Two centuries of biodiversity discovery and loss in Singapore.

There is an urgent need for reliable data on the impacts of deforestation on tropical biodiversity. The city-state of Singapore has one of the most detailed biodiversity records in the tropics, dating back to the turn of the 19th century. In 1819, Singapore was almost entirely covered in primary forest, but this has since been largely cleared. We compiled more than 200 y of records for 10 major taxonomic groups in Singapore (>50,000 individual records; >3,000 species), and we estimated extinction rates using recently developed and novel statistical models that account for "dark extinctions," i.e., extinctions of undiscovered species. The estimated overall extinction rate was 37% (95% CI [31 to 42%]). Extrapolating our Singapore observations to a future business-as-usual deforestation scenario for Southeast Asia suggests that 18% (95% CI [16 to 22%]) of species will be lost regionally by 2100. Our extinction estimates for Singapore and Southeast Asia are a factor of two lower than previous estimates that also attempted to account for dark extinctions. However, we caution that particular groups such as large mammals, forest-dependent birds, orchids, and butterflies are disproportionately vulnerable.

Climate predicts both visible and near-infrared reflectance in butterflies.

Climatic gradients frequently predict large-scale ecogeographical patterns in animal coloration, but the underlying causes are often difficult to disentangle. We examined ecogeographical patterns of reflectance among 343 European butterfly species and isolated the role of selection for thermal benefits by comparing animal-visible and near-infrared (NIR) wavebands. NIR light accounts for ~50% of solar energy but cannot be seen by animals so functions primarily in thermal control. We found that reflectance of both dorsal and ventral surfaces shows thermally adaptive correlations with climatic factors including temperature and precipitation. This adaptive variation was more prominent in NIR than animal-visible wavebands and for body regions (thorax-abdomen and basal wings) that are most important for thermoregulation. Thermal environments also predicted the reflectance difference between dorsal and ventral surfaces, which may be due to modulation between requirements for heating and cooling. These results highlight the importance of climatic gradients in shaping the reflectance properties of butterflies at a continent-wide scale.

The mitogenome of a Malagasy butterfly Malaza fastuosus (Mabille, 1884) recovered from the holotype collected over 140 years ago adds support for a new subfamily of Hesperiidae (Lepidoptera).

Malaza fastuosus is a lavishly patterned skipper butterfly from a genus that has three described species, all endemic to the mainland of Madagascar. To our knowledge, M. fastuosus has not been collected for nearly 50 years. To evaluate the power of our techniques to recover DNA, we used a single foreleg of an at least 140-year-old holotype specimen from the collection of the Natural History Museum London with no destruction of external morphology to extract DNA and assemble a complete mitogenome from next generation sequencing reads. The resulting 15 540 bp mitogenome contains 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and an A+T rich region, similarly to other Lepidoptera mitogenomes. Here we provide the first mitogenome also for Trapezitinae (Rachelia extrusus). Phylogenetic analysis of available skipper mitogenomes places Malaza outside of Trapezitinae and Barcinae + Hesperiinae, with a possible sister relationship to Heteropterinae. Of these, at least Heteropterinae, Trapezitinae, and almost all Hesperiinae have monocot-feeding caterpillars. Malaza appears to be an evolutionarily highly distinct ancient lineage, morphologically with several unusual hesperiid features. The monotypic subfamily Malazinae Lees & Grishin subfam. nov. (type genus Malaza) is proposed to reflect this morphological and molecular evidence.

Four hundred shades of brown: Higher level phylogeny of the problematic Euptychiina (Lepidoptera, Nymphalidae, Satyrinae) based on hybrid enrichment data.

Relationships within satyrine butterflies have been notoriously difficult to resolve using both morphology and Sanger sequencing methods, and this is particularly true for the mainly Neotropical subtribe Euptychiina, which contains about 400 described species. Known larvae of Euptychiina feed on grasses and sedges, with the exception of the genus Euptychia, which feed on mosses and lycopsids, and the butterflies occur widely in rainforest, cloudforest and grassland habitats, where they are often abundant. Several previous molecular and morphological studies have made significant progress in tackling the systematics of the group, but many relationships remain unresolved, with long-branch-attraction artifacts being a major problem. Additionally, the monophyly of the clade remains uncertain, with Euptychia possibly not being closely related to the remainder of the clade. Here we present a backbone phylogeny of the subtribe based on 106 taxa, 368 nuclear loci, and over 180,000 bps obtained through hybrid enrichment. Using both concatenation and species tree approaches (IQ-TREE, EXABAYES, ASTRAL), we can for the first time strongly confirm the monophyly of Euptychiina with Euptychia being the sister group to the remainder of the clade. The Euptychiina is divided into nine well supported clades, but the placement of a few genera such as Hermeuptychia, Pindis and the Chloreuptychia catharina group still remain uncertain. As partially indicated in previous studies, the genera Cissia, Chloreuptychia, Magneuptychia, Megisto, Splendeuptychia and Euptychoides, among others, were found to be highly polyphyletic and revisions are in preparation. The phylogeny will provide a strong backbone for the analysis of datasets in development that are much more taxonomically comprehensive but have orders of magnitude fewer loci. This study therefore represents a critical step towards resolving the higher classification and studying the evolution of this highly diverse lineage.

Serum Antibody Profile during Colonization of the Mouse Gut by Candida albicans: Relevance for Protection during Systemic Infection.

Candida albicans is a commensal microorganism in the oral cavity and gastrointestinal and urogenital tracts of most individuals that acts as an opportunistic pathogen when the host immune response is reduced. Here, we established different immunocompetent murine models to analyze the antibody responses to the C. albicans proteome during commensalism, commensalism followed by infection, and infection (C, C+I, and I models, respectively). Serum anti-C. albicans IgG antibody levels were higher in colonized mice than in infected mice. The antibody responses during gut commensalism (up to 55 days of colonization) mainly focused on C. albicans proteins involved in stress response and metabolism and differed in both models of commensalism. Different serum IgG antibody-reactivity profiles were also found over time among the three murine models. C. albicans gut colonization protected mice from an intravenous lethal fungal challenge, emphasizing the benefits of fungal gut colonization. This work highlights the importance of fungal gut colonization for future immune prophylactic therapies.

Male and female contributions to diversity among birdwing butterfly images.

Machine learning (ML) newly enables tests for higher inter-species diversity in visible phenotype (disparity) among males versus females, predictions made from Darwinian sexual selection versus Wallacean natural selection, respectively. Here, we use ML to quantify variation across a sample of > 16,000 dorsal and ventral photographs of the sexually dimorphic birdwing butterflies (Lepidoptera: Papilionidae). Validation of image embedding distances, learnt by a triplet-trained, deep convolutional neural network, shows ML can be used for automated reconstruction of phenotypic evolution achieving measures of phylogenetic congruence to genetic species trees within a range sampled among genetic trees themselves. Quantification of sexual disparity difference (male versus female embedding distance), shows sexually and phylogenetically variable inter-species disparity. Ornithoptera exemplify high embedded male image disparity, diversification of selective optima in fitted multi-peak OU models and accelerated divergence, with cases of extreme divergence in allopatry and sympatry. However, genus Troides shows inverted patterns, including comparatively static male embedded phenotype, and higher female than male disparity - though within an inferred selective regime common to these females. Birdwing shapes and colour patterns that are most phenotypically distinctive in ML similarity are generally those of males. However, either sex can contribute majoritively to observed phenotypic diversity among species.

DNA barcodes from over-a-century-old type specimens shed light on the taxonomy of a group of rare butterflies (Lepidoptera: Nymphalidae: Calinaginae).

We analyzed COI barcode sequences from 138 over-a-century old specimens of Calinaga including 36 name-bearing type specimens stored at the Natural History Museum London. These new data, combined with previously available RPS5 sequences, divide the Calinaga samples into four well-supported mitochondrial lineages that together with a novel wing-pattern analysis, support the recognition of six species (lhatso, buddha, brahma, aborica, formosana and davidis), with all other names subsumed either as subspecies or synonyms. One new taxon is described, Calinaga aborica naima Vane-Wright, ssp. n.

Revision of the "celia clade" of Pseudodebis Forster, 1964, with Two New Species and Notes on Papilio phorcys Fabricius, 1793 (Lepidoptera: Nymphalidae: Satyrinae).

The species-level classification of the "celia clade" of the nymphalid butterfly genus Pseudodebis Forster, 1964, is revised as part of ongoing revisionary work on this genus. The "celia clade" contains three species, of which two, Pseudodebis darrenthroopi Nakahara & Willmott, n. sp. and P. tigrillo Nakahara & Willmott, n. sp., are described and named herein based on morphology and molecular data. Consequently, we increase the described species diversity of Pseudodebis to 13, with a remarkable six species occurring in the trans-Andean region. We discuss five specific epithets associated with the clade and designate a neotype for Papilio celia Cramer, 1780, and lectotype for Taygetis keneza Butler, 1869, based on the same specimen, thus retaining the status of the former name as a senior objective synonym. We also provide a brief historical review for Papilio phorcys Fabricius, 1793, an enigmatic name currently synonymized under Papilio celia. Nevertheless, we were unable to locate the syntype(s) for this name and the identity of Papilio phorcys remains uncertain, so we retain the current synonymy as a parsimonious approach.

One Hundred Years of Solitude: rediscovery of Catasticta lycurgus (Godman amp; Salvin, 1880), a yellow butterfly from the Sierra Nevada de Santa Marta, Colombia (Lepidoptera: Pieridae).

Catasticta lycurgus is a striking endemic butterfly, restricted to high elevation habitats in the Sierra Nevada de Santa Marta, an isolated mountain range separate from the Andes in the north of Colombia. The type, which for almost a hundred years was the only known specimen, was collected in 1878 by Frederick Simons in the vicinity of Atánquez and was sent to the UK to be described by renowned naturalists Godman and Salvin in 1880. In 1972, explorers Adams and Bernard collected a second specimen of C. lycurgus in the locality of San Pedro at 2,900m of elevation in the Sierra Nevada de Santa Marta. These two specimens were the only known ones for many decades until recently, when Colombian entomologists found the species again in San Pedro de la Sierra and later, when a female was discovered in 2013. Here, we report the rediscovery of this rare and charismatic species, with new specimens collected near the type locality, which have not been reported previously. The female of C. lycurgus is described and illustrated for the first time as well the male genitalia of this species. We combine all information available to provide some insights on the systematic relationships of this species within the genus Catasticta Butler, discuss its distribution and provide a preliminary conservation assessment. Despite the newly collected specimens, the species remains very rare in the field and in collections.

Fifty years without a name: a new species of Splendeuptychia Forster (Lepidoptera: Nymphalidae: Satyrinae).

A new satyrine butterfly species, Splendeuptychia tupinamba Freitas, Huertas Rosa, sp. nov. (Nymphalidae: Satyrinae), is described. This species is found throughout a large geographical range in Brazil, Argentina and Paraguay, predominantly in the Cerrado domain, with some records in neighboring Amazonia and Atlantic Forest. Morphology and molecular data indicate that this species is part of a clade that includes Splendeuptychia ashna (the type species of the genus Splendeuptychia), and several species placed in the recently described genus Nubila Viloria, Andrade Henao, 2019.

A new euptychiine butterfly species from south Brazil and taxonomic rearrangements for Taydebis Freitas, 2013 and Hermeuptychia Forster, 1964 (Lepidoptera: Nymphalidae: Satyrinae).

A new species of Taydebis Freitas, 2003 from south Brazil is described using comparative morphology and species distributions. Also, based on morphology, we transfer Neonympha melobosis Capronnier, 1874 (formerly placed in Paryphthimoides Forster, 1964) to Taydebis, and recognize Euptychia peculiaris Butler, 1874 as its junior synonym (syn. nov.). Furthermore, the monotypic Prenda Freitas Mielke, 2011 is herein treated as junior synonym of Taydebis based on morphology, molecular and ecological evidence. Species of Taydebis are endemic and restricted to south Brazil, and now comprises three species: Taydebis guria Zacca, Casagrande Mielke sp. nov., T. melobosis comb. nov. and T. clarissa Freitas Mielke comb. nov. To continue clarifying Euptychiina taxonomy, Euptychia undulata Butler, 1867 (also formerly placed in Paryphthimoides) is transferred to Hermeuptychia Forster, 1964, and we provide additional information on its taxonomy, morphology, and distribution. Diagnoses, illustrations, and distributional maps are provided for all taxa except T. clarissa comb. nov.

Revalidation of Vareuptychia Forster, 1964, description of Vanima gen. nov., and notes on Euptychia cleophes Godman amp; Salvin, 1889 (Lepidoptera: Nymphalidae: Satyrinae).

Vareuptychia Forster, 1964 stat. rest. is revalidated and comprises two species, V. similis (Butler, 1867) comb. rest. and V. themis (Butler, 1867) comb. nov. Vanima Zacca, Casagrande Mielke gen. nov. is described to contain Euptychia labe Butler, 1870 (the type species), E. palladia Butler, 1867 and E. lesbia Staudinger, [1886]. The taxonomy of these two genera was initially revised based on morphological and distributional data, and subsequently tested and supported with a Maximum Likelihood analysis using four genes (COI, GAPDH, RpS5 and EF1-a). Lectotypes are designated for Euptychia similis Butler, 1867, E. themis Butler, 1867, E. undina Butler, 1870 and E. lesbia Staudinger, [1886]. No DNA sequences were obtained for Euptychia cleophes Godman Salvin, 1889 but its transfer to Megisto Hübner, [1819] is supported by morphological evidence. For all taxa treated in this study, a taxonomic catalog, diagnosis, (re)description and illustrations of adults, venation and genitalia are provided, as well as comments on intraspecific variation, sexual dichromatism, ecology and distribution maps.

Deep learning on butterfly phenotypes tests evolution's oldest mathematical model.

Traditional anatomical analyses captured only a fraction of real phenomic information. Here, we apply deep learning to quantify total phenotypic similarity across 2468 butterfly photographs, covering 38 subspecies from the polymorphic mimicry complex of Heliconius erato and Heliconius melpomene. Euclidean phenotypic distances, calculated using a deep convolutional triplet network, demonstrate significant convergence between interspecies co-mimics. This quantitatively validates a key prediction of Müllerian mimicry theory, evolutionary biology's oldest mathematical model. Phenotypic neighbor-joining trees are significantly correlated with wing pattern gene phylogenies, demonstrating objective, phylogenetically informative phenome capture. Comparative analyses indicate frequency-dependent mutual convergence with coevolutionary exchange of wing pattern features. Therefore, phenotypic analysis supports reciprocal coevolution, predicted by classical mimicry theory but since disputed, and reveals mutual convergence as an intrinsic generator for the unexpected diversity of Müllerian mimicry. This demonstrates that deep learning can generate phenomic spatial embeddings, which enable quantitative tests of evolutionary hypotheses previously only testable subjectively.

A revision of the new genus Amiga Nakahara, Willmott & Espeland, gen. n., described for Papilioarnaca Fabricius, 1776 (Lepidoptera, Nymphalidae, Satyrinae).

We here propose a new, monotypic genus, Amiga Nakahara, Willmott & Espeland, gen. n., to harbor a common Neotropical butterfly, described as Papilioarnaca Fabricius, 1776, and hitherto placed in the genus Chloreuptychia Forster, 1964. Recent and ongoing molecular phylogenetic research has shown Chloreuptychia to be polyphyletic, with C.arnaca proving to be unrelated to remaining species and not readily placed in any other described genus. Amigaarnaca gen. n. et comb. n. as treated here is a widely distributed and very common species ranging from southern Mexico to southern Brazil. A neotype is designated for the names Papilioarnaca and its junior synonym, Papilioebusa Cramer, 1780, resulting in the treatment of the latter name as a junior objective synonym of the former. A lectotype is designated for Euptychiasericeella Bates, 1865, which is treated as a subspecies, Amigaarnacasericeella (Bates, 1865), comb. n. et stat. n., based on molecular and morphological evidence. We also describe two new taxa, Amigaarnacaadela Nakahara & Espeland, ssp. n. and Amigaarnacaindianacristoi Nakahara & Marín, ssp. n., new subspecies from the western Andes and eastern Central America, and northern Venezuela, respectively.

TUP1-mediated filamentation in Candida albicans leads to inability to colonize the mouse gut.

AIM: To investigate the role of Candida albicans TUP1-mediated filamentation in the colonization of the mice gut. MATERIALS & METHODS: We used molecular genetics to generate a strain where filamentation is regulated by altering the expression of the TUP1 gene with tetracyclines. RESULTS: The colonization rates reached with the TUP1REP-RFPREP strain were lower compared with wild-type strain and completely absent after induction of filamentation. No differences in the susceptibility to bile salts nor in the adhesion to the mouse intestine epithelium were observed. CONCLUSION: Blockage of C. albicans in a filamentous form impedes gut cell colonization in the mouse.

Description of a new species of Euptychiina (Lepidoptera: Nymphalidae: Satyrinae) from South America.

A new species of Magneuptychia Forster, 1964 (Lepidoptera: Nymphalidae, Satyrinae), Magneuptychia andrei Zacca, Casagrande & Mielke sp. n., is described and illustrated from Venezuela, French Guiana, Trinidad and Tobago and northern Brazil. A comparative diagnosis between the new species and Magneuptychia ocypete (Fabricius, 1776), M. fugitiva Lamas, [1997] and Cissia terrestris (Butler, 1867) is also provided due the similarities in wing pattern.

Systematic revision of the Andean butterfly genus Orophila Staudinger, 1886 (Lepidoptera: Nymphalidae: Biblidinae).

A systematic review of the Neotropical butterfly genus Orophila Staudinger, 1886 based on morphological characters and geographical distribution is presented. Four species are recognized: O. campaspe (Hewitson, 1869) stat. rest., O. cardases (Hewitson, 1869), O. cecidas (Hewitson, 1869) stat. rest. and O. diotima (Hewitson, 1852). Other changes proposed include treating Orophila diotima footei (Lamas, 2003) syn. n. and O. cardases zurita (Fruhstorfer, 1916) syn. n. as synonyms of other taxa. Illustrations of adult males and male genitalia of all taxa are presented and the importance of morphological characters in both males and females is evaluated. Female specimens and genitalia are illustrated for the first time for O. c. cardases, O. cecidas and O. diotima. Lectotypes are designated for two nominal taxa.

iCollections methodology: workflow, results and lessons learned.

The Natural History Museum, London (NHMUK) has embarked on an ambitious programme to digitise its collections. The first phase of this programme was to undertake a series of pilot projects to develop the workflows and infrastructure needed to support mass digitisation of very large scientific collections. This paper presents the results of one of the pilot projects - iCollections. This project digitised all the lepidopteran specimens usually considered as butterflies, 181,545 specimens representing 89 species from the British Isles and Ireland. The data digitised includes, species name, georeferenced location, collector and collection date - the what, where, who and when of specimen data. In addition, a digital image of each specimen was taken. A previous paper explained the way the data were obtained and the background to the collections that made up the project. The present paper describes the technical, logistical, and economic aspects of managing the project.

iCollections methodology: workflow, results and lessons learned.

The Natural History Museum, London (NHMUK) has embarked on an ambitious programme to digitise its collections. The first phase of this programme was to undertake a series of pilot projects to develop the workflows and infrastructure needed to support mass digitisation of very large scientific collections. This paper presents the results of one of the pilot projects - iCollections. This project digitised all the lepidopteran specimens usually considered as butterflies, 181,545 specimens representing 89 species from the British Isles and Ireland. The data digitised includes, species name, georeferenced location, collector and collection date - the what, where, who and when of specimen data. In addition, a digital image of each specimen was taken. A previous paper explained the way the data were obtained and the background to the collections that made up the project. The present paper describes the technical, logistical, and economic aspects of managing the project.

iCollections - Digitising the British and Irish Butterflies in the Natural History Museum, London.

BACKGROUND: The Natural History Museum, London (NHMUK) has embarked on an ambitious programme to digitise its collections . The first phase of this programme has been to undertake a series of pilot projects that will develop the necessary workflows and infrastructure development needed to support mass digitisation of very large scientific collections. This paper presents the results of one of the pilot projects - iCollections. This project digitised all the lepidopteran specimens usually considered as butterflies, 181,545 specimens representing 89 species from the British Isles and Ireland. The data digitised includes, species name, georeferenced location, collector and collection date - the what, where, who and when of specimen data. In addition, a digital image of each specimen was taken. This paper explains the way the data were obtained and the background to the collections which made up the project. NEW INFORMATION: Specimen-level data associated with British and Irish butterfly specimens have not been available before and the iCollections project has released this valuable resource through the NHM data portal.