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The snake pipefish, Entelurus aequoreus (Linnaeus, 1758), is a slender, up to 60 cm long, northern Atlantic fish that dwells in open seagrass habitats and has recently expanded its distribution range. The snake pipefish is part of the family Syngnathidae (seahorses and pipefish) that has undergone several characteristic morphological changes, such as loss of pelvic fins and elongated snout. Here, we present a highly contiguous, near chromosome-scale genome of the snake pipefish assembled as part of a university master’s course. The final assembly has a length of 1.6 Gbp in 7,391 scaffolds, a scaffold and contig N50 of 62.3 Mbp and 45.0 Mbp and L50 of 12 and 14, respectively. The largest 28 scaffolds (>21 Mbp) span 89.7% of the assembly length. A BUSCO completeness score of 94.1% and a mapping rate above 98% suggest a high assembly completeness. Repetitive elements cover 74.93% of the genome, one of the highest proportions so far identified in vertebrate genomes. Demographic modeling using the PSMC framework indicates a peak in effective population size (50 – 100 kya) during the last interglacial period and suggests that the species might largely benefit from warmer water conditions, as seen today. Our updated snake pipefish assembly forms an important foundation for further analysis of the morphological and molecular changes unique to the family Syngnathidae.
Highlights
• Genomes for all five Natrix species, two represented by two distinct subspecies each, were sequenced.
• Two genomes were de-novo assembled to their 1.7 Gb length with a contig N50 of 4.6 Mbp and 1.5 Mbp.
• Evidence for interspecific hybridization, both between allopatric and widely sympatric species.
• Fossil-calibrated molecular clock using genomes indicates that species are ancient several million-year-old lineages.
• Our findings imply that speciation took place despite continued gene flow.
Abstract
Understanding speciation is one of the cornerstones of biological diversity research. Currently, speciation is often understood as a continuous process of divergence that continues until genetic or other incompatibilities minimize or prevent interbreeding. The Palearctic snake genus Natrix is an ideal group to study speciation, as it comprises taxa representing distinct stages of the speciation process, ranging from widely interbreeding parapatric taxa through parapatric species with very limited gene flow in narrow hybrid zones to widely sympatric species. To understand the evolution of reproductive isolation through time, we have sequenced the genomes of all five species within this genus and two additional subspecies. We used both long-read and short-read methods to sequence and de-novo-assemble two high-quality genomes (Natrix h. helvetica, Natrix n. natrix) to their 1.7 Gb length with a contig N50 of 4.6 Mbp and 1.5 Mbp, respectively, and used these as references to assemble the remaining short-read-based genomes. Our phylogenomic analyses yielded a well-supported dated phylogeny and evidence for a surprisingly complex history of interspecific gene flow, including between widely sympatric species. Furthermore, evidence for gene flow was also found for currently allopatric species pairs. Genetic exchange among these well-defined, distinct, and several million-year-old reptile species emphasizes that speciation and maintenance of species distinctness can occur despite continued genetic exchange.
The genus Jambu gen. nov. is proposed based on two new species: Jambu paru gen. et sp. nov. and Jambu manoa gen. et sp. nov. Hapalopus butantan is transferred to Jambu; consequently, Jambu butantan gen. et comb. nov. is proposed. The geographic distribution of J. butantan is extended on the basis of new material collected. The new genus and the new species are here diagnosed, described and illustrated. The shape of the genitalia of Jambu resembles that of Hapalopini but differs from most of them by the presence of type IV urticating setae. The presence of this type of urticating setae allows us to hypothesize that this new genus is phylogenetically related with Grammostolini. Males of Jambu differ from those of other genera of Grammostolini by the presence of a paraembolic apophysis on the palpal bulb. Females also differ from those of other Grammostolini by the spermathecae morphology, with one medial lamp-shaped or heart-shaped receptacle. The homology of some features and the taxonomic placement of the new genus are discussed.
The ant genus Syscia Roger, 1861 is a cryptobiotic group of the subfamily Dorylinae. In this study, eight species of this genus from Asia are recognized, including two new species, Syscia arcodorsa sp. nov. and S. zhoui sp. nov., both described from Guangxi in China. In addition, Cerapachys guizhouensis Zhou, 2006 is redescribed and transferred to Syscia as S. guizhouensis (Zhou, 2006) comb. nov. The species Syscia typhla Roger, 1861 is removed from the ant fauna of China. Lastly, a key to species of Syscia from Asia based on the worker caste is presented.
Four new species of the jumping spider genus Stenaelurillus Simon, 1886 are described from India: Stenaelurillus feral Tripathi, Kuni & Kadam sp. nov. (♂, from the Eastern Coastline), S. naldurg Kuni, Kadam & Tripathi sp. nov. (♂♀, from the Deccan Plateau), S. judithbleisterae Kadam, Tripathi & Kuni sp. nov. (♂♀, from the Western Ghats) and S. solapur Kuni, Tripathi & Kadam sp. nov. (♂♀, from the Deccan Plateau). Detailed diagnoses, descriptions, illustrations, natural history and distribution map are provided. Additionally, new locality records for the other five species within the states are presented and mapped.
In this study, I describe two new species of Macrobiotus based on morphological data collected through light and scanning electron microscopy. Both species are accompanied by DNA sequences from four commonly used molecular markers (18S rDNA, 28S rDNA, ITS-2, and COI). Macrobiotus ovovittatus sp. nov. was discovered in Greenland and can be distinguished from similar taxa of Macrobiotus by its continuous, solid, and clearly wrinkled egg surface, adorned with sparse, very small and irregularly spaced pores. Additionally, the terminal discs of egg processes are covered in multiple light-refracting dots, resembling crocheted napkins. Macrobiotus mileri sp. nov. was found in Israel and is characterized by unique pore arrangements in its body cuticle, expressed in two distinct animal forms: (i) forma porata with large pores arranged in five distinct patches and (ii) forma aporata with single, almost undetectable pores. It also features weakly defined convex terminal discs with smooth edges. Furthermore, the phylogenetic analyses conducted in this study offer the most updated phylogeny of superclade I within the family Macrobiotidae. This facilitates additional discussion concerning the interrelationships among species within the genus Macrobiotus and the circumscription of species groups within it.
In the vast abyssal plains northwest of Iceland, white glass sponges of the genus Caulophacus Schulze, 1886 were inhabited by reddish Bythocaris G.O. Sars, 1870 shrimps and pinkish amphipods. After in situ observations at 3700 m depth, in -1°C waters by a remotely operated vehicle, members of this assemblage were collected and preserved for molecular studies. Based on integrative taxonomic analyses, the amphipods were identified as a new species of the genus Halirages Boeck, 1871 – Halirages spongiae sp. nov. Lörz, Nack & Tandberg –, as described in detail below. Part of our integrative approach was to establish reference DNA barcodes for known species of Halirages. However, our investigation of material of Calliopiidae G.O. Sars, 1895 collected around Iceland and Norway revealed slight morphological discrepancies in all the described species of Halirages. Except for Halirages fulvocinctus (M. Sars, 1858), none of the encountered specimens of Calliopiidae fully matched a current species description. We illuminate the morphological characteristics of nine operational taxonomic units, which also represented clades in COI and 28S. We set the Icelandic samples in the context of Halirages from Canada and Norway. A key to the world species of Halirages is provided.
Cicadellinae is a relatively large subfamily of leafhoppers (Hemiptera: Cicadellidae) with a cosmopolitan distribution with most genera known to occur in the Neotropics. Mexico houses nearly 16% of the total genera and most are endemic, inhabiting threatened native forests. Here, a new unusual Mexican genus, Christopherus gen. nov., is described to accommodate a new species of Cicadellini, C. mictlantecuhtli sp. nov., collected in the endangered Cloud Forest of Sierra Juárez, Oaxaca State of Mexico, based on dry-pinned museum specimen data. The new taxa can be separated from other Neotropical Cicadellini genera easily using male genitalia features: (i) pygofer without processes, (ii) segment 10th without processes, (iii) paraphysis absent, and (iv) edeagus with single basal atrial process elongate and asymmetrical. The monotypic genus Gillonella with its type species, G. ampulla Nielson & Godoy, 1995, are redescribed. A detailed extensive morphological description and discussion to distinguish the new genus from allied red-striped Neotropical genera in Mexico, Central America, and South America are given. Distributional data for new taxa within Mexican forests is also provided.
A re-analysis of the morphological phylogeny of the Nopinae is made, based on an update in the description of Aamunops Galán-Sánchez & Álvarez-Padilla, 2022 and the addition of the recently described genera Nopsma Sánchez-Ruiz, Brescovit & Bonaldo, 2020 and Roddemberryus Sánchez-Ruiz & Bonaldo, 2023. Two new species, Aamunops hoof sp. nov. (male) and Aamunops yiselae sp. nov. (male and female), are also described, which allows a better understanding of the genus morphology and resulted in an emended diagnosis. The description of Aamunops has been updated to include several characteristics of the ultrastructural morphology, legs, chelicerae, palps and female genitalia. The inclusion of these new characters of Aamunops along with those of Nopsma and Roddemberryus in the previous data matrix resulted in a new, completely different hypothesis of the relationships of the nopine genera: Nopsma is part of a group formed by Cubanops and Nyetnops, while Aamunops and Roddemberryus are grouped with representatives of Tarsonops. The four-eyed Nopsides ceralbonus Chamberlin, 1924 was recovered as the most basal species of Nopinae. The relationships among genera of Nopinae and the phylogenetic position of three species, whose taxonomic position is doubtful (Cubanops luquillo Sánchez-Ruiz, Brescovit & Alayón, 2015, Orthonops confuso Galán-Sánchez & Álvarez-Padilla, 2022 and Tarsonops irataylori Bond & Taylor, 2013), is also discussed.
We describe a new species of karst-dwelling pitviper from Chumphon Province of Peninsular Thailand, in the Isthmus of Kra, based on morphological and molecular data (2427 bp from cyt b, ND4 and 16S rRNA mitochondrial DNA genes). Morphologically, Trimeresurus kraensis sp. nov. is distinguished from other congeners by the following combination of morphological characters: a dark/bottle-green dorsum with reddish-brown or purple crossbands; pale green venter lacking dark dots; stripes present on the lateral sides of the ventrals; internasals generally in contact; one large supraocular scale on each side of the head; iris pale copper; tail brown with dark purplish-brown crossbars; dorsal scales in 21–21–15 rows; ventral scales 167 in a single male, 169–171 in females; subcaudal scales 62 in a single male, 52–54 in females, all paired. White vertebral spots present in males, located on approximately every two or four dorsal scales; dark brown spots forming discontinuous pattern present on 1–3 lateral dorsal scale rows; males with reddish-brown postocular stripe with jagged edges. The new species differs from the morphologically similar species Trimeresurus venustus s. str. by a notable divergence in cytochrome b mitochondrial DNA gene sequences (p = 5.9%).
The beetle genus Pharaxonotha Reitter (Coleoptera: Erotylidae: Pharaxonothinae) is found in the cones of cycad genera in the New World, including species of Ceratozamia Brongn., Dioon Lindl., Microcycas (Miq.) A.DC and Zamia L. Its presence and diversity are analyzed for the 17 species of Zamia known to occur in Panama. Nine species are recognized, and five new species are described: Pharaxonotha clarkorum Pakaluk, P. confusa Pakaluk, P. fortunensis Tang, Skelley and Taylor new species, P. holzmani Tang, Skelley and Taylor new species, P. kirschii Reitter, P. manicatae Tang, Skelley and Taylor new species, P. panamensis Tang, Skelley and Taylor new species, P. pseudoparasitica Tang, Skelley and Taylor new species, and P. taylori Skelley and Tang. A key to species of Pharaxonotha in Panama is presented.
ZooBank registration. urn:lsid:zoobank.org:pub:C054B0D4-FD00-4AE7-BBA7-C75A12368561
A new species, Chlorocoris charluzae Thomas (Hemiptera: Heteroptera: Pentatomidae), is described from Panama. Eludocoris grandis Thomas is reported from Panama for the first time. The distribution of Chlorocoris rufispinus Dallas to include Panama is confirmed. Arawacoris Thomas, described as a subgenus of Chlorocoris Spinola, is elevated to full genus.
ZooBank registration. urn:lsid:zoobank.org:pub:F4E45B6C-5BD8-4B3E-B599-3BB61855B392
Pears, Pyrus pyrifolia (Burm.f.) Nak. (Rosaceae) are one of the most widely grown fruit trees in South Korea. Approximately 11% of the total pear production in 2022 was exported to countries such as the US and Vietnam. Exported pears must be free of pest species that are considered of quarantine importance by the importing countries. Herein, a list of scale insects (Hemiptera: Coccomorpha) associated with pear trees is updated. Additionally, Spilococcus pacificus (Borchsenius) is added to the list of mealybugs affecting pears in South Korea and is briefly diagnosed based on non-type specimens and illustrated using photographs. Information on its distribution and plant hosts are also provided.
ZooBank registration. urn:lsid:zoobank.org:pub:48A93063-EB78-402F-82CE-168540C90FE2
Pseudococcus longispinus (Targioni-Tozzetti) (Hemiptera: Pseudococcidae) is a widely-distributed pest that feeds on many economically important hosts, particularly tropical fruits and ornamentals. The potential distribution of this mealybug pest in South Korea remains a primary concern because of its high incidence of interceptions screened during inspection. Hence, this species prompted a modelling effort to assess its potential risk of introduction. Potential risk maps were developed for this pest with a CLIMEX model based on occurrence records under environmental data. The potential distribution of these pests in South Korea in the 2020s, 2050s and 2090s was projected based on the RCP 8.5 climate change scenario. Results showed that P. longispinus has little potential for invasion in the outdoor environment of South Korea due to high cold stress in the 2020s. However, some locations in Jejudo were predicted to be marginally suitable under future climate factors. In that respect, the results of this model prediction could be used to prepare a risk-based surveying program that improves the probability of detecting early P. longispinus populations.
ZooBank registration. urn:lsid:zoobank.org:pub:9E0CBFE6-E1AA-4B55-9E58-70B170E0FBD8
An overview of the genus Psephenops Grouvelle (Coleoptera: Psephenidae: Psepheninae) is provided with geographic distributions of the species. The taxonomic history of Psephenops smithi Grouvelle, the type species from Grenada and St. Vincent, and junior synonym Xexanchorinus latus Grouvelle from Grenada, is discussed, and lectotypes and paralectotypes are designated for both. Photographs of the type series and a non-type specimen with illustrated male genitalia, along with new distributional information for the species, are provided. The male, female, and associated larva of Psephenops trini Barr and Shepard, new species, are described and illustrated, as is the habitat of this species in Trinidad and Tobago. The Peruvian species Psephenus robacki Spangler is transferred from Psephenus Haldeman to Psephenops as Psephenops robacki (Spangler) new combination. Photographs of the female holotype are included, and possible new distributional records from Peru are reported.
ZooBank registration. urn:lsid:zoobank.org:pub:5C9ECB63-6A77-4FF6-8391-BF0F77BE5674
U.S. port of entry interception data revealed that Frankliniella Karny (Thysanoptera: Thripidae) was the most frequently intercepted genus of Thripidae. No published identification resource for intercepted Frankliniella is available to USDA port of entry entomology identifiers. A morphological review of intercepted species was conducted. A dichotomous key for the identification of intercepted slide mounted adult females was created. Morphological diagnosis, description of each species with their geographic region(s) of origin and frequency of interception is provided.
ZooBank registration. urn:lsid:zoobank.org:pub:403B362E-9A7F-4385-A0F1-9DB87FE09AD2
Members of the genus Centris Fabricius (Hymenoptera: Apoidea: Anthophila) constitute a significant component of the Neotropical (including insular) bee fauna, exhibiting high species richness, a moderate to large body size, and extensive interactions with various important plant groups. Females of most species possess specialized morphology adapted for collecting oils from flowers. This study documents the presence of the genus in Cuba, recognizing six species: C. aethiops Cresson, C. cornuta Cresson, C. fulviventris Cresson, C. poecila Lepeletier, C. taina Genaro and Breto new species, and C. tarsata F. Smith. Detailed information is provided for each species, encompassing a diagnosis, natural history, floral associations, seasonal occurrence, and distribution. Centris taina new species is described from Cuba, based on both sexes, which were previously misidentified as C. versicolor (Fabr.) for females and C. fasciatus F. Smith for males due to sexual dimorphism. Centris tarsata is reported as a new national record for Cuba, possibly introduced by humans from South America and now established and widely distributed across the entire island. A key to differentiate the Cuban species of Centris is presented.
ZooBank registration. urn:lsid:zoobank.org:pub:257916DF-2129-4694-876C-49C858046BF6
The subgenus Indonthophagus Kabakov, 2006 of Onthophagus Latreille, 1802 (Coleoptera: Scarabaeidae: Scarabaeinae: Onthophagini) is reviewed. A morphological definition of it is provided. A diagnosis, based both on external and internal characters, of the seven species deemed to belong to the group according to literature, is supplied. As a result, Onthophagus spinifex (Fabricius, 1781), previously placed with some uncertainty in the subgenus, is definitively excluded. A key to Indonthophagus species is also provided, as well as images of male, aedeagus and endophallus for each species. New country records of Onthophagus turbatus Walker, 1858 for Pakistan, Nepal and Bhutan are given.
ZooBank registration. urn:lsid:zoobank.org:pub:9D0CE9F2-35CF-449D-8984-1B4C722762F7
Mollusca is the second-largest animal phylum with over 100,000 species among eight distinct taxonomic classes. Across 1000 living species in the class Polyplacophora, chitons have a relatively constrained morphology but with some notable deviations. Several genera possess “shell eyes”, true eyes with a lens and retina that are embedded within the dorsal shells, which represent the most recent evolution of animal eyes. The phylogeny of major chiton clades is mostly well established, in a set of superfamily and higher-level taxa supported by various approaches including multiple gene markers, mitogenome-phylogeny and phylotranscritomic approaches as well as morphological studies. However, one critical lineage has remained unclear: Schizochiton was controversially suggested as a potential independent origin of chiton shell eyes. Here, with the draft genome sequencing of Schizochiton incisus (superfamily Schizochitonoidea) plus assembly of transcriptome data from other polyplacophorans, we present phylogenetic reconstructions using both mitochondrial genomes and phylogenomic approaches with multiple methods. Phylogenetic trees from mitogenomic data are inconsistent, reflecting larger scale confounding factors in molluscan mitogenomes. A consistent robust topology was generated with protein coding genes using different models and methods. Our results support Schizochitonoidea is a sister group to other Chitonoidea in Chitonina, in agreement with established classification. This suggests that the earliest origin of shell eyes is in Schizochitonoidea, which were also gained secondarily in other genera in Chitonoidea. Our results have generated a holistic review of the internal relationship within Polyplacophora, and a better understanding on the evolution of Polyplacophora.