Avian egg collections: museum collection bias driven by shape and size

Avian eggs exhibit substantial intra- and interspecific variation in shape, size and colour. Considerable efforts have been made to better understand the evolutionary drivers behind such variation, often using museum egg collections. Usually it is assumed that museum collections accurately represent the variation seen in natural populations, but this may not be the case if there is collection bias. Collection bias may lead to the over-representation of certain egg traits in collections, due to the aesthetic (or other) preferences of collectors. The aim of this study is to begin to look for the occurrence of potential collection bias in museum egg collections by comparing three shape indices (pointedness/asymmetry, elongation and polar asymmetry) and egg volume between subsets of eggs in museum collections with those of recently sampled eggs in the field for three different bird species: common guillemot Uria aalge, razorbill Alca torda and northern fulmar Fulmarus glacialis. We found no evidence of collection bias in our sampled razorbill and northern fulmar museum collection eggs, but some evidence for a bias in sampled museum collection eggs of common guillemots. Since the guillemot's egg differs from most bird eggs in being pyriform, we suggest that collection bias by historic egg collectors may be more prevalent in species with extreme egg traits. Researchers using museum egg collections to examine questions relating to egg shape should be aware of collection bias risks and consider how to minimise the effect of these possible biases on accumulated datasets.     

An associated partial skeleton of Jainosaurus cf. septentrionalis (Dinosauria: Sauropoda) from the Late Cretaceous of Chhota Simla,Central India

Abstract: The Cretaceous dinosaur fauna of Indo‐Pakistan has remained poorly understood because of a lack of associated and articulated remains, proliferation of named species, and an incomplete understanding of the dinosaur clades present (e.g. abelisaurid theropods; titanosaur sauropods). Continued work on existing collections, and new discoveries of dinosaur material from India, Pakistan and elsewhere in Gondwana, has begun to resolve the composition and affinities of Indo‐Pakistani dinosaurs. Here, we provide archival evidence that documents associations between postcranial remains of a sauropod collected from Chhota Simla, India by C. A. Matley in the 1930s and later described as ‘Titanosaurus sp.’ This partial skeleton, which represents only the fifth such documented association from Indo‐Pakistan, is referable to Jainosaurus cf. septentrionalis and provides a fuller understanding of its anatomy and phylogenetic affinities.     

The comparative osteology and phylogenetic relationships of African and South American lungfishes (Sarcopterygii: Dipnoi)

Lepidosirenidae is a clade of freshwater lungfishes that include the extant South American Lepidosiren paradoxa Fitzinger, 1837 and African species of the genus Protopterus. These genera have been geographically separated since the break‐up of Gondwana in the Early Cretaceous, but they display similar biology and morphology. Species were distinguished by a combination of features such as head‐to‐body ratios, the number of pairs of ribs, and the presence of external gills, but no discrete skeletal characters were identified, and no comparative studies including all extant species have been published. I used computed tomography (CT), X‐ray photography, and specimens from museum collections to describe the skeletal morphology of all species of lepidosirenid in a comparative context. I digitally disarticulated the bones in each specimen to compile a comparative atlas of the cranial and pectoral elements of all extant lungfishes, which has the potential to increase the correct identifications of specimens in museum collections. The morphology of the frontoparietal, parasphenoid, supraorbital, and suboperculum differ between species. I used those characters, along with molecular sequence data from the ribosomal RNA gene 16S, to run combined morphological and molecular phylogenetic analyses. Lepidosirenidae is monophyletic in all analyses, but the interrelationships of the species of Protopterus vary with the different sources of character data. © 2015 The Linnean Society of London     

Three phyla—Two type specimens—One shell: History of a snail shell revealed by modern imaging technology

In a recent revision of the gastropod genus Bellardiella, it became evident that the neotype of B. crassilabris had numerous borings over its entire shell surface. Superficial and light microscopical observation of the shell showed that the borings were made by a bryozoan belonging to the genus Penetrantia. Conventional techniques such as endocasting with the dissolution of the shell are impossible for type material. The application of non‐destructive micro‐CT‐scanning of the shell revealed the three‐dimensional arrangement of the entire colony within the shell. Careful analysis of the structure of the autozooids of the colony revealed that the species could not be assigned to any known species; we accordingly describe it as Penetrantia bellardiellae Schwaha, n. sp. The application of micro‐CT not only allowed the depiction of the new bryozoan species but also revealed the remains of a hermit crab located within the shell. The shell of Bellardiella crassilabris thus represents the type specimen of two species and contains a member of a third phylum inside. To our knowledge, this is a unique case, which also emphasizes the usefulness of micro‐CT imaging for precious specimens as well as the importance of historical museum collections.     

Nuclear DNA from a 180‐year‐old study skin reveals the phylogenetic position of the Kinglet Calyptura Calyptura cristata (Passeriformes: Tyrannides)

The Kinglet Calyptura Calyptura cristata is one of the most enigmatic bird species in South America, known only from specimens collected in the 19th century and a few recent observations. Knowledge of its biology is scanty and its systematic position is obscure. Traditionally, Calyptura was placed in the Cotingidae, but associated with genera that are now known to fall outside the Cotingidae. In an attempt to clarify its phylogenetic position, sequence data from four nuclear markers were obtained from a 180‐year‐old museum study skin of Calyptura, and incorporated into a comprehensive dataset of tyrant flycatchers, cotingas, manakins and allies. Our analyses demonstrate that Calyptura is most closely related to Platyrinchus and Neopipo and that these three genera constitute a deep branch in the clade containing the Rhynchocyclidae (tody‐tyrants and flatbills) and Tyrannidae (typical tyrant flycatchers). The Calyptura specimen is one of the oldest avian museum specimens from which a substantial amount of nuclear DNA sequence data have been obtained, and highlights the immense value of museum collections for DNA‐based phylogenetic studies.     

First record of albinism in the lanternshark family,Etmopteridae

A single albino specimen of the lanternshark, Lucifer's dogfish (Etmopterus lucifer), is reported here. The specimen was found among museum collections, having been captured near Cape Palliser, off the North Island of New Zealand in 1984. Morphometrics are reported, and with no retainment of pigmentation, the specimen is considered a complete albino. This is the first record of albinism for the family Etmopteridae and one of a handful of records for any deep-sea chondrichthyans.     

<Emphasis Type="Italic">Rainfordia opercularis</Emphasis>, a liopropomin serranid (Teleostei: Serranidae: Epinephelinae): corroborative evidence from settlement-stage larvae

Rainfordia opercularis was described in 1923 from a single specimen taken in Edgecumbe Bay, Queensland, Australia. The species is rare in museum collections, and the larvae have not been described. In 1999, two settlement-stage larvae (20–21 mm in standard length) were collected in light traps set off Lizard Island, Great Barrier Reef, Queensland. The smaller of the two has one thin, flexible, extremely elongate dorsal-fin spine encased in a pigmented sheath. The larger specimen lacks an elongate dorsal-fin spine and exhibits caudal-fin pigment characteristic of adults. A combination of features in one or both of the settlement-stage larvae support the placement of Rainfordia in the epinepheline-serranid tribe Liopropomini: presence of an elongate, filamentous dorsal-fin spine serially associated with the first dorsal-fin pterygiophore; presence of a spine on the inner preopercular ridge; presence of dense pigment on the frontals; absence of an elongate spine at the angle of the preopercle; and absence of supraorbital spination. Supplementary material to this paper is available in electronic format at     

World revision of Ortheziola Šulc (Homoptera: Coccoidea: Ortheziidae) with descriptions of eleven new species

Soil samples and museum collections were analysed from all zoogeographic regions of the world. From this material eleven new species of Ortheziola?ulc are described from Africa and the U.K., five additional species are redescribed and a key is presented for the identification of all sixteen species. A slightly modified concept of the genus is presented and several new characters are given as diagnostic of the genus. A phylogenetic hypothesis is given based on analysis of the morphological features of adult females. Results show that Ortheziola is most diverse in eastern Africa where relatively more advanced species occur. Basal species occur primarily in western Africa and Asia.     

Simple technique for distinguishing Yellow‐bellied Flycatchers from Cordilleran and Pacific‐slope flycatchers

Flycatchers of the genus Empidonax are readily misidentified in the field, in the hand, and even in museum collections. We describe a novel plumage feature that can be used to distinguish Yellow‐bellied Flycatchers (E. flaviventris) from the two species that comprise the Western Flycatcher complex, Cordilleran Flycatchers (E. occidentalis) and Pacific‐slope Flycatchers (E. difficilis). The length of the buffy fringing on the anterior edge of each secondary feather, visible on the folded wing, is significantly shorter in Yellow‐bellied Flycatchers than in Western flycatchers, with minimal overlap. A definitive identification can be made using a simple formula that includes measurements of wing chord and the length of the buffy fringing along the outer edge of the first secondary (S1). This method provides definitive in‐hand identification, and the difference in length of the buffy fringing on the secondaries is also a useful field mark for visual identification. Testing our method with 113 museum specimens that had been identified a priori based on locality, we correctly identified 112 specimens. The exception was a specimen from Illinois that had been assumed to be a Yellow‐bellied Flycatcher. However, based on our formula, it was a Western flycatcher and analysis of its mtDNA sequence confirmed this result, proving the utility of our method.     

Dinosaurs from the Maastrichtian-type area (southeastern Netherlands,northeastern Belgium)

In comparison to pre-1980 records of nonavian dinosaur remains from the Maastrichtian type strata, material collected during the past 20 years is both fairly common and diverse, consisting mostly of isolated cranial and post-cranial remains of hadrosaurids. With the exception of the type specimen of Megalosaurus bredai Seeley, a fragmentary right femur, no theropod material is represented in collections screened by us. In the present contribution, specimens recognised in various collections subsequent to our last tabulation (1999) are illustrated and briefly discussed. Although we are fully aware that the material is too limited to draw meaningful conclusions from, the specimens are here tied-in with a preliminary sequence-stratigraphic interpretation of the type Maastrichtian, which is currently being refined by strontium-isotope studies of coleoid cephalopods. To cite this article: J.W.M. Jagt, E.W.A. Mulder, A.S. Schulp, R.W. Dortangs, R.H.B. Fraaije, C. R. Palevol 2 (2003) 67–76.     

The case of an arctic wild ass highlights the utility of ancient DNA for validating problematic identifications in museum collections

Museum collections are essential for reconstructing and understanding past biodiversity. Many museum specimens are, however, challenging to identify. Museum samples may be incomplete, have an unusual morphology, or represent juvenile individuals, all of which complicate accurate identification. In some cases, inaccurate identification can lead to false biogeographic reconstructions with cascading impacts on paleontological and paleoecological research. Here, we analyzed an unusual Equid mandible found in the Far North of the Taymyr peninsula that was identified morphologically as Equus hemionus, an ancestor of present‐day Asiatic wild asses. If correct, this identification represents the only finding of a putative Late Pleistocene hemione in the Arctic region, and is therefore critical to understanding wild ass evolution and paleoecology. To confirm the accuracy of this specimen's taxonomic assignment, we used ancient DNA and mitochondrial hybridization capture to identify and place this specimen in the larger equid phylogeny. We find that the specimen is actually a member of E. caballus, the ancestor of domestic horses. Our study demonstrates the utility of ancient DNA to validate morphological identification, in particular of incomplete, otherwise problematic, or taxonomically unusual museum specimens.     

Re-examination of the historical range of the greater prairie chicken using provenance data and DNA analysis of museum collections

The extent to which a species has declined within its historical range is commonly used as an important criterion in categorizing the conservation status of wild populations. The greater prairie chicken (Tympanuchus cupido) has been extirpated from much of the area it once inhabited. However, within a large part of this area the species is not considered to be native, warranting no recovery effort or special protection. Demographic analysis based on provenance data from 238 specimens from museum collections in addition to genetic analyses of 100 mtDNA sequences suggest this species was native to the northern prairies, extending from central Minnesota to Alberta, Canada. Provenance data from 1879 to 1935 indicate that T. cupido would have required colonization and establishment of populations on an average 11,905 km² every year, with an estimated per capita growth rate of 8.9% per year. These rates seem unrealistic given the limited dispersal and high mortality rates reported for this species. A survey of mtDNA sequences from “original” and “expanded” ranges revealed no differences in levels of sequence diversity within ranges (π=0.018; SE=0.004) but significant levels of genetic differentiation (F _ST=0.034; P=0.013), which suggest that these populations have been relatively isolated for significant evolutionary time periods. DNA mismatch distributions fit a sudden expansion model consistent with a post-Pleistocene expansion of the species, which coincides with the expansion of prairies into the Canadian plains about 9000 years before present. This study demonstrates the value of museum collections as stores of ecological and genetic information fundamental for the conservation of natural populations, and suggests that the current status of the greater prairie chicken should be re-evaluated within all areas where this species may occur, but is now considered non-native.     

Old and new DNA unweave the phylogenetic position of the eastern Atlantic gall crab Detocarcinus balssi (Monod, 1956) (Decapoda: Cryptochiridae)

Phylogeny reconstructions based on mtDNA and nDNA have become the standard in studies on relationships between taxa. Difficulties in obtaining material, for example because of small endemic distributions, often lead to gaps in datasets. Collections in natural history museums can provide us with material to fill these gaps, but extracting DNA from historical specimens can be challenging. We used a PCR protocol for small amounts of sample material and high PCR yield on eggs of specimens of the coral‐dwelling gall crab family Cryptochiridae collected in 1984, including material from the eastern Atlantic species Detocarcinus balssi. We obtained DNA sequences from seven older museum specimens using newly developed primers, which we combined with COI sequences from recently collected material. Results show that D. balssi is closest to the Indo‐Pacific species Utinomiella dimorpha and not closely related to one of the other three Atlantic Cryptochiridae species. The remaining newly acquired DNA sequences from museum material cluster with the respective sequences from recently collected specimens.     

Can museum egg specimens be used for proteomic analyses?

Background  

Mass spectrometry and proteomic analyses have become powerful tools for the analysis of proteins and peptides. Investigation of proteins contained in the various layers of the avian eggshell has focused entirely on domesticated species. It has been widely assumed that this existing research can inform the study of wild bird species despite the fact that the vast majority of the diversity in avian species (~95%) exists outside the Orders to which domestic and poultry species belong. Museum collections offer a potentially valuable source of material for studying composition of wild avian eggshell matrix proteins. We used museum and fresh eggshells of common quails Coturnix coturnix to compare the protein composition of their organic matrices. Four eggs of domestic chickens were analysed simultaneously as a control for comparison to the fresh and museum quail eggs. The determination of the proteins was carried out using enzymatic cleavage followed by high-performance mass spectrometry.     

Dinosaurs of Portugal

A synthesis on the state of art on dinosaur knowledge in Portugal is presented. The following genera have been recognized: Ceratosaurus, Torvosaurus, Lourinhanosaurus, Allosaurus, cf. Compsognathus, Stokesosaurus, cf. Richardoestesia, cf. Archaeopteryx, Euronychodon, cf. Paronychodon, Dinheirosaurus, Lourinhasaurus, Lusotitan, cf. Pleurocoelus, Lusitanosaurus, Dacentrurus, Dracopelta, Phyllodon, Hypsilophodon, Alocodon, Trimucrodon, Draconyx, Iguanodon, and Taveirosaurus. Most are from Late Jurassic localities at the Lourinhã area and Guimarota. A new genus, Lusotitan, is here raised to include the Late Jurassic ‘Brachiosaurus’ atalaiensis. Lower Cretaceous until Cenomanian material is scarce, except for dinosaur footprints. An interesting Late-Cretaceous, mostly small dinosaur association has been collected between Aveiro and Taveiro. To cite this article: M.T. Antunes, O. Mateus, C. R. Palevol 2 (2003) 77–95.     

Diversity biases in terrestrial mammalian assemblages and quantifying the differences between museum collections and published accounts: A case study from the Miocene of Nevada

Understanding diversity through time in the fossil record has primarily relied on the raw count of species within a given time interval, or species richness. These estimates are often derived from published fossil data, and standardized for sample size or geographic area. However, most methods that standardize richness by sample size are sensitive to changes in evenness, which introduces a potential problem with relying on published records: published accounts could be more even than the museum collections from which they are drawn. We address this bias in the context of mammalian paleodiversity, comparing published and museum collections of the Hemphillian Thousand Creek fauna to those of the Barstovian Virgin Valley fauna. We rarified specimen data, both number of identified specimens (NISP) and minimum number of individuals (MNI), and presence/absence data to compare published and museum data within and between faunas. Within faunas, published numbers of specimens are more even than museum samples, but the difference for localities in Virgin Valley is not significant. Neither published nor museum numbers of specimens indicate a significant difference between faunas, but the diversity pattern is reversed between the two data sets. Presence/absence rarefactions show no differences between sources; here, published data adequately sample the underlying museum records. Specimen-based evenness is not accurate in the published sample, and therefore we suggest that future studies of diversity in terrestrial mammalian assemblages must assess unpublished collections. Additionally, NISP data for Thousand Creek are more even than MNI data, suggesting that relying solely on NISP for assessing species diversity can also be misleading. Because publication bias alters richness and evenness, diversity estimates using published data must be circumspect about data sources.