590 Tiere (Zoologie)
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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.
Background: In the speciation continuum, the strength of reproductive isolation varies, and species boundaries are blurred by gene flow. Interbreeding among giraffe (Giraffa spp.) in captivity is known, and anecdotal reports of natural hybrids exist. In Kenya, Nubian (G. camelopardalis camelopardalis), reticulated (G. reticulata), and Masai giraffe sensu stricto (G. tippelskirchi tippelskirchi) are parapatric, and thus, the country might be a melting pot for these taxa. We analyzed 128 genomes of wild giraffe, 113 newly sequenced, representing these three taxa.
Results: We found varying levels of Nubian ancestry in 13 reticulated giraffe sampled across the Laikipia Plateau most likely reflecting historical gene flow between these two lineages. Although comparatively weaker signs of ancestral gene flow and potential mitochondrial introgression from reticulated into Masai giraffe were also detected, estimated admixture levels between these two lineages are minimal. Importantly, contemporary gene flow between East African giraffe lineages was not statistically significant. Effective population sizes have declined since the Late Pleistocene, more severely for Nubian and reticulated giraffe.
Conclusions: Despite historically hybridizing, these three giraffe lineages have maintained their overall genomic integrity suggesting effective reproductive isolation, consistent with the previous classification of giraffe into four species.
Background: In the speciation continuum the strength of reproductive isolation varies, and species boundaries are blurred by gene flow. Interbreeding among giraffe (Giraffa spp.) in captivity is known and anecdotal reports of natural hybrids exist. In Kenya, Nubian (G. camelopardalis camelopardalis), reticulated (G. reticulata), and Masai giraffe sensu stricto (G. tippelskirchi tippelskirchi) are parapatric, and thus the country might be a melting pot for these taxa. We analyzed 128 genomes of wild giraffe, 113 newly sequenced, representing these three taxa.
Results: We found varying levels of Nubian ancestry in 13 reticulated giraffe sampled across the Laikipia Plateau most likely reflecting historical gene flow between these two lineages. Although comparatively weaker signs of ancestral gene flow and potential mitochondrial introgression from reticulated into Masai giraffe were also detected, estimated admixture levels between these two lineages are minimal. Importantly, contemporary gene flow between East African giraffe lineages was not statistically significant. Effective population sizes have declined since the Late Pleistocene, more severely for Nubian and reticulated giraffe.
Conclusions: Despite historically hybridizing, these three giraffe lineages have maintained their overall genomic integrity suggesting effective reproductive isolation, consistent with the previous classification of giraffe into four species.
Green spaces represent the only natural areas in several cities around the world, providing good shelters for the local fauna. Based on this premise, many ecological studies have been conducted focused on these areas. Most of these works are about insects, particularly butterflies and beetles. Our study is centered on a different group: green lacewings (Neuroptera: Chrysopidae). These insects exhibit a similar feeding behavior to some other groups, such as beetles. We estimated diversity, richness, distribution, abundance and similarity employing two methods: sweep netting and suction trapping. Also, oviposition hosts were identified in 20 different green spaces. Approximately 740 specimens were collected representing 15 species in five genera. Seven species are new state records for Yucatán, Mexico. We identified about 300 species of plants, if which 75 are considered ovipositional associated hosts. Our work is the first of its kind, employing green lacewings in an urban ecological model and additionally providing new information about chrysopids in South Mexico. We encourage the conduct of similar studies not only in Mexico but also in other Central and South American countries.
ZooBank registration. urn:lsid:zoobank.org:pub:2EDE9BDC-ECDD-4613-82A0-36C6877DD6A7
Three species of bees (Hymenoptera: Apidae, Colletidae) are newly recorded for Guatemala: Centris obscurior Michener, Centris vidua Mocsáry, and Zikanapis inbio (Michener, Engel and Ayala). We discuss aspects of their biology and circumstances of the collecting events and provide information on their presently known distribution.
ZooBank registration. urn:lsid:zoobank.org:pub:A19C3260-B215-4F61-AF9C-72D88DD06456
The Neotropical eucnemid genus, Dyscolotaxia Horn, is revised following the examination of specimens from five collections, examination of the published original description of Plesiofornax tetratoma Chassain, and from images provided by Fernanda Salazar-Buenaño (QCAZI). Dyscolotaxia championi Horn is redescribed with included descriptions of the male genitalia and a female specimen. Three new species of false click beetles (Coleoptera: Eucnemidae) are described from the Neotropical region. These new species are: Dyscolotaxia chiriquiensis (Panama), Dyscolotaxia hispaniolensis (Dominican Republic) and Dyscolotaxia picea (Ecuador). Amazotaxia new genus is described from South America for Plesiofornax tetratoma Chassain, creating Amazotaxia tetratoma (Chassain) new combination. Morphology of both Dyscolotaxia and Amazotaxia in relation to Pleisofornax Cocquerel are reviewed along with biogeographical hypotheses for these groups. An identification key is provided for species of Dyscolotaxia in the Neotropical region. Images for all species of Dyscolotaxia and Amazotaxia are provided.
A century and a half since the time of Hewitson, we are experiencing a renaissance in species discovery fueled by whole genome sequencing. A large-scale genomic analysis of Hesperiidae Latreille, 1809 (Lepidoptera), including primary type specimens, reveals a deluge of species new to science. One hundred of them (one in a new genus) are described here from the New World (type localities are given in parenthesis): Drephalys (Drephalys) diovalis Grishin, new species (Ecuador: Napo), Euriphellus panador Grishin, new species (Ecuador: Esmeraldas), Euriphellus panamicus Grishin, new species (Panama: Panama), Cecropterus (Thorybes) viridissimus Grishin, new species (Ecuador: Zamora-Chinchipe), Cecropterus (Murgaria) dariensis Grishin, new species (Panama: Darien), Urbanus (Urbanus) mericuti Grishin, new species (Ecuador: Napo), Telegonus (Telegonus) pastus Grishin, new species (Panama: Panama), Autochton (Autochton) dora Grishin, new species (Ecuador: Pastaza), Astraptes centralis Grishin, new species (Panama: Colón), Aguna claxonica Grishin, new species (Ecuador: Napo), Aguna esmeralda Grishin, new species (Ecuador: Esmeraldas), Aguna lata Grishin, new species (Guyana), Ridens angulinea Grishin, new species (Peru: Cuzco), Pythonides lera Grishin, new species (Peru: Cuzco), Pythonides latemarginatus Grishin, new species (Panama: Panama), Gindanes variegatus Grishin, new species (Brazil: Mato Grosso), Milanion (Milanion) virga Grishin, new species (Brazil: Rondônia), Milanion (Milanion) furvus Grishin, new species (Panama: Panama), Milanion (Milanion) laricus Grishin, new species (Ecuador: Napo), Charidia ronda Grishin, new species (Brazil: Rondônia), Pseudodrephalys tinas Grishin, new species (Peru: Loreto), Pseudodrephalys argus Grishin, new species (Suriname: Para), Achlyodes calvus Grishin, new species (Brazil: Santa Catarina), Spioniades artemis Grishin, new species (Panama: Panama), Spioniades artemidoides Grishin, new species (Brazil: Santa Catarina), Myrinia orieca Grishin, new species (Ecuador: Orellana), Myrinia aragua Grishin, new species (Venezuela: Aragua), Myrinia maculosa Grishin, new species (Guatemala), Myrinia manchada Grishin, new species (Guyana), Polyctor (Fenops) lamperus Grishin, new species (Panama: Darien), Nisoniades (Nisoniades) lutum Grishin, new species (Mexico: Guerrero. ), Bolla (Stolla) vena Grishin, new species (Venezuela: Aragua), Staphylus (Vulga) vula Grishin, new species (Mexico: Veracruz), Staphylus (Vulga) vulga Grishin, new species (Panama: Darien), Staphylus (Staphylus) rotundalus Grishin, new species (Ecuador: Napo), Staphylus (Staphylus) yucatanus Grishin, new species (Mexico: Quintana Roo/Yucatan), Heliopetes (Heliopetes) lana Grishin, new species (Guatemala), Canesia ella Grishin, new species (Venezuela: Barinas), Paches (Paches) loxeca Grishin, new species (Ecuador: Morona-Santiago), Clito congruens Grishin, new species (Panama: Colón), Cycloglypha corax Grishin, new species (Brazil: Rio de Janeiro), Festivia peruvia Grishin, new species (Peru: Huánuco), Decinea notata Grishin, new species (Ecuador: Napo), Pompeius fuscus Grishin, new species (Brazil: Minas Gerais), Vernia clara Grishin, new species (Panama: Chiriquí), Oligoria (Oligoria) obtena Grishin, new species (Ecuador: Napo), Thespieus mandal Grishin, new species (Brazil: Rio de Janeiro), Psoralis (Saniba) magnamacus Grishin, new species (Panama: Darien), Alychna ayonis Grishin, new species (Ecuador: Napo), Wahydra banios Grishin, new species (Ecuador: Tungurahua), Wahydra cuzcona Grishin, new species (Peru: Cuzco), Cynea (Cynea) aureofimbra Grishin, new species (Ecuador), Cynea (Nycea) quada Grishin, new species (Ecuador: Napo), Cynea (Quinta) achirae Grishin, new species (Mexico: Tamaulipas), Eutus amazonicus Grishin, new species (Peru: Madre de Dios), Eutus incus Grishin, new species (Peru: Cuzco), Eutus septemaculatus Grishin, new species (Brazil: Mato Grosso), Godmia viridicapita Grishin, new species (Ecuador: Napo), Rhomba pulla Grishin, new species (Peru: Cuzco), Niconiades victoria Grishin, new species (Mexico: Tamaulipas), Lancephallus purpurus Grishin, new genus and new species (Guyana), Mnasicles (Remella) ecua Grishin, new species (Ecuador: Pichincha), Amblyscirtes (Amblyscirtes) aeratus Grishin, new species (Mexico: Oaxaca), Amblyscirtes (Mastor) chrysoplea Grishin, new species (Mexico: Oaxaca), Amblyscirtes (Mastor) chrysomisa Grishin, new species (Mexico: Chiapas), Amblyscirtes (Flor) meridus Grishin, new species (Mexico: Veracruz), Rectava chiriquensis Grishin, new species (Panama: Chiriquí), Cobalopsis adictys Grishin, new species (Panama: Veraguas), Cymaenes melaporphyrus Grishin, new species (Mexico: San Luis Potosí), Lerema (Morys) ecuadorica Grishin, new species (Ecuador: Pichincha), Saturnus obscurior Grishin, new species (Panama: Darien), Cantha zoirodicta Grishin, new species (Peru: Madre de Dios), Cantha meiodicta Grishin, new species (Peru: Madre de Dios), Phlebodes duplex Grishin, new species (Guatemala: Cayuga), Lychnuchus (Enosis) valle Grishin, new species (Colombia: Valle), Eutychide ochoides Grishin, new species (Peru: Cuzco), Dion bora Grishin, new species (Panama: Darien), Dion occida Grishin, new species (Peru: Madre de Dios), Eprius (Eprius) veledinus Grishin, new species (Ecuador: Pichincha), Radiatus panamensis Grishin, new species (Panama: Panama), Pheraeus pulcher Grishin, new species (Peru: Madre de Dios), Callimormus rades Grishin, new species (Panama: Panama), Gubrus lubens Grishin, new species (Ecuador: Loja), Ludens labens Grishin, new species (Panama: Darien), Rigga isa Grishin, new species (Ecuador: Napo), Flaccilla lactea Grishin, new species (Peru: Cuzco), Falga athena Grishin, new species (Panama: Darien), Panoquina jay Grishin, new species (Peru: Loreto), Calpodes salianus Grishin, new species (Peru: Madre de Dios), Calpodes stingo Grishin, new species (Ecuador: Sucumbíos), Aides nobra Grishin, new species (Panama: Colón), Thracides pavo Grishin, new species (Mexico: Tabasco), Talides eluta Grishin, new species (Peru: Cuzco), Talides laeta Grishin, new species (Peru: Cuzco), Neoxeniades angustior Grishin, new species (Brazil: Rio de Janeiro), Damas zea Grishin, new species (Guyana), Tromba xantha Grishin, new species (Mexico: Veracruz), Perichares fura Grishin, new species (Ecuador: Pichincha), Carystoides (Balma) goliath Grishin, new species (Colombia: Valle), and Agathymus galeana Grishin, new species (Mexico: Nuevo Leon). Additionally, we present evidence to support 22 taxa as species (not subspecies or synonyms) and synonymize one genus and four species. Namely, the following taxa are species: Milanion pilta Evans, 1953 (not Milanion pilumnus Mabille and Boullet, 1917), Milanion latior Mabille and Boullet, 1917 (not a synonym of Milanion marciana Godman and Salvin, 1895), Charidia pilea Evans, 1953, and Charidia pocus Evans, 1953 (not Charidia lucaria (Hewitson, 1868)), Paches (Paches) gloriosus Röber, 1925 and Paches (Paches) loxana Evans, 1953 (not Paches (Paches) loxus (Westwood, 1852)), Spioniades anta Evans, 1953 (not Spioniades abbreviata (Mabille, 1888)), Decinea onasima (Hewitson, 1877) and Decinea formosus (Hayward, 1940) (not Decinea dama (Herrich-Schäffer, 1869)), Thespieus guerreronis (Dyar, 1913) (not Thespieus dalman (Latreille, [1824])), Cynea (Nycea) erebina (Möschler, 1879) and Cynea (Nycea) cleochares (Mabille, 1891) (not Cynea (Cynea) diluta (Herrich-Schäffer, 1869)), Amblyscirtes (Mastor) repta Evans, 1955 (not Amblyscirtes (Flor) florus (Godman, 1900)), Saturnus tiberius (Möschler, 1883), Saturnus conspicuus (E. Bell, 1941), Saturnus meton (Mabille, 1891), and Saturnus obscurus (E. Bell, 1941) (not Saturnus reticulata (Plötz, 1883)), Phlebodes sifax Evans, 1955 (not Phlebodes campo (E. Bell, 1947)), Eutychide ochus Godman, 1900 and Eutychide rogersi (Kaye, 1914) (not a subspecies and a synonym, respectively, of Eutychide subcordata (Herrich-Schäffer, 1869)), Falga mirabilis Evans, 1955, Falga jacta Evans, 1955, and Falga ombra Evans, 1955 (not Falga jeconia (A. Butler, 1870)); and the following taxa are junior subjective synonyms: Libra Evans, 1955 (of Phemiades Hübner, [1819]), Papilio clito Fabricius, 1787 of Milanion hemes hemes (Cramer, 1777), Pamphila hycsos Mabille, 1891 of Cynea (Nycea) erebina (Möschler, 1879), Hesperia olympia Plötz, 1882 of Eutychide subcordata (Herrich-Schäffer, 1869), and Hesperia ocrinus Plötz, 1882 of Aides aegita (Hewitson, 1866). Furthermore, we propose new combinations for genus-species: Lychnuchus (Enosis) ponka (Evans, 1955) (not Thoon Godman, 1900), and species-subspecies: Charidia pocus mayo Evans, 1953 (not Charidia lucaria (Hewitson, 1868)), Decinea onasima boliviensis (E. Bell, 1930) (not Decinea dama (Herrich-Schäffer, 1869)), Cynea (Nycea) erebina somba Evans, 1955 (not Pamphila hycsos Mabille, 1891), Saturnus tiberius suffuscus (Hayward, 1940) (not Saturnus reticulata (Plötz, 1883)), and Falga mirabilis odol Evans, 1955 (not Falga jeconia (A. Butler, 1870)). Then, Milanion pilumnus var. hemestinus Mabille and Boullet, 1917 is a junior subjective synonym of Milanion pilumnus pilumnus Mabille and Boullet, 1917, not of Milanion leucaspis (Mabille, 1878). Lectotypes are designated for nine taxa (names in original combinations below): Pellicia bromias Godman and Salvin, 1894 (Mexico: Veracruz, Atoyac), Nisoniades perforata Möschler, 1879 (Colombia), Helias ascalaphus Staudinger, 1876 (central Panama), Pamphila hycsos Mabille, 1891 (Colombia), Amblyscirtes fluonia Godman, 1900 (Mexico: Guerrero, Xocomanatlan), Mastor anubis Godman, 1900 (Mexico: Guerrero, Omiltemi), Eutychide ochus Godman, 1900 (Mexico: Veracruz, Atoyac), Cobalus subcordata Herrich-Schäffer, 1869 (Southeast Brazil), and Thracides xanthura Godman, 1901 (Panama: Chiriquí Province, Bugaba). A neotype is designated for Eudamus briccius Plötz, 1881 (Guyana: Iwokrama Forest).
ZooBank registration. urn:lsid:zoobank.org:pub:ACDF923B-906D-460E-9707-259E0ECDBCA8
Plagiosarus transversus Vlasak and Santos-Silva, new species (Cerambycidae: Lamiinae: Acanthoderini), is described from Costa Rica. The rank of Plagiosarus melampus congestus Bates, 1885 is discussed.
ZooBank registration. urn:lsid:zoobank.org:pub:71496BE9-C69F-43B4-AF33-E3376DA6E083
Trichodesma nancyae, new species (Coleoptera: Ptinidae), is described from Mexico. The species is illustrated and diagnosed, bringing the total number of extant species in the genus to 73. Lectotypes for Trichodesma beyeri Fall, Trichodesma scripta Champion, and Trichodesma texana Schaeffer are here designated. Habitus and label photographs are provided for types of 12 of the 13 species occurring in Mexico.
ZooBank registration. urn:lsid:zoobank.org:pub:F608D6CF-885B-49EA-9E8C-F0A12AE39424