Article

A large-scale molecular phylogeny of flesh flies (Diptera: Sarcophagidae)

October 2014
Systematic Entomology 39(4):783–799

DOI:10.1111/syen.12086

Authors:

Krzysztof Szpila

Nicolaus Copernicus University

Andrzej Grzywacz

Nicolaus Copernicus University

Thomas Pape

Natural History Museum of Denmark

The available data for Sarcophagidae in GenBank were analysed in order to reconstruct the most comprehensive phylogeny to date. GenBank was explored for nine markers that are commonly used in various molecular and phylogenetic studies of flesh flies. We obtained data for 187 species and constructed an aligned dataset with 9241 characters. However, the matrix suffered from 74% missing data due to a low number of sequences for some markers and in most of the cases only short fragments of the analysed genes were available. The reconstructed tree was taxonomically biased towards the subfamilies Paramacronychiinae (12% of the described species) and Sarcophaginae (8.6% of the described species) and specifically the genus Sarcophaga. The third subfamily Miltogramminae was represented by only 0.7% of described species. Moreover, about half of the included species were of forensic importance, while the percentage of such species in the entire family was estimated at 7%. Many nodes had very low support, so in order to increase the support and thereby identify a ‘core topology’, we pruned ‘rogue’ taxa and applied different substitution models. Both strategies improved support considerably, although some nodes still were left unresolved. An analysis of the distribution of bootstrap values across chronograms showed that the weakest phylogenetic signal is restricted to that part of the tree which coincides with the onset of rapid radiations mainly within the genus Sarcophaga. Our study is concordant with phylogenies obtained by other authors, with the most noteworthy exception being the subfamily Paramacronychiinae emerging as paraphyletic with regard to the Miltogramminae, which is in strong conflict with morphological evidence. We discuss the new findings in the light of traditional taxonomical classifications of Sarcophagidae and recent molecular studies.

Museomics and phylogenomics with protein-encoding ultraconserved elements illuminate the evolution of life history and phallic morphology of flesh flies (Diptera: Sarcophagidae)

Article

Full-text available

Dec 2021

Eliana Buenaventura

Background The common name of the Flesh flies (Sarcophagidae) usually relates them with organisms feeding on decomposing organic matter, although the biology of one of the largest radiations among insects also includes predation, coprophagy, and even kleptoparasitism. The question of whether the ancestor of all sarcophagids was a predator or a decomposer, or in association to which host have sarcophagids evolved, has thus always piqued the curiosity of flesh fly specialists. Such curiosity has often been hindered by both the impossibility of having a well-supported phylogeny of Sarcophagidae and its sister group to trace live habits and the scarcity of information on the biology of the group. Using a phylogenomic dataset of protein-encoding ultraconserved elements from representatives of all three subfamilies of Sarcophagidae as ingroup and a large Calyptratae outgroup, a robust phylogenetic framework and timescale are generated to understand flesh fly systematics and the evolution of their life histories. Results The evolutionary history for Sarcophagidae reconstructed here differs considerably from previous hypotheses. Within subfamily Sarcophaginae, a group of predatory flies, including genera Lepidodexia and Boettcheria , emerged as sister-group to the rest of Sarcophaginae. The genera Oxysarcodexia , Ravinia , and Tricharaea , long considered archaic and early-branching coprophagous and sarcosaprophagous lineages, were found nested well within the Sarcophaginae as sister-group to the sarcosaprophagous Microcerella . Predation on invertebrates is suggested as the ancestral and dominant strategy throughout the early evolution of flesh flies. Several transitions from predation to sarcosaprophagy and coprophagy occur across the sarcophagid phylogenetic tree, in contrast with almost no transitions from sarcosaprophagy or coprophagy to predatory habits. Regarding the morphological evolution of flesh flies, there might be a concerted evolution of male genitalia traits, such as the phallotrema position and the juxta, or the vesica and the folding of the phallotrema. One diversification rate shift was inferred in the evolution of sarcophagids, which is related to the origin of genus Sarcophaga . Conclusions This study has a significant impact on understanding sarcophagid evolution and highlights the importance of having a robust phylogenetic framework to reconstruct the ancestral character state of biological and morphological characters. I discuss the evolution of life histories of the family in relation to their hosts or substrates and outline how sarcosaprophagy, coprophagy, and kleptoparasitism behavior on various hosts may have evolved from predation on invertebrates. This study provides a phylogenetic framework for further physiological and comparative genomic work between predatory, sarcosaprophagous, coprophagous, and kleptoparasitic lineages, which could also have significant implications for the evolution of diverse life histories in other Diptera.

Museomics and protein-encoding ultraconserved elements illuminate the evolution of life history and phallic morphology of flesh flies (Diptera: Sarcophagidae)

Preprint

Full-text available

Feb 2021

Eliana Buenaventura

Background: The common name of the Flesh flies (Sarcophagidae) usually relates them with organisms feeding on decomposing organic matter, although the biology of one of the largest radiations among insects also includes predation, coprophagy, and even kleptoparasitism. The question of whether the ancestor of all sarcophagids was a predator or a decomposer, or in association to which host have sarcophagids evolved, has thus always piqued the curiosity of flesh fly specialists. Such curiosity has often been hindered by both the impossibility of having a well-supported phylogeny of Sarcophagidae and its sister group to trace live habits and the scarcity of information on the biology of the group. Using a phylogenomic dataset of ultraconserved elements from nearly all lineages of Sarcophagidae, a robust phylogenetic framework and timescale are generated to understand flesh fly systematics and the evolution of their life histories. Results: The evolutionary history for Sarcophagidae reconstructed here differs considerably from previous hypotheses. Within subfamily Sarcophaginae, a group of predatory flies, including genera Lepidodexia and Boettcheria, emerged as sister-group to the rest of Sarcophaginae. The genera Oxysarcodexia, Ravinia, and Tricharaea, long considered archaic and early-branching coprophagous and sarcosaprophagous lineages, were found nested well within the Sarcophaginae as sister-group to the sarcosaprophagous Microcerella. Predation on invertebrates is suggested as the ancestral and dominant strategy throughout the early evolution of flesh flies. Several switches from predation to sarcosaprophagy occur across the sarcophagid phylogenetic tree, in contrast with almost no switches from sarcosaprophagy or coprophagy to predatory habits. Regarding the morphological evolution of flesh flies, there might a concerted evolution of male genitalia traits, such as the phallotrema position and the juxta, or the vesica and the folding of the phallotrema. One diversification rate shift was inferred in the evolution of sarcophagids, which is associated with the genus Sarcophaga. Conclusions: This study has a significant impact on understanding sarcophagid evolution and highlights the importance of having a robust phylogenetic framework. I discuss the evolution of life histories of the family in relation to their hosts or substrates and outline how sarcosaprophagy, coprophagy, and kleptoparasitism behavior on various hosts may have evolved from predation on invertebrates. This study has established the framework for further physiological and comparative genomic work between predatory, sarcosaprophagous, coprophagous, and kleptoparasitic lineages, which could also have significant implications for the evolution of diverse life histories in other Diptera.

A phylotranscriptomic framework for flesh fly evolution (Diptera, Calyptratae, Sarcophagidae)

Article

Dec 2020
CLADISTICS

The Sarcophagidae (flesh flies) comprise a large and widely distributed radiation within the Calyptratae (Diptera). Larval feeding habits are ecologically diverse and include sarcosaprophagy, coprophagy, herbivory, invertebrate and vertebrate predation, and kleptoparasitism. To elucidate the geographic origin and evolution of flesh fly life‐history, we inferred a backbone phylogeny based on transcriptomic data from 26 sarcophagid species covering all three subfamilies plus 15 outgroups. The phylogeny was inferred using maximum parsimony and maximum likelihood methods based on a series of supermatrices, one set with overall information content improved by MARE (2290 loci), one set with 100% gene coverage for all included species (587 loci), and the last set including mitochondrial and nuclear genes (589 loci) and additional taxa. In order to obtain a more detailed hypothesis, we utilized the supertree approach to combine results from the present study with previously published hypotheses. This resulted supertree covers 84 of the one hundred currently recognized sarcophagid genera and formed the basis for the ancestral state reconstructions. The monophyletic Sarcophagidae is well‐supported as sister to {Mystacinobiidae + Oestridae}, and relationships at the subfamily level are inferred as {Sarcophaginae, (Paramacronychiinae + Miltogramminae)}. The Sarcophagidae and each subfamily originated in the Americas, with Sarcophaginae diversifying mainly in the Neotropics, whereas the major radiation of both Miltogramminae and Paramacronychiinae occurred in the Palaearctic. Sarcosaprophagy is reconstructed as the ancestral larval feeding habit of the family Sarcophagidae and each subfamily. The ancestral sarcophagid larva probably utilized dead invertebrates as food, and the food spectrum expanded together with the diversification of breeding strategies. Particularly, kleptoparasitism in Miltogramminae is derived from sarcosaprophagy and may be seen as having derived from the breeding biology of ‘lower’ miltogrammines, the larvae of which feed on buried vertebrate carrion.

Protein‐encoding ultraconserved elements provide a new phylogenomic perspective of Oestroidea flies (Diptera: Calyptratae)

Article

Full-text available

Jul 2020

The diverse superfamily Oestroidea with more than 15 000 known species includes among others blow flies, flesh flies, bot flies and the diverse tachinid flies. Oestroidea exhibit strikingly divergent morphological and ecological traits, but even with a variety of data sources and inferences there is no consensus on the relationships among major Oestroidea lineages. Phylogenomic inferences derived from targeted enrichment of ultraconserved elements or UCEs have emerged as a promising method for resolving difficult phylogenetic problems at varying timescales. To reconstruct phylogenetic relationships among families of Oestroidea, we obtained UCE loci exclusively derived from the transcribed portion of the genome, making them suitable for larger and more integrative phylogenomic studies using other genomic and transcriptomic resources. We analysed datasets containing 37–2077 UCE loci from 98 representatives of all oestroid families (except Ulurumyiidae and Mystacinobiidae) and seven calyptrate outgroups, with a total concatenated aligned length between 10 and 550 Mb. About 35% of the sampled taxa consisted of museum specimens (2–92 years old), of which 85% resulted in successful UCE enrichment. Our maximum likelihood and coalescent‐based analyses produced well‐resolved and highly supported topologies. With the exception of Calliphoridae and Oestridae all included families were recovered as monophyletic with the following conclusions: Oestroidea is monophyletic with Mesembrinellidae as sister to the remaining oestroid families; Oestridae is paraphyletic with respect to Sarcophagidae; Polleniidae is sister to Tachinidae; Rhinophoridae sister to (Luciliinae (Toxotarsinae (Melanomyinae + Calliphorinae))); Phumosiinae is sister to Chrysomyinae and Bengaliinae is sister to Rhiniidae. These results support the ranking of most calliphorid subfamilies as separate families.

Comparative analysis of mitochondrial genomes among the subfamily Sarcophaginae (Diptera: Sarcophagidae) and phylogenetic implications

Article

Jun 2020
INT J BIOL MACROMOL

The subfamily Sarcophaginae is extremely diverse in morphology, habit and geographical distribution, and usually considered to be of significant ecological, medical, and forensic significance. In the present study, 18 mitochondrial genomes (mitogenomes) of sarcophagid flies were first obtained. The rearrangement and orientation of genes were identical with that of ancestral insects. The degrees of compositional heterogeneity in the datasets were extremely low. Furthermore, 13 protein-coding genes were evolving under purifying selection. The phylogenic relationship of the genus-group taxa Boettcheria + (Sarcophaga + (Peckia + (Ravinia + Oxysarcodexia))) was strongly supported. Four subgenera were recovered as monophyletic (Liopygia, Liosarcophaga, Pierretia, Heteronychia) in addition to Parasarcophaga as polyphyletic. The sister-relationships between S. dux and S. aegyptiaca, S. pingi and S. kawayuensis were recovered, respectively. Moreover, the molecular phylogenetic relationships among the subgenera Helicophagella, Kozlovea, Kramerea, Pandelleisca, Phallocheira, Pseudothyrsocnema, Sinonipponia and Seniorwhitea were rarely put forward prior to this study. This study provides insight into the population genetics, molecular biology, and phylogeny for the subfamily Sarcophaginae, especially for the subgeneric classification of Sarcophaga. However, compared with the enormous species diversity of flesh flies, the available mitogenomes are still limited for recovering the phylogeny of Sarcophaginae.

A new species of Sarcophaga (Pandelleisca) (Diptera, Sarcophagidae) from Turkey

Article

Full-text available

Jun 2020

Gamze Pekbey

A new species, Sarcophaga (Pandelleisca) mersinensis sp. nov. is described from the Mediterranean region of Turkey. The male terminalia are documented with line drawings, photographs and scanning electron microscope images. The species is compared with the two most similar species, Sarcophaga (Pandelleisca) baudeti (Lehrer) and Sarcophaga (Pandelleisca) theodori (Lehrer), both known from Israel. A key is provided to the western Palaearctic species of Pandelleisca Rohdendorf.

Anchored hybrid enrichment challenges the traditional classification of flesh flies (Diptera: Sarcophagidae)

Article

Full-text available

Oct 2019

Sarcophagidae is one of the most species‐rich families within the superfamily Oestroidea. This diversity is usually represented by three lineages: Miltogramminae, Paramacronychiinae and Sarcophaginae. Historically, the phylogenetic relationships among these lineages have been elusive, due to poorly supported hypotheses or small taxon sets, or both. This study provides a dramatic increase in molecular data, more balanced sampling of all three lineages from all biogeographical regions and a reassessment of morphological characters using scanning electron microscopy in the most comprehensive assessment of subfamily‐level phylogeny in Sarcophagidae to date. This analysis of the largest molecular dataset ever produced for a phylogenetic analysis of a fly lineage, with 950 loci from anchored hybrid enrichment comprising 435 930 bp from 101 species, revealed Paramacronychiinae as sister to Miltogramminae, not to Sarcophaginae, as suggested by adult morphology. Maximum likelihood analysis produced a well‐supported topology, with 91% of the nodes receiving strong bootstrap proportions (> 97%). In contrast to the molecular data, three out of nine morphological characters studied point to a sister‐group relationship of (Sarcophaginae + Paramacronychiinae) and the remaining six characters are either silent on subfamily relationships or in need of further study. Re‐examination of morphological structures provides new insights into the evolution of male genitalic traits within Sarcophagidae and highlights their convergence producing conflicting phylogenetic signal. Our phylogeny reconciles older and widely used systems of classification with tree‐based thinking and sets up a classification of flesh flies that is more aligned with their evolutionary history.

Phylogeny, evolution and male terminalia functionality of Sarcophaginae (Diptera: Sarcophagidae)

Article

Aug 2018

The first comprehensive genus-level phylogeny of the subfamily Sarcophaginae is presented. A morphology-based phylogenetic analysis using parsimony is performed with 141 terminal taxa representing all 50 nominal genera of Sarcophaginae. In total, 222 morphological characters are coded, 150 of which are from the male terminalia. The homology of relevant male terminalia structures is assessed for the first time across the entire subfamily. Of 38 polyspecific genera represented by more than one species, the monophyly of 33 genera was recovered. This cladistic study found the genera Lepidodexia, Retrocitomyia, Sarcodexiopsis and Titanogrypa to be non-monophyletic as currently defined. Of nine monospecific genera, Mecynocorpus changes its status from monospecific to polyspecific with the discovery of a new species, Promayoa also becomes polyspecific with the transfer of one Titanogrypa species, and the remaining seven monospecific genera remain as such. Support was obtained for treating Sarcodexia as a subgenus of Peckia, and for treating Helicobia and Lipoptilocnema as valid genera rather than subgenera of Sarcophaga, and Halliosca as a valid genus rather than a subgenus of Lepidodexia. Morphological synapomorphies are discussed for all genera, including reviewed character interpretations of previous authors. We are here presenting a much more unifying interpretation of the Sarcophaginae acrophallus. New insights into the functional aspects of the sarcophagine phallus are presented. Our phylogeny shows the early lineages in Sarcophaginae as being mostly dung breeding, while lineages emerging later have more diverse life habits, including necrophagy and parasitism. Based on our phylogeny, 46 genera are recognized. The following nominal genus-group taxa are synonymized, with the junior synonym receiving a new status as subgenus under its respective senior synonym: under genus Dexosarcophaga Townsend, 1917 is subgenus Cistudinomyia Townsend, 1917, syn. nov. and stat. nov.; under Lepidodexia Brauer and Bergenstamm, 1891 is subgenus Archimimus Reinhard, 1952, syn. nov. and stat. nov.; under Malacophagomyia Lopes, 1966 is subgenus Dodgeisca Rohdendorf, 1971, syn. nov. and stat. nov.; under Sarcofahrtiopsis Hall, 1933 is subgenus Pacatuba Lopes, 1975, syn. nov. and stat. nov.; and under Udamopyga Hall, 1938 is subgenus Carinoclypeus Dodge, 1965, syn. nov. and stat. nov. One nominal taxon is raised from subgenus to valid genus: Halliosca Lopes, 1975, stat. nov. (from Lepidodexia Brauer and Bergenstamm, 1891). A morphological circumscription is provided for all the genera of Sarcophaginae. © 2018 The Linnean Society of London, Zoological Journal of the Linnean Society.

Odd, outsized, and obscure: Sarcophaga (Hadroxena) karakoncolos sp. n. (Diptera: Sarcophagidae) from Turkey

Article

Full-text available

May 2018

A new species of flesh fly, Sarcophaga karakoncolos sp. n., is described based on a single adult male from Turkey (Isparta Province, Anatolia), characterised by its very large size (almost 22mm in body length) and by a unique combination of morphological features. These, together with available molecular data, do not support inclusion of the new species in any of the currently recognised subgenera of Sarcophaga, and it is placed in a new subgenus, Hadroxena subg. n.

Molecular phylogeny of Miltogramminae (Diptera: Sarcophagidae): Implications for classification, systematics and evolution of larval feeding strategies

Article

Jul 2017
MOL PHYLOGENET EVOL

Miltogramminae is one of the phylogenetically most poorly studied taxa of the species-rich family Sarcophagidae (Diptera). Most species are kleptoparasites in nests of solitary aculeate wasps and bees, although parasitoids and saprophagous species are also known, and the ancestral miltogrammine life habit remains unsettled. Here, we present for the first time a comprehensive phylogenetic tree consisting of 58 representatives of Miltogramminae, reconstructed using sequence data from three mitochondrial (COI, cytB, ND4) and one nuclear (Ef-1α) genes. Our phylogenetic hypothesis suggests that: (1) Miltogramminae are sister to Paramacronychiinae, (2) Miltogramminae can be divided into the “lower miltogrammines” containing two clades of mainly saprophages and a clade of “higher miltogrammines” with mainly kleptoparasitic species, (3) only three genera turn out to be non-monophyletic: Miltogramma, Senotainia and Pterella and (4) the genus Sarcotachina, which traditionally has been considered as belonging to the Paramacronychiinae, is placed in one of the clades of “lower miltogrammines”. Ancestral state reconstruction of larval feeding strategy and five larval characters reveals that the ancestor of Miltogramminae was likely a saprophage retaining plesiomorphic oral ridges and a cephaloskeleton with sclerotized dorsal bridge. Synapomorphies like large pseudocephalic sensory organs and well-developed cuticular sculpture, suggest that the ancestral first instar larva actively searched for a buried food supply.

Rogue taxa identification and exclusion in the molecular phylogeny of the hyperdiverse genus Sarcophaga (Diptera: Sarcophagidae)

Conference Paper

Jan 2016

Eliana Buenaventura

Molecular phylogeny of the hyperdiverse genus Sarcophaga (Diptera: Sarcophagidae), and comparison between algorithms for identification of rogue taxa

Article

Apr 2017
CLADISTICS

The hyperdiverse genus Sarcophaga Meigen, with about 890 valid species arranged within 169 subgenera, accounts for almost half of the diversity of the subfamily Sarcophaginae. Current phylogenetic hypotheses for this genus are poorly supported or based on small taxon sets, or both. Here, we use molecular data from the genes COI and 28S to reconstruct the phylogeny of Sarcophaga based on the most comprehensive sampling for the group to date: 144 species from 47 subgenera, including representatives from all regional faunas for the first time. Of the total sequences of Sarcophaga used in the present study, 94.7% were newly generated. The secondary structure of the D1-D3 expansion segments of 28S is presented for the first time for the family Sarcophagidae, and is used in a multiple sequence alignment. Branch support and tree resolution increased remarkably through rogue taxa identification and exclusion. Rogue behaviour was explained mostly as a missing data problem. The RogueNaRok web service and the algorithms chkmoves, IterPCR and prunmajor implemented in the computer program TNT were equally good at identifying critical rogue species, but chkmoves and IterPCR also identified rogue clades. Pruning rogues increased the number of monophyletic subgenera in consensus trees from one to six out of 19 subgenera with more than one representative species. Bayesian inference, maximum-likelihood and parsimony analyses recovered more monophyletic subgenera after the removal of rogue taxa, with parsimony showing the largest improvements in branch support and resolution. Although with low support, Nearctic taxa were found to be the earliest diverging lineages, followed by a subsequent diversification of Old World faunas, which is in agreement with currently available evidence of a New World origin and early diversification of Sarcophaga.

Revising Spider Egg-predating Fly Records (Diptera: Sarcophagidae): New Insights on Prey, Taxonomy, and Distribution of Sarcophaga (Mehria) lorosa Hall in Southern South America

Article

Full-text available

Apr 2024

Flesh flies (Diptera: Sarcophagidae) exhibit a wide range of feeding habits including necrophagy, coprophagy, kleptoparasitism, parasitism, and predation. Among them are species of Sarcophaga Meigen belonging to the subgenera Baranovisca Lopes and Mehria Enderlein that are specialized predators of spider eggs. These flies hover around spider webs and lay their larvae on the spider egg sac. While progress has been made on the taxonomy of Baranovisca and Mehria in recent decades, our knowledge about their biology, prey selection, and distribution remains limited, restricting our understanding of the evolutionary dynamics of Sarcophagidae-Araneae interactions. Here, we describe and illustrate the first record of S. (M.) lorosa Hall preying on egg sacs of Metepeira galatheae (Thorell) (Araneae: Araneidae) in Chile. The taxonomy of S. (M.) lorosa is revised, with two new junior synonyms proposed: Weyrauchimyia ruficauda Lopes and Tibana, syn. nov., and Arachnidomyia travassosi Tibana and Mello, syn. nov. Furthermore, we present an annotated catalog that comprehensively reviews the existing records of spider egg-predating Sarcophagidae, and provide an overview of the evolution of Sarcophagidae-Araneae interactions. Our catalog includes information on at least four species of Baranovisca and 10 species of Mehria that have been documented as preying on eggs from species of various spider families, such as Araneidae, Cheiracanthiidae, Clubionidae, Philodromidae, Salticidae, and Tetragnathidae. These records cover all biogeographical regions except the Afrotropical. Our results enhance our understanding of the evolution of Sarcophagidae-Araneae interactions.

Anchored phylogenomics and revised classification of the Miltogramminae (Diptera: Sarcophagidae)

Article

Full-text available

Oct 2023
SYST ENTOMOL

The Miltogramminae (Diptera: Sarcophagidae) includes 600 species across >40 genera, which constitute 20% of global Sarcophagidae. While molecular phylogenetic hypotheses have been produced for this group, critical problems persist, including the presence of paraphyletic genera, uncertain relationships between genera, a bias of sampling towards Palaearctic taxa, and low support for many branches. The present study remedies these issues through the application of Anchored Hybrid Enrichment (AHE) to a sample including 60% of the currently recognised genera (16% of known species) representing all biogeo-graphic regions except the Neotropical. An alignment of 1,281 concatenated loci was analysed with maximum likelihood (RAxML, IQ-TREE), Bayesian inference (ExaBayes) and coalescent-based approaches (ASTRAL, SVDquartets), which resulted in highly supported and concordant topologies, providing unprecedented insight into the relationships of this subfamily of flesh flies, allowing a major update to miltogrammine classification. The AHE phylogenetic hypothesis supports the monophyly of a large proportion of genera. The monophyly of Metopia Meigen is restored by synonymy with Aenigmetopia Malloch, syn.n. To achieve monophyly of Miltogramma Meigen, eight species are transferred from Pterella Robineau-Desvoidy. The genus Pterella is shown to be paraphyletic in its current circum-scription, and to restore generic monophyly Pterella is restricted to contain only Pt. grisea (Meigen). Erioprocta Enderlein, stat.rev., is resurrected. The genus Senotainia Macquart is reconstructed as paraphyletic. The monotypic genus Metopodia Brauer & Bergenstamm is synonymised with Taxigramma Macquart, syn.n. In light of our phylogenetic hypotheses, a new Miltogramminae tribal classification is proposed, composed of six tribes.

Comparative Mitogenomics of Flesh Flies: Implications for Phylogeny

Article

Full-text available

Aug 2022

Simple Summary Flesh flies (Diptera: Sarcophagidae) make up the second-largest family of Oestroidea. They are well known for their veterinary, forensic, and medical importance due to their extremely diverse feeding habits, making them a hotspot in dipterology research. Therefore, efforts have been devoted to accumulating the mitochondrial genomes of Sarcophagidae. However, the mitogenome of flesh flies has mostly been sequenced for the genus Sarcophaga of the subfamily Sarcophaginae, and the other two subfamilies, Miltogramminae and Paramacronychiinae, have barely been touched. Here, we sequenced the mitochondrial genomes of five sarcophagid species from four genera representing all three subfamilies and investigated the phylogeny and evolution of flesh flies from the perspective of the mitogenome via comprehensive comparative analyses employing all mitogenomic data. This study will broaden our knowledge of flesh flies and make contributions to forensics, veterinary science, entomology, and ecology. Abstract Flesh flies (Diptera: Sarcophagidae) represent a rapid radiation belonging to the Calyptratae. With more than 3000 known species, they are extraordinarily diverse in terms of their breeding habits and are therefore of particular importance in human and veterinary medicine, forensics, and ecology. To better comprehend the phylogenetic relationships and evolutionary characteristics of the Sarcophagidae, we sequenced the complete mitochondrial genomes of five species of flesh flies and performed mitogenomic comparisons amongst the three subfamilies. The mitochondrial genomes match the hypothetical condition of the insect ancestor in terms of gene content and gene arrangement. The evolutionary rates of the subfamilies of Sarcophagidae differ significantly, with Miltogramminae exhibiting a higher rate than the other two subfamilies. The monophyly of the Sarcophagidae and each subfamily is strongly supported by phylogenetic analysis, with the subfamily-level relationship inferred as (Sarcophaginae, (Miltogramminae, Paramacronychiinae)). This study suggests that phylogenetic analysis based on mitochondrial genomes may not be appropriate for rapidly evolving groups such as Miltogramminae and that the third-codon positions could play a considerable role in reconstructing the phylogeny of Sarcophagidae. The protein-coding genes ND2 and ND6 have the potential to be employed as DNA markers for species identification and delimitation in flesh flies.

A review of earthworm-parasitizing Oestroidea (Diptera), with ecological and morphological notes on three species of Sarcophaga

Thesis

Jan 2021

Daniel Schönberger

A comprehensive review of all earthworm-parasitizing genera within the Oestroidea superfamily (namely Bellardia Robineau-Desvoidy, Calliphora Robineau-Desvoidy, Onesia Robineau-Desvoidy, Pollenia Robineau-Desvoidy and Sarcophaga Meigen) was conducted, including a list of rearing records found in the SMNS (Staatliches Museum für Naturkunde Stuttgart, Germany) and NHMUK (Natural History Museum, London, UK) collections. Sarcophaga flies and earthworms were collected in the field at eight localities around Stuttgart (Germany). Besides, a morphological and molecular analysis (using COI DNA-barcoding) of Sarcophaga (Sarcophaga) carnaria (Linnaeus), S. (S.) variegata (Scopoli) and S. (S.) subvicina Rohdendorf was performed to revise existing identification keys. In total, 126 males and 54 females were used for the morphological analysis, and 51 females were identified using DNA-barcoding. The review showed that some species of Bellardia, Onesia, Pollenia and Sarcophaga (s. str.) can be considered as earthworm endoparasitoids. Due to the lack of recorded observations, species of Calliphora could not be confirmed as earthworm parasitoids. In total, 172 Sarcophaga specimens belonging to twelve species were collected in the field, and one living earthworm was found infected with three larvae of S. variegata. Dissected females of S. subvicina can be split from S. carnaria and S. variegata by exhibiting a length/width ratio of sternite 7 greater than 0.9 (smaller than 0.9 in S. carnaria and S. variegata). Females of S. carnaria could not be reliably differentiated morphologically from those of S. variegata. The distributions of dusting and setation on syntergosternite 7+8 could not be confirmed as sufficiently reliable characters to differentiate male S. subvicina from S. carnaria and S. variegata, as used in a previously published key.

Comparative analysis of the mitochondrial genomes of flesh flies and their evolutionary implication

Article

Jan 2021
INT J BIOL MACROMOL

Flesh flies (Diptera: Sarcophagidae) include a large and widely distributed rapid radiation within the Calyptratae. They are vital for the ecosystem, as well as economic, forensic, and evolutionary studies, because of their extremely diverse habits as larvae. Phylogenetic studies of Sarcophagidae have been reaching convergence, which leads the opportunity to elucidate the evolution of these fast-evolving insects from the perspective of mitochondrial genome. Complete mitochondrial genome of eight species was sequenced, and comparative mitochondrial genomic analysis between subfamilies were conducted. Mitochondrial genomes of these flesh flies are conserved in gene content with gene arrangement, same as the inferred ancestral insect, and the nucleotide composition is highly biased towards A + T like other flesh flies. The evolutionary rates of Sarcophagidae vary considerably across subfamilies, with that of Miltogramminae higher than the other two subfamilies. Phylogenetic analysis strongly supports monophyly of Sarcophagidae and each subfamily, with subfamily-level relationship inferred as (Sarcophaginae, (Miltogramminae, Paramacronychiinae)). The main topological inconsistency of all reconstructions is the relationship within Miltogramminae and Sarcophaga, which might be caused by their rapid evolution. Our study indicates that the mitochondrial genomes of flesh flies are highly conserved, and they are practically useful for phylogenetic inference of calyptrates.

Latitudinal patterns in phylogenetic and functional diversity of Diptera in temperate bogs

Article

Mar 2019

Conservation of biodiversity is growing in interest, and wetlands are disappearing at an alarming rate, so understanding how communities are assembled and how interactions among species and ecosystems influence evolution is critical to the management of threatened habitats. We compared diversity and assemblages of peatland Diptera within and between ecoregions in Québec, Canada. We then determined the phylogenetic structure of peatland Diptera communities and how the structure differed with spatial scale (trap, site, ecoregion). Finally, we tested alpha and beta diversity along environmental and spatial gradients to determine which processes influence Diptera communities and diversity. Bogs across the three ecoregions support similar abundance, species richness, and functional diversity. We found that the major forces structuring Diptera assemblages in bogs across Québec are stochastic processes such as dispersal limitations. However, those random patterns change to clustering when anthropogenic disturbances modify the landscape. Assembly rules are mostly dictated by patch and landscape parameters specific to each ecoregion affecting dispersal and establishment between sites. Conservation of mobile organisms in habitats such as bogs will depend on conservation plans focusing on both patch quality and surrounding landscape, and that different conservation strategies need to be applied in different ecoregions.

DNA Barcoding for identifying synanthropic flesh flies (Diptera, Sarcophagidae) of Colombia

Article

Feb 2018
ACTA TROP

Tracking wetland community evolution using Diptera taxonomic, functional and phylogenetic structure

Article

Nov 2017

Different processes drive spatial variation in community composition. Standard measures of composition are useful in species‐based conservation and ecology, but they may be less informative in the context of evolutionary history and functional diversity. Functional and phylogenetic approaches are increasingly used to test mechanisms driving biodiversity patterns. We studied 28 families of flies (Diptera) with a range of functional characteristics in three wetland classes (bogs, swamps, marshes) in Quebec, Canada. We examined taxonomic, phylogenetic and functional structure of communities and assessed whether rarity is deterministic or stochastic. Beta‐ and phylobeta‐diversity were also examined for relatedness to local environmental conditions, patch area, and/or surrounding landscape. Phylogenetic community structure analyses had high value and complementarity to standard measures. Environmental filtering acted on bog communities during assembly, as they emerged from a slow peat accumulation process and the plant composition is characteristic as few species can survive in these acidic and low nutrient conditions. Subsequently, community assembly happened randomly. Neutral processes of community assembly are more important in marshes and swamps, as dispersal limitation explained species abundance dynamics of small and common Diptera species. The assembly of marsh communities is a balance between neutral processes and environmental filtering, while assembly in swamps can be seen as neutral. Clustering increased with environmental extremes, indicating environmental filtering. Rare species tended to be less closely related to common species. They have unique habitat requirements, and the high diversity is maintained by temporal turnover of species with similar traits filtered by the environment.

The genus-group names of Sarcophagidae (Insecta: Diptera) proposed by A.Z. Lehrer and Y.G. Verves

Article

Full-text available

Nov 2022

In: Evenhuis, N.L. & Pape, T. (eds.), Systema Dipterorum Nomenclatural Notes. II. Bishop Museum Occasional Papers 143: 37–90. A conspectus of all genus-group names of Sarcophagidae proposed by A.Z. Lehrer and Y.G. Verves is provided as an authority source for updating Systema Dipterorum, with two Appendices listing new synonymies, new statuses and new combinations as resulting from the adopted classification. By First Reviser action, Paraphalloides Lehrer, 2013 is selected as the correct original spelling, with the alternative spelling Paraphaloides thereby becoming an incorrect original spelling.

Wing measurements are a possible tool for the identification of European forensically important Sarcophagidae

Article

Full-text available

Sep 2022
FORENSIC SCI INT

The flesh flies are a group of insects well known for their forensic importance. Reliable identification of these flies relies on the use of either molecular markers or the morphology of the male genital apparatus. Identification of female flesh flies is more time consuming and less reliable than their male counterparts. This is particularly problematic for forensic entomology practitioners, because female flesh flies are more abundant than males in carrion arthropod assemblages. As such, it is critical that alternative methods for flesh fly identification are established that are equally effective for both sexes. One promising technique is the use of wing measurements, which have been shown to be reliable for the identification of some groups of necrophagous Diptera from several geographical regions. We applied this method to the European Sarcophagidae for the first time, using a dataset of 881 specimens representing 29 species and 5 genera. Species identifications were based on 15 landmarks located at wing vein junctions. We also combined our results with data from previous studies of Calliphoridae and Muscidae which utilised the same methodology, enabling the testing of family level identification using wing morphometrics. Species identifications using wing measurements had varied success. While some species were successfully identified without error, others, particularly from the genus Sarcophaga, were often misclassified. Notably, in several species wing measurements successfully identified both males and females. The results presented here suggest that wing measurements are a promising complementary method to other methods for the identification of necrophagous Sarcophagidae especially in material unsorted at the family level. It can also be used to double check identification performed by a taxonomist using traditional methods.

Predicting the Weathering Time by the Empty Puparium of Sarcophaga peregrina (Diptera: Sarcophagidae) with the ANN Models

Article

Full-text available

Sep 2022

Simple Summary The weathering time of cuticular hydrocarbons from the puparium could assist in estimating the postmortem interval (PMI) of decomposed corpses. However, the composition of cuticular hydrocarbons in the puparium is complicated and has not been well studied for sarcophagid species. Therefore, we examined the compounds of Sarcophaga peregrina (Robineau-Desvoidy, 1830) at varying temperatures and used various machine learning models to predict the weathering time. The artificial neural network (ANN) model may be optimal for weathering time estimation. Abstract Empty puparium are frequently collected at crime scenes and may provide valuable evidence in cases with a long postmortem interval (PMI). Here, we collected the puparium of Sarcophaga peregrina (Diptera: Sarcophagidae) (Robineau-Desvoidy, 1830) for 120 days at three temperatures (10 °C, 25 °C, and 40 °C) with the aim to estimate the weathering time of empty puparium. The CHC profiles were analyzed by gas chromatography-mass spectrometry (GC-MS). The partial least squares (PLS), support vector regression (SVR), and artificial neural network (ANN) models were used to estimate the weathering time. This identified 49 CHCs with a carbon chain length between 10 and 33 in empty puparium. The three models demonstrate that the variation tendency of hydrocarbon could be used to estimate the weathering time, while the ANN models show the best predictive ability among these three models. This work indicated that puparial hydrocarbon weathering has certain regularity with weathering time and can gain insight into estimating PMI in forensic investigations.

Flesh flies (Diptera: Sarcophagidae) of Kalamaili Mountain Ungulate Nature Reserve (China: Xinjiang): checklist and description of four new species

Article

Nov 2021

A checklist of the flesh flies occurring in Kalamaili Mountain Ungulate Nature Reserve, Xinjiang, NW China, is presented, based on material collected from 2009 to 2017. The checklist includes 18 genera and 46 species, 12 of which are new records for China. Four new species are described: Asiosarcophila kashanensis sp. nov., Miltogramma szpilai sp. nov., Sphecapatodes superciliosa sp. nov., and Sphecapatodes xinjiangensis sp. nov. Extensive documentation of the male and female habitus, details of the head, and the specialised setae of the male fore tarsus is given for all species where relevant, except for those already well illustrated in other publications. The male terminalia of almost all species of Paramacronychiinae and Sarcophaginae recorded from Kalamaili are illustrated with focus-stacked photographs.

Towards a new classification of Muscidae (Diptera): a comparison of hypotheses based on multiple molecular phylogenetic approaches

Article

Feb 2021
SYST ENTOMOL

Muscidae are a megadiverse dipteran family that exhibits extraordinary diversity in morphology and life history as both immatures and adults. The classification of Muscidae has been long debated, and most higher-level relationships remain unknown. In this study, we used multilocus Sanger sequencing (mS-seq), anchoredhybrid enrichment (AHE) and restriction-site associated DNA sequencing (RAD-seq)approaches to examine relationships within Muscidae. The results from AHE andRAD-seq largely correspond to those obtained from mS-seq in terms of overall topology,yet phylogenomic approaches received much higher nodal support. The results from all molecular approaches contradict the traditional classification based predominantlyon adult morphology, but provide an opportunity to re-interpret the morphology of immature stages. Rearrangements in Muscidae classification are proposed as follows:(i) Mesembrina Meigen and Polietes Rondani are transferred from Muscinae to Azeliinae; (ii) Reinwardtiinae stat. rev.is resurrected as a subfamily distinct from Azeliinae; (iii) Eginia Robineau-Desvoidy, Neohelina Malloch, Syngamoptera Schnabl and Xenotachina Malloch are transferred to Reinwardtiinae stat. rev.

Genetic diversity of Calliphora vicina (Diptera: Calliphoridae) in the Iberian Peninsula based on cox1 , 16S and ITS2 sequences

Article

Dec 2020

The study of Diptera at the scene of a crime can provide essential information for the interpretation of evidence. Phylogeographic reconstruction could help differentiate haplotypes of a dipteran species in a geographical area, clarifying, for example, the details of a possible relocation of a corpse. In addition, inferring the ancestral areas of distribution helps to understand the current status of the species and its biogeographic history. One of the most important species in forensic entomology is Calliphora vicina Rovineau-Desvoidy, 1830 (Diptera: Calliphoridae). The aim of this work is to increase our knowledge of this species in the Iberian Peninsula using 464 specimens from Spain and Portugal. These samples were identified using morphological keys and by molecular methods using fragments of the cox1, 16S and ITS2 genes. The phylogeographic history of these populations was inferred from haplotype networks and the reconstruction of ancestral areas of distribution. The molecular results corroborated the morphological identifications of the samples. Phylogeographic networks showed no geographical structure, as haplotypes are shared among almost all populations. reconstruct ancestral state in phylogenies analyses showed a high rate of movement among populations, possibly related to human activity. These results suggest that this species had a very rapid and recent spatial and demographic expansion throughout the Iberian Peninsula.

A new flesh fly species of Oxysarcodexia Townsend from the Brazilian Atlantic Forest and redescription of Oxysarcodexia xon (Dodge, 1968)

Article

Full-text available

Aug 2020

A new Neotropical species of Oxysarcodexia Townsend (Diptera, Sarcophagidae) from Atlantic Forest of southeastern Brazil, Oxysarcodexia digitata sp. nov., is described and illustrated based on male and female specimens. This new species resembles O. fraterna Lopes, O. nitida Soares & Mello-Patiu, O. notata Soares & Mello-Patiu, O. vittata (Walker), and O. xon (Dodge), but can be distinguished based on differences in phallic elements. Additionally, the male of Oxysarcodexia xon (Dodge, 1968) is redescribed and illustrated, its female is described for the first time, and new records is presented.

Oxysarcodexia Townsend, 1917 (Diptera: Sarcophagidae)—a centennial conspectus

Article

Aug 2020

A taxonomic conspectus is presented for the genus Oxysarcodexia Townsend, 1917, which is one of the most species-rich genera of New World flesh flies. It has its center of diversity in the Neotropical Region, with some species reaching into the Nearctic and a few species introduced to the Australasian and Oceanian Regions. Species within this genus are primarily dung-breeders, but some species have also been bred from vertebrate carcasses. Oxysarcodexia is defined and diagnosed, and a diagnosis, distributional data and known biological data are provided for each species together with figures of the habitus and male terminalia. Oxysarcodexia currently comprises 91 valid species, including six species newly described herein: O. alectoris sp. n. (French Guiana), O. angulosa sp. n. (Costa Rica), O. ariozanoi sp. n. (Brazil), O. graminifolia sp. n. (Colombia and Ecuador), O. maiae sp. n. (Ecuador), and O. rimata sp. n. (Ecuador). Two nominal species based on a male holotype, Oxysarcodexia bomplandi (Hall, 1937) and O subsericans (Walker, 1858), were left unidentified pending examination of their terminalia. Four nominal species, O. aureiceps (Macquart, 1855), O. dorisae Dodge, 1965, O. flavifrons (Macquart, 1846) and O. neivae Mattos, 1919, all described solely based on females, are considered of uncertain status pending a comprehensive study of females of this genus. Asioboettcheria Verves, 2001 is proposed as a junior synonym of Oxysarcodexia Townsend, 1917, syn. n., Oxysarcodexia cuernavaca Dodge, 1966 is proposed as a junior synonym of O. ventricosa (Wulp, 1895), syn. n., and Stackelbergeola papei Nandi, 1994 is proposed as a junior synonym of O. thornax (Walker, 1849), syn. n. A lectotype is designated for Sarcophaga varia Walker, 1836 [= O. varia (Walker, 1836)]. The newly-described O. ariozanoi and O. maiae are included in the “xon group” (former “Xarcophaga group”). New country-level distributional records are provided for O. adunca Lopes, 1975 (Ecuador), O. berlai Lopes, 1975 (Peru), O. cocais Carvalho-Filho, Sousa & Esposito, 2017 (Argentina), O. insolita Lopes, 1946 (Ecuador), O. jamesi Dodge, 1968 (Costa Rica), O. marina (Hall, 1938) (Brazil), O. nitida Soares & Mello-Patiu, 2010 (Ecuador), O. notata Soares & Mello-Patiu, 2010 (Brazil and Ecuador), and O. terminalis (Wiedemann, 1830) (Paraguay).

Mitochondrial DNA-Based Identification of Forensically Important Flesh Flies (Diptera: Sarcophagidae) in Thailand

Article

Full-text available

Dec 2019

Flesh flies (Sarcophagidae) are necrophagous insects initially colonizing on a corpse. The species-specific developmental data of the flies collected from a death scene can be used to estimate the minimum postmortem interval (PMImin). Thus, the first crucial step is to correctly identify the fly species. Because of the high similarity among species of flesh flies, DNA-based identification is considered more favorable than morphology-based identification. In this study, we demonstrated the effectiveness of combined sequences (2216 to 2218 bp) of cytochrome c oxidase subunit I and II genes (COI and COII) for identification of the following 14 forensically important flesh fly species in Thailand: Boettcherisca nathani Lopes, Fengia ostindicae (Senior-White), Harpagophalla kempi (Senior-White), Liopygia ruficornis (Fabricius), Lioproctia pattoni (Senior-White), Lioproctia saprianovae (Pape & Bänziger), Parasarcophaga albiceps (Meigen), Parasarcophaga brevicornis (Ho), Parasarcophaga dux (Thomson), Parasarcophaga misera (Walker), Sarcorohdendorfia antilope (Böttcher), Sarcorohdendorfia inextricata (Walker), Sarcorohdendorfia seniorwhitei (Ho) and Seniorwhitea princeps (Wiedemann). Nucleotide variations of Thai flesh flies were evenly distributed throughout the COI-COII genes. Mean intra- and interspecific variations ranged from 0.00 to 0.96% and 5.22% to 12.31%, respectively. Using Best Match (BM) and Best Close Match (BCM) criteria, identification success for the combined genes was 100%, while the All Species Barcodes (ASB) criterion showed 76.74% success. Maximum Likelihood (ML) and Bayesian Inference (BI) phylogenetic analyses yielded similar tree topologies of monophyletic clades between species with very strong support values. The achieved sequences covering 14 forensically important flesh fly species including newly submitted sequences for B. nathani, F. ostindicae and S. seniorwhitei, can serve as a reliable reference database for further forensic entomological research in Thailand and in other areas where those species occur.

Muscle attachment site patterns for species determination in West Palaearctic Wohlfahrtia (Diptera: Sarcophagidae) of medical and veterinary importance

Article

Full-text available

Dec 2019

The flesh fly genus Wohlfahrtia Brauer & Bergenstamm contains at least six species of medical and veterinary importance. Traditional methods of species identification in specimens of Wohlfahrtia, however, are restricted mostly to adult forms. Muscle attachment site (MAS) patterns allow for species determination in larval forms. MAS patterns in third instar larvae of six common West Palearctic species of Wohlfahrtia have been analyzed for this study. As in previously investigated Calliphoridae and Sarcophagidae, MAS patterns were found to be species specific. A genus pattern was established to be used as base for comparison in further species determination. For the first time a tool is provided for species identification of such broad range in larvae of Wohlfahrtia species. Wohlfahrtia patterns are composed of a significantly higher number of MAS than patterns found in Sarcophaga. Specifics of the six species analyzed are explained in detail. The larvae of the well-known species W. magnifica, an obligate traumatic myiasis agent, had to be excluded from the analysis as a great number of spines on the outside obscure muscle attachment sites on the inside of the cuticle.

Redefinition of Cornexcisia Fan & Kano, 2000 (Diptera: Sarcophagidae), with the first description of the female of Sarcophaga kurahashii (Shinonaga & Tumrasvin, 1979)

Article

Full-text available

Sep 2019

Sarcophaga Meigen, 1826 is proposed as a senior synonym of Cornexcisia Fan & Kano, 2000, syn. nov. and Fanzideia Xue, Verves & Du, 2011, syn. nov. Cornexcisia Fan & Kano, 2000, stat. rev. is given status as a subgenus and is considered a senior synonym of Fanzideia Xue, Verves & Du, 2011, syn. nov. at the subgeneric level. Cornexcisia is argued to contain S. (Cornexcisia) longicornuta (Fan & Kano, 2000), comb. nov., S. (C.) cygnocerca (Xue, Verves & Du, 2011), comb. nov., S. (C.) kurahashii (Shinonaga & Tumrasvin, 1979), subgen. comb. nov. (from Phallosphaera Rohdendorf) and S. (C.) suthep Pape & Bänziger, 2003, subgen. comb. nov. (from Rosellea Rohdendorf). Sarcophaga (C.) kurahashii is newly recorded from China (Yunnan), the male is redescribed and the female is described for the first time, supported by photographs, illustrations and mitochondrial cytochrome oxidase subunit I (COI) gene sequences. Species of Cornexcisia share an exceptionally long postpedicel in the female and the following apomorphic distiphallic appendages in the male: juxta ventro-proximally with an apically divided arm with cuticular pile, and lateral styli bifurcated from the base with each branch elongate, gently curved and slightly expanded apically. A key to the species of Cornexcisia is provided.

Identification of Forensically Important Flesh Flies Using the Cytochrome C Oxidase Subunits I and II Genes

Article

May 2019

Forensically important flesh flies (Diptera: Sarcophagidae) often are not morphologically distinguishable, especially at the immature stage. In addition, female flies are quite similar in general morphology, making accurate identifications difficult. DNA-based technologies, particularly mitochondrial DNA (mtDNA), have been used for species-level identification. The cytochrome oxidase subunits I and II (COI-COII) sequences of Iranian Sarcophagidae are still unavailable in GenBank. In this study as many as 648 (540 males and 106 females) fly specimens from family Sarcophagidae, representing 10 sarcophagid species, including eight forensically important species were collected from seven locations in five Iranian provinces. Of these, 150 male specimens were identified based on both morphology of male genitalia and DNA sequencing analysis. Sequence data from the COI-COII regions for 10 flesh fly species collected in Iran were generated for the first time. Digestion of COI-COII region by restriction enzymes RsaI, EcoRV, and HinfI provided distinct restriction fragment length polymorphism profiles among the species and can serve as molecular markers for species determination. Phylogenetic analysis represented that the COI-COII sequences are helpful for delimitation of sarcophagid species and implementation in forensic entomology. However, the application of the COI-COII fragment as a species identifier requires great caution and additional species and markers should be studied to ensure accurate species identification in the future.

Review of the Brazilian species of Udamopyga Hall, 1938 (Diptera: Sarcophagidae), with the description of a new species and a key to males and females

Article

Oct 2018

Udamopyga Hall, 1938 sensu stricto previously comprised 20 species: three from the Nearctic Region and 17 from the Neotropics. A comparative morphological study of the seven species so far recorded from Brazil is presented, including a newly described species from the Brazilian Atlantic Forest, Udamopyga squamata sp. nov., with emphasis on the terminalia and the addition of new diagnostic characters. An identification key to the adults of both sexes of these species is provided.

A brief review of forensically important flesh flies (Diptera: Sarcophagidae)

Article

Full-text available

Mar 2018

Forensic entomology could provide valuable data for the minimum postmortem interval (PMImin) estimation and other relevant information, such as causes and circumstances of death. Some representatives of flesh flies are one of the dominant necrophagous insects during early stages of decomposition, demonstrating unique biological characteristics compared with other necrophagous flies. Moreover, they lead to global health concerns as carriers of various pathogenic micro-organisms, and dominantly result in the traumatic myiasis. Thus, sarcophagid flies are considered important in decomposition processes for PMImin estimation. However, the utility of sarcophagid flies has been seriously hampered by limited ecological, biological and taxonomic knowledge of them. The aim of this paper is to provide a brief review on the species, distribution and biological habit of forensically important sarcophagid flies. In addition, the relation between traumatic myiasis and flesh flies, molecular identification methods and developmental pattern of flesh flies are summarized.

Taxon sampling to address an ancient rapid radiation: A supermatrix phylogeny of early brachyceran flies (Diptera)

Article

Full-text available

Nov 2017
SYST ENTOMOL

Early diverging brachyceran fly lineages underwent a rapid radiation approximately 180 Ma, coincident in part with the origin of flowering plants. This region of the fly tree includes 25 000 described extant species with diverse ecological roles such as blood-feeding (haematophagy), parasitoidism, predation, pollination and wood-feeding (xylophagy). Early diverging brachyceran lineages were once considered a monophyletic group of families called Orthorrhapha, based on the shared character of a longitudinal break in the pupal skin made during the emergence of the adult. Yet other morphological and molecular evidence generally supports a paraphyletic arrangement of ‘Orthorrhapha’, with strong support for one orthorrhaphan lineage – dance flies and relatives – as the closest relative to all higher flies (Cyclorrhapha), together called Eremoneura. In order to establish a comprehensive estimate of the relationships among orthorrhaphan lineages using a thorough sample of publicly available data, we compiled and analysed a dataset including 1217 taxa representing major lineages and 20 molecular markers. Our analyses suggest that ‘Orthorrhapha’ excluding Eremoneura is not monophyletic; instead, we recover two main lineages of early brachyceran flies: Homeodactyla and Heterodactyla. Homeodactyla includes Nemestrinoidea (uniting two parasitic families Acroceridae + Nemestrinidae) as the closest relatives to the large SXT clade, comprising Stratiomyomorpha, Xylophagidae and Tabanomorpha. Heterodactyla includes Bombyliidae with a monophyletic Asiloidea (exclusive of Bombyliidae) as the closest relatives to Eremoneura. Reducing missing data, modifying the distribution of genes across taxa, and, in particular, removing rogue taxa significantly improved tree resolution and statistical support. Although our analyses rely on dense taxonomic sampling and substantial gene coverage, our results pinpoint the limited resolving power of Sanger sequencing-era molecular phylogenetic datasets with respect to ancient, hyperdiverse radiations.

A new species and new records of Oxysarcodexia Townsend (Diptera: Sarcophagidae) from Brazil

Article

Full-text available

Aug 2017
REV BRAS ENTOMOL

Figs. 1–6. Oxysarcodexia cocais sp. nov., male terminalia of holotype. (1) Epandrium, surstylus and cercus, left lateral view; (2) Right pregonite and postgonite, lateral view; (3) Cerci, dorsal view; (4) Sternite 5, ventral view; (5) Phallus, ventral view; (6) Phallus with an arrow pointing to the triangular projection, lateral view. Scale bars = 3 mm. (Abbreviations: ar, arm; bs, base; cl, cleft; j, juxta; ls, lateral stylus; ms, median stylus; prg, pregonite; ptg, postgonite; ve, vesica.)

DNA barcoding allows identification of European Fanniidae (Diptera) of forensic interest

Article

Jun 2017

In forensic entomology practice, species identification is a prerequisite for any further analysis of collected material. Although morphology based taxonomy may be hindered by a range of factors, these are not obstacles for a molecular identification approach, so-called DNA barcoding. The Fanniidae are a dipteran family that is attracted to and breeds in decomposing animal carrion and dead human bodies. However, morphological identification of fanniids, both at adult and immature stages, is considered to be difficult, particularly for non-experts. We investigated the usefulness of molecular taxonomy methods as an alternative/supplement for morphology-based identification in European Fanniidae of forensic interest. The material used in this study was collected from various regions in Asia, Europe and North America. We sequenced a barcode region of the mitochondrial cytochrome c oxidase subunit I (COI) in 27 species. For 13 species, including some taxa breeding in dead bodies, this study describes COI sequences for the first time. Our analysis revealed that both mini-barcode and full-length COI barcode sequences give very high specimen identification success. Despite the large number of COI barcode sequences referring to Fanniidae in the BOLD and GenBank databases, previous identification of forensically relevant Fanniidae was hindered by uneven taxonomic sampling. The majority of available sequences refer to species that are not of medico-legal interest, and many species of forensic interest are unrepresented or represented only by a single sequence. Because of erroneous data that are present in depository databases, DNA barcoding must be used with caution and cannot be considered to be the sole alternative to other identification methods Wolbachia infections in the examined material did not disrupt specimen identification. The obtained results will facilitate precise identification of European Fanniidae of forensic interest, badly preserved material with degraded DNA, as well as matching of unidentified females and immature stages to already described specimens.

To be or not to be a valid genus: The systematic position of Ophyra R.-D. revised (Diptera: Muscidae)

Article

Full-text available

May 2017
SYST ENTOMOL

Ophyra Robineau-Desvoidy is one of the better-studied genera of the family Muscidae (Diptera). The larvae of species of this genus feed on highly decomposed organic matter of various origins, and may reveal predatory behaviour as they mature. These feeding habits, combined with the widespread distribution and close association with human dwellings of some species, give the genus commercial and medico-legal importance. However, the systematic position of Ophyra has been a matter of debate for many years. Ophyra has been considered by muscid workers to be either a valid genus or a junior synonym of Hydrotaea Robineau-Desvoidy. A lack of agreement about the systematic position of Ophyra has led to serious errors, particularly in the applied literature. Recent molecular and morphological studies provided contradictory information on the validity of the genus and its subfamilial classification. We revise the systematic position of Ophyra herein by means of molecular phylogenetic reconstruction. Our results are incongruent with opinions on the systematic position of Ophyra based on previously published molecular phylogenies, although they correspond with the concept of the genus based on adult morphology. All analyses of the concatenated dataset revealed Ophyra as monophyletic and placed within a paraphyletic Azeliini. Depending on the phylogenetic approach, Ophyra was placed within either a monophyletic, paraphyletic or polyphyletic Hydrotaea, yet always closely related to a certain group of species. We conclude that Ophyra, as currently defined, should not be considered a valid name, yet a detailed reconstruction of the genus Hydrotaea awaits future studies with greater increases in both taxon sampling and the number of molecular markers.

Sarcophaga maxima sp. nov. (Diptera: Sarcophagidae: Sarcophaginae), a new Australian flesh fly recognised by morphology and DNA barcoding: A new Australian Sarcophaga

Article

Feb 2017

A new species, Sarcophaga (Sarcorohdendorfia) maxima sp. nov., supported by both morphological and DNA barcoding data, is described from Queensland and New South Wales, Australia. The major morphological features of the new species are listed, and the male terminalia are documented with both photography and scanning electron microscopy. Sarcophaga alcicornis Hardy, 1932 is transferred from subgenus Lioproctia Enderlein to Sarcorohdendorfia Baranov.

Molecules and morphology unite Sarcophaga (Stackelbergeola) Rohdendorf and S. (Rohdendorfisca) Grunin within megadiverse Sarcophaga Meigen (sensu lato) (Diptera, Sarcophagidae)

Article

Full-text available

Oct 2016

The largest genus of the family Sarcophagidae (Insecta, Diptera), Sarcophaga Meigen (sensu lato), has ~160 subgenera; however, the validity and phylogenetic relationships of these are still unclear, impeding progress in evolutionary studies. This study presents a phylogenetic hypothesis for selected subgenera of Sarcophaga s.l. based on COI sequences (685 bp) for 87 species representing 27 valid subgenera. The subgenera Stackelbergeola Rohdendorf and Rohdendorfisca Grunin are reconsidered in the light of new molecular, morphological and biological data. The female is described for the first time for a representative of both subgenera, and Sarcophaga (Rohdendorfisca) flagellifera (Grunin) is shown to be a parasitoid of tettigoniid grasshoppers. As the male of Sarcophaga (Stackelbergeola) sushkini (Rohdendorf) is insufficiently documented in the literature, a redescription is provided based on material from Xinjiang, thereby providing the first record of this subgenus and species from China. Detailed documentation through photographs, scanning electron microscopy and illustrations of the adult morphology is also provided. The subgenera Stackelbergeola and Rohdendorfisca are shown to be monophyletic, together forming a monophylum supported by molecular and morphological data, and they are placed in a wider phylogenetic context of the megadiverse genus Sarcophaga s.l.

A Species-Level Phylogeny of Extant Snakes with Description of a New Colubrid Subfamily and Genus

Article

Full-text available

Sep 2016
PLOS ONE

Background: With over 3,500 species encompassing a diverse range of morphologies and ecologies, snakes make up 36% of squamate diversity. Despite several attempts at estimating higher-level snake relationships and numerous assessments of generic- or species-level phylogenies, a large-scale species-level phylogeny solely focusing on snakes has not been completed. Here, we provide the largest-yet estimate of the snake tree of life using maximum likelihood on a supermatrix of 1745 taxa (1652 snake species + 7 outgroup taxa) and 9,523 base pairs from 10 loci (5 nuclear, 5 mitochondrial), including previously unsequenced genera (2) and species (61). Results: Increased taxon sampling resulted in a phylogeny with a new higher-level topology and corroborate many lower-level relationships, strengthened by high nodal support values (> 85%) down to the species level (73.69% of nodes). Although the majority of families and subfamilies were strongly supported as monophyletic with > 88% support values, some families and numerous genera were paraphyletic, primarily due to limited taxon and loci sampling leading to a sparse supermatrix and minimal sequence overlap between some closely-related taxa. With all rogue taxa and incertae sedis species eliminated, higher-level relationships and support values remained relatively unchanged, except in five problematic clades. Conclusion: Our analyses resulted in new topologies at higher- and lower-levels; resolved several previous topological issues; established novel paraphyletic affiliations; designated a new subfamily, Ahaetuliinae, for the genera Ahaetulla, Chrysopelea, Dendrelaphis, and Dryophiops; and appointed Hemerophis (Coluber) zebrinus to a new genus, Mopanveldophis. Although we provide insight into some distinguished problematic nodes, at the deeper phylogenetic scale, resolution of these nodes may require sampling of more slowly-evolving nuclear genes.

High regional genetic diversity and lack of host-specificity in Ostrinia nubilalis (Lepidoptera: Crambidae) as revealed by mtDNA variation

Article

Full-text available

Aug 2016

The European corn borer (Ostrinia nubilalis) infests a wide array of host plants and is considered one of the most serious pests of maize in Europe. Recent studies suggest that individuals feeding on maize in Europe should be referred to O. nubilalis (sensu nov.), while those infesting dicots as Ostrinia scapulalis (sensu nov.). We test if the clear genetic distinctiveness among individuals of O. nubilalis living on maize vs. dicots is tracked by mitochondrial DNA (mtDNA). We used fragments of COI and COII genes of 32 individuals traditionally recognized as O. nubilalis collected on three host plants, maize, mugwort and hop, growing in different parts of Poland. In addition, we reconstructed the mtDNA phylogeny of Ostrinia species based on our data and sequences retrieved from GenBank to assess host and/or biogeographic patterns. We also compared haplotype variation found in Poland (east-central Europe) with other regions (Anatolia, Eastern Europe, Balkans, Far East, North America). Our study showed high mtDNA diversity of O. nubilalis in Poland in comparison with other regions and revealed rare haplotypes likely of Asian origin. We did not find distinct mtDNA haplotypes in larvae feeding on maize vs. dicotyledonous plants. Phylogenetic analyses showed an apparent lack of mtDNA divergence among putatively distinct lineages belonging to the O. nubilalis group as identical haplotypes are shared by Asian and European individuals. We argue that human-mediated dispersal, hybridization and sporadic host jumps are likely responsible for the lack of a geographic pattern in mtDNA variation.

New record of Phylloteles hyalipennis (Baranov, 1934) (Diptera: Miltogramminae) from North India, with morphology, life cycle and SEM study of immature stages

Article

Dec 2024

Phylogeny of Urostylididae (Heteroptera: Pentatomoidea) reveals rapid radiation and challenges traditional classification

Article

Full-text available

Jan 2023

Urostylididae, a phytophagous heteropteran family that feeds on the sap of various trees and shrubs, comprises 8 genera and 173 species. Its phylogeny has received little attention, and no studies have revealed its generic monophyly or relationships. We present the first molecular phylogeny of Urostylididae based on complete mitogenomes and nuclear ribosomal genes from almost all genera and representative species, using maximum likelihood analysis and Bayesian inference. All phylogenetic results showed overall consistent topological relationships, indicating polyphyly of the three most speciose genera, Urolabida, Urochela, and Urostylis. Among the three monotypic genera, Chelurotropella formed a stable relationship with Urochela wui in all trees, Cobbenicoris was a stable sister group of Urostylis fici but with position variation among trees, and Urochellus formed a sister group with Urostylis cuneata or species of two or more genera in different trees. The smaller genus Tessaromerus was always sister to Urostylis tricarinata, but their positions varied among trees. Thus, the currently recognized genera of Urostylididae are unreliable. Furthermore, our phylogenetic results suggested some topological incongruence among the trees produced with different analytical methods and data sets, mainly among deep internal nodes, with short branches and low support values. Given the quartet‐based evaluation system and branch patterns, Urostylididae underwent rapid radiation resulting in incomplete lineage sorting and introgression in our data sets, making our phylogenetic analyses more sensitive to the data or method used. Moreover, the rapid radiation might have caused morphological homoplasy of diagnostic characters of genera, leading to taxonomic confusion for Urostylididae. Therefore, a thorough taxonomic revision of this family is needed.

Entomologia sądowa – definicja, zakres, wybrane kierunki badań

Article

Full-text available

Dec 2022

Marcin Kadej

Entomologia sądowa jest wąską specjalnością naukową dynamicznie rozwijającą się w ostatnich latach. Ma ona wybitnie utylitarny charakter, o czym świadczy jej stosowanie w wielu postępowaniach, w tym sprawach kryminalistycznych. Wiedza o owadach – ich biologii, ekologii, behawiorze – jest niezwykle przydatna do wnioskowania o czasie jaki upłynął od momentu zgonu (PMI), zawsze wtedy, gdy inne standardowe metody są zawodne. W tym celu wielu naukowców na całym świecie prowadzi różnorodne badania nad owadami nekrofilnymi. Zebrane w ten sposób informacjenie tylko przyczyniają się do lepszego rozumienia roli owadów w procesach przemiany materii, ale także podnoszą jakość wnioskowania o PMI. Z uwagi na liczbę i specyfikę prowadzonych badań entomologię sądową należy uznać za specjalność naukową o wybitnie interdyscyplinarnym charakterze – budującą pomosty między innymi specjalizacjami badawczymi w obrębie biologii, chemii czy medycyny sądowej. W obszarze poznawczym jest jeszcze wiele wątków wymagających dalszych pogłębionych analiz, wiele gatunków czeka na opracowanie modeli rozwojowych, ustalenie wieku ich stadiów rozwojowych, a w końcu opisanie interakcji między gatunkami konkurującymi o ten sam zasób pokarmowy. W niniejszym artykule przedstawiono kierunki badawcze zakorzenione w entomologii sądowej, świadczące o jej wielkim potencjale naukowym.

DNA-based and taxonomic identification of forensically important Sarcophagidae (Diptera) in southeastern Spain

Article

Nov 2020
SCI JUSTICE

Studying dipterans at the scene of a death can provide essential information for interpreting the evidence and help to reconstruct the events happened to a corpse in the past. Molecular tools have been employed for identification at specific levels in the cases of cryptic species or poorly conserved specimens. Identification of specimens is essential in forensic entomology since each species has a specific growth rate, which determines the calculation of the minimum post mortem interval (minPMI). In addition, phylogeographic reconstruction within a species can help to differentiate the haplotypes from a geographic area, thereby helping to clarify the possible relocation of a corpse. The morphological identification of Sarcophagidae species is often difficult, especially for the females. This is an important Diptera family since some of its species are among the first to reach a corpse, especially in warm areas. In this study, we compared the sarcophagids found in human corpses in forensic cases in Alicante (southeast of Spain) with specimens collected from baited traps in the same area and surrounding provinces. In total, 189 specimens were collected, comprising 72 from forensic cases and 117 from baited traps. Molecular identification was conducted by sequencing the cox1 mitochondrial gene and analyzing the sequences using ABGD, GMYC, and BIN species delimitation methods. The median joining algorithm in the PopART program was used to construct phylogeographic networks. Eight species in the family Sarcophagidae were identified. The most widely collected species were Sarcophaga argyrostoma and Sarcophaga tibialis. The haplotype networks obtained for these species did not indicate a clear geographic distribution of haplotypes. The S. argyrostoma samples from Alcoy were clearly isolated. The results demonstrated that this method is useful for identifying Sarcophagidae samples in forensic investigations and it can be employed for minPMI estimation.

The genus Peckia Robineau-Desvoidy (Diptera: Sarcophagidae) in the Brazilian Amazon: a new species, new records, descriptions of female terminalia and key to species

Article

Sep 2018

Flesh flies of the genus Peckia Robineau-Desvoidy, 1830 were studied from the Brazilian Amazon region. The male terminalia of all species are illustrated. The female terminalia are described and illustrated for all species for which the female is known. The female terminalia of six species are described for the first time; those of seven species are redescribed and documented through new illustrations. A new species of the subgenus Pattonella Enderlein, 1928, Peckia (Pattonella) juruti sp. nov., is described. It is similar to Peckia (Pattonella) smarti (Lopes, 1941) in the shape of the cercus and distiphallus, but differs in the shape of the gonites, juxta and capitis. Peckia (Peckia) hillifera (Aldrich, 1916) is recorded from Brazil for the first time; Peckia (Euboettcheria) florencioi (Prado & Fonseca, 1932) is newly reported for the Brazilian Amazon. A key to the 21 species of Peckia so far recorded from the Brazilian Amazon is provided, allowing the identification of both sexes where known. The females of only five of these species remain unknown.

First mitogenome for the subfamily Miltogramminae (Diptera: Sarcophagidae) and its phylogenetic implications

Article

Full-text available

Oct 2017

The mitochondrial genome of Mesomelena mesomelaena (Loew, 1848) is the first to be sequenced in the flesh fly subfamily Miltogramminae (Diptera: Sarcophagidae). The 14,559 bp mitogenome contains 37 typical metazoan mitochondrial genes: 13 protein-coding genes, two ribosomal RNA genes and 22 transfer RNA genes, with the same locations as in the insect ground plan. All the protein-coding genes have the start codon ATN, except for cox1 (TCG). Eight protein-coding genes have the stop codon TAA, while the remaining five have the stop codon T (cox1, cox2, nad5, and nad4) or TAG (cytb). Synonymous and non-synonymous substitution rates (Ks and Ka) for each protein-coding gene indicate that these genes evolved primarily under negative (or purifying) selection (Ka < Ks). Phylogeny of Sarcophagidae is proposed based on all the sarcophagid mitogenomes in GenBank, and the subfamily topology is reconstructed as (Sarcophaginae (Paramacronychiinae, Miltogramminae)). © Institute of Entomology, Biology Centre, Czech Academy of Sciences, České Budějovice.

Corrigendum to “Multilocus and multiregional phylogeny reconstruction of the genus Sarcophaga (Diptera, Sarcophagidae)” [Mol. Phylogen. Evol. 107 (2017) 619–629]

Article

Jan 2017
MOL PHYLOGENET EVOL

Multilocus and multiregional phylogeny reconstruction of the genus Sarcophaga (Diptera, Sarcophagidae)

Article

Jan 2017
MOL PHYLOGENET EVOL

The flesh-fly genus Sarcophaga is extremely diverse and contains ca. 30% of the species in the family Sarcophagidae (∼3000 species). The phylogenetic position of the genus-group taxa Helicobia, Lipoptilocnema, and Peckia remains uncertain with respect to the hyperdiverse Sarcophaga, due to conflicting phylogenetic trees and insufficient sampling in recent studies. We present maximum-likelihood and Bayesian phylogenetic analyses of 145 species of 48 subgenera of the genus Sarcophaga from all biogeographic regions based on the molecular markers COI, 28 D1–D3 expansion regions, EF1α, and white. Our analyses find (Lipoptilocnema + Peckia) as the sister group of the monophyletic Sarcophaga. The genus Helicobia is placed outside Sarcophaga. Our hypotheses suggest that the ancestor shared by Sarcophaga and its sister clade originated in the Neotropical region, and the subsequent range expansion might be related to the formation of the Isthmus of Panama. This study supports the monophyly of most of the subgenera of Sarcophaga included here, and it shows the evolution of this genus to be a rapid radiation occurring in the Nearctic region with a subsequent dispersal into the Old World. The subgeneric clusters within Sarcophaga are in agreement with the current classification, with only Mauritiella, Rosellea, Helicophagella, Liosarcophaga, and Sarcorohdendorfia being non-monophyletic. We also validate the monotypic condition of 10 subgenera.

Order Diptera Linnaeus, 1758. In: Zhang, Z.-Q. (Ed.) Animal biodiversity: An outline of higher-level classification and survey of taxonomic richness

Article

Full-text available

Dec 2011

Bayesian phylogenetics with BEAUti and the BEAST 1.7

Article

Full-text available

Jan 2012
MOL BIOL EVOL

DNA-Based Identification and Molecular Systematics of Forensically Important Sarcophagidae (Diptera)

Article

Full-text available

Sep 2001

Sarcophagid flies have many characteristics that make them ideal forensic indicators. However, their utility is severely limited because it is difficult or impossible to determine the species of a sarcophagid larva, and in many instances an adult specimen, based on anatomy. We developed a database of mitochondrial DNA sequence data that makes it possible to identify all sarcophagid species likely to be found feeding on a human corpse at an urban location in Canada or the USA. Analyses were based on a 783 base pair region of the gene for cytochrome oxidase subunit one (COI). The species analyzed, including some of no forensic importance that were included for purposes of phylogenetic comparisons, were members of the genera Sarcophaga, Peckia, Blaesoxipha, Ravinia, Wohlfahrtia, Brachicoma (all Sarcophagidae), and Musca (Muscidae).

Catalogue of the Sarcophagidae of the World (Insecta: Diptera)

Article

Full-text available

Jan 1996

Thomas Pape

Systematics Of Bulbostyla, A New Subgenus Of Sarcophaga Meigen, And Change Of Status For Robackina Lopes (Diptera: Sarcophagidae)

Article

Full-text available

Jul 2010
ZOOTAXA

Sarcophaga (Bulbostyla) subgen. nov. is described as a new subgenus of Sarcophaga Meigen to accommodate some species previously assigned to the subgenus S. (Neobellieria) Blanchard. Sarcophaga (Bulbostyla) contains nine species: S. airosalis sp. nov., S. cadyi sp. nov. (type species), S. cuautla sp. nov., S. fattigina sp. nov., S. ironalis sp. nov., S. semimarginalis Hall, S. sternalis (Reinhard), S. subdiscalis Aldrich and S. yorkii Parker. All species are described and illustrated and a key to the species is provided. The species within the subgenus are morphologically uniform externally and are distinguished mostly on male genitalic characters. Phylogenetic relationships within Bulbostyla are unresolved based on morphological characters and will require consideration of additional characters, such as molecular sequence data. The genus-group taxon Robackina Lopes is removed from synonymy with the subgenus Sarcophaga (Neobellieria) and reinstated as a valid subgenus of Sarcophaga (stat. nov.) to accommodate the single New World species Sarcophaga triplasia Wulp. A lectotype is designated for S. triplasia. The subgenus and species are redescribed and illustrated.

Genomic Treasure Troves: Complet Genome Sequencing of Herbarium and Insect Museum Specimens

Article

Full-text available

Jul 2013
PLOS ONE

Unlocking the vast genomic diversity stored in natural history collections would create unprecedented opportunities for genome-scale evolutionary, phylogenetic, domestication and population genomic studies. Many researchers have been discouraged from using historical specimens in molecular studies because of both generally limited success of DNA extraction and the challenges associated with PCR-amplifying highly degraded DNA. In today's next-generation sequencing (NGS) world, opportunities and prospects for historical DNA have changed dramatically, as most NGS methods are actually designed for taking short fragmented DNA molecules as templates. Here we show that using a standard multiplex and paired-end Illumina sequencing approach, genome-scale sequence data can be generated reliably from dry-preserved plant, fungal and insect specimens collected up to 115 years ago, and with minimal destructive sampling. Using a reference-based assembly approach, we were able to produce the entire nuclear genome of a 43-year-old Arabidopsis thaliana (Brassicaceae) herbarium specimen with high and uniform sequence coverage. Nuclear genome sequences of three fungal specimens of 22-82 years of age (Agaricus bisporus, Laccaria bicolor, Pleurotus ostreatus) were generated with 81.4-97.9% exome coverage. Complete organellar genome sequences were assembled for all specimens. Using de novo assembly we retrieved between 16.2-71.0% of coding sequence regions, and hence remain somewhat cautious about prospects for de novo genome assembly from historical specimens. Non-target sequence contaminations were observed in 2 of our insect museum specimens. We anticipate that future museum genomics projects will perhaps not generate entire genome sequences in all cases (our specimens contained relatively small and low-complexity genomes), but at least generating vital comparative genomic data for testing (phylo)genetic, demographic and genetic hypotheses, that become increasingly more horizontal. Furthermore, NGS of historical DNA enables recovering crucial genetic information from old type specimens that to date have remained mostly unutilized and, thus, opens up a new frontier for taxonomic research as well.

Missing data and the accuracy of Bayesian phylognetics

Article

Full-text available

May 2008

The effect of missing data on phylogenetic methods is a potentially important issue in our attempts to reconstruct the Tree of Life. If missing data are truly problematic, then it may be unwise to include species in an analysis that lack data for some characters (incomplete taxa) or to include characters that lack data for some species. Given the difficulty of obtaining data from all characters for all taxa (e.g., fossils), missing data might seriously impede efforts to reconstruct a comprehensive phylogeny that includes all species. Fortunately, recent simulations and empirical analyses suggest that missing data cells are not themselves problematic, and that in- complete taxa can be accurately placed as long as the overall number of characters in the analysis is large. How- ever, these studies have so far only been conducted on parsimony, likelihood, and neighbor-joining methods. Although Bayesian phylogenetic methods have become widely used in recent years, the effects of missing data on Bayesian analysis have not been adequately studied. Here, we conduct simulations to test whether Bayesian analyses can accurately place incomplete taxa despite extensive missing data. In agreement with previous studies of other methods, we find that Bayesian analyses can accurately reconstruct the position of highly incomplete taxa (i.e., 95% missing data), as long as the overall number of characters in the analysis is large. These results suggest that highly incomplete taxa can be safely included in many Bayesian phylogenetic analyses.

Molecular phylogenetics of the Muscidae (Diptera : Calyptratae): new ideas in a congruence context

Article

Full-text available

Jun 2007

Hypotheses about the evolution of Muscidae have long been the subject of continuous re-evaluation and reinterpretation. Current understandings of the relationships among these flies are based mainly on a single set of characters and are therefore questionable. Our understanding of muscid phylogeny thus needs greater support and further corroboration from additional suites of characters. In the current study, we analysed phylogenetic relationships among 24 species of muscid flies (18 genera and six subfamilies) using 2989 characters derived from sequences of mitochondrial (COI and COII) and nuclear genes (CAD and EF-1α). Data from each gene partition were analysed both in combined and separate phylogenetic analyses using maximum parsimony, maximum likelihood, and Bayesian inference. Support was found for the monophyly of the Muscidae in all analyses and for a sister-group relationship between Coenosiini and Phaoniinae. The latter group was placed in a clade with sampled species of Reinwardtiini and Cyrtoneurininae. The genera Ophyra and Hydrotaea were placed in the Muscinae and a sister-group relationship for Musca and Stomoxys was supported. Sampled species of Polietina form a monophyletic lineage, while Morellia was found to be paraphyletic. Combined analysis of gene partitions improved support and resolution for resulting topologies despite significant incongruence between data partitions found through application of the Incongruence Length Difference test.

Molecular Systematics of the Calliphoridae (Diptera: Oestroidea): Evidence From One Mitochondrial and Three Nuclear Genes

Article

Full-text available

Feb 2013

Approximately 8% of calyptrate species diversity comes from the Calliphoridae, which includes flies of medical, veterinary, and forensic importance. The status of family Calliphoridae has for years been the central systematic problem of the superfamily Oestroidea, and phylogenetic relationships between the key groups of the Calliphoridae are unresolved and controversial. We reconstructed phylogenies of the Calliphoridae within the larger context of the other Oestroidea based on 5,189 bp of combined data from one mitochondrial (cytochrome oxidase subunit one) and three nuclear (carbamoylphosphate synthetase, elongation factor one alpha, and 28S ribosomal RNA) genes using maximum parsimony, maximum likelihood, and Bayesian methods. Trees obtained from the different phylogenetic methods were almost identical. Calliphoridae is polyphyletic, with the phylogenetic position of Mesembrinellinae still uncertain but clearly outside the lineage that includes other Calliphoridae and some noncalliphorids, and Polleniinae is the sister group of the family Tachinidae. Strong support for a sister group relationship between Rhiniinae and traditional calliphorid subfamilies conflicts with a recent proposal to give Rhiniinae family status. All calliphorid subfamilies (except Calliphorinae) for which we had more than one species were monophyletic. Melanomyinae was nested within Calliphorinae. Toxotarsinae was more closely related to Calliphorinae rather than, as indicated by morphology, to Chrysomyinae. Efforts to resolve the relationships of the Oestroid families were largely inconclusive, although the monophyly of the superfamily was strongly supported.

Relaxed Phylogenetics and the Palaeoptera Problem: Resolving Deep Ancestral Splits in the Insect Phylogeny

Article

Full-text available

Dec 2012
SYST BIOL

The order in which the three groups of winged insects (the Pterygota) diverged from their common ancestor has important implications for understanding the origin of insect flight. But despite this importance, the split between the Odonata (dragonflies and damselflies), Ephemeroptera (mayflies) and Neoptera (the other winged orders) remains very much unresolved. Indeed, previous studies have obtained strong apparent support for each of the three possible branching patterns. Here, we present a systematic reinvestigation of the basal pterygote split. Our results suggest that outgroup choice and limited taxon sampling have been major sources of systematic error, even for datasets with a large number of characters (e.g., in phylogenomic datasets). In particular, a dataset of 113 taxa provides consistent support for the Palaeoptera hypothesis (the grouping of Odonata with Ephemeroptera), while results from datasets with fewer taxa give inconsistent results, and are highly sensitive to minor changes in data and methods. We also focus on recent methods that exploit temporal information using fossil calibrations, combined with additional assumptions about the evolutionary process, and so reduce the influence of outgroup choice. These methods are shown to provide more consistent results, for example, supporting Palaeoptera, even for datasets that previously supported other hypotheses. Together, these results have implications for understanding insect origins and for resolving other problematic splits in the tree of life.

Using Supermatrices for Phylogenetic Inquiry: An Example Using the Sedges

Article

Full-text available

Oct 2012
SYST BIOL

In this paper, we use supermatrix data-mining methods to reconstruct a large, highly inclusive phylogeny of Cyperaceae from nucleotide data available on GenBank. We explore the properties of these trees and their utility for phylogenetic inference, and show that even the highly incomplete alignments characteristic of supermatrix approaches may yield very good estimates of phylogeny. We present a novel pipeline for filtering sparse alignments to improve their phylogenetic utility by maximizing the partial decisiveness of the matrices themselves through a technique we call "phylogenetic scaffolding," and we present a new method of scoring tip instability (i.e. "rogue taxa") based on the I statistic implemented in the software Mesquite. The modified statistic, which we call I(S), is somewhat more straightforward to interpret than similar statistics, and our implementation of it may be applied to very large sets of large trees. The largest sedge trees presented here contain over 1,500 tips (about one quarter of all sedge species), and are based on multi-gene alignments with over 20,000 sites and over 90% missing data. These trees match well with previously supported phylogenetic hypotheses, but have lower overall support values and less resolution than more heavily filtered trees. Our best-resolved trees are characterized by stronger support values than any previously published sedge phylogenies, and show some relationships that are incongruous with previous studies. Overall, we show that supermatix methods offer powerful means of pursuing phylogenetic study, and that these tools have high potential value for many systematic biologists.

Hemisphere-scale differences in conifer evolutionary history

Article

Full-text available

Sep 2012
P NATL ACAD SCI USA

Fundamental differences in the distribution of oceans and landmasses in the Northern and Southern Hemispheres potentially impact patterns of biological diversity in the two areas. The evolutionary history of conifers provides an opportunity to explore these dynamics, because the majority of extant conifer species belong to lineages that have been broadly confined to the Northern or Southern Hemisphere during the Cenozoic. Incorporating genetic information with a critical review of fossil evidence, we developed an age-calibrated phylogeny sampling ∼80% of living conifer species. Most extant conifer species diverged recently during the Neogene within clades that generally were established during the later Mesozoic, but lineages that diversified mainly in the Southern Hemisphere show a significantly older distribution of divergence ages than their counterparts in the Northern Hemisphere. Our tree topology and divergence times also are best fit by diversification models in which Northern Hemisphere conifer lineages have higher rates of species turnover than Southern Hemisphere lineages. The abundance of recent divergences in northern clades may reflect complex patterns of migration and range shifts during climatic cycles over the later Neogene leading to elevated rates of speciation and extinction, whereas the scattered persistence of mild, wetter habitats in the Southern Hemisphere may have favored the survival of older lineages.

Pruning Rogue Taxa Improves Phylogenetic Accuracy: An Efficient Algorithm and Webservice

Article

Full-text available

Sep 2012
SYST BIOL

The presence of rogue taxa (rogues) in a set of trees can frequently have a negative impact on the results of a bootstrap analysis (e.g., the overall support in consensus trees). We introduce an efficient graph-based algorithm for rogue taxon identification as well as an interactive web-service implementing this algorithm. Compared to our previous method, the new algorithm is up to four orders of magnitude faster, while returning qualitatively identical results. Because of this significant improvement in scalability, the new algorithm can now identify substantially more complex and compute-intensive rogue taxon constellations. On a large and diverse collection of real-world datasets, we show that our method yields better supported reduced/pruned consensus trees than any competing rogue taxon identification method. Using the parallel version of our open-source code, we successfully identified rogue taxa in a set of 100 trees with 116,334 taxa each. For simulated datasets we show that, when removing/pruning rogue taxa with our method from a tree set, we consistently obtain bootstrap consensus trees as well as maximum likelihood trees that are topologically closer to the respective true trees.

Darriba D, Taboada GL, Doallo R, Posada D.. jModelTest 2: more models, new heuristics and parallel computing. Nat Methods 9: 772

Article

Full-text available

Jul 2012
Br J Pharmacol

Sensitivity analysis, molecular systematics and natural history evolution of Scathophagidae (Diptera: Cyclorrhapha: Calyptratae)

Article

Full-text available

Feb 2007
CLADISTICS

The 60 000 described species of Cyclorrhapha are characterized by an unusual diversity in larval life-history traits, which range from saprophagy over phytophagy to parasitism and predation. However, the direction of evolutionary change between the different modes remains unclear. Here, we use the Scathophagidae (Diptera) for reconstructing the direction of change in this relatively small family (≈ 250 spp.) whose larval habits mirror the diversity in natural history found in Cyclorrhapha. We subjected a molecular data set for 63 species (22 genera) and DNA sequences from seven genes (12S, 16S, Cytb, COI, 28S, Ef1-alfa, Pol II) to an extensive sensitivity analysis and compare the performance of three different alignment strategies (manual, Clustal, POY). We find that the default Clustal alignment performs worst as judged by character incongruence, topological congruence and branch support. For this alignment, scoring indels as a fifth character state worsens character incongruence and topological congruence. However, manual alignment and direct optimization perform similarly well and yield near-identical trees, although branch support is lower for the direct-optimization trees. All three alignment techniques favor the upweighting of transversion. We furthermore confirm the independence of the concepts “node support” and “node stability” by documenting several cases of poorly supported nodes being very stable and cases of well supported nodes being unstable. We confirm the monophyly of the Scathophagidae, its two constituent subfamilies, and most genera. We demonstrate that phytophagy in the form of leaf mining is the ancestral larval feeding habit for Scathophagidae. From phytophagy, two shifts to saprophagy and one shift to predation has occurred while a second origin of predation is from a saprophagous ancestor. © The Willi Hennig Society 2006.

Molecular phylogeny of the Calyptratae (Diptera: Cyclorrhapha) with an emphasis on the superfamily Oestroidea and the position of Mystacinobiidae and McAlpine's fly

Article

Full-text available

Aug 2010
SYST ENTOMOL

The dipteran clade Calyptratae is comprised of approximately 18 000 described species (12% of the known dipteran diversity) and includes well-known taxa such as houseflies, tsetse flies, blowflies and botflies, which have a close association with humans. However, the phylogenetic relationships within this insect radiation are very poorly understood and controversial. Here we propose a higher-level phylogenetic hypothesis for the Calyptratae based on an extensive DNA sequence dataset for 11 noncalyptrate outgroups and 247 calyptrate species representing all commonly accepted families in the Oestroidea and Hippoboscoidea, as well as those of the muscoid grade. DNA sequences for genes in the mitochondrial (12S, 16S, cytochrome c oxidase subunit I and cytochrome b) and nuclear genome [18S, 28S, the carbamoyl phosphate synthetase region of CAD (rudimentary), Elongation factor one alpha] were used to reconstruct the relationships. We discuss problems relating to the alignment and analysis of large datasets and emphasize the advantages of utilizing a guide tree-based approach for the alignment of the DNA sequences and using the leaf stability index to identify ‘wildcard’ taxa whose excessive instability obscures the phylogenetic signal. Our analyses support the monophyly of the Calyptratae and demonstrate that the superfamily Oestroidea is nested within the muscoid grade. We confirm that the monotypic family Mystacinobiidae is an oestroid and further revise the composition of the Oestroidea by demonstrating that the previously unplaced and still undescribed ‘McAlpine’s fly’ is nested within this superfamily as a probable sister group to Mystacinobiidae. Within the Oestroidea we confirm with molecular data that the Calliphoridae are a paraphyletic grade of lineages. The families Sarcophagidae and Rhiniidae are monophyletic, but support for the monophyly of Tachinidae and Rhinophoridae depends on analytical technique (e.g. parsimony or maximum likelihood). The superfamilies Hippoboscoidea and Oestroidea are consistently found to be monophyletic, and the paraphyly of the muscoid grade is confirmed. In the overall relationships for the calyptrates, the Hippoboscoidea are sister group to the remaining Calyptratae, and the Fanniidae are sister group to the nonhippoboscoid calyptrates, whose relationships can be summarized as (Muscidae (Oestroidea (Scathophagidae, Anthomyiidae))).

Order Diptera Linnaeus, 1758

Article

Full-text available

Jan 2011
ZOOTAXA

Phylogeny of the Sympetrinae (Odonata: Libellulidae): Further evidence of the homoplasious nature of wing venation

Article

Full-text available

Jan 2008
SYST ENTOMOL

Abstract Sympetrinae is the largest subfamily of the diverse dragonfly family Libellulidae. This subfamily, like most libellulid subfamilies, is defined currently by a few wing venation characters, none of which are synapomorphies for the taxon. In this study, we used DNA sequence data from the nuclear locus elongation factor-1α and the mitochondrial loci 16S and 12S rRNA, together with 38 wing venation characters, to test the monophyly of the Sympetrinae and several other libellulid subfamilies. No analysis recovered Sympetrinae as monophyletic, partly because of the position of Leucorrhinia (of the subfamily Leucorrhininae) as a strongly supported sister to Sympetrum (of Sympetrinae) in all analyses. The subfamilies Brachydiplactinae, Leucorrhininae, Trameinae and Trithemistinae were also found not to be monophyletic. Libellulinae was the only subfamily supported strongly as monophyletic. Consistency indices and retention indices of wing venation characters used to define various subfamilies were closer to zero than unity, showing that many of these characters were homoplasious, and therefore not useful for a classification scheme within Libellulidae.

Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics

Article

Full-text available

May 2012
SYST BIOL

The field of phylogenetics is on the cusp of a major revolution, enabled by new methods of data collection that leverage both genomic resources and recent advances in DNA sequencing. Previous phylogenetic work has required labor-intensive marker development coupled with single-locus polymerase chain reaction and DNA sequencing on clade-by-clade and locus-by-locus basis. Here, we present a new, cost-efficient, and rapid approach to obtaining data from hundreds of loci for potentially hundreds of individuals for deep and shallow phylogenetic studies. Specifically, we designed probes for target enrichment of >500 loci in highly conserved anchor regions of vertebrate genomes (flanked by less conserved regions) from five model species and tested enrichment efficiency in nonmodel species up to 508 million years divergent from the nearest model. We found that hybrid enrichment using conserved probes (anchored enrichment) can recover a large number of unlinked loci that are useful at a diversity of phylogenetic timescales. This new approach has the potential not only to expedite resolution of deep-scale portions of the Tree of Life but also to greatly accelerate resolution of the large number of shallow clades that remain unresolved. The combination of low cost (~1% of the cost of traditional Sanger sequencing and ~3.5% of the cost of high-throughput amplicon sequencing for projects on the scale of 500 loci × 100 individuals) and rapid data collection (~2 weeks of laboratory time) are expected to make this approach tractable even for researchers working on systems with limited or nonexistent genomic resources.

Creating the CIPRES Science Gateway for Inference of Large Phylogenetic Trees

Conference Paper

Full-text available

Dec 2010

Understanding the evolutionary history of living organisms is a central problem in biology. Until recently the ability to infer evolutionary relationships was limited by the amount of DNA sequence data available, but new DNA sequencing technologies have largely removed this limitation. As a result, DNA sequence data are readily available or obtainable for a wide spectrum of organisms, thus creating an unprecedented opportunity to explore evolutionary relationships broadly and deeply across the Tree of Life. Unfortunately, the algorithms used to infer evolutionary relationships are NP-hard, so the dramatic increase in available DNA sequence data has created a commensurate increase in the need for access to powerful computational resources. Local laptop or desktop machines are no longer viable for analysis of the larger data sets available today, and progress in the field relies upon access to large, scalable high-performance computing resources. This paper describes development of the CIPRES Science Gateway, a web portal designed to provide researchers with transparent access to the fastest available community codes for inference of phylogenetic relationships, and implementation of these codes on scalable computational resources. Meeting the needs of the community has included developing infrastructure to provide access, working with the community to improve existing community codes, developing infrastructure to insure the portal is scalable to the entire systematics community, and adopting strategies that make the project sustainable by the community. The CIPRES Science Gateway has allowed more than 1800 unique users to run jobs that required 2.5 million Service Units since its release in December 2009. (A Service Unit is a CPU-hour at unit priority).

Molecular phylogenetics: Principles and practice

Article

Full-text available

Mar 2012
NAT REV GENET

Phylogenies are important for addressing various biological questions such as relationships among species or genes, the origin and spread of viral infection and the demographic changes and migration patterns of species. The advancement of sequencing technologies has taken phylogenetic analysis to a new height. Phylogenies have permeated nearly every branch of biology, and the plethora of phylogenetic methods and software packages that are now available may seem daunting to an experimental biologist. Here, we review the major methods of phylogenetic analysis, including parsimony, distance, likelihood and Bayesian methods. We discuss their strengths and weaknesses and provide guidance for their use.

Bayesian phylogenetics with BEAUti and the BEAST 1.7. Molecular Biology and Evolution, 29, 1969-1973

Article

Full-text available

Feb 2012
MOL BIOL EVOL

Computational evolutionary biology, statistical phylogenetics and coalescent-based population genetics are becoming increasingly central to the analysis and understanding of molecular sequence data. We present the Bayesian Evolutionary Analysis by Sampling Trees (BEAST) software package version 1.7, which implements a family of Markov chain Monte Carlo (MCMC) algorithms for Bayesian phylogenetic inference, divergence time dating, coalescent analysis, phylogeography and related molecular evolutionary analyses. This package includes an enhanced graphical user interface program called Bayesian Evolutionary Analysis Utility (BEAUti) that enables access to advanced models for molecular sequence and phenotypic trait evolution that were previously available to developers only. The package also provides new tools for visualizing and summarizing multispecies coalescent and phylogeographic analyses. BEAUti and BEAST 1.7 are open source under the GNU lesser general public license and available at http://beast-mcmc.googlecode.com and http://beast.bio.ed.ac.uk

The sarcophagid flies from Peninsular Malaysia (Diptera: Sarcophagidae)

Article

Jan 2009

The collections of Malayan Sarcophagidae preserved in the National Science Museum and the National Institute of Infectious Diseases, Tokyo and made by the present authors during the field surveys in the Peninsular Malaysia between 2004 and 2008 are dealt with. A total of two subfamilies, 20 genera and 45 species is listed. A new species, Boettcherisca highlandica sp. nov. is described and illustrated.

The flies from Sarawak, East Malaysia (Diptera : Muscidae, Calliphoridae, Sarcophagidae and Tachinidae)

Article

Dec 2007

The collection of Muscidae, Calliphoridae, Sarcophagidae and Tachinidae made by the first author during the field surveys in Sarawak, East Malaysia between 2005 and 2006 is dealt with. A total of 39 genera and 67 species are listed. A new species of the sarcophagid fly, Parasarcophaga omari sp. nov. is described and illustrated.

Analysis of Phylogenetics and Evolution with R

Book

Jan 2006

Emmanuel Paradis

Bayes factors

Article

Jan 1995

vol Garli: genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion [doctoral dissertation], Austin: Univ

Article

Jan 2006

D.J. Zwickl

The world Blaesoxipha Loew, 1861 (Diptera: Sarcophagidae)

Article

Jan 1994

Thomas Pape

Three New Species of Sarcophaga (Insecta: Diptera: Sarcophagidae) from Timor, with a Lectotype Designation for Myophora peronii

Article

May 2004

Three new species of Sarcophaga Meigen, 1826 are described from Timor (Indonesia), viz., Sarcophaga (Sarcorohdendorfia) ikat sp.n., S. (S.) uncus sp.n., and S. (Lioproctia) serratocudo sp.n. The nominal taxon Myophora peronii Robineau-Desvoidy, 1830, with the type locality Timor and previously considered a nomen dubium, is revised and proposed as a senior synonym of Sarcophaga tibialis Macquart, 1851, syn.n. Prevailing usage is maintained through reversed priority: Myophora peronii qualifies as a nomen oblitum, while Sarcophaga tibialis is shown to qualify as a nomen protectum. The delimitation of several Sarcophaga subgenera, Johnstonimyia Lopes, 1959, Sarcorohdendorfia Baranov, 1938, Seniorwhitea Rohdendorf, 1937, and Lioproctia Enderlein, 1928, is briefly discussed and three species are transferred from S. (Johnstonimyia) to S. (Sarcorohdendorfia): S. (Sarcorohdendorfia) gorokaensis Sugiyama, Shinonaga and Kano, 1988; S. (Sarcorohdendorfia) hugoi Pape, 1996; and S. (Sarcorohdendorfia) vanuatu Pape, 1991. The apparently convergent evolution of golden abdominal coloration in several species of Sarcophaga on Timor is discussed.

Katoh K, Misawa K, Kuma KI, Miyata T.. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30: 3059-3066

Article

Jul 2002
NUCLEIC ACIDS RES

Kazutaka Katoh

A multiple sequence alignment program, MAFFT, has been developed. The CPU time is drastically reduced as compared with existing methods. MAFFT includes two novel techniques. (i) Homo logous regions are rapidly identified by the fast Fourier transform (FFT), in which an amino acid sequence is converted to a sequence composed of volume and polarity values of each amino acid residue. (ii) We propose a simplified scoring system that performs well for reducing CPU time and increasing the accuracy of alignments even for sequences having large insertions or extensions as well as distantly related sequences of similar length. Two different heuristics, the progressive method (FFT‐NS‐2) and the iterative refinement method (FFT‐NS‐i), are implemented in MAFFT. The performances of FFT‐NS‐2 and FFT‐NS‐i were compared with other methods by computer simulations and benchmark tests; the CPU time of FFT‐NS‐2 is drastically reduced as compared with CLUSTALW with comparable accuracy. FFT‐NS‐i is over 100 times faster than T‐COFFEE, when the number of input sequences exceeds 60, without sacrificing the accuracy.

The First Instar of European Miltogramminae (Diptera: Sarcophagidae)

Book

Jan 2010

Krzysztof Szpila

The present study provides a detailed account of first instar morphology for the subfamily Miltogramminae. The larvae of 72 European species are described and illustrated. Documentation of larval morphology for 52 species is published for the first time. Material was obtained by keeping wild-caught females under laboratory conditions or by dissecting dry specimens from museum collections. Larvae were subsequently prepared for analysis by light and scanning electron (SEM) microscopy. Several relative measures were used to define the shape of the following structures: antenna, antennal dome, antennal basal ring, first sensillum basiconicum of maxillary palpus, labrum, intermediate sclerite and basal sclerite. For each species, morphology was analyzed in detail for all body segments. Morphological characters of larvae were illustrated as black and white drawings, microscope slide photographs and SEM images. Unusual morphological variability was observed with regard to most characters and several structures that are entirely unique among the Oestroidea are described for the first time. Cuticular sculpture and elongation of the first sensillum basiconicum of the maxillary palpus (mentioned previously as possible apomorphies in the subfamily) are present in almost all of the described larvae. For 20 species the presented data were compared with descriptions in the earlier literature. This comparison revealed several discrepancies, mainly regarding the interpretation of shape for particular elements of the cephaloskeleton, or the presence of cuticular structures. Morphological variability of first instar Miltogramminae is discussed in light of current knowledge on morphology of the early preimaginal instars in the Oestroidea superfamily. According to general evolutionary trends in higher Diptera, from saprophagy to parasitism or predation, the set of seven plesiomorphic larval characters is defined. Among the Miltogramminae, the first instar of Phyllotelini bears the highest number of these characters. In contrast to an earlier hypothesis, the saprophagy of various buried resources is suggested in the present work to be the ancestral life habit of the whole subfamily. First instar morphological data are in many points in conflict with current systematics of the taxon, which emphasizes the necessity of further research on the systematics and phylogeny of Miltogramminae.

Bayes Factor

Article

Jun 1995

In a 1935 paper and in his book Theory of Probability, Jeffreys developed a methodology for quantifying the evidence in favor of a scientific theory. The centerpiece was a number, now called the Bayes factor, which is the posterior odds of the null hypothesis when the prior probability on the null is one-half. Although there has been much discussion of Bayesian hypothesis testing in the context of criticism of P-values, less attention has been given to the Bayes factor as a practical tool of applied statistics. In this article we review and discuss the uses of Bayes factors in the context of five scientific applications in genetics, sports, ecology, sociology, and psychology. We emphasize the following points:

Analysis of Phylogenetics and Evolution With R (Second Edition)

Article

Jan 2012

Emmanuel Paradis

Updates on the nomenclature of the Australian Sarcophagidae (Diptera) along with descriptions of two new species of Sarcophaga (sensu lato)

Article

Jun 2013

Two new species, Sarcophaga (Sarcosolomonia) collessi sp. nov. and Sarcophaga (Sarcorohdendorfia) clavus sp. nov., both collected in Queensland, Australia, are described, and the following four new synonymies are proposed: Sarcophaga horti Blackith and Blackith, 1988 syn. nov. of Sarcophaga bancroftorum Johnston and Tiegs, 1921; Sarcophaga fergusonina Hardy, 1940 syn. nov. of Sarcophaga assimilis Macquart, 1851; Sarcophaga brevicornis Ho, 1934 syn. nov. of Sarcophaga kohla Johnston and Hardy, 1923a; and Sarcophaga triplex Hardy, 1943 syn. nov. of Sarcophaga furcata Hardy, 1932.

A key to the Australian Sarcophagidae (Diptera) with special emphasis on Sarcophaga (sensu lato)

Article

Jun 2013

The Australian Sarcophagidae (Diptera) currently comprise 84 species, classified into ten genera from the subfamilies Miltogramminae and Sarcophaginae. A key is provided to the Australian sarcophagids, allowing for separation into subfamilies and genera, along with the identification of all species of Sarcophaga (sensu lato). A comprehensive database of illustrations and photographs of male terminalia, as well as updated biological information, is given for each species of Sarcophaga s.l.

Phylogenetic relationships of flesh flies in the subfamily Sarcophaginae based on three mtDNA fragments (Diptera: Sarcophagidae)

Article

Jan 2013

In an effort to improve our knowledge of the phylogenetic relationships among species and genera of the subfamily Sarcophaginae, we analysed data from three mitochondrial gene fragments. Sequence data for portions of the genes cytochrome oxidase I (COI), cytochrome oxidase II (COII) and dehydrogenase subunit 4 (ND4) were obtained from 43 species of Sarcophagidae representing 15 genera. We used a Bayesian approach to simultaneously choose how best to partition the data and which substitution model to apply to each partition. Phylogenetic relationships were inferred using Bayesian Inference and Maximum Likelihood methods. Our results are consistent with monophyly of the subfamily Sarcophaginae (posterior probability 1; bootstrap support 93%), as well as with monophyly of several genera within the Sarcophaginae (including Sarcophaga s.l.; posterior probability 1; bootstrap support 97%). We found support for a sister‐group relationship between Ravinia Robineau‐Desvoidy and Oxysarcodexia Townsend, which has been hypothesised by past authors on the basis of morphological similarities, although this was supported only in the Bayesian analyses (posterior probability 0. 81–0. 98), and for some novel supra‐generic clades. Contrary to a recent morphological hypothesis, we do not find Helicobia Coquillett to be nested within Sarcophaga Meigen; our data suggest, but do not strongly support, a hypothesis that Peckia Robineau‐Desvoidy is the sister group to Sarcophaga.

TNT, a free program for phylogentic analysis

Article

Jan 2008

Phylogeny of Heteronychia: the largest lineage of Sarcophaga (Diptera: Sarcophagidae)

Article

Oct 2013

Sarcophaga Meigen is one of the megadiverse genera of true flies, with approximately 850 valid species worldwide. The genus is divided into about 160 subgenera, the validity of a vast majority of which has never been verified using cladistic methods. This paper deals with the mainly Palaearctic subgenus Heteronychia Brauer & Bergenstamm, which comprises 89 species and is thus the largest subunit of Sarcophaga. We performed a cladistic analysis of the group based exclusively on male morphological characters. Parsimony analyses were run on a matrix of 84 characters for 88 species. Species of the subgenera Discachaeta Enderlein and Notoecus Stein were also included in the matrix. A further analysis was carried out using a subset of characters from the terminalia alone (70 characters). The results show that the clade formed by Heteronychia, Discachaeta, and Notoecus is monophyletic, with Discachaeta emerging as polyphyletic whereas Sarcophaga (Notoecus) longestylata Strobl is nested within the Sarcophaga filia‐group. Character states supporting Heteronychia and the few well‐supported species‐groups are discussed in detail. The following synonymies are proposed: Discachaeta = Heteronychia (syn. nov.) and Notoecus = Heteronychia (syn. nov.). The paper also includes a historical background of the taxon in relation to the classification of the genus Sarcophaga over the past two centuries, as well as a terminological review of the male terminalia, particularly of the distiphallus. © 2013 The Linnean Society of London

Unlocking the vault: Next-generation museum population genomics

Article

Sep 2013
MOL ECOL

Natural history museum collections provide unique resources for understanding how species respond to environmental change, including the abrupt, anthropogenic climate change of the past century. Ideally, researchers would conduct genome-scale screening of museum specimens to explore the evolutionary consequences of environmental changes, but to date such analyses have been severely limited by the numerous challenges of working with the highly degraded DNA typical of historic samples. Here, we circumvent these challenges by using custom, multiplexed, exon capture to enrich and sequence ~11 000 exons (~4 Mb) from early 20th-century museum skins. We used this approach to test for changes in genomic diversity accompanying a climate-related range retraction in the alpine chipmunks (Tamias alpinus) in the high Sierra Nevada area of California, USA. We developed robust bioinformatic pipelines that rigorously detect and filter out base misincorporations in DNA derived from skins, most of which likely resulted from postmortem damage. Furthermore, to accommodate genotyping uncertainties associated with low-medium coverage data, we applied a recently developed probabilistic method to call single-nucleotide polymorphisms and estimate allele frequencies and the joint site frequency spectrum. Our results show increased genetic subdivision following range retraction, but no change in overall genetic diversity at either nonsynonymous or synonymous sites. This case study showcases the advantages of integrating emerging genomic and statistical tools in museum collection-based population genomic applications. Such technical advances greatly enhance the value of museum collections, even where a pre-existing reference is lacking and points to a broad range of potential applications in evolutionary and conservation biology.

Area and rapid radiation of Hawaiian Bidens (Asteraceae)

Article

Jul 2012
J BIOGEOGR

Aim To estimate the rate of adaptive radiation of endemic Hawaiian Bidens and to compare their diversification rates with those of other plants in Hawaii and elsewhere with rapid rates of radiation. Location Hawaii. Methods Fifty‐nine samples representing all 19 Hawaiian species, six Hawaiian subspecies, two Hawaiian hybrids and an additional two Central American and two African Bidens species had their DNA extracted, amplified by polymerase chain reaction and sequenced for four chloroplast and two nuclear loci, resulting in a total of approximately 5400 base pairs per individual. Internal transcribed spacer sequences for additional outgroup taxa, including 13 non‐Hawaiian Bidens , were obtained from GenBank. Phylogenetic relationships were assessed by maximum likelihood and Bayesian inference. The age of the most recent common ancestor and diversification rates of Hawaiian Bidens were estimated using the methods of previously published studies to allow for direct comparison with other studies. Calculations were made on a per‐unit‐area basis. Results We estimate the age of the Hawaiian clade to be 1.3–3.1 million years old, with an estimated diversification rate of 0.3–2.3 species/million years and 4.8 × 10 ⁻⁵ to 1.3 × 10 ⁻⁴ species Myr ⁻¹ km ⁻² . Bidens species are found in Europe, Africa, Asia and North and South America, but the Hawaiian species have greater diversity of growth form, floral morphology, dispersal mode and habitat type than observed in the rest of the genus world‐wide. Despite this diversity, we found little genetic differentiation among the Hawaiian species. This is similar to the results from other molecular studies on Hawaiian plant taxa, including others with great morphological variability (e.g. silverswords, lobeliads and mints). Main conclusions On a per‐unit‐area basis, Hawaiian Bidens have among the highest rates of speciation for plant radiations documented to date. The rapid diversification within such a small area was probably facilitated by the habitat diversity of the Hawaiian Islands and the adaptive loss of dispersal potential. Our findings point to the need to consider the spatial context of diversification – specifically, the relative scale of habitable area, environmental heterogeneity and dispersal ability – to understand the rate and extent of adaptive radiation.

Utility of COI, CAD and morphological data for resolving relationships within the genus Sarcophaga (sensu lato) (Diptera: Sarcophagidae): A preliminary study

Article

May 2013
MOL PHYLOGENET EVOL

Currently there are ∼3,000 known species of Sarcophagidae (Diptera), which are classified into 173 genera in three subfamilies. Almost 25% of sarcophagids belong to the genus Sarcophaga (sensu lato) however little is known about the validity of, and relationships between the ∼150 (or more) subgenera of Sarcophaga s.l. In this preliminary study, we evaluated the usefulness of three sources of data for resolving relationships between 35 species from 14 Sarcophaga s.l. subgenera: the mitochondrial COI barcode region, ∼800 bp of the nuclear gene CAD, and 110 morphological characters. Bayesian, maximum likelihood (ML) and maximum parsimony (MP) analyses were performed on the combined dataset. Much of the tree was only supported by the Bayesian and ML analyses, with the MP tree poorly resolved. The genus Sarcophaga s.l. was resolved as monophyletic in both the Bayesian and ML analyses and strong support was obtained at the species-level. Notably, the only subgenus consistently resolved as monophyletic was Liopygia. The monophyly of and relationships between the remaining Sarcophaga s.l. subgenera sampled remain questionable. We suggest that future phylogenetic studies on the genus Sarcophaga s.l. consider COI, CAD, and morphological data for analyses. We also advocate the use of additional data and a range of inference strategies to assist with resolving relationships within Sarcophaga s.l.

Revision of the New World genus Peckia Robineau-Desvoidy (Diptera: Sarcophagidae)

Article

Mar 2013
ZOOTAXA

The New World and largely Neotropical genus Peckia Robineau-Desvoidy, 1830 is revised with a key to all species. Peckia is considered a senior synonym of Guanoxipha Lehrer, 2012, n. syn. and of Sarcodexia Townsend, 1892, n. syn., the first one under Squamatodes Curran and the latter maintained as a valid subgenus, which here is redefined giving the new generic combinations Peckia (Sarcodexia) lambens (Wiedemann, 1830), n. comb. and P. (S.) notata (Lopes, 1935), n. comb.; and the new subgeneric affiliations P. (S.) aequata (Wulp, 1895), P. (S.) chirotheca (Hall, 1933), P. (S.) dominicana (Lopes, 1982), P. (S.) florencioi (Prado & Fonseca, 1932), P. (S.) roppai (Lopes & Tibana, 1982) and P. (S.) tridentata (Hall, 1937). Peckia virgo (Pape, 1994) is transferred from subgenus Euboettcheria Townsend, 1927 to subgenus Squamatodes Curran, 1927. Sarcophaga adolenda Lopes, 1935 is transferred from its current position in Peckia to the genus Retrocitomyia Lopes, 1982, n. comb. A total of 67 species are recognized and grouped in the subgenera Euboettcheria, Pattonella Enderlein, 1928, Peckia Robineau-Desvoidy, 1830 (sensu stricto), Sarcodexia and Squamatodes. Nine new species are described, viz., Peckia (Euboettcheria) santamariae n. sp. (Colombia), Peckia (Euboettcheria) cacao n. sp. (Costa Rica), Peckia (Euboettcheria) calixtoi n. sp. (Puerto Rico), Peckia (Euboettcheria) hernandosi n. sp. (Ecuador), Peckia (Pattonella) kladosoides n. sp. (Colombia), Peckia (Peckia) cocopex n. sp. (Costa Rica: Cocos Island), Peckia (Peckia) sarmientoi n. sp. (Ecuador), Peckia (Peckia) rosalbae n. sp. (Colombia) and Peckia (Sarcodexia) cocos n. sp. (Costa Rica: Cocos Island). The following new synonymies are proposed as junior synonyms under their respective species: under Peckia (Euboettcheria) tridentata (Hall, 1937) is Euboettcheria alvarengai Lopes & Tibana, 1982, n. syn.; under Peckia (Peckia) chrysostoma (Wiedemann, 1830) is Paraphrissopoda hugolopesiana Lehrer, 2006, n. syn.; under Peckia (Peckia) pexata (Wulp, 1895) are Sarcophaga concinnata Williston, 1896, n. syn., Sarcophaga otiosa Williston, 1896, n. syn. and Paraphrissopoda catiae Lehrer, 2006, n. syn.; under Peckia (Peckia) rubella (Wiedemann, 1830) is Sarcophaga capitata Aldrich, 1916, n. syn. and under Peckia (Squamatodes) trivittata (Curran, 1927) is Squamatodes stahli Dodge, 1966, n. syn. Lectotypes are designated for Sarcophaga aequata Wulp, 1895, Sarcophaga concinnata Williston, 1896, Sarcophaga otiosa Williston, 1896 and Sarcophaga volucris Wulp, 1895. Paraphrissopoda alvesia Lehrer, 2006 is deemed an unavailable name as no depository was given for the putative type material.

MESQUITE: a modular system for evolutionary analysis

Article

Nov 2009
EVOLUTION

MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform

Article

Jul 2002

A multiple sequence alignment program, MAFFT, has been developed. The CPU time is drastically reduced as compared with existing methods. MAFFT includes two novel techniques. (i) Homo logous regions are rapidly identified by the fast Fourier transform (FFT), in which an amino acid sequence is converted to a sequence composed of volume and polarity values of each amino acid residue. (ii) We propose a simplified scoring system that performs well for reducing CPU time and increasing the accuracy of alignments even for sequences having large insertions or extensions as well as distantly related sequences of similar length. Two different heuristics, the progressive method (FFT-NS-2) and the iterative refinement method (FFT-NS-i), are implemented in MAFFT. The performances of FFT-NS-2 and FFT-NS-i were compared with other methods by computer simulations and benchmark tests; the CPU time of FFT-NS-2 is drastically reduced as compared with CLUSTALW with comparable accuracy. FFT-NS-i is over 100 times faster than T-COFFEE, when the number of input sequences exceeds 60, without sacrificing the accuracy.

Identification of forensically important Sarcophaga species (Diptera: Sarcophagidae) using the mitochondrial COI gene

Article

Sep 2012
INT J LEGAL MED

The identification of species of the forensically important genus Sarcophaga is very difficult and requires strong taxonomic expertise. In this study, we sequenced the mitochondrial cytochrome c oxidase subunit I (COI) gene of 126 specimens of 56 W European Sarcophaga species and added GenBank data to our database to yield a total dataset of 270 COI sequences from 99 Sarcophaga species to evaluate the COI gene as a molecular diagnostic tool for species identification in this genus. Using two simple criteria (Best Match, BM and Best Close Match, BCM), we showed that the identification success using a mini-barcode region of 127 bp was very low (80.7-82.5 %) and the use of this region is not recommended as a species identifier. In contrast, identification success was very high using the standard barcode region (658 bp) or using the entire COI region (1,535 bp) (98.2-99.3 %). Yet, there was a low interspecific sequence divergence (<2 %) in six species groups so that for 16 out of the 99 species (nine of which are of forensic importance), the use of COI barcodes as species identifier should be done with care. For these species, additional markers will be necessary to achieve a 100 % identification success. We further illustrate how such reference databases can improve local reference databases for forensic entomologists.

TNT, a free program for phylogenetic analysis

Article

Jul 2008
CLADISTICS

The main features of the phylogeny program TNT are discussed. Windows versions have a menu interface, while Macintosh and Linux versions are command-driven. The program can analyze data sets with discrete (additive, non-additive, step-matrix) as well as continuous characters (evaluated with Farris optimization). Effective analysis of large data sets can be carried out in reasonable times, and a number of methods to help identifying wildcard taxa in the case of ambiguous data sets are implemented. A variety of methods for diagnosing trees and exploring character evolution is available in TNT, and publication-quality tree-diagrams can be saved as metafiles. Through the use of a number of native commands and a simple but powerful scripting language, TNT allows the user an enormous flexibility in phylogenetic analyses or simulations. © The Willi Hennig Society 2008.

Towards a phylogeny of the flesh flies (Diptera: Sarcophagidae): Morphology and phylogenetic implications of the acrophallus in the subfamily Sarcophaginae

Article

Apr 2010
ZOOL J LINN SOC-LOND

The morphology of the acrophallus, the distal portion of the male phallus carrying the phallotreme, was studied in 72 exemplar species representing 56 genera and subgenera of the flesh fly subfamily Sarcophaginae. For 42 of those species, scanning electron microscopy was used to clarify the phallic morphology. Terms used to describe the male genitalia were updated based on new interpretations of homology. Male genitalic characters, combined with other morphological characters of adult males and females and of larvae, were used to construct a phylogeny. The monophyly of the subfamily was supported, and some generic-level sister-group relationships proposed in the literature, but without previous cladistic analyses, were also supported. The genus Blaesoxipha Loew, as currently recognized, was not monophyletic in our analysis. The genus Helicobia Coquillett is synonymized with Sarcophaga Meigen syn. nov. and treated as a subgenus of the latter. The Sarcophaga subgenera Neobellieria Blanchard and Mehria Enderlein were not monophyletic. Many of the clades in the analysis were supported primarily or exclusively by male genitalic character states, highlighting the importance of the male genitalia as a source of morphological characters for sarcophagine phylogeny. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 158, 740–778.

A new genus of Paramacronychiinae (Diptera: Sarcophagidae), argued from a genus‐level cladistic analysis

Article

Jan 2002
SYST ENTOMOL

Thomas Pape

Primorya gen.n. is described as a new genus of the flesh fly subfamily Paramacronychiinae, including the type species and sole member Primorya ussuriensis sp.n. from the Russian Far East. Arguments for erecting a new genus are obtained from a phylogenetic analysis of all paramacronychiine genera. Goniophyto suenagai (Kurahashi), comb.n. is transferred from Wohlfahrtiodes Villeneuve and included in a broadened concept of Goniophyto Townsend, and Agria cicadina (Kato) , comb.n. is transferred from Angiometopa Brauer & Bergenstamm. A key to all paramacronychiine genera is provided.

Troubleshooting Molecular Phylogenetic Analyses

Article

Nov 2002
Annu Rev Ecol Systemat

The number, size, and scope of phylogenetic analyses using molecular data has increased steadily in recent years. This has simultaneously led to a dramatic improvement in our understanding of phylogenetic relationships and a better appre-ciation for an array of methodological problems that continue to hinder progress in phylogenetic studies of certain data sets and/or particular parts of the tree of life. This review focuses on several persistent problems, including rooting, conflict among data sets, weak support in trees, strong but evidently incorrect support, and the computa-tional issues arising when methods are applied to the large data sets that are becoming increasingly commonplace. We frame each of these issues as a specific problem to be overcome, review the relevant theoretical and empirical literature, and suggest solu-tions, or at least strategies, for further investigation of the issues involved.

The utility of Mitochondrial DNA fragments for genetic identification of forensically important sarcophagid flies (Diptera: Sarcophagidae) in China

Article

Mar 2012
TROP BIOMED

Species-diagnostic anatomical characters of fleshflies are not known for most immature stages or even adults, and an existing key may be incomplete or difûcult for nonspecialists to use. The use of sarcophagids for PMI estimations has been greatly hampered by their highly similar morphological characters. DNA-based method can be used as a supplemental means of morphological method in identification of forensically important sarcophagid flies. However, relying solely on single DNA fragment for delimiting species is considered to be unreliable, especially when the fragment was small. Sequence data of selected regions of the cytochrome oxidase subunit two (COII) and 16S ribosomal RNA (16S rRNA) genes of the most important Chinese fleshfly taxa associated with cadavers are presented, which can be instrumental for implementation of the Chinese Sarcophagidae database. Phylogenetic analysis of the sequenced segments showed that all sarcophagid specimens were properly assigned into five species, which indicated the possibility of separation congeneric species with the short fragments.

A large-scale molecular phylogeny of flesh flies (Diptera: Sarcophagidae)

Abstract

No full-text available

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