Molecular Phylogeny of Deer (Cervidae: Artiodactyla)

A review of the genus Rusa in the indo-malayan archipelago and conservation efforts

Genus Rusa, belonging to the deer family Cervidae is native to the Indo-Malaya Archipelago (IMA). However, detailed information on the Rusa genus in the IMA is limited. This review provides comprehensive information on the Rusa genus in the IMA including, threats and conservation efforts. There are four species of deer in Rusa genus, which is Sambar deer (Rusa unicolor), Javan deer (Rusa timorensis), Visayan spotted deer (Rusa alfredi) and Philippine deer (Rusa marianna). Despite their wide distribution in the South Asian and Southeast Asian regions, they are under serious threats. Some conservation efforts that are being done to protect and conserve them among others are; (1) facilities protection, (2) habitat enrichment programme, (3) Ex-situ conservation, (4) legislations, and (5) captive breeding. Conservation through genetics is also an important step in conserving these species. Recommendations for conservation of the genus are also discussed; 1. maintenance of ecosystem. 2. more effective monitoring system on the existing protected area. 3. ex-situ conservation, and 4. habitat monitoring.

The systematics of the Cervidae: a total evidence approach

Systematic relationships of cervids have been controversial for decades. Despite new input from molecular systematics, consensus could only be partially reached. The initial, gross (sub) classification based on morphology and comparative anatomy was mostly supported by molecular data. The rich fossil record of cervids has never been extensively tested in phylogenetic frameworks concerning potential systematic relationships of fossil cervids to extant cervids. The aim of this work was to investigate the systematic relationships of extant and fossil cervids using molecular and morphological characters and make implications about their evolutionary history based on the phylogenetic reconstructions. To achieve these objectives, molecular data were compiled consisting of five nuclear markers and the complete mitochondrial genome of 50 extant and one fossil cervids. Several analyses using different data partitions, taxon sampling, partitioning schemes, and optimality criteria were undertaken. In addition, the most extensive morphological character matrix for such a broad cervid taxon sampling was compiled including 168 cranial and dental characters of 41 extant and 29 fossil cervids. The morphological and molecular data were analysed in a combined approach and other comprehensive phylogenetic reconstructions. The results showed that most Miocene cervids were more closely related to each other than to any other cervids. They were often positioned between the outgroup and all other cervids or as the sister taxon to Muntiacini. Two Miocene cervids were frequently placed within Muntiacini. Plio- and Pleistocene cervids could often be affiliated to Cervini, Odocoileini or Capreolini. The phylogenetic analyses provide new insights into the evolutionary history of cervids. Several fossil cervids could be successfully related to living representatives, confirming previously assumed affiliations based on comparative morphology and introducing new hypotheses. New systematic relationships were observed, some uncertainties persisted and resolving systematics within certain taxa remained challenging.

Whole-genome sequencing of wild Siberian musk deer (Moschus moschiferus) provides insights into its genetic features

Background

Siberian musk deer, one of the seven species, is distributed in coniferous forests of Asia. Worldwide, the population size of Siberian musk deer is threatened by severe illegal poaching for commercially valuable musk and meat, habitat losses, and forest fire. At present, this species is categorized as Vulnerable on the IUCN Red List. However, the genetic information of Siberian musk deer is largely unexplored.

Results

Here, we produced 3.10 Gb draft assembly of wild Siberian musk deer with a contig N50 of 29,145 bp and a scaffold N50 of 7,955,248 bp. We annotated 19,363 protein-coding genes and estimated 44.44% of the genome to be repetitive. Our phylogenetic analysis reveals that wild Siberian musk deer is closer to Bovidae than to Cervidae. Comparative analyses showed that the genetic features of Siberian musk deer adapted in cold and high-altitude environments. We sequenced two additional genomes of Siberian musk deer constructed demographic history indicated that changes in effective population size corresponded with recent glacial epochs. Finally, we identified several candidate genes that may play a role in the musk secretion based on transcriptome analysis.

Conclusions

Here, we present a high-quality draft genome of wild Siberian musk deer, which will provide a valuable genetic resource for further investigations of this economically important musk deer.

Exploring genetic diversity and phylogenic relationships of Chinese cattle using gene mtDNA 16S rRNA

The objective of this research was to characterize the genetic diversity and phylogenetic diversity among 12 cattle breeds (10 Chinese breeds and two foreign taurine breeds as controls) utilizing gene mtDNA 16S rRNA. The complete sequences of the mtDNA 16S rRNA genes of the 251 animals were 1570 bp long. The mean percentages of the four nitrogen bases were 37.8 % for adenine (A), 23.7 % for thymine (T), 20.9 % for cytosine (C), and 17.6 % for guanine (G). The mtDNA 16S rRNA gene base percentages had a strong bias towards A  +  T. All detected nucleotide variations in gene mtDNA 16S rRNA were either transitions (62.3 %) or transversions (37.7 %); no indels (insertions and deletions) were found. A total of 40 haplotypes were constructed based on these mutations. A total of 36 haplotypes of these 40 haplotypes were present in 10 Chinese cattle breeds. The haplotype diversity of all Chinese cattle populations was 0.903 ± 0.077 , while the nucleotide diversity was 0.0071 ± 0.0039 . Kimura's two-parameter genetic distances between pairs of the studied 12 breeds ranged from 0.001 to 0.010. The phylogenetic analysis assigned the 10 Chinese breeds to two distinct lineages that likely differed in their percentage of Bos taurus and Bos indicus ancestry.

Characterization of the complete mitogenome of Indian Mouse Deer, Moschiola indica (Artiodactyla: Tragulidae) and its evolutionary significance

The mitochondrial genome of Indian mouse deer (Moschiola indica) was sequenced, assembled and characterized for the first time using 22 pairs of polymerase chain reaction (PCR) primers. The mitogenome of M. indica which is 16,444 bp in size was found very similar to most vertebrates in organisation that harbours 13 protein-coding genes, 22 transfer RNA, 2 ribosomal RNA and 1A + T-rich region. Its comparison with over 52 mitogenomes of the order Artiodactyla, showed a conserved nature of gene organisation, codon usage, gene orientation and evolutionary rates of proteins except that M. indica possesses an extra copy of trnF. The complete mitogenome and protein-coding genes of M. indica were found to be highly A + T biased. Rate of protein evolution was highest in atp8 and lowest in cox3. Further, a higher purifying selection pressure was found to be acting on family Tragulidae compared to Bovidae and Cervidae. The phylogenetic analysis of M. indica placed the Tragulidae as sister-group of all other ruminants, similar to previous analyses. Moschiola forms the sister-group to the other two tragulid genera Tragulus (from Asia) and Hyemoschus (from Africa), which is unexpected as usually the Asian species are thought to form a monophyletic group.

Bony labyrinth morphology clarifies the origin and evolution of deer

Deer are an iconic group of large mammals that originated in the Early Miocene of Eurasia (ca. 19 Ma). While there is some consensus on key relationships among their members, on the basis of molecular- or morphology-based analyses, or combined approaches, many questions remain, and the bony labyrinth has shown considerable potential for the phylogenetics of this and other groups. Here we examine its shape in 29 species of living and fossil deer using 3D geometric morphometrics and cladistics. We clarify several issues of the origin and evolution of cervids. Our results give new age estimates at different nodes of the tree and provide for the first time a clear distinction of stem and crown Cervidae. We unambiguously attribute the fossil Euprox furcatus (13.8 Ma) to crown Cervidae, pushing back the origin of crown deer to (at least) 4 Ma. Furthermore, we show that Capreolinae are more variable in bony labyrinth shape than Cervinae and confirm for the first time the monophyly of the Old World Capreolinae (including the Chinese water deer Hydropotes) based on morphological characters only. Finally, we provide evidence to support the sister group relationship of Megaloceros giganteus with the fallow deer Dama.

Systematic relationships of five newly sequenced cervid species

Cervid phylogenetics has been puzzling researchers for over 150 years. In recent decades, molecular systematics has provided new input for both the support and revision of the previous results from comparative anatomy but has led to only partial consensus. Despite all of the efforts to reach taxon-wide species sampling over the last two decades, a number of cervid species still lack molecular data because they are difficult to access in the wild. By extracting ancient DNA from museum specimens, in this study, we obtained partial mitochondrial cytochrome b gene sequences for Mazama bricenii, Mazama chunyi, Muntiacus atherodes, Pudu mephistophiles, and Rusa marianna, including three holotypes. These new sequences were used to enrich the existing mitochondrial DNA alignments and yielded the most taxonomically complete data set for cervids to date. Phylogenetic analyses provide new insights into the evolutionary history of these five species. However, systematic uncertainties within Muntiacus persist and resolving phylogenetic relationships within Pudu and Mazama remain challenging.

Multi level ecological fitting: indirect life cycles are not a barrier to host switching and invasion

Many invasive species are able to escape from coevolved enemies and thus enjoy a competitive advantage over native species. However, during the invasion phase, non-native species must overcome many ecological and/or physiological hurdles before they become established and spread in their new habitats. This may explain why most introduced species either fail to establish or remain as rare interstitials in their new ranges. Studies focusing on invasive species have been based on plants or animals where establishment requires the possession of preadapted traits from their native ranges that enables them to establish and spread in their new habitats. The possession of preadapted traits that facilitate the exploitation of novel resources or to colonize novel habitats is known as 'ecological fitting'. Some species have evolved traits and life histories that reflect highly intimate associations with very specific types of habitats or niches. For these species, their phenological windows are narrow, and thus the ability to colonize non-native habitats requires that a number of conditions need to be met in accordance with their more specialized life histories. Some of the strongest examples of more complex ecological fitting involve invasive parasites that require different animal hosts to complete their life cycles. For instance, the giant liver fluke, Fascioloides magna, is a major parasite of several species of ungulates in North America. The species exhibits a life cycle whereby newly hatched larvae must find suitable intermediate hosts (freshwater snails) and mature larvae, definitive hosts (ungulates). Intermediate and definitive host ranges of F. magna in its native range are low in number, yet this parasite has been successfully introduced into Europe where it has become a parasite of native European snails and deer. We discuss how the ability of these parasites to overcome multiple ecophysiological barriers represents an excellent example of 'multiple-level ecological fitting'.

Life history and biology of Fascioloides magna (Trematoda) and its native and exotic hosts

Host-parasite interactions are model systems in a wide range of ecological and evolutionary fields and may be utilized for testing numerous theories and hypotheses in terms of both applied and fundamental research. For instance, they are important in terms of studying coevolutionary arms races, species invasions, and in economic terms the health of livestock and humans. Here, I present a comprehensive description of the life history, biogeography, and biology of the giant liver fluke, Fascioloides magna, and both its intermediate and definitive hosts. F. magna is native to North America where it uses several species of freshwater snails (Lymnaeidae) as intermediate hosts and four main species of ungulates as definitive hosts. The fluke has also been introduced into parts of Europe where it is now established in two lymnaeid snail species and three ungulate species. This study gives a comprehensive description of different developmental stages of the fluke in its two host classes, as well as detailed notes on historical and present distributions of F. magna in North America and Europe as well as in its snail and deer hosts (with range maps provided). Aberrant and dead-end hosts are also discussed in detail, and descriptive phylogenies are provided for all of the organisms. I briefly discuss how F. magna represents a model example of multiple-level ecological fitting, a phenomenon not yet described in the empirical literature. Lastly, I explore possible future scenarios for fluke invasion in Europe, where it is currently expanding its range.

Immunolocalization of cytoskeletal proteins in the testes of two Asian cervids: water deer (Hydropotes inermis) and Reeves' muntjac (Muntiacus reevesi)

In order to gather basic reproductive information of the water deer and Reeves' muntjac, the immunolocalization of the cytoskeleton proteins in the testes and epididymides of these two species was investigated. The distribution pattern of cytoskeletal proteins in these two species was similar. The desmin was detected in the peritubular myoid cells of the testes and the sub-epithelial cells of the epididymal ducts. Vimentin was observed in the myoid cells, Leydig cells and perinuclear region of the Sertoli cells. Intense immunoreactions for α-smooth muscle actin were restricted to the smooth vascular muscle cells and the peritubular myoid cells in the testes. From the present results, it appears that these distribution patterns of cytoskeletal proteins may be common in the cervids.