Museum Specimens Research Articles

Lions & sea lions & bears, oh my: utilizing museum specimens to study the ossification sequence of carnivoran taxa

BackgroundMammalian skeletons are largely formed before birth. Heterochronic changes in skeletal formation can be investigated by comparing the order of ossification for different elements of the skeleton. Due to the challenge of collecting prenatal specimens in viviparous taxa, opportunistically collected museum specimens provide the best material for studying prenatal skeletal development across many mammalian species. Previous studies have investigated ossification sequence in a range of mammalian species, but little is known about the pattern of bone formation in Carnivora. Carnivorans have diverse ecologies, diets, and biomechanical specializations and are well-suited for investigating questions in evolutionary biology. Currently, developmental data on carnivorans is largely limited to domesticated species. To expand available data on carnivoran skeletal development, we used micro-computed tomography (micro-CT) to non-invasively evaluate the degree of ossification in all prenatal carnivoran specimens housed in the Harvard Museum of Comparative Zoology. By coding the presence or absence of bones in each specimen, we constructed ossification sequences for each species. Parsimov-based genetic inference (PGi) was then used to identify heterochronic shifts between carnivoran lineages and reconstruct the ancestral ossification sequence of Carnivora.ResultsWe used micro-CT to study prenatal ossification sequence in six carnivora species: Eumetopias jubatus (Steller sea lion, n = 6), Herpestes javanicus (small Indian mongoose, n = 1), Panthera leo (lion, n = 1), Urocyon cinereoargenteus (gray fox, n = 1), Ursus arctos arctos (Eurasian brown bear, n = 1), and Viverricula indica (small Indian civet, n = 5). Due to the relatively later stage of collection for the available specimens, few heterochronic shifts were identified. Ossification sequences of feliform species showed complete agreement with the domestic cat. In caniforms, the bear and fox ossification sequences largely matched the dog, but numerous heterochronic shifts were identified in the sea lion.ConclusionsWe use museum specimens to generate cranial and postcranial micro-CT data on six species split between the two major carnivoran clades: Caniformia and Feliformia. Our data suggest that the ossification sequence of domestic dogs and cats are likely good models for terrestrial caniforms and feliforms, respectively, but not pinnipeds.

Defining conservation areas through diversity parameters and museum specimens: a case study for craneflies

Defining conservation areas through diversity parameters and museum specimens: a case study for craneflies

Scouts vs. usurpers: alternative foraging strategies facilitate coexistence between neotropical Cathartid vultures

Understanding how diverse assemblages of scavengers can coexist on shared ecological resources is a fundamental challenge in community ecology. However, current approaches typically focus on behaviour at carcass provisioning sites, missing how important differences in movement behaviour and foraging strategies can facilitate sympatric species coexistence. Such information is particularly important for vultures – obligate scavengers representing the most endangered avian foraging guild. Their loss from ecosystems can trigger trophic cascades, mesopredator release and disease outbreaks. We provide the first‐ever analyses of GPS location data from wild King Vultures Sarcoramphus papa and Greater Yellow‐headed Vultures Cathartes melambrotus, coupled with trait data (from both wild‐living and museum specimens) and visitation data from camera traps deployed at provisioned carcasses, to characterize vulture flight behaviour and strategies in the Peruvian Amazon. We found marked species differences in several key movement characteristics, including: King Vultures having home‐ranges five times larger, average flight heights four times greater and ground speeds 40% faster than those of Greater Yellow‐headed Vultures. Despite these differences, both species flew similar distances each day (on average), probably due to King Vultures taking 50% fewer flights and spending 40% less time in the air per day. Consistent with these patterns, King Vulture body mass was more than double that of the Greater Yellow‐headed Vulture, with a substantially larger hang wing index (a measure of long‐distance flight efficiency). At carcasses, Greater Yellow‐headed Vultures typically arrived first but were rapidly outnumbered by both King and Black Vultures Coragyps atratus. We find that the movement behaviour of obligate apex scavengers in the western Amazon is linked to their ability to coexist – Greater Yellow‐headed Vultures, a smaller stature ‘scouting’ species adapted to fly low, forage early and arrive first at carcasses, are ultimately displaced by larger‐bodied, wider ranging King Vultures at large ephemeral carrion resources. Expansion of future GPS tracking initiatives could facilitate the exploration of direct facultative interactions from animal movement data and give further insight into how diverse communities assemble and interact.

Two New Species of Emesis Fabricius, 1807 from Northwestern South and Central America (Lepidoptera: Riodinidae)

Two new species and a subspecies, Emesis (Aphacites) hypoaithos, Callaghan, Trujano-Ortega & Ríos-Málaver, sp. nov., Emesis (Aphacites) hypoaithos ochros, Callaghan, Trujano-Ortega & Ríos-Málaver, ssp. nov., Emesis (Tenedia) pacis, Callaghan, Trujano-Ortega & Ríos-Málaver, sp. nov. are described from Northwestern South and Central America. The biology, habits, habitat, and distribution of these taxa are described from museum specimens and field observations. Male and female genitalia of the new taxa are illustrated and compared with similar taxa for proper identification.

The Complete Genome Sequences of 12 Species of Enteromius (Cyprinidae, Cypriniformes, Actinopteri).

We present the complete genome sequences of 12 species of Enteromius. Illumina sequencing was performed on genetic material from museum specimens. The reads were assembled using a de novo method followed by a finishing step. The raw and assembled data are publicly available via Genbank.

Phenotypic plasticity in tropical butterflies is linked to climatic seasonality on a macroevolutionary scale.

Phenotypic plasticity can be adaptive in fluctuating environments by providing rapid environment-phenotype matching and this applies particularly in seasonal environments. African Bicyclus butterflies have repeatedly colonized seasonal savannahs from ancestral forests around the Late Miocene and many species now exhibit seasonal polyphenism. On a macroevolutionary scale, it can be expected that savannah species will exhibit higher plasticity due to them experiencing stronger environmental seasonality than forest species. We quantified seasonality using environmental niche modelling, and surveyed the degree of plasticity in a key wing pattern element (eyespot size) using museum specimens. We show that species occurring in highly seasonal environments display strong plasticity, while species in less seasonal or aseasonal environments exhibit surprisingly variable degrees of plasticity, including strong to no plasticity. Furthermore, eyespot size plasticity has a moderate phylogenetic signal and the ancestral Bicyclus likely exhibited some degree of plasticity. We propose hypotheses to explain the range of plasticity patterns seen in less seasonal environments, and generate testable predictions for the evolution of plasticity in Bicyclus. Our study provides one of the most compelling cases showing links between seasonality and phenotypic plasticity on a macroevolutionary scale and the potential role of plasticity in facilitating the colonization of novel environments.

Museum Genomics approach to study the taxonomy and evolution of Woolly-necked storks using historic specimens

Abstract The accessibility of genomic tools in evolutionary biology has allowed for a thorough exploration of various evolutionary processes associated with adaptation and speciation. However, genomic studies in natural systems present numerous challenges, reflecting the inherent complexities of studying organisms in their native habitats. The utilization of museum specimens for genomics research has received increased attention in recent times, facilitated by advancements in ancient DNA techniques. In this study, we have utilized a museum genomics approach to analyze historic specimens of Woolly-necked storks (Ciconia sps.) and examine their genetic composition, taxonomic status, and explore the evolutionary and adaptive trajectories of populations over the years. The Woolly-necked storks are distributed in Asia and Africa with a taxonomic classification that has been a matter of ambiguity. Asian and African Woollynecks were recently recognized as different species based on their morphological differences, however, their genomic validation was lacking. In this study, we have used ∼70-year-old museum samples for whole-genome population-scale sequencing. Our study has revealed that Asian and African Woollyneck are genetically distinct, consistent with the current taxonomic classification based on morphological features. However, we also found a high genetic divergence between the Asian sub-species C. e. neglecta and C. e. episcopus suggesting this classification requires a detailed examination to explore processes of ongoing speciation. Because taxonomic classification directly impacts conservation efforts, and there is evidence of declining populations of Asian Woollynecks in Southeast Asia, our results highlight that population-scale studies are urgent to determine the genetic, ecological, and phylogenetic diversity of these birds.

Molecular phylogeny and biogeography of the aquatic dance fly subfamily Clinocerinae (Diptera: Empididae)

AbstractThis study presents the first molecular phylogenetic analysis of the Clinocerinae, challenging the traditionally accepted monophyly of this subfamily. DNA was extracted from fresh and museum specimens representing all biogeographical regions. Maximum likelihood (ML) and Bayesian inference (BI) phylogenetic analyses were performed based on sequences from two mitochondrial genes, cytochrome c oxidase subunit I (COI) and cytochrome β, and three nuclear genes, carbomoylphosphate synthase domain of rudimentary, elongation factor‐1α and isocitrate dehydrogenase. Through molecular data and morphological examination, our results reveal a division within Clinocerinae, distinguishing ‘typical’ or Clinocerinae (s.s.) from several genera, specifically Afroclinocera Sinclair, Asymphyloptera Collin and Proagomyia Collin, possibly lending support for a reclassification of these genera outside Clinocerinae. Bergenstammia Mik is proposed as a junior synonym of Phaeobalia Mik, syn. n., and the following new combinations are recognized: Phaeobalia albanica (Wagner) comb. n., Phaeobalia aurinae (Pusch & Wagner) comb. n., Phaeobalia carniolica (Horvat) comb. n., Phaeobalia frigida (Vaillant) comb. n., Phaeobalia glacialis (Palaczyk & Słowińska) comb. n., Phaeobalia multiseta (Strobl) comb. n., Phaeobalia nudimana (Vaillant) comb. n., Phaeobalia nudipes (Loew) comb. n., Phaeobalia pulla (Vaillant & Wagner) comb. n., Phaeobalia pyrenaica (Vaillant & Vinçon) comb. n., Phaeobalia slovaca (Wagner) comb. n. and Phaeobalia thomasi (Vaillant & Vinçon) comb. n. Re‐evaluation of the genus Roederiodes resulted in the following new combinations: Clinocerella macedonicus (Wagner & Horvat) comb. n. and Clinocerella montenegrinus (Wagner & Horvat) comb. n. The origins of Clinocerinae (s.s.) are traced back to the Holarctic region, Laurasian origin, with a likely complex history of dispersal events into the Southern Hemisphere. Based on current knowledge, the greatest generic and species richness is confined to the Palaearctic Region. These findings provide valuable insights into the evolutionary relationships and distribution patterns of Clinocerinae (s.s.), challenging existing taxonomic classifications and shedding light on their historical biogeography.

Status and distribution of Paraguayan Procyonidae and Mephitidae (Mammalia: Carnivora)

Two species of procyonid (Nasua nasua and Procyon cancrivorus) and one species of mephitid (Conepatus chinga) have long been documented to occur in Paraguay, but very little has been published about their ecology in the country since the early 19th Century works of Azara and Rengger. Data on the distribution and status of these species in the country is collated from museum specimens, published literature and reliable observations to provide a basis for future research. A hierarchical approach is taken towards types of record and maps are provided that distinguish these for all species. All three species remain common in the Chaco region west of the Paraguay River, and all are considered of Least Concern. However, this region is experiencing high levels of deforestation and data to assess the potential declines of the species is unavailable. The two species of procyonid are also widespread in the Oriental region, but the status of Conepatus chinga there is unclear. There are multiple reports from the Atlantic Forest region but documentation is limited to fecal molecular samples. Clarifying the distribution of that species in the Oriental region is a priority for research.

Life history of an evolutionary distinct aquatic caecilian amphibian (genus Potomotyphlus) in eastern Amazonia, Brazil

Abstract Basic ecological data for caecilians are relatively lacking. This study presents the first comprehensive ecological investigation of the Amazonian aquatic caecilian Potomotyphlus kaupii, utilizing a large sample size. We collected population data over a 14-month period, and also used data of museum specimens, both from Belém, State of Pará, Brazil. Our analysis focused on sex ratio, sexual size dimorphism (SSD), female fecundity, and ecological observations. No significant differences in adult sex ratio were found. SSD was found in some characters such as circumference at midbody and body mass with females being larger than males, while males had a wider and longer cloacal disc. We provide the first determination of the approximate size at which males diverge from females in the terminal portion of the body, demonstrating an allometric growth pattern of the cloacal region. Female size showed a positive correlation with the number of ovarian eggs, indicating an important reproductive strategy. Furthermore, a novel behaviour in P. kaupii was documented. We expand the understanding of Gymnophiona biology, in particular of a fully aquatic species, and provide support for future ecological and conservation research on caecilians.

Genetics, geography, and subspecies status of American mink in Florida, with an emphasis on Neogale vison evergladensis

Historical records of American mink (Neogale vison) in Florida suggest they occur in four populations, each currently recognized as a separate subspecies. The Everglades mink (N. v. evergladensis) is a state-listed threatened subspecies, and the Atlantic salt marsh mink (N. v. lutensis) and Gulf salt marsh mink (N. v. halilimnetes) are both Species of Greatest Conservation Need, but support for their taxonomic status is limited. We acquired 62 samples of mink for genetic analysis using mtDNA and microsatellite data with the objective of assessing the subspecies status of mink in Florida with an emphasis on evergladensis. We also compared historical and current range estimates of mink subspecies in Florida using museum specimens, public sightings, and detection records from scientific studies. All estimates of FST were significant when evergladensis was paired with other subspecies and both assignment tests and the Principal Coordinate Analysis separated evergladensis from other subspecies. The single mtDNA haplotype from evergladensis was not found elsewhere in Florida but was present in a subspecies outside of Florida (vulgivaga). Genetic diversity was lowest in evergladensis and highest for vulgivaga from Louisiana. We found support for lutensis as a separate taxonomic unit and assignment tests found some support for the genetic distinctiveness of halilimnetes. Sample sizes limited analyses in halilimnetes and prevented any conclusions about the subspecies status of mink in the Panhandle. Based on current range estimates, mink from evergladensis, lutensis, and halilimnetes are geographically isolated from one another and supports the genetic analysis. Using a more modern definition of subspecies that includes genetics, distribution, and ecology, we conclude that the data supports multiple subspecies of mink in Florida.

Museum skins enable identification of introgression associated with cytonuclear discordance.

Increased sampling of genomes and populations across closely related species has revealed that levels of genetic exchange during and after speciation are higher than previously thought. One obvious manifestation of such exchange is strong cytonuclear discordance, where the divergence in mitochondrial DNA (mtDNA) differs from that for nuclear genes more (or less) than expected from differences between mtDNA and nuclear DNA (nDNA) in population size and mutation rate. Given genome-scale datasets and coalescent modelling, we can now confidently identify cases of strong discordance and test specifically for historical or recent introgression as the cause. Using population sampling, combining exon capture data from historical museum specimens and recently collected tissues we showcase how genomic tools can resolve complex evolutionary histories in the brachyotis group of rock-wallabies (Petrogale). In particular, applying population and phylogenomic approaches we can assess the role of demographic processes in driving complex evolutionary patterns and assess a role of ancient introgression and hybridisation. We find that described species are well supported as monophyletic taxa for nDNA genes, but not for mtDNA, with cytonuclear discordance involving at least four operational taxonomic units (OTUs) across four species which diverged 183-278 kya. ABC modelling of nDNA gene trees supports introgression during or after speciation for some taxon pairs with cytonuclear discordance. Given substantial differences in body size between the species involved, this evidence for gene flow is surprising. Heterogenous patterns of introgression were identified but do not appear to be associated with chromosome differences between species. These and previous results suggest that dynamic past climates across the monsoonal tropics could have promoted reticulation among related species.

A taxonomic revision of the sponge-associated genus Thoracactis Gravier, 1918 (Anthozoa: Zoantharia) based on an integrated approach

Abstract The integrated approach of molecular phylogenetic and morphological analyses has revolutionized the systematics and our understanding of the evolutionary relationships of marine taxa. One such group is the hexacorallian order Zoantharia Rafinesque, 1815. The monotypic genus Thoracactis Gravier, 1918 has been little investigated since its placement within the order Zoantharia more than 100 years ago. Here, we examined museum specimens collected from the Cape Verde Islands (eastern Atlantic) and newly collected specimens from Brazil (southwestern Atlantic), using a combined molecular and morphological approach. Our results conclusively show Thoracactis to be referable to the family Parazoanthidae. Morphological data show that Thoracactis topsenti Gravier, 1918, the type species of this monotypic genus, has a cyclically transitional arrangement of its sphincter muscle, and this arrangement has previously been reported from the Parazoanthidae. Thoracactis can be distinguished from other hexasterophoran glass-sponge-associated genera (Churabana Kise, Montenegro & Reimer, 2022, Parachurabana Kise, 2023, and Vitrumanthus Kise, Montenegro & Reimer, 2022) by a combination of morphological, ecological and molecular phylogenetic data. In addition, molecular phylogenetic analyses clearly indicate that Thoracactis topsenti is placed within Parazoanthidae. These results are yet another demonstration of the utility of comprehensive combined approaches. From now, research attention should focus on the revision of remaining taxonomic questions within the family Epizoanthidae, with the goal of a comprehensively revised suborder Macrocnemina within reach.

A new genus of Cicadellini (Hemiptera: Cicadellidae) from the Oaxacan Cloud Forest, with taxonomic notes on allied red-striped genera

Cicadellinae is a relatively large subfamily of leafhoppers (Hemiptera: Cicadellidae) with a cosmopolitan distribution with most genera known to occur in the Neotropics. Mexico houses nearly 16% of the total genera and most are endemic, inhabiting threatened native forests. Here, a new unusual Mexican genus, Christopherus gen. nov., is described to accommodate a new species of Cicadellini, C. mictlantecuhtli sp. nov., collected in the endangered Cloud Forest of Sierra Juárez, Oaxaca State of Mexico, based on dry-pinned museum specimen data. The new taxa can be separated from other Neotropical Cicadellini genera easily using male genitalia features: (i) pygofer without processes, (ii) segment 10th without processes, (iii) paraphysis absent, and (iv) edeagus with single basal atrial process elongate and asymmetrical. The monotypic genus Gillonella with its type species, G. ampulla Nielson & Godoy, 1995, are redescribed. A detailed extensive morphological description and discussion to distinguish the new genus from allied red-striped Neotropical genera in Mexico, Central America, and South America are given. Distributional data for new taxa within Mexican forests is also provided.

Link between Monkeypox Virus Genomes from Museum Specimens and 1965 Zoo Outbreak.

We used pathogen genomics to test orangutan specimens from a museum in Bonn, Germany, to identify the origin of the animals and the circumstances of their death. We found monkeypox virus genomes in the samples and determined that they represent cases from a 1965 outbreak at Rotterdam Zoo in Rotterdam, the Netherlands.

Identification of long-preserved specimens reveals the historical geographic range of the Patagonian lamprey Geotria macrostoma (Burmeister, 1868) in southern South America.

The lamprey genus Geotria Gray, 1851 currently includes only two species: G. australis and G. macrostoma. However, taxonomic relationships within the genus have traditionally been ambiguous and difficult to establish due to the extreme changes in morphology, dentition, and coloration that lampreys undergo during their life cycles, particularly during upstream migration and sexual maturation. Consequently, several lamprey specimens held in museum collections have remained unidentified, especially those from Argentina. In this study, a series of morphometric characters were subjected to discriminant function analysis (DFA) to identify the lamprey species collected during 1867-2004 from the de la Plata River and Patagonia. These specimens are housed at the Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" in Buenos Aires, the Museo de Historia Natural de Montevideo, and the Naturhistoriska riksmuseet in Stockholm. Based on the proportions of the length of the oral disc, prebranchial, and pre-caudal body regions, and the depth of the trunk, DFA provided conclusive evidence that the specimens corresponded to the recently revalidated G. macrostoma (Burmeister, 1868), which was originally incorrectly named as Petromyzon macrostomus Burmeister, 1868, Exomegas macrostomus (Berg, 1899), Geotria chilensis (Berg, 1895), and Geotria macrostoma f. gallegensis Smitt, 1901, as well as other nontype museum individuals of uncertain taxonomic status. The identifications of these long-preserved museum specimens provided key information on the historical geographic range of Argentinian lampreys and suggest that the disappearance of the species reported from northern localities (the Pampean Region) can be attributed to the degradation of their critical habitats, primarily caused by anthropogenic impact and climate change.

Investigating flock-associated mimicry: examining the evidence for, and drivers of, plumage mimicry in the greater and lesser necklaced laughingthrush.

Visual mimicry is less understood in birds than in other taxa. The interspecific social dominance mimicry (ISDM) hypothesis asserts that subordinate species resemble dominant ones to reduce aggression. Plumage mimicry has also been consistently noted in mixed-species flocks (MSFs), suggesting a connection to grouping behaviour, although it is unclear whether this is linked to ISDM. We studied greater necklaced laughingthrush (GNLT, Pterorhinus pectoralis) and lesser necklaced laughingthrush (LNLT, Garrulax monileger), which were recently placed in different genera. Measurements of 162 museum specimens showed LNLT converging in sympatry with GNLT in necklace colour, but diverging in necklace to body ratio, with proportionally smaller necklaces. The species were closely associated in six of seven MSF systems from Nepal to China. In a study of foraging behaviour in Nepal, aggression was rare between the species, LNLT followed GNLT and had lower foraging rates when further from GNLT. Our data suggest a link between this MSF-associated mimicry and ISDM, and that the subordinate LNLT may be the mimic and gain more from the resemblance. The species spend much time together in dense and poorly lit vegetation, where the LNLTs resemblance to GNLTs potentially allows them to forage closer to GNLTs than would be otherwise possible.

Description of a tetrapod trackway from the early Carboniferous Bonaventure Formation of New Brunswick, Canada

The Bonaventure Formation is an early Carboniferous fossil-bearing rock unit that crops out in northern New Brunswick and eastern Quebec, eastern Canada. Here, we describe CMNFV 10013, a tetrapod trackway found in Bonaventure Formation outcrops on Heron Island, New Brunswick, by Robert Wheelock Ells in 1879. The specimen shows at least seven prints including two pes-manus couples, one of which is sufficiently well preserved to be attributable to Hylopus isp. Several underprints significantly depart from typical Hylopus tracks and emphasise the importance of considering taphonomy when identifying fossil trackways. CMNFV 10013 is the first described fossil reported from the Bonaventure Formation. It extends the Carboniferous Maritimes Basin tetrapod trackway record northwards and represents one of the oldest tetrapod trackways from Canada. Reviewing the global record of Hylopus isp. reveals CMNFV 10013 is also one of the earliest Hylopus found. This global record also reveals that Hylopus occurrences are clustered around the paleotropics, possibly suggesting a biogeographical preference. This specimen highlights the importance of describing forgotten museum specimens. Future research should focus on undescribed museum specimens and contributing to existing collections through fieldwork in the promising rocks of Heron Island.

Nanoscale millefeuilles produce iridescent bill ornaments in birds.

Colors are well studied in bird plumage but not in other integumentary structures. In particular, iridescent colors from structures other than plumage are undescribed in birds. Here, we show that a multilayer of keratin and lipids is sufficient to produce the iridescent bill of Spermophaga haematina. Furthermore, that the male bill is presented to the female under different angles during display provides support for the hypothesis that iridescence evolved in response to sexual selection. This is the first report of an iridescent bill, and only the second instance of iridescence in birds in which melanosomes are not involved. Furthermore, an investigation of museum specimens of an additional 98 species, showed that this evolved once, possibly twice. These results are promising, as they suggest that birds utilize a wider array of physical phenomena to produce coloration and should further stimulate research on nonplumage integumentary colors.

Pathogen prospecting of museums: Reconstructing malaria epidemiology

Malaria is a disease of global significance. Ongoing changes to the earth’s climate, antimalarial resistance, insecticide resistance, and socioeconomic decline test the resilience of malaria prevention programs. Museum insect specimens present an untapped resource for studying vector-borne pathogens, spurring the question: Do historical mosquito collections contain Plasmodium DNA, and, if so, can museum specimens be used to reconstruct the historical epidemiology of malaria? In this Perspective, we explore molecular techniques practical to pathogen prospecting, which, more broadly, we define as the science of screening entomological museum specimens for human, animal, or plant pathogens. Historical DNA and pathogen prospecting provide a means of describing the coevolution of human, vector, and parasite, informing the development of insecticides, diagnostics, therapeutics, and vaccines.