The role of chromosome variation in the speciation of the red brocket deer complex: the study of reproductive isolation in females

Small Fishes, Big Issues: Species Delimitation in Hemigrammus Marginatus, Gill, 1958 (Acestrorhamphidae: Pristellinae) from Brazilian Coastal Basins Based on Integrative Genetics

The small characins represent a systematic puzzle in the Neotropical ichthyofauna as a result of independent miniaturization processes, adaptive convergence and lack of diagnostic characters for several genera. In order to diminish the taxonomic uncertainties and the evolutionary pathways in Hemigrammus, we carried out an integrative genetic analysis in the putatively widespread Hemigrammus marginatus Ellis, 1958 by combining cytogenetic and molecular data based on the mitochondrial Cytochrome C Oxidase subunit I (COI). Specimens of H. marginatus from the type locality in Itapicuru River basin and other two populations from coastal rivers in northeastern Brazil were analyzed and compared with the available data from other regions in South America. Conspicuous macro and microkaryotypic differences were detected between the samples from northeastern and southern Brazil (Upper Paraná River basin). Likewise, the DNA barcoding and species delimitation analyses recovered distinct Molecular Operational Taxonomical Units within H. marginatus. Therefore, the population from the type locality should be referred to as H. marginatus stricto sensu, representing a restricted characin taxon from coastal drainages (including the São Francisco River basin) along northeastern Brazil, while other populations of this small characin fish need to be taxonomically revised and managed as unique lineages.

The role of dispersal of repetitive DNAs in the diversification of bristlenose plecos (Loricariidae, Hypostominae, Ancistrus) from South Atlantic Coastal drainages

Sea-level changes during the Pleistocene and the geomorphological history have largely molded the intricate shaping of coastal drainages in Eastern South America. Therefore, freshwater fishes from this region are promising models to infer how riverine isolation and reconnections affected their genetic diversification and geographic distribution. In the present study, we provided a detailed cytogenomic analysis of Ancistrus multispinis and Ancistrus brevipinnis, including the physical mapping of repetitive DNA classes, to verify whether chromosome differentiation would be related to the split between two major watersheds in Southern Brazil. Both species of Ancistrus shared the same modal diploid number (2n=52) and karyotype formulae (14 metacentric, 8 submetacentric and 30 subtelo/acrocentric chromosomes), besides single and terminal 18S ribosomal cistrons, (CGG)10 microsatellite sequences interspersed with heterochromatin in nucleolar organizer regions and a dispersed content of (AC)15 and (GT)15 microsatellites. In turn, the patterns of heterochromatin distribution, number of (GAG)10 microsatellites and 5S rDNA clusters diverged between both taxa. Most likely, these microstructural differences were determined by independent evolutionary processes, strongly associated to the geographic isolation between watersheds. Furthermore, the mapping of repetitive DNAs revealed a dynamic reorganization of genomes of Ancistrus, being useful for the taxonomic disambiguation in this complex group of Neotropical fish.

Effect of oxytocin and cloprostenol on the seminal parameters of red brocket deer (Mazama rufa) during the electroejaculation procedure

Successful implementation of conservation programs for endangered species requires biological material for use in reproductive biotechnologies. This enhances reproductive efficiency and helps increase the populations of critically endangered species. One way to facilitate the exchange of genetics between captive and free-ranging animals is through the creation of cryogenic banks that store cryopreserved gametes. In particular, semen cryopreservation allows for this exchange to occur. We evaluated whether the use of exogenous hormones (such as oxytocin and prostaglandin) prior to electroejaculation increases seminal volume, sperm concentration, and the number of doses produced in the red brocket deer (Mazama rufa). We also evaluate whether seminal parameters vary over the three stimulation cycles of the same electroejaculation procedure. The treatments did not affect ejaculate volume (p = 0.402), the number of sperm cells in the ejaculates (p = 0.926), total doses produced (p = 0.684), sperm mass movement (p = 0.229), sperm cell concentration (p = 0.106), and acrosome integrity (p = 0.210). The use of hormones has potential in reducing the need for stressful stimuli in electroejaculation, but the choice of hormones must take into account their effects on semen quality.

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.

Karyotypic changes and diversification time in Epinephelidae groupers (Perciformes). Implications on reproductive isolation

Groupers (Epinephelidae and Serranidae) have attracted special attention to fish farming, and their species offer good opportunities for successful hybridizations. Cytogenetic data allow a better understanding of the role of karyotypic diversification in the acquisition of post-zygotic reproductive isolation (RI). Thus, chromosomal analyses were performed on E. striatus (Caribbean Sea), E. coioides and E. tauvina (Indo-Pacific Region), using standard procedures and mapping of six repetitive DNA classes by the in situ hybridization. The three species have 2n=48 chromosomes. The karyotypes of E. coioides and E. striatus are composed only of acrocentric chromosomes (FN=48), while E. tauvina has 8 submetacentric chromosomes (FN=56). Heterochromatin has a preferential centromeric distribution, and the microsatellite repeats are dispersed throughout the chromosomes of all species. The 18S and 5S rDNA sites are unique but show a colocalization arrangement in E. tauvina and E. striatus. The chromosomal organization suggests that the three species still maintain a significant amount of syntenic regions. The range of the karyotype divergence and the RI levels showed low, but goes turn proportionally greater in relation to the divergence time between the parental species. The slow acquisition of postzygotic RI is consistent with the high karyotype homogeneity presented by Epinephelidae family.

Karyotype Diversification and Chromosome Rearrangements in Squamate Reptiles

Karyotype diversification represents an important, yet poorly understood, driver of evolution. Squamate reptiles are characterized by a high taxonomic diversity which is reflected at the karyotype level in terms of general structure, chromosome number and morphology, and insurgence of differentiated simple or multiple-sex-chromosome systems with either male or female heterogamety. The potential of squamate reptiles as unique model organisms in evolutionary cytogenetics has been recognised in recent years in several studies, which have provided novel insights into the chromosome evolutionary dynamics of different taxonomic groups. Here, we review and summarize the resulting complex, but promising, general picture from a systematic perspective, mapping some of the main squamate karyological characteristics onto their phylogenetic relationships. We highlight how all the major categories of balanced chromosome rearrangements contributed to the karyotype evolution in different taxonomic groups. We show that distinct karyotype evolutionary trends may occur, and coexist, with different frequencies in different clades. Finally, in light of the known squamate chromosome diversity and recent research advances, we discuss traditional and novel hypotheses on karyotype evolution and propose a scenario of circular karyotype evolution.

Evaluation of minimally invasive estrus synchronization protocols in brown brocket deer (Subulo gouazoubira)

This study aimed to evaluate minimally invasive protocols for estrus synchronization in the brown brocket deer (Subulo gouazoubira). Females were submitted to Latin square design, in different treatments. All females received 0.25 mg of estradiol benzoate on the first day of treatment, concomitant with one of the following sources of progesterone: (1) DIP: an intravaginal progesterone releasing device for eight days, (2) MGA1x: once a day (in the morning) oral dose of 1 mg melengestrol acetate for eight days, (3) MGA2x: twice a day (morning and afternoon) oral doses of 0.5 mg of MGA for eight days, (4) P4LA: a single i.m. administration of 75 mg of long-acting progesterone (P4LA). Eight days after the beginning of each treatment, females received an i.m. administration of 265 µg of prostaglandin (PGF2α; cloprostenol). Treatment efficacy was evaluated by manifestation of behavioral estrus after treatment and concentration of fecal progesterone metabolites (FPM). The time to onset of estrus in treatment P4LA was significantly longer (180 ± 38.9 h) compared to DIP (63 ± 6.6 h), MGA1x (53 ± 14.4 h) and MGA2x (41 ± 10.1 h) (P = 0.008). According to individual baseline FPM and FPM concentration during the days after estrus, the corpus luteum formation was suggested in all females which responded to the treatments (93.75 %). Low synchrony, longer interval between PGF2α administration and onset of estrus suggest that the P4LA dose (75 mg) is too high and not effective for S. gouazoubira. DIP, MGA 1x and MGA 2x, were effective in estrus synchronization.

Chromosome-length genome assembly and karyotype of the endangered black-footed ferret (Mustela nigripes)

The black-footed ferret (Mustela nigripes) narrowly avoided extinction to become an oft-cited example of the benefits of intensive management, research, and collaboration to save a species through ex situ conservation breeding and reintroduction into its former range. However, the species remains at risk due to possible inbreeding, disease susceptibility, and multiple fertility challenges. Here, we report the de novo genome assembly of a male black-footed ferret generated through a combination of linked-read sequencing, optical mapping, and Hi-C proximity ligation. In addition, we report the karyotype for this species, which was used to anchor and assign chromosome numbers to the chromosome-length scaffolds. The draft assembly was ~2.5 Gb in length, with 95.6% of it anchored to 19 chromosome-length scaffolds, corresponding to the 2n = 38 chromosomes revealed by the karyotype. The assembly has contig and scaffold N50 values of 148.8 kbp and 145.4 Mbp, respectively, and is up to 96% complete based on BUSCO analyses. Annotation of the assembly, including evidence from RNA-seq data, identified 21,406 protein-coding genes and a repeat content of 37.35%. Phylogenomic analyses indicated that the black-footed ferret diverged from the European polecat/domestic ferret lineage 1.6 million yr ago. This assembly will enable research on the conservation genomics of black-footed ferrets and thereby aid in the further restoration of this endangered species.

Chromosome-Length Assembly of the Baikal Seal (Pusa sibirica) Genome Reveals a Historically Large Population Prior to Isolation in Lake Baikal

Pusa sibirica, the Baikal seal, is the only extant, exclusively freshwater, pinniped species. The pending issue is, how and when they reached their current habitat—the rift lake Baikal, more than three thousand kilometers away from the Arctic Ocean. To explore the demographic history and genetic diversity of this species, we generated a de novo chromosome-length assembly, and compared it with three closely related marine pinniped species. Multiple whole genome alignment of the four species compared with their karyotypes showed high conservation of chromosomal features, except for three large inversions on chromosome VI. We found the mean heterozygosity of the studied Baikal seal individuals was relatively low (0.61 SNPs/kbp), but comparable to other analyzed pinniped samples. Demographic reconstruction of seals revealed differing trajectories, yet remarkable variations in Ne occurred during approximately the same time periods. The Baikal seal showed a significantly more severe decline relative to other species. This could be due to the difference in environmental conditions encountered by the earlier populations of Baikal seals, as ice sheets changed during glacial–interglacial cycles. We connect this period to the time of migration to Lake Baikal, which occurred ~3–0.3 Mya, after which the population stabilized, indicating balanced habitat conditions.

Cytogenetic Mapping of Cattle BAC Probes for the Hypothetical Ancestral Karyotype of the Family Cervidae

Cervids are characterized by their greatest karyotypic diversity among mammals. A great diversity of chromosome numbers in notably similar morphological groups leads to the existence of several complexes of cryptic species and taxonomic uncertainties. Some deer lineages, such as those of Neotropical deer, stand out for a rapid chromosomal reorganization and intraspecific chromosome polymorphisms, which have not been properly explored yet. For that reason, we contribute to the study of deer karyotype diversity and taxonomy by producing and characterizing new molecular cytogenetic markers for the gray brocket deer (Subulo gouazoubira), a deer species that retained the hypothetical ancestral karyotype of Cervidae. We used bacterial artificial chromosome (BAC) clones derived from the cattle genome (Bos taurus) as markers, which were hybridized on S. gouazoubira metaphase chromosomes. In total, we mapped 108 markers, encompassing all gray brocket deer chromosomes, except the Y chromosome. The detailed analysis of fluorescent in situ hybridization results showed 6 fissions and 1 fusion as interchromosomal rearrangements that have separated cattle and gray brocket deer karyotypes. Each group of BAC probes derived from bovine chromosome pairs 1, 2, 5, 6, 8, and 9 showed hybridization signals on 2 different chromosomes, while pairs 28 and 26 are fused in tandem in a single acrocentric chromosome in S. gouazoubira. Furthermore, the BAC markers detected the occurrence of intrachromosomal rearrangements in the S. gouazoubira chromosomes homologous to pair 1 and the X chromosome of cattle. We present a karyotypic map of the 108 new markers, which will be of great importance for future karyotypic evolution studies in cervids and, consequently, help in their conservation and taxonomy resolution.

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.

How Important Are Structural Variants for Speciation?

Understanding the genetic basis of reproductive isolation is a central issue in the study of speciation. Structural variants (SVs); that is, structural changes in DNA, including inversions, translocations, insertions, deletions, and duplications, are common in a broad range of organisms and have been hypothesized to play a central role in speciation. Recent advances in molecular and statistical methods have identified structural variants, especially inversions, underlying ecologically important traits; thus, suggesting these mutations contribute to adaptation. However, the contribution of structural variants to reproductive isolation between species—and the underlying mechanism by which structural variants most often contribute to speciation—remain unclear. Here, we review (i) different mechanisms by which structural variants can generate or maintain reproductive isolation; (ii) patterns expected with these different mechanisms; and (iii) relevant empirical examples of each. We also summarize the available sequencing and bioinformatic methods to detect structural variants. Lastly, we suggest empirical approaches and new research directions to help obtain a more complete assessment of the role of structural variants in speciation.

Assisted Reproductive Technology in Neotropical Deer: A Model Approach to Preserving Genetic Diversity

Simple Summary

Deer species in the Neotropical region have undergone a decline of their populations. Although conservation of their natural habitat is considered the best way to assist the species, the speed of occupation of these areas and the anthropic actions are so fast that the efforts are, at times, insufficient. As free-living populations decrease, there is a descent in the genetic diversity and an increase in crossbreeding between related individuals (inbreeding). Genetic diversity is essential for survival, since it enables natural selection to occur, providing adaptation and maintenance of the species. To protect the genetic diversity, it is possible to use reproductive techniques and conserve different types of cells, which can be used in the future to reestablish any alleles that have been lost by the populations.

Abstract

One of the most significant challenges in deer is the ability to maintain genetic diversity, avoiding inbreeding and sustaining population health and reproduction. Although our general knowledge of reproductive physiology is improving, it appears that the application of assisted reproductive technology (ART) will more efficiently advance wildlife conservation efforts and preserve genetic diversity. The purpose of this review is to present the most important results obtained with the use of ART in Neotropical deer. Thus, the state-of-the-art for estrus synchronization, semen technology, artificial insemination, and in vivo embryo production will be presented. In vitro embryo production (IVP) is also a biotechnology that is taking initial steps in deer. In this aspect, the approach with the proteomics of ovarian follicular fluid is being used as a tool for a better understanding of oocyte maturation. Finally, cell banks and the use of interspecific somatic cell nuclear transfer (iSCNT) as well as the use of stem cells for gametes differentiation are promising techniques.

Chromosomal Polymorphism and Speciation: The Case of the Genus Mazama (Cetartiodactyla; Cervidae)

Chromosomal polymorphism plays a major role in speciation processes in mammals with high rates of karyotypic evolution, as observed in the family Cervidae. One remarkable example is the genus Mazama that comprises wide inter- and intra-specific chromosomal variability. To evaluate the impact of chromosomal polymorphisms as reproductive barriers within the genus Mazama, inter-specific hybrids between Mazama gouazoubira and Mazama nemorivaga (MGO × MNE) and intra-specific hybrids between cytotypes of Mazama americana (MAM) differing by a tandem (TF) or centric fusion (Robertsonian translocations—RT) were evaluated. MGO × MNE hybrid fertility was evaluated by the seminal quality and testicular histology. MAM hybrids estimation of the meiotic segregation products was performed by sperm-FISH analysis. MGO × MNE hybrids analyses showed different degrees of fertility reduction, from severe subfertility to complete sterility. Regarding MAM, RT, and TF carriers showed a mean value for alternate segregation rate of 97.74%, and 67.23%, and adjacent segregation rate of 1.80%, and 29.07%, respectively. Our results suggested an efficient post-zygotic barrier represented by severe fertility reduction for MGO × MNE and MAM with heterozygous TF. Nevertheless, RT did not show a severe effect on the reproductive fitness in MAM. Our data support the validity of MGO and MNE as different species and reveals cryptic species within MAM.

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.

Collection and in vitro maturation of Mazama gouazoubira (brown brocket deer) oocytes obtained after ovarian stimulation

In vitro production of embryos has gained prominence as a tool for use in wildlife conservation programmes in situ and ex situ. However, the development of this technique depends on steps that include ovarian stimulation, collection and oocyte maturation. The purpose of this study was to assess the feasibility of an ovarian stimulation protocol for follicular aspiration, the efficiency of videolaparoscopy for follicular aspiration and test a medium for in vitro oocyte maturation for the species Mazama gouazoubira. Five females were submitted to repeated ovarian stimulation (hormone protocol using controlled internal drug release), and estradiol benzoate on D0 and eight injections of follicle-stimulating hormone, once every 12 h, from D4 onwards at 30-day intervals. Fourteen surgical procedures were performed in superstimulated females, resulting in the collection of 94 oocytes and an average of 17.1 ± 9.1 follicles observed, 13.5 ± 6.6 follicles aspirated and 7.2 ± 3.7 oocytes collected per surgery. After collection, the oocytes were submitted to in vitro maturation for 24 h and stained with Hoechst 33342 dye to evaluate their nuclear status; 64.5% of the oocytes reached MII and 16.1% were spontaneously activated by parthenogenesis. The nuclear status of oocytes that did not undergo in vitro maturation was evaluated; 80.9% were found to be immature.

Low invasive estrous synchronization protocol for wild animals: an example with melengestrol acetate in brown brocket deer (Mazama gouazoubira)

Deer are sensitive to stressful stimuli by handling and their reproductive physiology could be altered by these procedures, making it necessary to develop less invasive protocols for ART. Melengestrol acetate (MGA), a synthetic progestin administered orally, appears as an alternative for estrous synchronization protocols (ESP), such as reported in cattle. Firstly, we compared two MGA doses (0.5 and 1.0 mg/day/animal), which would have suppression effect in estrous behavior (EB). Eight females were randomly and equally distributed in Group 1 (G1) and Group 2 (G2), which received 0.5 and 1.0 mg/day/animal respectively for 15 days (D1 to D15). Two cloprostenol (CP) applications were performed on D0 and D11. Estrus detection (ED) was performed every day. All females from G1 displayed estrus during treatment period, whereas all females from G2 displayed estrus after treatment, suggesting a suppressive effect of 1.0 mg in the EB. Once the suppressive MGA dose (1.0 mg) was defined, we used this dose for assessing ESP. The same eight females received 1.0 mg/animal for eight days (D-8 to D-1), followed by 0.25 mg of estradiol benzoate on D-8 and 265 μg of CP on D0. Feces for fecal progesterone metabolites (FPM) measurement were collected from D0 until seven days after the last day of estrus. Seven females displayed estrus between 12 and 72 h after CP application, which was followed by a significant increase in FPM levels (except female MG6), suggesting the formation of corpus luteum. After ED, females were placed with a fertile male to assess the fertility of the protocol. Pregnancy was confirmed by ultrasound 30 days after mating in 3/6 individuals. Although the low effectiveness of MGA protocol, it should be considered as a promising alternative in deer ESP since this protocol has less stressful effect on the animal during reproductive management when compared to other ESP.

Designation of a neotype for Mazama americana (Artiodactyla, Cervidae) reveals a cryptic new complex of brocket deer species

Mazamaamericana (red brocket deer) is the genus-type species (first species described for this genus) and the basis for the identity of other Mazama species. Mazamaamericana is one of the most abundant and widely distributed deer species in the neotropical forest. However, recent studies suggest that this taxon belongs to a species complex. Our goal was to collect an animal at the type locality (topotype) in French Guiana with the aim of characterizing the morphological (biometric, craniometric), cytogenetic (Giemsa, C-banding, G-banding and NOR) and molecular (mitochondrial DNA) features. The comparisons showed that the collected specimen was very similar morphologically to specimens from other South American populations, but it was cytogenetically and molecularly very different from any of the cytotypes already described for this species, corroborating the existence of a complex of cryptic species. The data suggest that the M.americana topotype is a different species from all the cytotypes already described in the literature and which occupy the southern region of the Amazon River. The characterization and designation of the M.americana neotype is the first step toward a taxonomic reorganization of the genus Mazama, with the potential identification of new species.

In Vitro Development and Mitochondrial Gene Expression in Brown Brocket Deer (Mazama gouazoubira) Embryos Obtained by Interspecific Somatic Cell Nuclear Transfer

The genetic diversity of Neotropical deer is increasingly jeopardized, owing to declining population size. Thus, the formation of cryobanking of somatic cells is important for the preservation of these species using cloning. The transformation of these cells into viable embryos has been hampered by a lack of endangered species oocytes. Accordingly, the aim of this study was to produce brown brocket deer embryos by interspecific somatic cell nuclear transfer (iSCNT), using goat or cattle oocytes as cytoplasts, and to elucidate embryo mitochondrial activity by measuring the expression levels of ATP6, COX3, and ND5. Cattle embryos produced by in vitro fertilization (IVF) were used as a control. There were no differences in the development of embryos produced by traditional SCNT and iSCNT when using either the goat cytoplasts (38.4% vs. 25.0% cleaved and 40.0% vs. 50.0% morula rates, respectively) or cattle cytoplast (72.8% vs. 65.5% cleaved and 11.3% vs. 5.9% blastocyst rates, respectively). Concerning the gene expression, no significant difference was observed when goat oocytes were used as cytoplasts. However, when using cattle oocytes and 16S as a reference gene, the iSCNT upregulated COX3, when compared with SCNT group. In contrast, when GAPDH was used as a reference gene, all the evaluated genes were upregulated in the iSCNT group, when compared with the IVF group. When compared with the SCNT group, only the expression of ATP6 was statistically different. In conclusion, it was demonstrated that interspecific nuclear transfer is a potentially useful tool for conservation programs of endangered similar deer species.

Prevalence of chromosome anomalies in a deer farm with fertility decline in Malaysia

BACKGROUND

A number of factors are known to reduce fertility rate in animals and one of the important categories of such factors is chromosome anomalies. They can occur with or without causing phenotypic abnormalities on animals; in some cases, they may directly affect meiosis, gametogenesis and the viability of conceptus. In many instances, balanced structural rearrangements can be transmitted to offspring, affecting fertility in subsequent generations.

AIM

This work investigated the occurrence of chromosome aberrations in Rusa timorensis, Rusa unicolor and Axis axis raised in a nucleus deer farm in Malaysia with a history of declining fertility of unknown origin.

MATERIALS & METHODS

Blood samples were collected from 60 animals through venipuncture, cultured for 72 h and arrested at metaphase. SmartType® and Ideokar® software were used to karyotype the chromosomes.

RESULTS

We found 15 out of the 60 animals screened from both sexes harbor some form of chromosome aberration. Chromosomal aberrations exist at the rate of 25% and may not be unconnected with the observed reduced fertility on the farm. Further investigations should be carried out, especially on the offspring of the studied animals to transmission of these aberrations. The animals that are confirmed to transmit the chromosomal aberrations should be culled to arrest the propagation of their abnormalities.

Acoustic parameters of courtship and human-directed friendly vocalisations in seven species of Neotropical deer in captivity

Context Polygynous deer rut vocalisations have been found to be highly conspicuous, typical of the species and important in sexual selection. Information about vocalisations is not available for Neotropical species (subfamily Odocoileinae). Aims The objective was to record courtship vocalisations from all Neotropical deer available, looking for differences among species useful for taxonomic identification, characterise the vocalisations according to acoustic parameters and to try to determine functions. Methods Four species of brocket deer (red, Mazama americana (n = 9); grey, M. gouazoubira (n = 7); Amazonian brown, M. nemorivaga (n = 3); Brazilian dwarf, M. nana (n = 1)), and one individual each of marsh (Blastocerus dichotomus), white-tailed (Odocoileus virginianus) and taruca (Hippocamellus antisensis) deer were recorded in captivity at two institutions, in conditions of courtship or human interaction. The acoustic analysis was performed with Praat. Data from the first three species of Mazama were analysed statistically with a multilevel model with two layers. Key results In the context of courting either females or humans, male deer produced low-intensity, short-duration (0.1–0.3 s) bleats with fundamental frequencies (F0) between 100 and 400 Hz; calls were similar among species. The duration of these calls for Amazonian brown brocket males was significantly longer than for males of the other two species. Females of two species had longer-duration calls than did males, in friendly interactions with humans. F0 differences among species for both friendly and courtship calls were almost significant for males of M. gouazoubira. Individual differences were highly significant for both duration and mean F0. Mean F0 for courtship calls of adult males was not correlated with body size in six of the seven species, in contrast to the theory of acoustic allometry. Conclusions The production of male courtship bleats is probably a basic feature of Odocoiline deer and is probably important in sexual selection and female choice. The differences from one species to another are not sufficient for taxonomic use but may be incipient isolating mechanisms between grey and Amazonian brown brocket deer. Implications Studies of deer vocalisations have shown their importance in sexual selection and their incredible variety in closely related species and subspecies, but they have dealt mainly with Old World deer. This study fills a gap in our knowledge, as the first on Neotropical deer, which constitute six genera and 17 species and are widely distributed in the Americas. These data are important for future studies on the function and phylogeny of deer vocalisations.

Azaperone and xylazine: A pharmacological combination to facilitate captive deer management for red brocket deer (Mazama americana)

The care and management of deer in captivity is challenging, especially in the case of red brocket deer (Mazama americana), whose routine management using physical restraint is difficult. Our study evaluated the effects of azaperone and xylazine combination for immobilizing red brocket deer and allow for the standard capture and handling protocols (e.g., biological material, horn cutting, and trimming) to be conducted safely. Six adult, captive, red brocket deer received an intramuscular injection of either 1 mg/kg azaperone and 0.5 mg/kg xylazine (AX0.5) or 1 mg/kg azaperone and 1 mg/kg xylazine (AX1.0). Sedation latency, sternal recumbency, safe handling, and quality of the sedation were evaluated to provide an overview of how the immobilizing drugs affected managing the species in captivity. Additionally, heart rate, respiratory rate, mean arterial pressure, rectal temperature, pH, PaO₂, PaCO₂, SaO₂, HCO₃^-, BE, Na⁺, K⁺ and serum lactate were also measured. The latency period of the animals in the AX0.5 group was greater than that of the animals in the AX1.0 group (7 ± 6.6 min vs. 5 ± 2.0 min), as was the time for them to assume sternal recumbency (12 ± 9.7 min vs. 6 ± 3.1 min). However, the time after the initial dose at which the animals could safely be handled (14 ± 4.5 min vs. 12 ± 5.2 min), and the time until the end of the safe handling period (75 ± 12.3 min vs. 85 ± 6.8 min) were similar for both groups. Animals in both groups showed physiological stability during all evaluations, but hypoxemia was observed in one animal in each group. We conclude that both drug combinations are safe and effective at sedating red brocket deer in captivity and suggest that the procedure be performed with oxygen supplementation to reduce the potential for hypoxia.

Intraspecific chromosome polymorphisms can lead to reproductive isolation and speciation: an example in red brocket deer (Mazama americana)

The red brocket (Mazama americana) is a South American deer with a wide geographical distribution that presents different chromosomal variants depending on their location. At least six different cytotypes belonging to two distinct evolutionary lineages have been described. This study aimed to verify the existence of postzygotic reproductive isolation between cytotypes of M. americana by comparative evaluation of pure and hybrid males. Seven 18-month-old bucks were submitted to seminal collection and evaluation and testicle histological evaluations. The pure males showed normal parameters for sperm quality and testicular histology. Hybrids from the same evolutionary lineage (≤3 chromosomes different from the progenitors) showed similar results to pure males, except for the reduced ratio of round spermatids to pachytene spermatocytes. Hybrids between cytotypes of different evolutionary lineages (≥10 chromosomes different from progenitors) presented azoospermia and evidence of testicular degeneration. Despite the striking morphological similarities, we can conclude that populations with more distinct karyotypes possess an effective reproductive barrier; moreover, there is evidence that reproductive isolation mechanisms exist between some closer karyotypes, corroborating the hypothesis that M. americana is best characterized as a superspecies. Thus, the future description of several new species for this taxon is expected, since the tendency is to establish efficient mechanisms of postzygotic reproductive isolation, preventing the introgression and fusion of genomes from different populations through chromosome variation.

Intrapopulation Chromosomal Polymorphism in Mazama gouazoubira (Cetartiodactyla; Cervidae): The Emergence of a New Species?

Mazama gouazoubira is a small deer species widely distributed in South America. Previous studies have shown that this species presents intraspecific chromosomal polymorphisms, which could affect fertility due to the effects of chromosomal rearrangements on gamete formation. Important aspects regarding the karyotype evolution of this species and the genus remain undefined due to the lack of information concerning the causes of this chromosomal variation. Nineteen individuals belonging to the Mazama gouazoubira population located in the Pantanal were cytogenetically evaluated. Among the individuals analyzed, 9 had B chromosomes and 5 carried a heterozygous centric fusion (2n = 69 and FN = 70). In 3 individuals, the fusion occurred between chromosomes X and 16, in 1 individual between chromosomes 7 and 21, and in another individual between chromosomes 4 and 16. These striking polymorphisms could be explained by several hypotheses. One is that the chromosome rearrangements in this species are recent and not fixed in the population yet, and another hypothesis is that they represent a balanced polymorphism and that heterozygotes have an adaptive advantage. On the other hand, these polymorphisms may negatively influence fertility and raise questions about sustainability or reproductive isolation of the population.

A gene-tree test of the traditional taxonomy of American deer: the importance of voucher specimens, geographic data, and dense sampling

The taxonomy of American deer has been established almost entirely on the basis of morphological data and without the use of explicit phylogenetic methods; hence, phylogenetic analyses including data for all of the currently recognized species, even if based on a single gene, might improve current understanding of their taxonomy. We tested the monophyly of the morphology-defined genera and species of New World deer (Odocoileini) with phylogenetic analyses of mitochondrial DNA sequences. This is the first such test conducted using extensive geographic and taxonomic sampling. Our results do not support the monophyly of Mazama, Odocoileus, Pudu, M. americana, M. nemorivaga, Od. hemionus, and Od. virginianus. Mazama contains species that belong to other genera. We found a novel sister-taxon relationship between "Mazama" pandora and a clade formed by Od. hemionus columbianus and Od. h. sitkensis, and transfer pandora to Odocoileus. The clade formed by Od. h. columbianus and Od. h. sitkensis may represent a valid species, whereas the remaining subspecies of Od. hemionus appear closer to Od. virginianus. Pudu (Pudu) puda was not found sister to Pudu (Pudella) mephistophiles. If confirmed, this result will prompt the recognition of the monotypic Pudella as a distinct genus. We provide evidence for the existence of an undescribed species now confused with Mazama americana, and identify other instances of cryptic, taxonomically unrecognized species-level diversity among populations here regarded as Mazama temama, "Mazama" nemorivaga, and Hippocamelus antisensis. Noteworthy records that substantially extend the known distributions of M. temama and "M." gouazoubira are provided, and we unveil a surprising ambiguity regarding the distribution of "M." nemorivaga, as it is described in the literature. The study of deer of the tribe Odocoileini has been hampered by the paucity of information regarding voucher specimens and the provenance of sequences deposited in GenBank. We pinpoint priorities for future systematic research on the tribe Odocoileini.

Using sperm morphometry and multivariate analysis to differentiate species of gray Mazama

There is genetic evidence that the two species of Brazilian gray Mazama, Mazama gouazoubira and Mazama nemorivaga, belong to different genera. This study identified significant differences that separated them into distinct groups, based on characteristics of the spermatozoa and ejaculate of both species. The characteristics that most clearly differentiated between the species were ejaculate colour, white for M. gouazoubira and reddish for M. nemorivaga, and sperm head dimensions. Multivariate analysis of sperm head dimension and format data accurately discriminated three groups for species with total percentage of misclassified of 0.71. The individual analysis, by animal, and the multivariate analysis have also discriminated correctly all five animals (total percentage of misclassified of 13.95%), and the canonical plot has shown three different clusters: Cluster 1, including individuals of M. nemorivaga; Cluster 2, including two individuals of M. gouazoubira; and Cluster 3, including a single individual of M. gouazoubira. The results obtained in this work corroborate the hypothesis of the formation of new genera and species for gray Mazama. Moreover, the easily applied method described herein can be used as an auxiliary tool to identify sibling species of other taxonomic groups.

Extensive Chromosomal Reorganization in the Evolution of New World Muroid Rodents (Cricetidae, Sigmodontinae): Searching for Ancestral Phylogenetic Traits

Sigmodontinae rodents show great diversity and complexity in morphology and ecology. This diversity is accompanied by extensive chromosome variation challenging attempts to reconstruct their ancestral genome. The species Hylaeamys megacephalus–HME (Oryzomyini, 2n = 54), Necromys lasiurus—NLA (Akodontini, 2n = 34) and Akodon sp.–ASP (Akodontini, 2n = 10) have extreme diploid numbers that make it difficult to understand the rearrangements that are responsible for such differences. In this study we analyzed these changes using whole chromosome probes of HME in cross-species painting of NLA and ASP to construct chromosome homology maps that reveal the rearrangements between species. We include data from the literature for other Sigmodontinae previously studied with probes from HME and Mus musculus (MMU) probes. We also use the HME probes on MMU chromosomes for the comparative analysis of NLA with other species already mapped by MMU probes. Our results show that NLA and ASP have highly rearranged karyotypes when compared to HME. Eleven HME syntenic blocks are shared among the species studied here. Four syntenies may be ancestral to Akodontini (HME2/18, 3/25, 18/25 and 4/11/16) and eight to Sigmodontinae (HME26, 1/12, 6/21, 7/9, 5/17, 11/16, 20/13 and 19/14/19). Using MMU data we identified six associations shared among rodents from seven subfamilies, where MMU3/18 and MMU8/13 are phylogenetic signatures of Sigmodontinae. We suggest that the associations MMU2entire, MMU6proximal/12entire, MMU3/18, MMU8/13, MMU1/17, MMU10/17, MMU12/17, MMU5/16, MMU5/6 and MMU7/19 are part of the ancestral Sigmodontinae genome.