Vertebrate Specimens Research Articles

Century-old chromatin architecture revealed in formalin-fixed vertebrates

Gene expression is regulated by changes in chromatin architecture intrinsic to cellular differentiation and as an active response to environmental stimuli. Chromatin dynamics are a major driver of phenotypic diversity, regulation of development, and manifestation of disease. Remarkably, we know little about the evolutionary dynamics of chromatin reorganisation through time, data essential to characterise the impact of environmental stress during the ongoing biodiversity extinction crisis (20th–21st century). Linking the disparate fields of chromatin biology and museum science through their common use of the preservative formaldehyde (a constituent of formalin), we have generated historical chromatin profiles in museum specimens up to 117 years old. Historical chromatin profiles are reproducible, tissue-specific, sex-specific, and environmental condition-dependent in vertebrate specimens. Additionally, we show that over-fixation modulates differential chromatin accessibility to enable semi-quantitative estimates of relative gene expression in vertebrates and a yeast model. Our approach transforms formalin-fixed biological collections into an accurate, comprehensive, and global record of environmental impact on gene expression and phenotype.

New age constraints for human entry into the Americas on the north Pacific coast

The timing of the initial peopling of the Americas is unresolved. Because the archaeological record necessitates discussion of human entry from Beringia into southern North America during the last glaciation, addressing this problem routinely involves evaluating environmental parameters then targeting areas suitable for human settlement. Vertebrate remains indicate landscape quality and are a key dataset for assessing coastal migration theories and the viability of coastal routes. Here, radiocarbon dates on vertebrate specimens and archaeological sites are calibrated to document species occurrences and the ages of human settlements across the western expansion and decay of the Cordilleran Ice Sheet (CIS) during the Late Wisconsin Fraser Glaciation in four subregions of the north Pacific coast of North America. The results show archaeological sites occur after glacial maxima and are generally consistent with the age of other securely dated earliest sites in southern North America. They also highlight gaps in the vertebrate chronologies around CIS maxima in each of the subregions that point to species redistributions and extirpations and signal times of low potential for human settlement and subsistence in a key portion of the proposed coastal migration route. This study, therefore, defines new age constraints for human coastal migration theories in the peopling of the Americas debate.

The new layout of the Museum of Zoology of the University of Catania (Italy) one year after its opening

On 9 July 2021 the Museum of Zoology of the University of Catania (Italy), the oldest Sicilian zoological museum whose foundation dates back to 1853 by Prof. Andrea Aradas, reopened to the public with a new layout, which involved the elimination of all the showcases in which the specimens were displayed. The new project instead envisaged that all the vertebrate specimens present in the main room, around 170, are arranged on open platforms and grouped according to systematic or biogeographical criteria. An emotional museum was thus created in which the elimination of the showcases and the possibility to walk among the exhibits without barriers or limitations increase the emotional and emphatic involvement of the visitor, helping the transmission of information on biodiversity and the relationship between man and nature.

From roads to biobanks: Roadkill animals as a valuable source of genetic data

To protect biodiversity we must understand its structure and composition including the bacteria and microparasites associated with wildlife, which may pose risks to human health. However, acquiring this knowledge often presents challenges, particularly in areas of high biodiversity where there are many undescribed and poorly studied species and funding resources can be limited. A solution to fill this knowledge gap is sampling roadkill (animals that die on roads as a result of collisions with circulating vehicles). These specimens can help characterize local wildlife and their associated parasites with fewer ethical and logistical challenges compared to traditional specimen collection. Here we test this approach by analyzing 817 tissue samples obtained from 590 roadkill vertebrate specimens (Amphibia, Reptilia, Aves and Mammalia) collected in roads within the Tropical Andes of Ecuador. First, we tested if the quantity and quality of recovered DNA varied across roadkill specimens collected at different times since death, exploring if decomposition affected the potential to identify vertebrate species and associated microorganisms. Second, we compared DNA stability across taxa and tissues to identify potential limitations and offer recommendations for future work. Finally, we illustrate how these samples can aid in taxonomic identification and parasite detection. Our study shows that sampling roadkill can help study biodiversity. DNA was recovered and amplified (allowing species identification and parasite detection) from roadkill even 120 hours after death, although risk of degradation increased overtime. DNA was extracted from all vertebrate classes but in smaller quantities and with lower quality from amphibians. We recommend sampling liver if possible as it produced the highest amounts of DNA (muscle produced the lowest). Additional testing of this approach in areas with different environmental and traffic conditions is needed, but our results show that sampling roadkill specimens can help detect and potentially monitor biodiversity and could be a valuable approach to create biobanks and preserve genetic data.

A record of Late Jurassic vertebrates from Texas

ABSTRACT We present the first description of Jurassic vertebrate fossils from Texas. The vertebrate specimens were collected from the Upper Jurassic Malone Formation in the Malone Mountains of western Texas. The specimens are fragmentary and not particularly diagnostic, but probably represent elements of plesiosaurians. One specimen is similar to the caudal vertebra of a pliosaurid plesiosaurian, whereas another may be a partial propodial of a small plesiosaurian. Additional bone fragments are not identifiable at this time. These vertebrates were discovered along with abundant plant and invertebrate fossils. Previous studies of the invertebrate fossils indicate a Kimmeridgian to Tithonian age for the Malone Formation, which is consistent with a single grain age of 151±2 Ma from detrital zircon U–Pb geochronology obtained in this study. The Malone Formation was deposited in shallow marine to marginal marine environments along the northern edge of the Chihuahua trough. It is correlative with the La Casita and La Caja Formations of northern Mexico, where similar marine vertebrates have been reported. The Malone Formation is also correlative with the Morrison Formation to the north.

A potentially fatal cranial pathology in a specimen of Tarchia.

Skulls of the Mongolian ankylosaurids Shamosaurus, Tarchia, and Saichania were scanned for information about their internal anatomy. Computed tomography (CT) imaging of the Tarchia skull revealed substantial internal anatomical differences from known Campanian North American taxa, particularly in the morphology of the airway. In addition, unexpected anomalies were detected within the airway and sinuses. The anomalies include multiple bilaterally distributed, variably sized hyperdense (mineralized) concretions within the airway and sinuses, the largest of which, positioned in the right nasal cavity medial to the supraorbitals, has an asymmetric ovoid shape that tapers caudally and which is partially encased within a hemispherical trabeculated osseous proliferation (sinus exostosis). Immediately adjacent to the exostosis is a subcircular transosseous defect in the prefrontal region of the skull roof that is partially filled with trabeculated ossified material with similar architectural features as the larger exostosis. Irregularities along the internal and external surfaces of the cranial vault may be associated. The radiologic features of the hemicircumferential exostosis suggest a chronic reactive osteoproliferation, possibly in response to an ongoing inflammatory reaction to primary sinus infection or, in combination with the unilateral transosseous defect, traumatically introduced infection with potentially fatal consequences. This report underscores the value of CT scanning of fossil vertebrate specimens, which in this case revealed large internal lesions of the skull that, at the time the scan was performed, were otherwise indiscernible.

Scientific collections of the Zoological Institute of the Russian Academy of Sciences, Saint Petersburg

The Zoological Institute of the Russian Academy of Sciences in St Petersburg is one of the oldest biological research institutions in Russia, housing the largest zoological collections in the country, both in terms of their size (number of specimens) and global diversity. It is also one of the largest zoological depositories in the world, with over 60 million specimens in its stores. In total, the Zoological Institute holds about 260,000 animal species, about a quarter of the world’s known diversity. The type collection includes several tens of hundreds of primary types, which are very important as the essential foundation for zoological nomenclature. The digitisation of scientific collections now plays an important role in ensuring the standardised accumulation and use of various data sets, as well as quick access to stored information. The digitised scientific collections of the Zoological Institute are published online for the public access. To date they have accumulated 146,695 taxa records and over 13,000 high quality images of invertebrate and vertebrate specimens and their original data labels. The Zoological Institute is not only a depository of animal specimens important for biodiversity inventories and studies, but also a unique bank of genetic resources of extant/extinct animals which can be studied using modern genetic technologies.

Quaternary ungulates of the Abismo Ponta de Flecha Cave, Ribeira of Iguape Valley, Southeast Brazil: Zooarchaeological and Paleoenvironmental aspects

The Ribeira de Iguape Valley, located in the south of the state of São Paulo, presents a complex system of caves developed from Precambrian carbonate rocks. The presence of such karstic system favored the preservation of numerous fossilized remains of Quaternary mammals. The Abismo Ponta de Flecha Cave, located in the municipality of Iporanga, is a vertical cave divided into several lateral galleries with abundant vertebrate specimens. Among the most common are the ungulates, a clade of mammals characterized mainly by the presence of hooves, represented by the Holoarctic ungulates families Cervidae, Tayassuidae, Tapiridae, and the South American native ungulate Toxodontidae. The most common family in the deposit is Tayassuidae, with several individuals assigned to the species Tayassu pecari, Dicotyles tajacu, as well as an indeterminate large Tayassuidae. The Cervidae remains found in the cave have two species assigned to the genus Mazama; M. americana and M. gouazoubira. A specimen of the Tapiridae family, Tapirus sp., was also found. Only one species attributed to the extinct family Toxodontidae, Toxodon platensis, was recorded. Many specimens of Tayassuidae and Cervidae were subadults, and one individual of Tayassu pecari was very young. The origin of the specimens might be the result of the transport of individual bone parts, the death of accidently trapped animals as well as the disposal of such remains by human groups that inhabited the region in the past.

Using Macro- and Microscale Preservation in Vertebrate Fossils as Predictors for Molecular Preservation in Fluvial Environments.

Simple SummaryFossils are the only direct evidence of life throughout Earth’s history. We examine the biology of ancient animals to learn about evolution and past ecosystems. Biomolecules are a relatively new source of information from fossil records because new technology is now being used in paleontology that makes it possible to detect molecular remains in fossils. However, molecules extracted from fossils are complex mixtures with environmental and other sources of organic compounds. Additionally, macroscale preservation is well-known to vary greatly across fossil localities. Therefore, a goal in molecular paleontology is to develop ways to predict where molecules may be preserved and differentiate between endogenous and exogenous sources. Here, we use a powerful combination of methods that focus on high-resolution mass spectrometry to evaluate the molecular-scale preservation of a dinosaur quarry from the Triassic Period. We found that despite very good overall preservation at this locality, there is no evidence of endogenous molecules, demonstrating that molecular preservation is variable and that good macro- and microscale preservation cannot necessarily be used as predictors for biomolecule preservation in the fossil record.Exceptionally preserved fossils retain soft tissues and often the biomolecules that were present in an animal during its life. The majority of terrestrial vertebrate fossils are not traditionally considered exceptionally preserved, with fossils falling on a spectrum ranging from very well-preserved to poorly preserved when considering completeness, morphology and the presence of microstructures. Within this variability of anatomical preservation, high-quality macro-scale preservation (e.g., articulated skeletons) may not be reflected in molecular-scale preservation (i.e., biomolecules). Excavation of the Hayden Quarry (HQ; Chinle Formation, Ghost Ranch, NM, USA) has resulted in the recovery of thousands of fossilized vertebrate specimens. This has contributed greatly to our knowledge of early dinosaur evolution and paleoenvironmental conditions during the Late Triassic Period (~212 Ma). The number of specimens, completeness of skeletons and fidelity of osteohistological microstructures preserved in the bone all demonstrate the remarkable quality of the fossils preserved at this locality. Because the Hayden Quarry is an excellent example of good preservation in a fluvial environment, we have tested different fossil types (i.e., bone, tooth, coprolite) to examine the molecular preservation and overall taphonomy of the HQ to determine how different scales of preservation vary within a single locality. We used multiple high-resolution mass spectrometry techniques (TOF-SIMS, GC-MS, FT-ICR MS) to compare the fossils to unaltered bone from extant vertebrates, experimentally matured bone, and younger dinosaurian skeletal material from other fluvial environments. FT-ICR MS provides detailed molecular information about complex mixtures, and TOF-SIMS has high elemental spatial sensitivity. Using these techniques, we did not find convincing evidence of a molecular signal that can be confidently interpreted as endogenous, indicating that very good macro- and microscale preservation are not necessarily good predictors of molecular preservation.

Acid-Free Staining Procedure to Demonstrate Nerves in Whole Vertebrate Specimens with the Differentiation of Bone and Cartilage

The value of clearing and staining whole organisms to study vertebrate anatomy is unquestionable. These methods have been developed for over a century leading to protocols to prepare triple-stained specimens to differentiate between bones, cartilage, and nerves. Despite their potential to advance the field of comparative anatomy, nerve-staining methods have been used by a small number of vertebrate systematists in part because of the inconsistently successful preparations. Here, we report on several modifications to the current Sudan black B protocols and propose a new acid-free protocol to differentiate among bone, cartilage, and nerves in whole small vertebrates. This method may also be used to stain solely bone and cartilage by eliminating the nerve-staining steps. The technique herein described is successful for preparing juveniles and adults (including miniatures).

A new exposure of the North Curry Sandstone Member (Dunscombe Mudstone Formation, Mercia Mudstone Group: Carnian, Triassic), near Taunton, Somerset (UK): The location of Charles Moore's vertebrate specimens resolved

There is renewed interest in a series of Carnian-aged sandstone units across the UK because they represent a unique event in the Late Triassic, the Carnian Pluvial Episode (CPE), from 233 to 232 Ma. The North Curry Sandstone Member of the Mercia Mudstone Group in Somerset is of particular importance because it yielded a rich fauna of shark, bony fish and amphibian remains in coarse-grained sandstones to Charles Moore in the 1860s. However, the exact location and age of his important collection had not been identified. Here, we demonstrate that the Moore collection comes from the North Curry Sandstone Member in a location in the village of Ruishton, just east of Taunton, where a new road cutting reveals both the bone-rich units and a complete succession through the CPE, a time of major climatic and biotic upheaval. The 16 m section comprises several sandstones interbedded with red-green mudstones, representing a terrestrial environment with lacustrine, evaporitic mud flat and fluvial deposits.

The bovids (Artiodactyla) from the Lower Pleistocene locality of Karnezeika (Southern Greece)

ABSTRACT More than 3000 fossil vertebrate specimens have been unearthed from the new Lower Pleistocene locality of Karnezeika, Peloponnese, Greece. The vast majority of the material (~90%) represents bovids, and their systematic study is provided herein. The bovid assemblage consists of four taxa. A significant portion of the collected bovid material belongs to a small sized gazelle, attributed to Gazella bouvrainae, and to the large Rupicaprini Gallogoral meneghinii. A relatively small sized form of Gazellospira torticornis has been recorded as well, and in addition the scarce dental material belonging to an unspecified Caprini form is mentioned as Caprini gen. et sp. indet. This combination of taxa is typical for the Middle Villafranchian of Greece (2.6–1.8 Ma).

Declining growth of natural history collections fails future generations.

New additions of vertebrate specimens to natural history collections are declining in the midst of widespread and accelerating environmental change. Reversing these trends in collecting efforts is essential for addressing future unforeseen ecological issues.

Evaluating the Existence of Vertebrate Deadfall Communities from the Early Jurassic Posidonienschiefer Formation

Large vertebrate carcasses contain significant amounts of nutrients that upon death are transferred from the water column to the benthos, enriching the immediate environment. The organisms exploiting these ephemeral resources vary as the carcass decays, creating an ecological succession: mobile scavengers arrive first, followed by enrichment opportunists, sulfophilic taxa, and lastly reef species encrusting the exposed bones. Such communities have been postulated to subsist on the carcasses of Mesozoic marine vertebrates, but are rarely documented in the Jurassic. In particular, these communities are virtually unknown from the Early Jurassic, despite the occurrence of several productive fossil Lagerstätte that have produced thousands of vertebrate bones and skeletons. We review published occurrences and present new findings related to the development of deadfall communities in the Toarcian Posidonienschiefer Formation of southwestern Germany, focusing on the classic locality of Holzmaden. We report the presence of the mobile scavenger, enrichment opportunist, and reef stages, and found potential evidence for the poorly documented sulfophilic stage. Although rare in the Posidonienschiefer Formation, such communities do occur in association with exceptionally preserved vertebrate specimens, complementing a growing body of evidence that a temporarily oxygenated benthic environment does not preclude exceptional vertebrate fossil preservation.

Evaluating the taphonomic consistency of microvertebrate assemblages at Natural Trap Cave, Wyoming, USA

Paleontological sites composed of small vertebrate specimens can contain hundreds-of-thousands of identifiable fossils, which can reveal community responses to environmental and trophic changes. However, the composition of these communities may be skewed if the taphonomic signatures of the deposits change over time and across strata. Here, we discuss the taphonomic processes that led to dense deposits of microvertebrate fossils at Natural Trap Cave, Wyoming, USA. We then evaluate the nature and consistency of the taphonomic signature across stratigraphic layers using bone breakage rates and bone processing information. Natural Trap Cave is a pitfall cave that has an excellent record of vertebrate communities over the last 35,000 years. Along the North Wall of the excavation site, microvertebrate fossils form a dense accumulation, raining down from a packrat (Neotoma) nest located ∼20 m above the floor of the cave. Using the breakage rates of micromammal limb bones, we evaluate whether the accumulation mechanism appears consistent across strata. We demonstrate that the variation in breakage rates from Natural Trap Cave's strata cluster together when compared to breakage rates for different predator types (mammalian carnivores, raptors, and owls). We then demonstrate that the variation in breakage rates from the three strata is less than would be expected if it were the result of a change in major predator type across the strata. Our analysis of depositional taphonomy at Natural Trap Cave provides confidence in the reliability of the microvertebrate community record, paving the way for future paleoecological analyses.

A strategy for a high enrichment of insect mitochondrial DNA for mitogenomic analysis.

Next-generation sequencing has dramatically fostered insect mitogenomic research in recent years. However, studies on the insect mitochondrial genome (mitogenome) assembly mainly rely on the sequencing data from total DNA, which is not cost-effective as a huge data from nuclear DNA are wasted. Besides, many mitogenomic studies require genomic information from individual organisms, whereas the DNA yield from small individual insects is too low to meet the sequencing requirements. Here, we describe a strategy for a high enrichment of insect mitochondrial DNA (mtDNA) using rolling circle amplification (RCA) technique. This strategy consists of standard DNA extraction, RCA enrichment, next-generation sequencing and mitogenome assembly. We have evaluated the performance of this strategy on nine insect species representing eight families of insecta, three other invertebrates, and even two vertebrate specimens. Results show that our strategy is especially suitable for insects, which allows almost all tested insect mtDNA contents to reach 80% and above. A further examination of enrichment efficiency of our strategy among different taxa shows that it is also applicable to other invertebrates and even some vertebrates such as Rhacophorus and ptyas species, although its enrichment efficiency in these groups is lower than that of insects. After treatment with our strategy, small flux sequencing data can realize the assembly of mitogenome with deep coverage, providing a solid base for subsequent mitogenome-based studies.

Anatomical self-efficacy of undergraduate students improves during a fully online biology course with at-home dissections.

Student enrollments in online college courses have grown steadily over the past decade, and college administrators expect this trend to continue or accelerate. Despite the growing popularity of online education, one major critique in the sciences is that students are not trained in the hands-on skills they may need for the workforce, graduate school, or professional school. For example, the Association of American Medical Colleges has recommended that medical schools evaluate applicants on their motor skills and observation skills, yet many online biology programs do not offer opportunities for students to develop these skills. In on-campus biology programs, students commonly develop these skills through hands-on animal dissections, but educators have struggled with how to teach dissections in an online environment. We designed a fully online undergraduate biology course that includes at-home, hands-on dissections of eight vertebrate specimens. Over three course offerings, we evaluated changes in four student outcomes: anatomical self-efficacy, confidence in laboratory skills, perceptions of support, and concerns about dissections. Here, we describe how we implemented at-home dissections in the online course and show that students taking the course gained anatomical self-efficacy and confidence in multiple laboratory skills. Based on open-ended responses, the students perceived that their experiences with the at-home dissections facilitated these gains. These results demonstrate that at-home, hands-on laboratories are a viable approach for teaching practical skills to students in fully online courses. We encourage science instructors to introduce at-home laboratories into their online courses, and we provide recommendations for instructors interested in implementing at-home laboratories.

Creating a National Biodiversity Database in Gabon and the Challenges of Mobilizing Natural History Data for Francophone Countries

Language is a major barrier for researchers wanting to digitize and publish collection data in Africa. Despite being the fifth most spoken language on Earth and the second most common in Africa, resources in French about digitization, data management, and publishing are lacking. Furthermore, French-speaking regions of Africa (primarily Central/West Africa and Madagascar) host some of the highest biodiversity on the continent and therefore are of great importance to scientists and decision-makers. Without having representation in online portals like the Global Biodiversity Information Facility (GBIF) and Integrated Digitized Biocollections (iDigBio), these important collections are effectively invisible. Producing relevant/applicable resources about digitization in French will help shine a light on these valuable natural history records and allow the data-holders in Africa to retain the autonomy of their collections. Awarded a GBIF-BID (Biodiversity Information for Development) grant in 2021, an international, multilingual network of partners has undertaken the important task of digitizing and mobilizing Gabon’s vertebrate collections. There are an estimated 13,500 vertebrate specimens housed in five institutions in different parts of Gabon. To date, the group has mobilized >4,600 vertebrate records to our recently launched Gabon Biodiversity Portal (https://gabonbiota.org/). The portal also hosts French guides for using Symbiota-based portals to manage, georeference, and publish natural history databases. These resources can provide much-needed guidance for other Francophone countries⁠—in Africa and beyond⁠—working to maximize the accessibility and value of their biodiversity collections.

A new Silurian fish close to the common ancestor of modern gnathostomes

The Silurian Period occupies a pivotal stage in the unfolding of key evolutionary events, including the rise of jawed vertebrates.1-4 However, the understanding of this early diversification is often hampered by the patchy nature of the Silurian fossil record,5 with the articulated specimens of jawed vertebrates only known in isolated localities, most notably Qujing, Yunnan, China.6-9 Here, we report a new Silurian maxillate placoderm, Bianchengichthys micros, from the Ludlow of Chongqing, with a near-complete dermatoskeleton preserved in articulation. Although geographically separated, the new taxon resembles the previously reported Qilinyu in possessing a unique combination of dermatoskeletal characters. However, the dermal bone of the mandible in Bianchengichthys unexpectedly differs from those in both Qilinyu and Entelognathus and displays a broad oral lamina carrying a line of tooth-like denticles, in addition to the marginal toothless flange. The external morphology of the pectoral fin is preserved and reveals an extensively scale-covered lobate part, flanked by a fringe of lepidotrichia-like aligned scales. The phylogenetic analysis reveals that Bianchengichthys is positioned immediately below Entelognathus plus modern gnathostomes. The discovery significantly widens the distribution of Silurian placoderm-grade gnathostomes in South China and provides a range of morphological disparity for the outgroup comparison to the earliest evolution of jaws, dentitions, and pectoral fins in modern gnathostomes. We also demonstrate that the previously reported Silurian placoderms from central Vietnam10 are maxillate placoderms close to Qilinyu, Silurolepis, and Bianchengichthys, corroborating the paleogeographic proximity between the Indochina and South China blocks during the Middle Paleozoic.11.

14C DATES AND STABLE ISOTOPE ECOLOGY OF MARINE VERTEBRATES IN THE LATE PLEISTOCENE-EARLY HOLOCENE CHAMPLAIN SEA

ABSTRACTThe late Pleistocene to early Holocene Champlain Sea provides a unique opportunity to study the development of marine ecosystems in a context of global climatic change. This study presents radiocarbon (14C) dates and stable isotope analyses on 15 vertebrate specimens from Champlain Sea sediments, including the Charlotte Whale, which is Vermont’s State marine fossil. Data are used in an attempt to investigate the timing of colonization and ecological dynamics in this newly formed sea. Using the average marine correction,14C dates on four specimens likely calibrate prior to or possibly synchronous with the accepted origination date for the Champlain Sea, implying larger marine reservoir effects than the average marine correction in the vertebrate tissues. Without knowing the specific marine reservoir offsets, it is not possible to calculate the timing of colonization or its relation to concurrent climatic change. Observed lower δ13C and δ15N values in walruses, a fin whale, and a right whale support consumption of prey from lower trophic levels such as bivalve mollusks, krill, and copepods. Higher isotopic values in beluga whales and a bird, the thick-billed murre, support consuming fish, such as cod and capelin. These isotopic data show comparable values and relationships as observed in modern arctic marine ecosystems.