is at least partly driven by major expansion of repetitive elements. In H. magnus, long interspersed nuclear elements alone exceed the entire genome size of some annulipalpian counterparts suggesting that caddisflies have high potential as a model for understanding genome size evolution in diverse insect lineages.

Nectopsyche of Ecuador: a new species from the high Andean páramo and redescription of Nectopsyche spiloma (Ross) (Trichoptera: Leptoceridae).

The male and female of a new species of long-horned caddisfly, Nectopsyche paramo, are described from the high Andes of Ecuador. The new species was found above 4,000 m, representing the highest recorded elevation for a species in the genus. The larval stage of the species is also described. Only a total of 13 larvae were collected during a 17-month sampling program and 11 adults, suggesting that the species is rare. Larvae were found mainly in leaf packs. A male and female were observed in a mating swarm ca. 3 m above a stream during late afternoon. In addition, we redescribe the adult male of Nectopsyche spiloma (Ross), previously known from Ecuador from unsubstantiated literature records.

New Atanatolica species from Ecuador (Trichoptera, Leptoceridae).

Four new species of Atanatolica Mosely are described from Ecuador: A.andina sp. n., A.angulata sp. n., A.curvata sp. n., and A.decouxi sp. n. These species belong to the A.dominicana group and constitute new records of the genus from Chimborazo, Imbabura, and Napo Provinces. Additionally, A.andina sp. n. represents the highest elevation recorded for any species in the genus at 3900 m. Size class data are also presented suggesting continuous larval growth for the probable larva of A.decouxi sp. n., described and illustrated here. A new distribution record is provided for A.manabi from Carchi Province.

New species and a new genus of Philopotamidae from the Andes of Bolivia and Ecuador (Insecta, Trichoptera).

A new genus and species of Philopotamidae (Philopotaminae), Aymaradellaboliviana, is described from the Bolivian Andes of South America. The new genus differs from other Philopotaminae by the loss of 2A vein in the hind wing and, in the male genitalia, the synscleritous tergum and sternum of segment VIII, and the elongate sclerotized dorsal processes of segment VIII. The first record of Hydrobiosella (Philopotaminae) in the New World is also provided with a new species from the Andes of Ecuador, Hydrobiosellaandina. In addition, a new species of the Neotropical genus Chimarrhodella (Chimarrinae), Chimarrhodellachoco, is described from the Choco-Andean region of Ecuador, and Chimarrhodellaperuviana (Ross) is recorded from Ecuador for the first time. Lastly, Wormaldiaimbrialis (Philopotaminae), new species, is described, also from the Ecuadorian Choco.

Fourteen new species of Oecetis McLachlan, 1877 (Trichoptera: Leptoceridae) from the Neotropical region.

BACKGROUND: The caddisfly genus Oecetis currently contains 534 valid species. Its larval stages are found in freshwaters around the world. The adults can be distinguished from other Leptoceridae by the unbranched forewing M vein and the exceptionally long maxillary palps. In the Neotropical region, 55 species of Oecetis have been recorded and most of them can be placed in one of the six species groups known from this biogeographical region: the avara-, falicia-, inconspicua-, punctata-, punctipennis-, and testacea-groups. More than 50% of the known diversity of Neotropical Oecetis has been described in the past 40 years. Here, we describe an additional 14 new species of Oecetis to further document the diversity of this genus in the Neotropical region. METHODS: The descriptions and illustrations presented here are based on male specimens. Specimens were collected with Malaise traps or ultraviolet light traps. They were preserved in alcohol or pinned as stated in material examined section. Specimens had their genitalia prepared in 85% lactic acid to better observe internal characters and illustrations were aided by the use of a microscope with drawing tube attached. RESULTS AND DISCUSSION: This study raises the number of species of Oecetis in the Neotropics from 55 to 69. Eight of the new species presented here could not be reliably placed in one of the known species groups (Oecetis acuticlasper n. sp., Oecetis flinti n. sp., Oecetis carinata n. sp., Oecetis cassicoleata n. sp., Oecetis blahniki n. sp., Oecetis gibbosa n. sp., Oecetis licina n. sp., and Oecetis pertica n. sp.). The others are placed in the punctata-group (Oecetis bidigitata n. sp., Oecetis quasipunctata n. sp.), testacea-group (Oecetis plenuspinosa n. sp.), and falicia-group (Oecetis calori n. sp., Oecetis hastapulla n. sp., Oecetis machaera n. sp.). Most of the diagnostic characters rely on structures of the inferior appendages and phallic apparatus, and the shape of tergum X.

Catalog of the Neotropical Trichoptera (Caddisflies).

The Neotropical caddisfly (Trichoptera) fauna is cataloged from a review of over 1,000 literature citations through 2015 (partial 2016) to include 3,262 currently recognized, valid species-group names in 25 families and 155 extant genera. Fourteen subspecies are included in the total as well as 35 fossil species and 1 fossil genus. The region covered includes all of Mexico, Central America, the Caribbean, and South America. Genus-group and species-group synonyms are listed. For each nominal species, information on the type locality, type depository, sex of type, distribution by country, and other pertinent taxonomic or biological information is included. Summary information on taxonomy, phylogeny, distribution, immature stages, and biology are provided for each family and genus where known. An extensive index to all nominal taxa is included to facilitate use of the catalog. The glossosomatid species Mexitrichia usseglioi Rueda Martín & Gibon, is transferred to Mortoniellacomb. n.

New Cernotina caddisflies from the Ecuadorian Amazon (Trichoptera: Polycentropodidae).

Two new species of the caddisfly genus Cernotina Ross, 1938 (Polycentropodidae) are described from the lowland Amazon basin of Ecuador, Cernotina tiputini, new species, and Cernotina waorani, new species. These represent the first new species described from this region. We also record from Ecuador for the first time Cernotina hastilis Flint, previously known from Tobago, and present new Ecuadorian locality records for C. cygnea Flint, and C. lobisomem Santos & Nessimian. The homology of the intermediate appendage of the male genitalia of this genus is established. The region surveyed is under severe environmental threat from logging, mining, and crude oil extraction, making the description of the biodiversity of the region imperative.

Two new species of the rare Neotropical caddisfly genus Amphoropsyche Holzenthal (Trichoptera, Leptoceridae).

Two new species in the rare, endemic Neotropical caddisfly genus Amphoropsyche Holzenthal, 1985 are described from Ecuador (A. carchisp. n.) and Peru (A. matsigenkasp. n.) bringing to 17 the number of species known in the genus. Almost all species are known from only a few individuals and from even fewer localities. The new species belong to a group of 10 other species that have tergum X in the male genitalia divided into a mesal process and a pair of lateral processes. Amphoropsyche carchi can be separated from those species by the rounded mesal concavity, the short mesobasal lobe, and the short 2nd article of the inferior appendage, while A. matsigenka can be diagnosed by the very slender and straight inferior appendage, which bears a pair of spine-like mesoventral projections. We also present a new record for Amphoropsyche tandayapa Holzenthal & Rázuri-Gonzales, 2011, from Ecuador, previously known only from the male holotype.

New species of the endemic Neotropical caddisfly genus Contulma from the Andes of Ecuador (Trichoptera: Anomalopsychidae).

The genus Contulma Flint (Trichoptera: Anomalopsychidae) is composed mostly of regionally endemic species occurring above 2,000 m, with a few more widespread species and some that are found at lower elevations. Adults of three new species of Contulma are described and illustrated from the Andes of Ecuador, Contulma lina, new species, Contulma quito, new species, and Contulma sangay, new species. These species are similar to previously described species from the region, including C. paluguillensis, C. nevada, and C. lancelolata. New provincial records are provided for C. bacula, C. cataracta, and C. echinata. Contulma duffi Oláh, 2016 is considered a junior, subjective synonym of C. penai, Holzenthal & Flint, 1995. Also, we provide an identification key to males of the 30 Contulma species now known.

Diversity and distribution of the Caddisflies (Insecta: Trichoptera) of Ecuador.

BACKGROUND: Aquatic insects and other freshwater animals are some of the most threatened forms of life on Earth. Caddisflies (Trichoptera) are highly biodiverse in the Neotropics and occupy a wide variety of freshwater habitats. In Andean countries, including Ecuador, knowledge of the aquatic biota is limited, and there is a great need for baseline data on the species found in these countries. Here we present the first list of Trichoptera known from Ecuador, a country that harbors two global biodiversity "hotspots." METHODS: We conducted a literature review of species previously reported from Ecuador and supplemented these data with material we collected during five recent field inventories from about 40 localities spanning both hotspots. Using species presence data for each Ecuadorian province, we calculated the CHAO 2 species estimator to obtain the minimum species richness for the country. RESULTS: We recorded 310 species, including 48 new records from our own field inventories for the country. CHAO 2 calculations showed that only 54% of the species have been found. Hydroptilidae and Hydropsychidae were the most species rich families. We report the family Xiphocentronidae for the first time from Ecuador as well as several new records of genera from different families. DISCUSSION: As in the neighboring Andean countries of Colombia and Peru, it is common to find undescribed species of caddisflies. There are vast areas of Ecuador and the northern Andes that are completely unexplored, and we expect that hundreds of new species are yet to be discovered.

New synonyms in the highly diverse caddisfly genus Smicridea (Trichoptera, Hydropsychidae).

In this paper, Smicridea (Rhyacophylax) repula Oláh & Johanson, 2012 is synonymized with Smicridea (Rhyacophylax) lobata (Ulmer, 1909), and the species Leptonema islamarga Botosaneanu, 2002 is transferred to Smicridea (Rhyacophylax) as a synonym of Smicridea lobata. Additionally, we present more detailed illustrations of the male genitalia of Smicridea (Rhyacophylax) lobata and Smicridea (Rhyacophylax) signata (Banks, 1903), and include notes on their distributions to aid in the identification of these two, often-confused species.

A new Ecuadorian species of the rare Neotropical caddisfly genus Amphoropsyche Holzenthal (Trichoptera, Leptoceridae).

A new species of the rare long-horned caddisfly genus Amphoropsyche Holzenthal is described from Ecuador, bringing the number of species known from the genus to 15. All species are very regional in their distributions and known only from very few specimens. The new species, Amphoropsyche real, is similar to a number of previously described species from Colombia (Amphoropsyche ayura, Amphoropsyche cauca, Amphoropsyche flinti, Amphoropsyche quebrada, and Amphoropsyche stellata) and Ecuador (Amphoropsyche napo and Amphoropsyche tandayapa). The males can be distinguished from the others by features of segment X of the male genitalia, especially the prominent midlateral and subapicodorsal spinelike setae. An updated taxonomic key to males of the genus is provided.