The SITE-100 Project: Site-Based Biodiversity Genomics for Species Discovery, Community Ecology, and a Global Tree-of-Life

Most insect communities are composed of evolutionarily diverse lineages, but detailed phylogenetic analyses of whole communities are lacking, in particular in species-rich tropical faunas. Likewise, our knowledge of the Tree-of-Life to document evolutionary diversity of organisms remains highly incomplete and especially requires the inclusion of unstudied lineages from species-rich ecosystems. Here we present the SITE-100 program, which is an attempt at building the Tree-of-Life from whole-community sampling of high-biodiversity sites around the globe. Combining the local site-based sets into a global tree produces an increasingly comprehensive estimate of organismal phylogeny, while also re-tracing evolutionary history of lineages constituting the local community. Local sets are collected in bulk in standardized passive traps and imaged with large-scale high-resolution cameras, which is followed by a parataxonomy step for the preliminary separation of morphospecies and selection of specimens for phylogenetic analysis. Selected specimens are used for individual DNA extraction and sequencing, usually to sequence mitochondrial genomes. All remaining specimens are bulk extracted and subjected to metabarcoding. Phylogenetic analysis on the mitogenomes produces a reference tree to which short barcode sequences are added in a secondary analysis using phylogenetic placement methods or backbone constrained tree searches. However, the approach may be hampered because (1) mitogenomes are limited in phylogenetic informativeness, and (2) site-based sampling may produce poor taxon coverage which causes challenges for phylogenetic inference. To mitigate these problems, we first assemble nuclear shotgun data from taxonomically chosen lineages to resolve the base of the tree, and add site-based mitogenome and DNA barcode data in three hierarchical steps. We posit that site-based sampling, though not meeting the criterion of “taxon-completeness,” has great merits given preliminary studies showing representativeness and evenness of taxa sampled. We therefore argue in favor of site-based sampling as an unorthodox but logistically efficient way to construct large phylogenetic trees.Copyright © 2022 Bian, Garner, Liu and Vogler. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. The attached file is the published version of the article

Species‐level image classification with convolutional neural network enables insect identification from habitus images

1. Changes in insect biomass, abundance, and diversity are challenging to track at sufficient spatial, temporal, and taxonomic resolution. Camera traps can capture habitus images of ground-dwelling insects. However, currently sampling involves manually detecting and identifying specimens. Here, we test whether a convolutional neural network (CNN) can classify habitus images of ground beetles to species level, and estimate how correct classification relates to body size, number of species inside genera, and species identity. 2. We created an image database of 65,841 museum specimens comprising 361 carabid beetle species from the British Isles and fine-tuned the parameters of a pretrained CNN from a training dataset. By summing up class confidence values within genus, tribe, and subfamily and setting a confidence threshold, we trade-off between classification accuracy, precision, and recall and taxonomic resolution. 3. The CNN classified 51.9% of 19,164 test images correctly to species level and 74.9% to genus level. Average classification recall on species level was 50.7%. Applying a threshold of 0.5 increased the average classification recall to 74.6% at the expense of taxonomic resolution. Higher top value from the output layer and larger sized species were more often classified correctly, as were images of species in genera with few species. 4. Fine-tuning enabled us to classify images with a high mean recall for the whole test dataset to species or higher taxonomic levels, however, with high variability. This indicates that some species are more difficult to identify because of properties such as their body size or the number of related species. 5. Together, species-level image classification of arthropods from museum collections and ecological monitoring can substantially increase the amount of occurrence data that can feasibly be collected. These tools thus provide new opportunities in understanding and predicting ecological responses to environmental change.This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. © 2019 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd. The attached file is the published pdf

Synopsis of the pelidnotine scarabs (Coleoptera, Scarabaeidae, Rutelinae, Rutelini) and annotated catalog of the species and subspecies

The pelidnotine scarabs (Scarabaeidae: Rutelinae: Rutelini) are a speciose, paraphyletic assemblage of beetles that includes spectacular metallic species (“jewel scarabs”) as well as species that are ecologically important as herbivores, pollinators, and bioindicators. These beetles suffer from a complicated nomenclatural history, due primarily to 20th century taxonomic and nomenclatural errors. We review the taxonomic history of the pelidnotine scarabs, present a provisional key to genera with overviews of all genera, and synthesize a catalog of all taxa with synonyms, distributional data, type specimen information, and 107 images of exemplar species. As a result of our research, the pelidnotine leaf chafers (a paraphyletic group) include 27 (26 extant and 1 extinct) genera and 420 valid species and subspecies (419 extant and 1 extinct). Our research makes biodiversity research on this group tractable and accessible, thus setting the stage for future studies that address evolutionary and ecological trends. Based on our research, 1 new species is described, 1 new generic synonym and 12 new species synonyms are proposed, 11 new lectotypes and 1 new neotype are designated, many new or revised nomenclatural combinations, and many unavailable names are presented. The following taxonomic changes are made: New generic synonym: The genus Heteropelidnota Ohaus, 1912 is a new junior synonym of Pelidnota MacLeay, 1819. New species synonyms: Plusiotis adelaida pavonacea Casey, 1915 is a syn. n. of Chrysina adelaida (Hope, 1841); Odontognathus gounellei Ohaus, 1908 is a revised synonym of Pelidnota ebenina (Blanchard, 1842); Pelidnota francoisgenieri Moore & Jameson, 2013 is a syn. n. of Pelidnota punctata (Linnaeus, 1758); Pelidnota genieri Soula, 2009 is a syn. n. of Pelidnota punctata (Linnaeus, 1758); Pelidnota lutea (Olivier, 1758) is a revised synonym of Pelidnota punctata (Linnaeus, 1758); Pelidnota (Pelidnota) texensis Casey, 1915 is a revised synonym of Pelidnota punctata (Linnaeus, 1758); Pelidnota (Strigidia) zikani (Ohaus, 1922) is a revised synonym of Pelidnota tibialis tibialis Burmeister, 1844; Pelidnota ludovici Ohaus, 1905 is a syn. n. of Pelidnota burmeisteri tricolor Nonfried, 1894; Rutela fulvipennis Germar, 1824 is syn. n. of Pelidnota cuprea (Germar, 1824); Pelidnota pulchella blanda Burmeister, 1844 is a syn. n. of Pelidnota pulchella pulchella (Kirby, 1819); Pelidnota pulchella scapularis Burmeister, 1844 is a syn. n. of Pelidnota pulchella pulchella (Kirby, 1819); Pelidnota xanthogramma Perty, 1830 is a syn. n. of Pelidnota pulchella pulchella (Kirby, 1819). New or revised statuses: Pelidnota fabricelavalettei Soula, 2009, revised status, is considered a species; Pelidnota rioensis Soula, 2009, stat. n., is considered a species; Pelidnota semiaurata semiaurata Burmeister, 1844, stat. rev., is considered a subspecies. New or comb. rev. and revised status: Plusiotis guaymi Curoe, 2001 is formally transferred to the genus Chrysina (C. guaymi (Curoe, 2001), comb. n.); Plusiotis transvolcanica Morón & Nogueira, 2016 is transferred to the genus Chrysina (C. transvolcanica (Morón & Nogueira, 2016), comb. n.). Heteropelidnota kuhnti Ohaus, 1912 is transferred to the genus Pelidnota (P. kuhnti (Ohaus, 1912), comb. n.); Odontognathus riedeli Ohaus, 1905 is considered a subspecies of Pelidnota rubripennis Burmeister, 1844 (Pelidnota rubripennis riedeli (Ohaus, 1905), revised status and comb. rev.); Pelidnota (Strigidia) acutipennis (F. Bates, 1904) is transferred to the genus Sorocha (Sorocha acutipennis (F. Bates, 1904), comb. rev.); Pelidnota (Odontognathus) nadiae Martínez, 1978 is transferred to the genus Sorocha (Sorocha nadiae (Martínez, 1978), comb. rev.); Pelidnota (Ganonota) plicipennis Ohaus, 1934 is transferred to the genus Sorocha (Sorocha plicipennis (Ohaus, 1934), comb. rev.); Pelidnota similis Ohaus, 1908 is transferred to the genus Sorocha (Sorocha similis (Ohaus, 1908), comb. rev.); Pelidnota (Ganonota) yungana Ohaus, 1934 is transferred to Sorocha (Sorocha yungana (Ohaus, 1934), comb. rev.); Pelidnota malyi Soula, 2010: 58, revised status; Xenopelidnota anomala porioni Chalumeau, 1985, revised subspecies status. To stabilize the classification of the group, a neotype is designated for the following species: Pelidnota thiliezi Soula, 2009. Lectotypes are designated for the following names (given in their original combinations): Pelidnota brevicollis Casey, 1915, Pelidnota brevis Casey, 1915, Pelidnota debiliceps Casey, 1915, Pelidnota hudsonica Casey, 1915, Pelidnota oblonga Casey, 1915, Pelidnota pallidipes Casey, 1915, Pelidnota ponderella Casey, 1915, Pelidnota strenua Casey, 1915, Pelidnota tarsalis Casey, 1915, Pelidnota texensis Casey, 1915, and Scarabaeus punctatus Linnaeus, 1758. The following published infrasubspecific names are unavailable per ICZN Article 45.6.1: Pelidnota (Odontognathus) cuprea var. coerulea Ohaus, 1913; Pelidnota (Odontognathus) cuprea var. rufoviolacea Ohaus, 1913; Pelidnota (Odontognathus) cuprea var. nigrocoerulea Ohaus, 1913; Pelidnota pulchella var. fulvopunctata Ohaus, 1913; Pelidnota pulchella var. sellata Ohaus, 1913; Pelidnota pulchella var. reducta Ohaus, 1913; Pelidnota unicolor var. infuscata Ohaus, 1913. The following published species name is unavailable per ICZN Article 11.5: Neopatatra synonyma Moore & Jameson, 2013. The following published species name is unavailable per application of ICZN Article 16.1: Parhoplognathus rubripennis Soula, 2008. Synopsis of the pelidnotine scarabs (Coleoptera, Scarabaeidae, Rutelinae, Rutelini) 3 The following published species name is unavailable per application of ICZN Article 16.4.1: Strigidia testaceovirens argentinica Soula, 2006, Pelidnota (Strigidia) testaceovirens argentinica (Soula, 2006), and Pelidnota testaceovirens argentinica (Soula, 2006). The following published species names are unavailable per application of ICZN Article 16.4.2: Homonyx digennaroi Soula, 2010; Homonyx lecourti Soula, 2010; Homonyx mulliei Soula, 2010; Homonyx simoensi Soula, 2010; Homonyx wagneri Soula, 2010; Homonyx zovii Demez & Soula, 2011; Pelidnota arnaudi Soula, 2009; Pelidnota brusteli Soula, 2010; Pelidnota chalcothorax septentrionalis Soula, 2009; Pelidnota degallieri Soula, 2010; Pelidnota lavalettei Soula, 2008; Pelidnota lavalettei Soula, 2009; Pelidnota dieteri Soula, 2011; Strigidia gracilis decaensi Soula, 2008, Pelidnota (Strigidia) gracilis decaensi (Soula, 2008), and Pelidnota gracilis decaensi (Soula, 2008); Pelidnota halleri Demez & Soula, 2011; Pelidnota injantepalominoi Demez & Soula, 2011; Pelidnota kucerai Soula, 2009; Pelidnota malyi Soula, 2010: 36-37; Pelidnota mezai Soula, 2009; Pelidnota polita darienensis Soula, 2009; Pelidnota polita orozcoi Soula, 2009; Pelidnota polita pittieri Soula, 2009; Pelidnota punctulata decolombia Soula, 2009; Pelidnota punctulata venezolana Soula, 2009; Pelidnota raingeardi Soula, 2009; Pelidnota schneideri Soula, 2010; Pelidnota simoensi Soula, 2009; Pelidnota unicolor subandina Soula, 2009; Sorocha carloti Demez & Soula, 2011; Sorocha castroi Soula, 2008; Sorocha fravali Soula, 2011; Sorocha jeanmaurettei Demez & Soula, 2011; Sorocha yelamosi Soula, 2011; Xenopelidnota bolivari Soula, 2009; Xenopelidnota pittieri pittieri Soula, 2009. Due to unavailability of the name Pseudogeniates cordobaensis Soula 2009, we describe the species as intentionally new (Pseudogeniates cordobaensis Moore, Jameson, Garner, Audibert, Smith, and Seidel, sp. n.)

Book reviews / The Lives of Beetles a Natural History of Coleoptera by Arthur V. Evans

Book review for The Royal Entomological Society on The Lives of Beetles: A natural history of Coleoptera by Arthur V. Evans.</p

The genome sequence of a ground beetle, Nebria brevicollis (Fabricius, 1792) [version 1; peer review: 2 approved]

We present a genome assembly from an individual female Nebria brevicollis (a ground beetle; Arthropoda; Insecta; Coleoptera; Carabidae). The genome sequence is 242 megabases in span. Most of the assembly is scaffolded into 15 chromosomal pseudomolecules, with the X sex chromosome assembled. The mitochondrial genome has also been assembled and is 25.2 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,021 protein-coding genes

Phyllobaenus obscurus Gorham 1883

Phyllobaenus obscurus (Gorham, 1883: 172) (Fig. 21) Original combination. Hydnocera obscura Types. Gorham referred to ten specimens, seven being from the type locality. The BMNH and MNHN house eight. The two remaining syntypes are from Rio Maria Linda and San Gerónimo. Series locality. Paso Antonio, Rio Maria Linda and San Gerónimo, Guatemala, and David, Chiriqui, Panama. Type locality. San Gerónimo, Guatemala. LECTOTYPE (here designated): Type [round label]; S. Geronimo, Guatemala, Champion; Type; B. C. A. Col. III. (2). Hydnocera obscura Gorham, Hydnocera obscura Gorham (BMNH; 1). PARALECTOTYPES: S. Geronimo, Guatemala, Champion; B. C. A. Col. III. (2). Hydnocera obscura Gorham (BMNH; 2); S. Geronimo, Guatemala, Champion; Hydnocera obscura Gorham; Museum Paris Coll Gorham 1914 [blue label]; Museum Paris ex. Coll. R. Oberthur [blue label] (MNHN; 2, sharing a cardmount); S. Geronimo, Guatemala, Champion; Museum Paris Coll Gorham 1914 [blue label]; Museum Paris ex. Coll. R. Oberthur [blue label] (MNHN; 1); Paso Antonio, 400 ft, Champion; B. C. A. Col. III. (2). Hydnocera obscura Gorham (BMNH; 1); David, Chiriqui, Champion; B. C. A. Col. III. (2). Hydnocera obscura Gorham (BMNH; 1).Published as part of Leavengood, John M. & Garner, Beulah H., 2014, Nomenclatural notes on some checkered beetle (Coleoptera: Cleridae) types of the Natural History Museum, London (BMNH), pp. 301-335 in Zootaxa 3760 (3) on page 312, DOI: 10.11646/zootaxa.3760.3.1, http://zenodo.org/record/24971

Allelidea viridis Blackburn 1891

Allelidea viridis Blackburn, 1891: 302 (Fig. 50) Original combination. Allelidea viridis Types. Blackburn referred to no fewer than three specimens in his description. Paralectotypes are deposited in the Australian Museum (2 specimens) and the South Australian Museum (1 specimen) (J. Bartlett, in litt.). Series/ Type locality. Mordialloc, Victoria LECTOTYPE (here designated): 3808 T Al. [?] [on card mount], Type [round, red-bordered label], Australia, Blackburn Coll., B. M. 1910 - 236, Allelidea viridis Blackb. (BMNH; 1).Published as part of Leavengood, John M. & Garner, Beulah H., 2014, Nomenclatural notes on some checkered beetle (Coleoptera: Cleridae) types of the Natural History Museum, London (BMNH), pp. 301-335 in Zootaxa 3760 (3) on pages 324-325, DOI: 10.11646/zootaxa.3760.3.1, http://zenodo.org/record/24971

Blaesiophthalmus accinctus Newman 1842

Blaesiophthalmus accinctus (Newman, 1842: 364) (Fig. 51) Original combination. Thanasimus accinctus Types. One found; number not specified. Series/ Type locality. Port Philip, South Australia. LECTOTYPE (here designated): Type [round, red-bordered label], Thanasimus accinctus Newm. Entomol 36 [4] (BMNH; 1). The assumption of the “ 364 ” is because Newman's labels included the page number of the description in The Entomologist (J. Bartlett, in litt.).Published as part of Leavengood, John M. & Garner, Beulah H., 2014, Nomenclatural notes on some checkered beetle (Coleoptera: Cleridae) types of the Natural History Museum, London (BMNH), pp. 301-335 in Zootaxa 3760 (3) on page 325, DOI: 10.11646/zootaxa.3760.3.1, http://zenodo.org/record/24971

Phyllobaenus aeneicollis Schenkling 1907

Phyllobaenus aeneicollis (Schenkling, 1907: 306) (Fig. 1) Original combination. Hydnocera aeneicollis Types. The designated paralectotypes do not share the type locality. However, Schenkling stated that multiple specimens were placed in the BMNH (and only one has the type locality; here designated the lectotype). Many others were apparently collected from different localities during the same expedition by H. H. Smith. Döbler (1982) substantiated all specimens from these localities as syntypes except for the Omilteme specimen, which we believe Döbler overlooked. Additional syntypes exist in the SDEI (Senckenberg Deutsches Entomologisches Institut, Müncheberg, Germany). Series locality. Schenkling identified the type locality corresponding to the designated lectotype. The series spans Chilpancingo, Amula and Omilteme, all in Guerrero, Mexico. Type locality. Chilpancingo, Guerrero, Mexico, 4600 ’ elevation. LECTOTYPE (here designated): Type [round, red-bordered label], Chilpancingo, Guerrero, 4600 ft., [Schenkling’s type label] (BMNH; 1). PARALECTOTYPES: Xucumanatlan, Guerrero, 7000 ft, July, H. H. Smith, [Schenkling det label] (BMNH; 1); Amula, Guerrero, 6000 ft, Aug., H. H. Smith, [Schenkling det label] (BMNH; 1); Chilpancingo, Guerrero, 4600 ft, Aug., H. H. Smith, [Schenkling det label] (BMNH; 1); Omilteme, Guerrero, 8000 ft, Aug., H. H. Smith, [Schenkling det label] (BMNH; 1).Published as part of Leavengood, John M. & Garner, Beulah H., 2014, Nomenclatural notes on some checkered beetle (Coleoptera: Cleridae) types of the Natural History Museum, London (BMNH), pp. 301-335 in Zootaxa 3760 (3) on pages 303-305, DOI: 10.11646/zootaxa.3760.3.1, http://zenodo.org/record/24971

Phyllobaenus lateralis Gorham 1883

Phyllobaenus lateralis (Gorham, 1883: 169) (Fig. 17) Original combination. Hydnocera lateralis = Phyllobaenus chapini (Wolcott, 1927: 81) [Hydnocera chapini], new synonymy Comments. The elytral and pronotal shapes described to distinguish lateralis from chapini were produced from a limited sample of specimens which did not properly illustrate their variation. The eyes, proportions of the head and pronotum, and parallel to sinuate elytral forms vary within the species and include intermediate forms. The plasticity in elytral margins and apices is typical of other Phyllobaenus species with the same elytral form (e.g., P. subulatus). Types. Gorham indicated eleven specimens. Seven are in the BMNH and three are in the MNHN. One syntype was deposited in another museum. While all are from the same locality, there are specimens bearing labels with different elevations from the type locality. The specimen marked “ type ” was collected at “ 2 – 3000 ft.” For now, only BCA specimens from the type locality with this elevation (of which 10 have been located) are considered to be part of the type series. Series/ Type locality. Volcan de Chiriqui, Panama. LECTOTYPE / PARALECTOTYPE (here designated): Syntype 1 + 2 / 7 [round, blue-bordered label], Type [round, red-bordered label], V. de Chiriqui, 2 – 3000 ft, Hydnocera lateralis Gorham, Champion, B. C. A. Col. III (2), Hydnocera lateralis Gorham (BMNH; 2 specimens on a single card mount; the lectotype indicated by LT and the paralectotype indicated by PLT, written on the card mount). PARALECTOTYPES: Syntype 3 + 4 / 7 [round, blue-bordered label], V. de Chiriqui, 2 – 3000 ft, Champion, B. C. A. Col. III (2), Hydnocera lateralis Gorham (BMNH; 2 specimens on a single card mount); Syntype [round, blue-bordered label], V. de Chiriqui, 2 – 3000 ft, Champion, B. C. A. Col. III (2), Hydnocera lateralis Gorham (BMNH; 3, with 5 /7, 6/ 7, and 7 / 7 on the Syntype labels); V. de Chiriqui, 2 – 3000 ft, Champion, Hydnocera lateralis Gorham, Museum Paris Coll Gorham 1914 [blue label], Museum Paris ex. Coll. R. Oberthur [blue label] (MNHN; 2, sharing a card mount); V. de Chiriqui, 2 – 3000 ft, Champion, Museum Paris Coll Gorham 1914 [blue label], Museum Paris ex. Coll. R. Oberthur [blue label] (MNHN; 1).Published as part of Leavengood, John M. & Garner, Beulah H., 2014, Nomenclatural notes on some checkered beetle (Coleoptera: Cleridae) types of the Natural History Museum, London (BMNH), pp. 301-335 in Zootaxa 3760 (3) on pages 310-311, DOI: 10.11646/zootaxa.3760.3.1, http://zenodo.org/record/24971