The systematics of the Cervidae: a total evidence approach

Hair Coat of the Water Deer Hydropotes inermis (Cervidae, Artiodactyla), a New Species in the Russian Fauna

The hair coat and hair microstructure of an adult male Hydropotes inermis from the Primorsky Krai of Russia were studied for the first time by light and scanning electron microscopy. Lack of abundant underfur, sparse hair, and a weak layering are characteristic of the species, which inhabits the temperate monsoon and tropical zones and does not need an efficient thermal protection. An alveolar and lattice medulla of the hair is similar to that of other deer, is well developed, and increases the heat-protective properties of the hair because seasonal and daily fluctuations in temperature and humidity can be significant. The cuticle pattern is similar to that of the deer tribes Alceini and Capreolini. The hair thickness and length are substantial on the back, sides, and thighs, and the coat thus provides reliable protection from mechanical damage when the water deer moves through thickets of bushes and grasses along riverbanks and swamps in its habitats. A knotty nature of hairs protects the skin from sharp outgrowths of aquatic and marsh plants.

Comparative karyotype analysis of the red brocket deer (M. americana sensu lato and M. rufa) complex: evidence of drastic chromosomal evolution and implications on speciation process

Chromosomal rearrangements are often associated with playing a role in the speciation process. However, the underlying mechanism that favors the genetic isolation associated with chromosomal changes remains elusive. In this sense, the genus Mazama is recognized by its high level of karyotype diversity among species with similar morphology. A cryptic species complex has been identified within the genus, with the red brocket deer (Mazama americana and Mazama rufa) being the most impressive example. The chromosome variation was clustered in cytotypes with diploid numbers ranging from 42 to 53 and was correlated with geographical location. We conducted an analysis of chromosome evolution of the red brocket deer complex using comparative chromosome painting and Bacterial Artificial Chromosome (BAC) clones among different cytotypes. The aim was to deepen our understanding of the karyotypic relationships within the red brocket, thereby elucidating the significant chromosome variation among closely related species. This underscores the significance of chromosome changes as a key evolutionary process shaping their genomes. The results revealed the presence of three distinct cytogenetic lineages characterized by significant karyotypic divergence, suggesting the existence of efficient post-zygotic barriers. Tandem fusions constitute the main mechanism driving karyotype evolution, following a few centric fusions, inversion X-autosomal fusions. The BAC mapping has improved our comprehension of the karyotypic relationships within the red brocket deer complex, prompting questions regarding the role of these changes in the speciation process. We propose the red brocket as a model group to investigate how chromosomal changes contribute to isolation and explore the implications of these changes in taxonomy and conservation.

Comparative Genomics Reveal Phylogenetic Relationship and Chromosomal Evolutionary Events of Eight Cervidae Species

Cervidae represents a family that is not only rich in species diversity but also exhibits a wide range of karyotypes. The controversies regarding the phylogeny and classification of Cervidae still persist. The flourishing development of the genomic era has made it possible to address these issues at the genomic level. Here, the genomes of nine species were used to explore the phylogeny and chromosomal evolutionary events of Cervidae. By conducting whole-genome comparisons, we identified single-copy orthologous genes across the nine species and constructed a phylogenetic tree based on the single-copy orthologous genes sequences, providing new insights into the phylogeny of Cervidae, particularly the phylogenetic relationship among sika deer, red deer, wapiti and Tarim red deer. Gene family analysis revealed contractions in the olfactory receptor gene family and expansions in the histone gene family across eight Cervidae species. Furthermore, synteny analysis was used to explore the chromosomal evolutionary events of Cervidae species, revealing six chromosomal fissions during the evolutionary process from Bovidae to Cervidae. Notably, specific chromosomal fusion events were found in four species of Cervus, and a unique chromosomal fusion event was identified in Muntiacus reevesi. Our study further completed the phylogenetic relationship within the Cervidae and demonstrated the feasibility of inferring species phylogeny at the whole-genome level. Additionally, our findings on gene family evolution and the chromosomal evolutionary events in eight Cervidae species lay a foundation for comprehensive research of the evolution of Cervidae.

Anaerobic fungi in the tortoise alimentary tract illuminate early stages of host-fungal symbiosis and Neocallimastigomycota evolution

Anaerobic gut fungi (AGF, Neocallimastigomycota) reside in the alimentary tract of herbivores. While their presence in mammals is well documented, evidence for their occurrence in non-mammalian hosts is currently sparse. Culture-independent surveys of AGF in tortoises identified a unique community, with three novel deep-branching genera representing >90% of sequences in most samples. Representatives of all genera were successfully isolated under strict anaerobic conditions. Transcriptomics-enabled phylogenomic and molecular dating analyses indicated an ancient, deep-branching position in the AGF tree for these genera, with an evolutionary divergence time estimate of 104-112 million years ago (Mya). Such estimates push the establishment of animal-Neocallimastigomycota symbiosis from the late to the early Cretaceous. Further, tortoise-associated isolates (T-AGF) exhibited limited capacity for plant polysaccharides metabolism and lacked genes encoding several carbohydrate-active enzyme (CAZyme) families. Finally, we demonstrate that the observed curtailed degradation capacities and reduced CAZyme repertoire is driven by the paucity of horizontal gene transfer (HGT) in T-AGF genomes, compared to their mammalian counterparts. This reduced capacity was reflected in an altered cellulosomal production capacity in T-AGF. Our findings provide insights into the phylogenetic diversity, ecological distribution, evolutionary history, evolution of fungal-host nutritional symbiosis, and dynamics of genes acquisition in Neocallimastigomycota.

Evolutionary insights on critically endangered Kashmir red deer or hangul (Cervus hanglu hanglu) through a mitogenomic lens

Background

The Kashmir red deer or Hangul (Cervus hanglu hanglu) is the only Tarim red deer species endemic to India. With a current estimated population size of fewer than 200 individuals, this critically endangered species is confined to the greater Dachigam landscape in Jammu and Kashmir. Poaching, habitat loss and fragmentation, resource competition with livestock, and small population size are the major conservation challenges for this species.

Methods

Blood sampling was conducted from two wild Hangul individuals during radio-collaring operations at Dachigam National Park, Kashmir in 2013 and 2020, respectively. Using next-generation sequencing approach, we sequenced the 16,351 bp long mitogenome of two wild-caught Hangul individuals (1 M:1 F at ~14× and ~10× coverage, respectively) from Dachigam National Park.

Results

The annotated sequences were identical with an AT-rich composition, including 13 protein-coding genes (11,354 bp), 22 tRNA genes (1,515 bp), two ribosomal genes (2,526 bp) and a non-coding control region (917 bp) in a conserved order like other red deer species. Bayesian phylogenetic reconstruction of the red deer complex revealed two major groups: the elaphoid and the wapitoid clades. Hangul formed a distinct clade with its other subspecies C. hanglu yarkandensis and is sister to the Hungarian red deer (C. elaphus hippelaphus). Divergence time analyses suggested that the Tarim deer species group separated ~1.55 Mya from their common ancestors and Hangul diverged ~0.75 Mya from closely related C. yarkandensis, corroborating with the known paleobiogeographic events related to refugia during glaciations in the Pleistocene era. This study provides baseline information on Hangul mitogenome for further research on phylogeography and other population parameters and helps in developing suitable conservation plans for this species.

Comparative studies of X chromosomes in Cervidae family

The family Cervidae is the second most diverse in the infraorder Pecora and is characterized by variability in the diploid chromosome numbers among species. X chromosomes in Cervidae evolved through complex chromosomal rearrangements of conserved segments within the chromosome, changes in centromere position, heterochromatic variation, and X-autosomal translocations. The family Cervidae consists of two subfamilies: Cervinae and Capreolinae. Here we build a detailed X chromosome map with 29 cattle bacterial artificial chromosomes of representatives of both subfamilies: reindeer (Rangifer tarandus), gray brocket deer (Mazama gouazoubira), Chinese water deer (Hydropotes inermis) (Capreolinae); black muntjac (Muntiacus crinifrons), tufted deer (Elaphodus cephalophus), sika deer (Cervus nippon) and red deer (Cervus elaphus) (Cervinae). To track chromosomal rearrangements during Cervidae evolution, we summarized new data, and compared them with available X chromosomal maps and chromosome level assemblies of other species. We demonstrate the types of rearrangements that may have underlined the variability of Cervidae X chromosomes. We detected two types of cervine X chromosome-acrocentric and submetacentric. The acrocentric type is found in three independent deer lineages (subfamily Cervinae and in two Capreolinae tribes-Odocoileini and Capreolini). We show that chromosomal rearrangements on the X-chromosome in Cervidae occur at a higher frequency than in the entire Ruminantia lineage: the rate of rearrangements is 2 per 10 million years.

Assessing the Taxonomic Status of the Gray Brocket Mazama simplicicornis argentina Lönnberg, 1919 (Artiodactyla: Cervidae)

Mazama simplicicornis argentina is the name that was given to describe a gray brocket collected by Lönberg in 1919 in the central Chaco region of Argentina. Subsequent authors, based on morphological similarities, considered this name to be a synonym for the species Subulo gouazoubira Fischer, 1814 from Paraguay. In the absence of genetic analyses to compare the Argentinian and Paraguayan gray brockets, we aimed to clarify the taxonomy of M. simplicicornis argentina through an integrative assessment using morphological, cytogenetical, and molecular data from its holotype and a current topotype. Qualitative skull features and cranio-morphometric results of M. simplicicornis argentina showed a great similarity with the S. gouazoubira neotype characters. The diploid chromosome number of M. simplicicornis argentina topotype corresponded with the karyotypical pattern of S. gouazoubira with 2n = 70 and FN = 70, showing a great similarity in all classic and molecular cytogenetic results and revealing the homologies between karyotypes. The phylogenetic analysis of mitochondrial genes used in this study (concatenated partial ND5 and Cytb gene) allocated the M. simplicicornis argentina specimens in the monophyletic clade of S. gouazoubira with a branch value of 100%. These results show that there is no discontinuity between the Argentinian and Paraguayan gray brockets. Therefore, the individuals originally described as M. simplicicornis argentina should be recognized as S. gouazoubira.

Evolution and development of the cetacean skull roof: a case study in novelty and homology

Skulls of living whales and dolphins (cetaceans) are telescoped-bones of the skull roof are overlapped by expanded facial bones and/or anteriorly extended occipital bones. Evolution of the underlying skull roof (calvarium), which lies between the telescoped regions, is relatively unstudied. We explore the evolution and development of the calvarium of toothed whales (odontocetes) by integrating fetal data with Oligocene odontocete fossils from North America, including eight neonatal and juvenile skulls of Olympicetus†. We identified two potential synapomorphies of crown Cetacea: contact of interparietals with frontals, and a single anterior median interparietal (AMI) element. Within Odontoceti, loss of contact between the parietals diagnoses the clade including Delphinida, Ziphiidae and Platanistidae (=Synrhina). Delphinida is characterized by a greatly enlarged interparietal. New fetal series of delphinoids reveal a consistent developmental pattern with three elements: the AMI and bilateral posterior interparietals (PIs). The PIs most resemble the medial interparietal elements of terrestrial artiodactyls, suggesting that the AMI of cetaceans could be a unique ossification. More broadly, the paucity of conserved anatomical relationships of the interparietals, as well as the fact that the elements often do not coalesce into a single bone, demonstrates that assessing homology of the interparietals across mammals remains challenging. This article is part of the theme issue 'The mammalian skull: development, structure and function'.

Patterns and determinants of the global herbivorous mycobiome

Despite their role in host nutrition, the anaerobic gut fungal (AGF) component of the herbivorous gut microbiome remains poorly characterized. Here, to examine global patterns and determinants of AGF diversity, we generate and analyze an amplicon dataset from 661 fecal samples from 34 mammalian species, 9 families, and 6 continents. We identify 56 novel genera, greatly expanding AGF diversity beyond current estimates (31 genera and candidate genera). Community structure analysis indicates that host phylogenetic affiliation, not domestication status and biogeography, shapes the community rather than. Fungal-host associations are stronger and more specific in hindgut fermenters than in foregut fermenters. Transcriptomics-enabled phylogenomic and molecular clock analyses of 52 strains from 14 genera indicate that most genera with preferences for hindgut hosts evolved earlier (44-58 Mya) than those with preferences for foregut hosts (22-32 Mya). Our results greatly expand the documented scope of AGF diversity and provide an ecologically and evolutionary-grounded model to explain the observed patterns of AGF diversity in extant animal hosts.

Revalidation of Passalites Gloger, 1841 for the Amazon brown brocket deer P.nemorivagus (Cuvier, 1817) (Mammalia, Artiodactyla, Cervidae)

Mazamanemorivaga (Cuvier, 1817) is a gray brocket deer that inhabits the Amazon region. An assessment of previous studies revealed inconsistencies in its current taxonomic classification, suggesting the need for an update in its genus classification. A taxonomic repositioning of this species is proposed through the collection of a specimen from its type locality (French Guiana) with subsequent morphological (coloring pattern, body measurements, and craniometry), cytogenetics (G Band, C Band, conventional Giemsa, Ag-NOR staining, and BAC probe mapping), and molecular phylogenetic analysis (mitochondrial genes Cyt B of 920 bp, COI I of 658 bp, D-loop 610 bp), and comparisons with other specimens of the same taxon, as well as other Neotropical deer species. The morphological and cytogenetic differences between this and other Neotropical Cervidae confirm the taxon as a unique and valid species. The phylogenetic analysis evidenced the basal position of the M.nemorivaga specimens within the Blastocerina clade. This shows early diversification and wide divergence from the other species, suggesting that the taxon should be transferred to a different genus. A taxonomic update of the genus name is proposed through the validation of Passalites Gloger, 1841, with Passalitesnemorivagus (Cuvier, 1817) as the type species. Future research should focus on evaluating the potential existence of other species within the genus Passalites, as suggested in the literature.

First description of the mitochondrial genomes of the Central American brocket deer Mazama temama (Kerr, 1792) and the Yucatán Peninsula brocket deer Odocoileus pandora Merriam, 1901

BACKGROUND

The Central American (Mazama temama) and the Yucatán Peninsula brocket deer (Odocoileus pandora) are deer species with cryptic habits, and little is known about their biology. Odocoileus pandora is listed as Vulnerable on the 2015 IUCN Red List of Threatened Species, while M. temama is considered Data Deficient; however, it currently faces a decreasing population trend.

METHODS AND RESULTS

We assembled the complete mitochondrial genome for two M. temama specimens and one complete and one partial for O. pandora from Illumina 150 bp paired-end reads. The mitogenomes of M. temama and O. pandora have a length of 16,479-16,480 and 16,419 bp, respectively, AT-biased; they consist of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and one non-coding control region, most of them follow a transcription direction in the heavy strand of the molecule. The mitochondrial genome of O. pandora shows some particularities compared to other deer species, like a shorter control region of 987-990 bp and a cytochrome b gene with a length of 1,143 bp. Our phylogenetic analyses confirm the close affinity of M. temama to South American M. americana and the nested position of the genus Odocoileus, including O. pandora, into the genus Mazama.

CONCLUSIONS

Here, we described for the first time the complete mitochondrial genome for these two species. While our study provides additional information about the taxonomic status of the northern neotropical brocket deer, further research is needed to solve the complicated taxonomy of neotropical deer.

Antler tine homologies and cervid systematics: A review of past and present controversies with special emphasis on Elaphurus davidianus

Antlers are the most conspicuous trait of cervids and have been used in the past to establish a classification of their fossil and living representatives. Since the availability of molecular data, morphological characters have generally become less important for phylogenetic reconstructions. In recent years, however, the appreciation of morphological characters has increased, and they are now more frequently used in addition to molecular data to reconstruct the evolutionary history of cervids. A persistent challenge when using antler traits in deer systematics is finding a consensus on the homology of structures. Here, we review early and recent attempts to homologize antler structures and objections to this approach, compare and evaluate recent advances on antler homologies, and critically discuss these different views in order to offer a basis for further scientific exchange on the topic. We further present some developmental aspects of antler branching patterns and discuss their potential for reconstructing cervid systematics. The use of heterogeneous data for reconstructing phylogenies has resulted in partly conflicting hypotheses on the systematic position of certain cervid species, on which we also elaborate here. We address current discussions on the use of different molecular markers in cervid systematics and the question whether antler morphology and molecular data can provide a consistent picture on the evolutionary history of cervids. In this context, special attention is given to the antler morphology and the systematic position of the enigmatic Pere David's deer (Elaphurus davidianus).

Ecomorphology of the cervid intermediate phalanx and its implications for palaeoenvironmental reconstruction

This paper reports on newly developed ecomorphological models for the cervid intermediate phalanx. Using a geometric morphometric approach, we quantitatively assess the overall gracility of the bone, the depth and concavity of the proximal articulation and the roundness and symmetry of the distal articulation in the intermediate phalanx, to establish relationships between morphology, locomotor behavior and environment. The morphology of the phalanx was found to vary along a gradient from gracile phalanges with shallow proximal articulations in forms adapted to yielding substrate, to robust phalanges with deeper proximal articulations in taxa adapted to firm substrate. Phylogeny and allometry are accounted for using regressions and phylogenetic comparative methods. Although the results indicate phylogeny explains part of the morphological variation, overall the shape of the intermediate phalanx appears mainly driven by differences in function. Consequently, this element promises to be a useful palaeoenvironmental proxy that can be applied on fossil assemblages with cervid remains.

Human and Animal Fascioliasis: Origins and Worldwide Evolving Scenario

Fascioliasis is a plant- and waterborne zoonotic parasitic disease caused by two trematode species: (i) Fasciola hepatica in Europe, Asia, Africa, the Americas, and Oceania and (ii) F. gigantica, which is restricted to Africa and Asia. Fasciolid liver flukes infect mainly herbivores as ruminants, equids, and camelids but also omnivore mammals as humans and swine and are transmitted by freshwater Lymnaeidae snail vectors. Two phases may be distinguished in fasciolid evolution. The long predomestication period includes the F. gigantica origin in east-southern Africa around the mid-Miocene, the F. hepatica origin in the Near-Middle East of Asia around the latest Miocene to Early Pliocene, and their subsequent local spread. The short postdomestication period includes the worldwide spread by human-guided movements of animals in the last 12,000 years and the more recent transoceanic anthropogenic introductions of F. hepatica into the Americas and Oceania and of F. gigantica into several large islands of the Pacific with ships transporting livestock in the last 500 years. The routes and chronology of the spreading waves followed by both fasciolids into the five continents are redefined on the basis of recently generated knowledge of human-guided movements of domesticated hosts. No local, zonal, or regional situation showing disagreement with historical records was found, although in a few world zones the available knowledge is still insufficient. The anthropogenically accelerated evolution of fasciolids allows us to call them "peridomestic endoparasites." The multidisciplinary implications for crucial aspects of the disease should therefore lead the present baseline update to be taken into account in future research studies.

Reevaluation of the status of the Central American brocket deer Mazama temama (Artiodactyla: Cervidae) subspecies based on morphological and environmental evidence

The Central American brocket deer (Mazama temama) is widespread across the Mesoamerican forests, yet it remains largely unknown. Three subspecies are recognized currently within M. temama using pelage coloration as the primary diagnostic character. However, it remains unclear if there is any pattern of morphological variation throughout its distribution. We compared two models of morphological subdivision, namely the traditional subspecies and another based on biogeographic provinces via 2D geometric morphometrics and ecological niche modeling. The second model presented a better fit to the observed variation in cranial shape and size. We found divergence in skull size between individuals from Mexico and Guatemala (northern group) relative to specimens from Honduras, Nicaragua, Costa Rica, and Panama (southern group), the latter being 8% larger than the northern group. Centroid size showed a significant correlation with geographic distance suggesting an isolation-by-distance pattern. Low geographical overlap between the two clusters suggests niche conservatism. Late Pleistocene dispersal from South to Central America and differences in available resources with subsequent isolation due to climatic barriers therefore may have promoted differentiation in size albeit without extensive changes in shape. In this context, the Motagua-Polochic-Jolotán fault system probably plays a key role in promoting morphological differentiation by climatic isolation. Finally, we suggest that M. t. temama (Kerr, 1792) and M. t. reperticia  Goldman, 1913 should remain as valid names for the two morphological and ecologically differentiated groups detected here.

Extrapolating the susceptibility of Eld’s deer (Rucervus eldii thamin) to chronic wasting disease from prion protein gene (PRNP) polymorphisms

Chronic wasting disease (CWD) is a prion disease of North American cervids. The transmission of CWD to endangered cervid species is of concern for captive breeding programs. Trans-species transmission could occur via direct contact with infected wild deer, or via prion contaminated fomites. Variation in the prion protein gene, PRNP, is associated with differences in CWD susceptibility among cervids. We therefore sequenced PRNP in 36 endangered Eld’s deer (Rucervus eldii thamin), detecting five synonymous and two non-synonymous SNPs. Three haplotypes were inferred, suggesting that genetic management in captive breeding programs has been effective at maintaining PRNP diversity. The haplotypes encoded two PrP protein variants. The more common Eld’s deer PrP variant encodes methionine at codon 208 and glutamine at codon 226. Because this protein variant is identical to a common PrP variant in white-tailed deer and mule deer and is especially common in white-tailed deer positive for CWD, we recommend reducing the frequency of this variant in the breeding stock, while implementing strict management practices to avoid exposure to wild North American cervids. The frequency of the other PrP variant, which differs from variants present in these North American cervids, was low. It has the potential to reduce susceptibility to CWD and thus could be increased in frequency. While PRNP haplotype frequencies should be shifted, genetic diversity should be maintained. Ultimately protein diversity may be protective should CWD infect the species, and trans-species polymorphisms are suggestive of past balancing selection and a potential fitness advantage for PRNP diversity.

Phylogeny and evolution of the genus Cervus (Cervidae, Mammalia) as revealed by complete mitochondrial genomes

Mitochondrial DNA (mtDNA) lineages are recognized as important components of intra- and interspecific biodiversity, and allow to reveal colonization routes and phylogeographic structure of many taxa. Among these is the genus Cervus that is widely distributed across the Holarctic. We obtained sequences of complete mitochondrial genomes from 13 Cervus taxa and included them in global phylogenetic analyses of 71 Cervinae mitogenomes. The well-resolved phylogenetic trees confirmed Cervus to be monophyletic. Molecular dating based on several fossil calibration points revealed that ca. 2.6 Mya two main mitochondrial lineages of Cervus separated in Central Asia, the Western (including C. hanglu and C. elaphus) and the Eastern (comprising C. albirostris, C. canadensis and C. nippon). We also observed convergent changes in the composition of some mitochondrial genes in C. hanglu of the Western lineage and representatives of the Eastern lineage. Several subspecies of C. nippon and C. hanglu have accumulated a large portion of deleterious substitutions in their mitochondrial protein-coding genes, probably due to drift in the wake of decreasing population size. In contrast to previous studies, we found that the relic haplogroup B of C. elaphus was sister to all other red deer lineages and that the Middle-Eastern haplogroup E shared a common ancestor with the Balkan haplogroup C. Comparison of the mtDNA phylogenetic tree with a published nuclear genome tree may imply ancient introgressions of mtDNA between different Cervus species as well as from the common ancestor of South Asian deer, Rusa timorensis and R. unicolor, to the Cervus clade.

Resurrection of the genus Subulo Smith, 1827 for the gray brocket deer, with designation of a neotype

The gray brocket deer, Mazama gouazoubiraG. Fischer, 1814, occurs in South America and presents an extensive degree of morphological and genetic variability. Previous phylogenetic research showed that the genus Mazama is polyphyletic and imposed the designation of a different genus-group name for M. gouazoubira. We aimed to review and clarify the taxonomy of M. gouazoubira through the proposal of updating the nomenclature for this taxon and by the characterization of specimens collected close to the original type locality (topotypes). The topotypes were characterized by morphological (general characterization and morphometry), cytogenetic (conventional staining, Ag-NOR, G- and C-banding, and fluorescence in situ hybridization), and phylogenetic (mitogenomes) approaches. We revealed chromosome homologies between cattle and M. gouazoubira using an entire set of cattle whole chromosome painting probes and propose an updated G-band idiogram for the species. The morphometric analysis did not discriminate the individuals of M. gouazoubira, including the topotypes, from other small brocket deer species. However, the phylogenetic analysis, based on a Bayesian inference tree of the mitogenomes, confirmed the polyphyly of the genus Mazama and supported the need to change the gray brocket deer genus-group name. Based on our revision, we validated the genus SubuloSmith, 1827, and fixed a type species for the genus. In the absence of the holotype, we denominated a neotype described by the collection of a male topotype in Paraguay. The nomenclature rearrangement presented here is a starting point that will assist in the taxonomic resolution of Neotropical deer.

Paleobiogeographical origins of Fasciola hepatica and F. gigantica in light of new DNA sequence characteristics of F. nyanzae from hippopotamus

Fascioliasis is a highly pathogenic disease affecting humans and livestock worldwide. It is caused by the liver flukes Fasciola hepatica transmitted by Galba/Fossaria lymnaeid snails in Europe, Asia, Africa, the Americas and Oceania, and F. gigantica transmitted by Radix lymnaeids in Africa and Asia. An evident founder effect appears in genetic studies as the consequence of their spread by human-guided movements of domestic ruminants, equines and Old World camelids in the post-domestication period from the beginning of the Neolithic. Establishing the geographical origins of fasciolid expansion is multidisciplinary crucial for disease assessment. Sequencing of selected nuclear ribosomal and mitochondrial DNA markers of F. nyanzae infecting hippopotamuses (Hippopotamus amphibius) in South Africa and their comparative analyses with F. hepatica and F. gigantica, and the two Fascioloides species, Fs. jacksoni from Asian elephants and Fs. magna from Holarctic cervids, allow to draw a tuned-up evolutionary scenario during the pre-domestication period. Close sequence similarities indicate a direct derivation of F. hepatica and F. gigantica from F. nyanzae by speciation after host capture phenomena. Phylogenetic reconstruction, genetic distances and divergence estimates fully fit fossil knowledge, past interconnecting bridges between continents, present fasciolid infection in the wild fauna, and lymnaeid distribution. The paleobiogeographical analyses suggest an origin for F. gigantica by transfer from primitive hippopotamuses to grazing bovid ancestors of Reduncinae, Bovinae and Alcelaphinae, by keeping the same vector Radix natalensis in warm lowlands of southeastern Africa in the mid-Miocene, around 13.5 mya. The origin of F. hepatica should have occurred after capture from primitive, less amphibious Hexaprotodon hippopotamuses to mid-sized ovicaprines as the wild bezoar Capra aegagrus and the wild mouflon Ovis gmelini, and from R. natalensis to Galba truncatula in cooler areas and mountainous foothills of Asian Near East in the latest Miocene to Early Pliocene, around 6.0 to 4.0 mya and perhaps shortly afterwards.

A Pleistocene Fight Club revealed by the palaeobiological study of the Dama-like deer record from Pantalla (Italy)

Here, we report on the exceptionally well-preserved deer record from the locality of Pantalla (central Italy), dated in the Early Pleistocene (ca. 2.1-2.0 million years ago). The fossils show a combination of characters that allows an unambiguous attribution to 'Pseudodama' nestii, of which they represent one of the most informative collections to date. Our comparisons-also conducted through CT-based methods on endocranial structures-reveal that the cranial and postcranial skeleton of 'P.' nestii displays a mosaic of intermediate characters between extant Dama and Cervus, but also that the affinities with Dama are prevalent. Some Cervus-like features especially in cranial morphology, can be interpreted as plesiomorphic characters supporting a basal position of 'Pseudodama' among the Cervini. Interestingly, three bone anomalies are described in the two male crania of 'P.' nestii from Pantalla and are interpreted as palaeotraumatological evidence resulting from different injuries suffered by the deer during their life. This allows opening a treasure trove of information on paleobiological aspects, including ontogeny and antler cycle and function.

Skull anatomy of the endangered Patagonian huemul deer(Hippocamelus bisulcus)

Studies of the normal skull anatomy of the Patagonian Huemul deer are scarce. Currently, the findings of bone lesions in the skull associated with metabolic imbalances are frequent in the literature. The objective of this study was to provide anatomical and morphometric data of the cranium and facies including a morphofunctional interpretation as a reference for clinical, ecomorphological and educational purposes. Five skulls were described, measured, scanned and digitally reconstructed. The presence of a caudal projection of the vomer bone, the absence of the facial tubercle and thin bones forming the cranial cavity were observed. Linear measurements allowed the skull to be classified as dolichocephalic, hyperlepten and ultra-dolichocranial. In conclusion, the Patagonian Huemul has a long head, an extremely long skull and a very narrow face. The thickness of the bones that made up the walls of the cranial cavity suggests chronic metabolic imbalances in response to mineral deficiency. The anatomical and morphometric data obtained in this study strongly emphasizes the relevance of considering the implementation of such management policies that aim at promoting an optimal nutritional context.

Cross-Species Analysis Reveals Co-Expressed Genes Regulating Antler Development in Cervidae

Antlers constitute an interesting model for basic research in regenerative biology. Despite decades of being studied, much is still unknown about the genes related to antler development. Here, we utilized both the genome and antlerogenic periosteum (AP) transcriptome data of four deer species to reveal antler-related genes through cross-species comparative analysis. The results showed that the global gene expression pattern matches the status of antler phenotypes, supporting the fact that the genes expressed in the AP may be related to antler phenotypes. The upregulated genes of the AP in three-antlered deer showed evidence of co-expression, and their protein sequences were highly conserved. These genes were growth related and likely participated in antler development. In contrast, the upregulated genes in antler-less deer (Chinese water deer) were involved mainly in organismal death and growth failure, possibly related to the loss of antlers during evolution. Overall, this study demonstrates that the co-expressed genes in antlered deer may regulate antler development.

Changes in Neuropeptide Prohormone Genes among Cetartiodactyla Livestock and Wild Species Associated with Evolution and Domestication

The impact of evolution and domestication processes on the sequences of neuropeptide prohormone genes that participate in cell–cell signaling influences multiple biological process that involve neuropeptide signaling. This information is important to understand the physiological differences between Cetartiodactyla domesticated species such as cow, pig, and llama and wild species such as hippopotamus, giraffes, and whales. Systematic analysis of changes associated with evolutionary and domestication forces in neuropeptide prohormone protein sequences that are processed into neuropeptides was undertaken. The genomes from 118 Cetartiodactyla genomes representing 22 families were mined for 98 neuropeptide prohormone genes. Compared to other Cetartiodactyla suborders, Ruminantia preserved PYY2 and lost RLN1. Changes in GNRH2, IAPP, INSL6, POMC, PRLH, and TAC4 protein sequences could result in the loss of some bioactive neuropeptides in some families. An evolutionary model suggested that most neuropeptide prohormone genes disfavor sequence changes that incorporate large and hydrophobic amino acids. A compelling finding was that differences between domestic and wild species are associated with the molecular system underlying ‘fight or flight’ responses. Overall, the results demonstrate the importance of simultaneously comparing the neuropeptide prohormone gene complement from close and distant-related species. These findings broaden the foundation for empirical studies about the function of the neuropeptidome associated with health, behavior, and food production.

Serological screening in wild ruminants in Germany, 2021/22: No evidence of SARS-CoV-2, bluetongue virus or pestivirus spread but high seroprevalences against Schmallenberg virus

Wildlife animals may be susceptible to multiple infectious agents of public health or veterinary relevance, thereby potentially forming a reservoir that bears the constant risk of re‐introduction into the human or livestock population. Here, we serologically investigated 493 wild ruminant samples collected in the 2021/2022 hunting season in Germany for the presence of antibodies against the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) and four viruses pathogenic to domestic ruminants, namely, the orthobunyavirus Schmallenberg virus (SBV), the reovirus bluetongue virus (BTV) and ruminant pestiviruses like bovine viral diarrhoea virus or border disease virus. The animal species comprised fallow deer, red deer, roe deer, mouflon and wisent. For coronavirus serology, additional 307 fallow, roe and red deer samples collected between 2017 and 2020 at three military training areas were included. While antibodies against SBV could be detected in about 13.6% of the samples collected in 2021/2022, only one fallow deer of unknown age tested positive for anti‐BTV antibodies, and all samples reacted negative for antibodies against ruminant pestiviruses. In an ELISA based on the receptor‐binding domain (RBD) of SARS‐CoV‐2, 25 out of 493 (5.1%) samples collected in autumn and winter 2021/2022 scored positive. This sero‐reactivity could not be confirmed by the highly specific virus neutralisation test, occurred also in 2017, 2018 and 2019, that is, prior to the human SARS‐CoV‐2 pandemic, and was likewise observed against the RBD of the related SARS‐CoV‐1. Therefore, the SARS‐CoV‐2 sero‐reactivity was most likely induced by another hitherto unknown deer virus belonging to the subgenus Sarbecovirus of betacoronaviruses.

High expression of canines in some Mediterranean roe deer populations against the general evolutionary trend

Upper canines do not usually appear in the roe deer Capreolus capreolus, Linnaeus 1758 and their occasional appearance represents the expression of a tooth, as a rudimentary canine, which has been suppressed in the evolution of the group. These dental anomalies could be potentially useful for tracing ancestral genes in local ecotypes and populations. We studied the skulls of 517 adult roe deer males from seven Iberian Peninsula hunting populations looking for canine occurrence and the variations depending on region and ecomorphological variety. A total of 18 specimens had canines (3.48 %) but a relationship was detected between the geographic origin and the canine presence. We found upper canines in three populations which were those located in the Tagus river basin, with 6.08 %, 10.91 % and 20 % prevalences, respectively. In the population with the highest prevalence, we also found a case of duplicated canines on either side of the upper jaw. Here, the high prevalence of upper canines against the evolutionary trend may be a sign of atavistic populations, possibly adapted to a less fibrous diet, in a geographical area connected through the Tagus river basin, and probably regarding one of the glacial refuges of the Iberian Peninsula.

Revalidation of Mazama rufa (Illiger 1815) (Artiodactyla: Cervidae) as a Distinct Species out of the Complex Mazama americana (Erxleben 1777)

The red brocket deer Mazama americana Erxleben, 1777 is considered a polyphyletic complex of cryptic species with wide chromosomal divergence. Evidence indicates that the observed chromosomal divergences result in reproductive isolation. The description of a neotype for M. americana allowed its genetic characterization and represented a comparative basis to resolve the taxonomic uncertainties of the group. Thus, we designated a neotype for the synonym Mazama rufa Illiger, 1815 and tested its recognition as a distinct species from the M. americana complex with the analysis of morphological, cytogenetic and molecular data. We also evaluated its distribution by sampling fecal DNA in the wild. Morphological data from craniometry and body biometry indicated an overlap of quantitative measurements between M. rufa and the entire M. americana complex. The phylogenetic hypothesis obtained through mtDNA confirmed the reciprocal monophyly relationship between M. americana and M. rufa, and both were identified as distinct molecular operational taxonomic units by the General Mixed Yule Coalescent species delimitation analysis. Finally, classic cytogenetic data and fluorescence in situ hybridization with whole chromosome painting probes showed M. rufa with a karyotype of 2n = 52, FN = 56. Comparative analysis indicate that at least fifteen rearrangements separate M. rufa and M. americana (sensu stricto) karyotypes, which confirmed their substantial chromosomal divergence. This divergence should represent an important reproductive barrier and allow its characterization as a distinct and valid species. Genetic analysis of fecal samples demonstrated a wide distribution of M. rufa in the South American continent through the Atlantic Forest, Cerrado and south region of Amazon. Thus, we conclude for the revalidation of M. rufa as a distinct species under the concept of biological isolation, with its karyotype as the main diagnostic character. The present work serves as a basis for the taxonomic review of the M. americana complex, which should be mainly based on cytogenetic characterization and directed towards a better sampling of the Amazon region, the evaluation of available names in the species synonymy and a multi-locus phylogenetic analysis.

Cytochrome b sequence of the Mazama americana jucunda Thomas, 1913 holotype reveals Mazama bororo Duarte, 1996 as its junior synonym

The small red brocket deer, Mazama bororo Duarte, 1996 was described based on karyotypical and morphological characters. However, the original description of Mazama americana jucunda suggested that this subspecies could represent the same taxon as Mazama bororo. This assumption was based on the type locality of Mazama americana jucunda and on morphological similarities between Mazama americana jucunda and Mazama bororo. To solve this question, we obtained DNA sequences of the holotype of Mazama americana jucunda and compared it with other species of Mazama, including the holotype of M. bororo. A phylogenetic tree was obtained to verify the relationships among these taxa. The results clearly showed that M. americana jucunda and M. bororo represent the same biological entity. Therefore, the oldest name available for the small red brocket occurring in the Atlantic Forest of southern Brazil should be Mazama jucunda, remaining M. bororo as a junior synonym. We emphasise the importance of using DNA from museum specimens, especially from holotypes, in order to obtain a more accurate taxonomic identification. We also highlight the importance of application of valid names for labelling all aspects of biodiversity research, as well as for monitoring and conservation efforts.

Roars, groans and moans: Anatomical correlates of vocal diversity in polygynous deer

Eurasian deer are characterized by the extraordinary diversity of their vocal repertoires. Male sexual calls range from roars with relatively low fundamental frequency (hereafter fo ) in red deer Cervus elaphus, to moans with extremely high fo in sika deer Cervus nippon, and almost infrasonic groans with exceptionally low fo in fallow deer Dama dama. Moreover, while both red and fallow males are capable of lowering their formant frequencies during their calls, sika males appear to lack this ability. Female contact calls are also characterized by relatively less pronounced, yet strong interspecific differences. The aim of this study is to examine the anatomical bases of these inter-specific and inter-sexual differences by identifying if the acoustic variation is reflected in corresponding anatomical variation. To do this, we investigated the vocal anatomy of male and female specimens of each of these three species. Across species and sexes, we find that the observed acoustic variability is indeed related to expected corresponding anatomical differences, based on the source-filter theory of vocal production. At the source level, low fo is associated with larger vocal folds, whereas high fo is associated with smaller vocal folds: sika deer have the smallest vocal folds and male fallow deer the largest. Red and sika deer vocal folds do not appear to be sexually dimorphic, while fallow deer exhibit strong sexual dimorphism (after correcting for body size differences). At the filter level, the variability in formants is related to the configuration of the vocal tract: in fallow and red deer, both sexes have evolved a permanently descended larynx (with a resting position of the larynx much lower in males than in females). Both sexes also have the potential for momentary, call-synchronous vocal tract elongation, again more pronounced in males than in females. In contrast, the resting position of the larynx is high in both sexes of sika deer and the potential for further active vocal tract elongation is virtually absent in both sexes. Anatomical evidence suggests an evolutionary reversal in larynx position within sika deer, that is, a secondary larynx ascent. Together, our observations confirm that the observed diversity of vocal behaviour in polygynous deer is supported by strong anatomical differences, highlighting the importance of anatomical specializations in shaping mammalian vocal repertoires. Sexual selection is discussed as a potential evolutionary driver of the observed vocal diversity and sexual dimorphisms.

Ecomorphology of the cervid calcaneus as a proxy for paleoenvironmental reconstruction

This study presents new ecomorphological models for the cervid calcaneus that can be used to make predictions about the nature of ancient environments. Using geometric morphometrics to quantitatively assess the length of the articular surface supporting the malleolus, the length and orientation of the tuber calcanei, and the position of the articular facets, we aimed to establish correlations between morphological traits, locomotor behavior, and environmental parameters in extant cervids. The morphology of the calcaneus was found to primarily vary with locomotor strategy and habitat, along a continuum from habitats with an open vegetation structure to habitats with a closed vegetation structure. Confounding factors, including sexual dimorphism, allometry, and phylogeny were accounted for using Principal Component Analysis, regressions and phylogenetic comparative methods. The results of our analyses suggested that these factors did not substantially obscure habitat predictions. As such, the calcaneus provides a valuable proxy for paleoenvironmental reconstruction that is broadly applicable to Quaternary fossil assemblages with a sufficiently large sample of cervids.

Artificial Reproductive Technology (ART) Applied to Female Cervids Adapted from Domestic Ruminants

There are about 150 Cervidae species on the IUCN Red List of Threatened Species. Only a small part is counted among farm animals, and most of them are free roaming. The universality and large numbers of representatives of cervids such as red deer (Cervus elaphus) and roe deer (Capreolus capreolus) may predispose these species to be used as models for research on reintroduction or assisted reproduction of deer at risk of extinction. We outlined the historical fluctuation of cervids in Europe and the process of domestication, which led to breeding management. Consequently, the reproductive techniques used in domestic ruminants were adapted for use in female deer which we reviewed based on our results and other available results. We focused on stress susceptibility in cervids depending on habitat and antropopression and proposed copeptin as a novel diagnostic parameter suitable for stress determination. Some reproductive biotechniques have been adopted for female cervids with satisfactory results, e.g., in vitro fertilization, while others still require methodological refinement, e.g., cryopreservation of oocytes and embryos.

Spatial variation in antler investment of Apennine red deer

Heterogeneity in resource availability and quality can trigger spatial patterns in the expression of sexually selected traits such as body mass and weaponry. While relationships between habitat features and phenotypic quality are well established at broad geographical scales, information is poor on spatial patterns at finer, intrapopulation scales. We analyzed biometric data collected on 1965 red deer Cervus elaphus males over 20 years from a nonmigratory population living on two sides of a mountainous ridge, with substantial differences in land cover and habitat quality but similar climate and population density. We investigate spatial patterns in (i) body mass, (ii) antler mass, and (iii) antler investment. We also tested for site- and age-specific patterns in allometric relationship between body mass and antler mass. Statistically significant fine-scale spatial variations in body mass, antler mass, and, to a lesser extent, antler allocation matched spatial differences in land cover. All three traits were greater in the northern slope, characterized by higher habitat heterogeneity and greater availability of open habitats, than in the southern slope. Moreover, the allometric relationship between body mass and antler mass differed among age-classes, in a pattern that was consistent between the two mountain slopes. Our results support the occurrence of spatial patterns in the expression of individual attributes also at a fine, intrapopulation scale. Our findings emphasize the role of environmental heterogeneity in shaping spatial variations of key life-history traits, with potential consequences for reproductive success.

Confirmed archaeological evidence of water deer in Vietnam: relics of the Pleistocene or a shifting baseline?

Studies of archaeological and palaeontological bone assemblages increasingly show that the historical distributions of many mammal species are unrepresentative of their longer-term geographical ranges in the Quaternary. Consequently, the geographical and ecological scope of potential conservation efforts may be inappropriately narrow. Here, we consider a case-in-point, the water deer Hydropotes inermis, which has historical native distributions in eastern China and the Korean peninsula. We present morphological and metric criteria for the taxonomic diagnosis of mandibles and maxillary canine fragments from Hang Thung Binh 1 cave in Tràng An World Heritage Site, which confirm the prehistoric presence of water deer in Vietnam. Dated to between 13 000 and 16 000 years before the present, the specimens are further evidence of a wider Quaternary distribution for these Vulnerable cervids, are valuable additions to a sparse Pleistocene fossil record and confirm water deer as a component of the Upper Pleistocene fauna of northern Vietnam. Palaeoenvironmental proxies suggest that the Tràng An water deer occupied cooler, but not necessarily drier, conditions than today. We consider if the specimens represent extirpated Pleistocene populations or indicate a previously unrecognized, longer-standing southerly distribution with possible implications for the conservation of the species in the future.

The intriguing giant deer from the Bate cave (Crete): could paleohistological evidence question its taxonomy and nomenclature?

The research describes for the first time a possible case of pituitary gigantism in fossil mammals, precisely in deer. The pathology was detected in 2 long bones (tibia and metatarsus) belonging to an individual of an unusual large size found at the Bate cave (Rethymnon, Northern Crete). It formed the basis of Candiacervus major, the largest among the endemic deer species recorded in the Pleistocene-Early Holocene of Crete. Radiological and histomorphological examinations highlighted a reduction in cortical bone thickness and the presence of wide lacunae inside of the bone tissue. The pathological conditions suggest a pituitary gigantism diagnosis also supported by some morphological evidence, such as the extremely elongated distal part of the metatarsal diaphysis, the proportionally small proximal epiphysis, and some bone gracility. The diagnosis of a case of pituitary gigantism as presumed responsible for the extraordinary elongation of the tibia and the metatarsal bone is intriguing as they are, respectively, the paratype and the holotype of the C. major. The species represents a case of a deviation from the "island rule" in Pleistocene large mammals. The new evidence recommends a taxonomic and nomenclatural revision of this species. The main outcomes of this research are as follows: (i) a case of pituitary gigantism is described for the first time in an extinct mammal; (ii) it is underlined that paleohistology may provide interesting clues for disentangling taxonomic and nomenclatural issues; (iii) one of the very few cases of gigantism in insular mammals is being questioned.

Reassessment of the enigmatic ruminant Miocene genus Amphimoschus Bourgeois, 1873 (Mammalia, Artiodactyla, Pecora)

Amphimoschus is an extinct Eurasian ruminant genus, mostly recorded in Europe, without a close living relative and, hence, an unknown systematic position. This genus is known from around 50 localities from the late early to the middle Miocene. Two species were described during 180 years, but since their first description during the late 19^th century and early 20^th century, hardly any detailed taxonomic work has been done on the genus. Over the years, extensive collecting and excavating activities have enriched collections with more and more complete material of this still rare and enigmatic animal. Most interestingly, a number of skull remains have been unearthed and are promising in terms of providing phylogenetic information. In the present paper, we describe cranial material, the bony labyrinth, the dentition through 780 teeth and five skulls from different ontogenetic stages. We cannot find a clear morphometric distinction between the supposedly smaller and older species Amphimoschus artenensis and the supposedly younger and larger species A. ponteleviensis. Accordingly, we have no reason to retain the two species and propose, following the principle of priority (ICZN chapter 6 article 23), that only A. ponteleviensis Bourgeois, 1873 is valid. Our studies on the ontogenetic variation of Amphimoschus does reveal that the sagittal crest may increase in size and a supraorbital ridge may appear with age. Despite the abundant material, the family affiliation is still uncertain.

Satellite DNA in Neotropical Deer Species

The taxonomy and phylogenetics of Neotropical deer have been mostly based on morphological criteria and needs a critical revision on the basis of new molecular and cytogenetic markers. In this study, we used the variation in the sequence, copy number, and chromosome localization of satellite I-IV DNA to evaluate evolutionary relationships among eight Neotropical deer species. Using FISH with satI-IV probes derived from Mazama gouazoubira, we proved the presence of satellite DNA blocks in peri/centromeric regions of all analyzed deer. Satellite DNA was also detected in the interstitial chromosome regions of species of the genus Mazama with highly reduced chromosome numbers. In contrast to Blastocerus dichotomus, Ozotoceros bezoarticus, and Odocoileus virginianus, Mazama species showed high abundance of satIV DNA by FISH. The phylogenetic analysis of the satellite DNA showed close relationships between O. bezoarticus and B. dichotomus. Furthermore, the Neotropical and Nearctic populations of O. virginianus formed a single clade. However, the satellite DNA phylogeny did not allow resolving the relationships within the genus Mazama. The high abundance of the satellite DNA in centromeres probably contributes to the formation of chromosomal rearrangements, thus leading to a fast and ongoing speciation in this genus, which has not yet been reflected in the satellite DNA sequence diversification.

Species assignment in forensics and the challenge of hybrids

Forensic identification of species is in growing demand, particularly from law enforcement authorities in the areas of wildlife, fisheries and hunting as well as food authentication. Within the non-human forensic genetics expanding applications' field, the major current difficulties result from the lack of standards and genetic databases as well as the poor or absent taxonomic definition of several groups. Here we focus on a forensically important and overlooked problem in species identification: the exclusive use of uniparental markers, a common practice in current genetic barcoding methodologies, may lead to incorrect or impossible assignment whenever hybrids can occur (frequently, not only in domesticates, but also in the wild). For example, if one of these cases involves a mammal, and mitochondrial DNA alone is used (which in instances may be the only type of DNA sequence available in databases), the sample will be wrongfully assigned to the female parental species, completely missing the detection of a possible hybrid animal. The importance of this issue in the forensic contributions to food authentication, wildlife and conservation genetics is analyzed. We present a cautionary guidance on the forensic reporting of results avoiding this error.

A new viewpoint on antlers reveals the evolutionary history of deer (Cervidae, Mammalia)

Recent molecular phylogeny of deer revealed that the characters of antlers previously focused on are homoplasious, and antlers tend to be considered problematic for classification. However, we think antlers are important tools and reconsidered and analysed the characters and structures to use them for classification. This study developed a method to describe the branching structure of antlers by using antler grooves, which are formed on the antlers by growth, and then projecting the position of the branching directions of tines on the burr circumference. By making diagrams, comparing the branching structure interspecifically, homologous elements (tines, beams, and processes) of the antlers of 25 species of 16 genera were determined. Subsequently, ancestral state reconstruction was performed on the fixed molecular phylogenetic tree. It was revealed that Capreolinae and Cervini gained respective three-pointed antlers independently, and their subclades gained synapomorphous tines. We found new homologous and synapomorphous characters, as the antler of Eld’s deer, which has been classified in Rucervus, is structurally close to that of Elaphurus rather than that of Rucervus, consistent with molecular phylogeny. The methods of this study will contribute to the understanding of the branching structure and phylogeny of fossil species and uncover the evolutionary history of Cervidae.