Phylogenomics of several deer species revealed by comparative chromosome painting with Chinese muntjac paints

A set of Chinese muntjac (Muntiacus reevesi) chromosome-specific paints has been hybridized onto the metaphases of sika deer (Cervus nippon, CNI, 2n = 66), red deer (Cervus elaphus, CEL, 2n = 62) and tufted deer (Elaphodus cephalophus, ECE, 2n = 47). Thirty-three homologous autosomal segments were detected in genomes of sika deer and red deer, while 31 autosomal homologous segments were delineated in genome of tufted deer. The Chinese muntjac chromosome X probe painted to the whole X chromosome, and the chromosome Y probe gave signals on the Y chromosome as well as distal region of the X chromosome of each species. Our results confirmed that exclusive Robertsonian translocations have contributed to the karyotypic evolution of sika deer and red deer. In addition to Robertsonian translocation, tandem fusions have played a more important role in the karyotypic evolution of tufted deer. Different types of chromosomal rearrangements have led to great differences in the genome organization between cervinae and muntiacinae species. Our analysis testified that six chromosomal fissions in the proposed 2n = 58 ancestral pecoran karyotype led to the formation of 2n = 70 ancestral cervid karyotype and the deer karyotypes is more derived compare with those of bovid species. Combining previous cytogenetic and molecular systematic studies, we analyzed the genome phylogeny for 11 cervid species.     

Phylogeography,population genetics and conservation of the European red deer Cervus elaphus

• 1 During the Last Glacial Maximum, European red deer Cervus elaphus occurred in refugia in Iberia/southern France, Italy, the Balkans and the Carpathians. Most of Europe, including large parts of the east and north‐east, is now inhabited by red deer from the western lineage. The eastern lineage is largely confined to south‐eastern Europe; a third lineage comprises Sardo‐Corsican and Barbary red deer.
• 2 Sardo‐Corsican, Barbary and Mesola red deer are genetically unique units. They exhibit low levels of genetic diversity and deserve particular protection, since conservation strategies should target genetic information.
• 3 Hybridization between sika Cervus nippon and red deer occurs rarely, but may lead to extensive introgression, particularly in parts of the British Isles. Further expansion of both species may lead to increased hybridization in continental Europe.
• 4 Although hunting has an impact on red deer gene pools, the main threat today is habitat fragmentation in human‐dominated landscapes. The resulting increase in genetic drift and inbreeding reduces variability in isolated populations and may lead to inbreeding depression. To support vital meta‐populations, migration corridors should be established.

     

Red and sika deer in the British Isles,current management issues and management policy

The red deer (Cervus elaphus) is one of the most widely distributed species of deer in Europe. Due to its economic value as game species or its negative impacts on forestry, agriculture and conservation areas, most populations are currently managed, with strategies and intensity of the management varying between countries. In Britain, and less certainly in Ireland, red deer have been continuously present since the end of the last glaciation and constitute the largest population of red deer in Europe. Although they thrived in the past when forests were abundant, the current distribution of red deer in the British Isles is uneven, with the largest numbers being found in Scotland and few and more localised populations in England, Wales and the Republic of Ireland. In the British Isles, as in many other parts of Europe, there is a long history of man interacting with deer populations including local extinctions, multiple translocations and introductions of exotic species of deer. Among introduced exotic species of deer, the Japanese sika (Cervus nippon) is the one of most concern. After introduction of small numbers at multiple locations in Britain and Ireland from 1860 onwards, sika have increased in population number and range in areas with good forest cover, and where they overlap with red deer there is a risk of hybridisation. Due to recent increases in numbers and range of red and sika deer, both species pose a range of management challenges which are not easy to solve. In this review we summarise the history and status of these two species in Great Britain and Ireland, describe current management and discuss management options for the future.     

Introgression of exotic Cervus (nippon and canadensis) into red deer (Cervus elaphus) populations in Scotland and the English Lake District

Since the mid‐19th century, multiple introductions of Japanese sika deer (Cervus nippon nippon) and North American wapiti (C. canadensis) have taken place in the British Isles. While wapiti have generally been unsuccessful, sika have been very successful, especially in Scotland where they now overlap at least 40% of the range of native red deer (C. elaphus). Hybridization between these two species and red deer has been demonstrated in captivity and in the wild. Using a panel of 22 microsatellite loci that are highly diagnostic between red deer and sika, and moderately diagnostic between red deer and wapiti, we investigated the extent of introgression between these species in 2,943 deer sampled from around Scotland and from the English Lake District using the Bayesian clustering software STRUCTURE. We also used a diagnostic mitochondrial marker for red deer and sika. Our survey extends previous studies indicating little introgression of wapiti nuclear alleles into red deer, in particular in Northern Scotland, Kintyre, and the Lake District. We found a new area of extensive sika introgression in South Kintyre. In the North Highlands, we show for the first time geographically scattered evidence of past hybridization followed by extensive backcrossing, including one red‐like individual with sika introgression, two sika‐like individuals with red deer introgression, and six individuals that were apparently pure sika at the nuclear markers assessed but which carried red deer mitochondria. However, there has not been a collapse of assortative mating in this region. Similarly, in the English Lake District red deer, we found only traces of past sika introgression. No sika alleles were detected in the Central Highlands or the Hebridean red deer refugia. We make suggestions for management to prevent further spread of sika alleles into red deer and vice versa.     

Suppression of Regeneration in New Zealand Mountain Beech Forests is Dependent on Species of Introduced Deer

We compared the impacts on forest regeneration of introduced sika (Cervus nippon) and red (Cervus elaphus) deer in New Zealand. Plot data were used to compare mountain beech (Nothofagus solandri var. cliffortioides) regeneration between a region with sika deer, and four regions without sika deer. All regions surveyed had red deer present. In the region where sika deer had been present for more than a decade, there was evidence of poor mountain beech seedling regeneration. In the four regions without sika deer, there was evidence of a strong regenerative response at stands with low occupancy by trees. When compared to larger deer species, sika deer have a digestive morphology allowing greater dietary versatility, which may result in them impeding forest regeneration where red deer do not. In contrast to mountain beech, some small-leaved shrub species may have been competitively advantaged by intensive browsing from sika deer. This is contra to a current view that small-leaved shrub species with interlacing branches were able to tolerate browsing from extinct ratite birds, but not introduced deer. Sika deer have been introduced into countries where other deer species are indigenous, such as Canada, Denmark, Great Britain, Czech Republic, Ireland and the United States of America. Because of their dietary advantage, sika deer may have a greater potential to impede forest regeneration and competitively exclude larger deer species, particularly at low basal area sites where impacts on tree regeneration are likely to be greatest.     

Investigating temporal changes in hybridization and introgression in a predominantly bimodal hybridizing population of invasive sika (Cervus nippon) and native red deer (C. elaphus) on the Kintyre Peninsula,Scotland

We investigated temporal changes in hybridization and introgression between native red deer (Cervus elaphus) and invasive Japanese sika (Cervus nippon) on the Kintyre Peninsula, Scotland, over 15 years, through analysis of 1513 samples of deer at 20 microsatellite loci and a mtDNA marker. We found no evidence that either the proportion of recent hybrids, or the levels of introgression had changed over the study period. Nevertheless, in one population where the two species have been in contact since ～1970, 44% of individuals sampled during the study were hybrids. This suggests that hybridization between these species can proceed fairly rapidly. By analysing the number of alleles that have introgressed from polymorphic red deer into the genetically homogenous sika population, we reconstructed the haplotypes of red deer alleles introduced by backcrossing. Five separate hybridization events could account for all the recently hybridized sika‐like individuals found across a large section of the Peninsula. Although we demonstrate that low rates of F1 hybridization can lead to substantial introgression, the progress of hybridization and introgression appears to be unpredictable over the short timescales.     

Expanding ranges of wild and feral deer in Great Britain

1. It is often stated that wild deer in Great Britain are increasing in range and number. This study presents the first quantified estimate of national range expansion for all six species. From national surveys of deer presence in 10 km squares between 1972 and 2002, the red deer range is estimated to have expanded at a compound rate of 0.3% per year, fallow deer at 1.8%, Chinese water deer at 2.0%, roe deer at 2.3%, Japanese sika at 5.3% and Reeves’ muntjac at 8.2%. 2. Each species is expected to expand its range further for the foreseeable future. The most widespread species, roe deer, is predicted to be present within 79% of all 10 km squares in mainland Britain within 10 years. 3. Deer range expansion brings a combination of benefits and costs, and some degree of management is considered necessary to limit both environmental damage and deer suffering.     

A survey of the hybridisation status of Cervus deer species on the island of Ireland

Red deer (Cervus elaphus) did not recolonise Ireland after the last glaciation, but the population in Co. Kerry is descended from an ancient (c. 5000 BP) introduction and merits conservation. During the mid-19th century exotic species including North American wapiti (C. canadensis) and Japanese sika deer (C. nippon nippon) were introduced to Ireland, mainly via Powerscourt Park, Co. Wicklow. While wapiti failed to establish, sika thrived, dispersed within Co. Wicklow and were translocated to other sites throughout Ireland. Red deer and sika are known to have hybridised in Ireland, particularly in Co. Wicklow, but an extensive survey with a large, highly diagnostic marker panel is required to assess the threat hybridisation potentially poses to the Co. Kerry red deer population. Here, 374 individuals were genotyped at a panel of 22 microsatellites and at a single mtDNA marker that are highly diagnostic for red deer and Japanese sika. The microsatellites are also moderately diagnostic for red deer and wapiti. Wapiti introgression was very low [trace evidence in 2 (0.53 %) individuals]. Despite long-standing sympatry of red deer and sika in the area, no red deer-sika hybrids were detected in Co. Kerry suggesting strong assortative mating by both species in this area. However, 80/197 (41 %) of deer sampled in Co. Wicklow and 7/15 (47 %) of deer sampled in Co. Cork were red-sika hybrids. Given their proximity and that hybrids are less likely to mate assortatively than pure individuals, the Co. Cork hybrids pose a threat to the Co. Kerry red deer.     

Identifying threshold densities for wild deer in the UK above which negative impacts may occur

• 1 At high densities, deer populations may have adverse effects upon and within their environment. In this review we explore published and unpublished information to derive density thresholds for deer species in relation to impacts upon agriculture, forestry, conservation habitats, road traffic, and human and livestock health in the UK. Impact levels are affected by many factors other than absolute density. We therefore seek to establish the range of densities within which negative impacts might start to occur and which should trigger objective monitoring of actual impacts.
• 2 In commercial forestry, a threshold of 4 deer per 100ha has been suggested. Unfenced native woodlands seem to regenerate naturally if there are fewer than 4–5 large deer or fewer than 25 roe deer Capreolus capreolus per 100ha; open habitats may suffer only light or moderate impacts from red deer Cervus elaphus at landscape densities of 7–8 per 100ha.
• 3 Woodland bird species may have declined where deer densities are high but absolute thresholds seem impossible to establish. One study suggests maximum diversity at about 8 white‐tailed deer Odocoileus virginianus per 100ha.
• 4 Deer–vehicle collisions are affected by various factors in addition to deer density, but British and American studies suggest that accident frequencies decline at densities below 7–8 per 100ha.
• 5 Fallow deer Dama dama populations may maintain bovine TB (bTB) infection at much lower densities (25/100ha) than red or roe deer (91/100ha and 200/100ha, respectively) assuming 100% prevalence. Even at 30% prevalence a density of 75 fallow deer per 100ha could maintain bTB within the population.
• 6 We conclude that deer density alone is unlikely to be a good predictor of impact, and suggest that long‐term management should be based on assessment both of actual impacts and apparent density of deer.

     

Predicting the status of wild deer as hosts of <Emphasis Type="Italic">Mycobacterium bovis</Emphasis> infection in Britain

Control of livestock diseases can become complicated when wild animals are involved. The Eurasian badger (Meles meles) is considered the principle wildlife host of Mycobacterium bovis (which causes bovine tuberculosis, bTB) in Great Britain and Ireland, but wild deer have also been implicated. Whether wild deer are likely to perpetuate bTB in cattle depends on the exposure risks they pose, the mode of pathogen transmission, the distances over which the disease can be transported and whether they can maintain infection within their own populations independently of other sources. We evaluated the likely host status of each of four species of wild British deer (red, roe, fallow and Reeves' muntjac) and the badger across a range of densities typically observed in Britain by manipulating the reproductive number equation proposed by Anderson and May (1991). We estimate that roe deer almost certainly act as spillover hosts at densities lower than 30 km⁻², red deer below 16 km⁻², muntjac below 6 km⁻², fallow below 4 km⁻² and the badger below 2 km⁻². We also estimate that muntjac will almost certainly act as maintenance hosts at densities above 56 km⁻², fallow above 47 km⁻² and badgers above 24 km⁻². For densities between these values, we cannot be certain of the host status of these species, and for red and roe deer we cannot be certain of host status under most natural conditions typically experienced in parts of Britain experiencing high incidence of bTB in cattle. However, enhanced transmission rates resulting from artificially high densities such as might be experienced at supplementary feeding sites may be sufficient to promote independent maintenance of infection. We were not able to confidently assign host status to any species over a wide range of densities, but conclude that this is likely to reflect reality, where host status may be affected as much by, for example, demographic fluctuations as it is by population density. Our results imply densities below which populations of wild deer inhabiting cattle bTB hotspots ought to be maintained in order to control the possibility of them perpetuating the cycle of intra- and interspecific M. bovis transmission.     

Use of melengestrol acetate in feed for contraception in herds of captive ungulates

Herds of blackbuck antelope (Antilopa cervicapra) and barasingha (Cervus duvauceli), axis (Cervus axis), sambar (Cervus unicolor), and Formosan sika (Cervus nippon taiwanaus) deer at the Wildlife Conservation Society/Bronx Zoo (WCS/BZ) were fed melengestrol acetate (MGA) at a concentration of 0.000154% in pelleted feed for various periods of times during 1991–2001. The target dose per animal of MGA was 1–2 mg per day. Contraceptive rates during treatment were 100% for blackbuck antelope and barasingha, sambar, and sika deer, and approximately 93% for axis deer. There were no observed adverse effects from MGA treatment on gestation. Post‐treatment reproductive rates were lower than pretreatment rates. Zoo Biol 22:455–463, 2003. © 2003 Wiley‐Liss, Inc.     

Polymorphism and genetic control of erythrocyte 6-phosphogluconate dehydrogenase in the genus Cervus

A study of 11 enzyme systems in blood samples of Cervus dama, C. elaphus, C. nippon and hybrids C. elaphus X nippon has revealed an erythrocyte 6-phosphogluconate dehydrogenase polymorphism in the hybrid populations. Genetic analysis suggests that this enzyme is controlled by one gene locus with two codominant alleles, one specific for pure Japanese sika deer, the other for pure red deer as well as for fallow deer, while both alleles have been found in the red X sika hybrids.     

Evaluation of introgressive hybridization among Cervidae in Japan's Kinki District via two novel genetic markers developed from public NGS data

Hybridization and backcrossing of native populations with introduced species can lead to introgression and genetic alteration. In this study, we evaluated introgression in 43 deer from a potential hybrid zone around Okinoshima Island, Kinki District, Japan. This region witnessed the migration of a hybrid population (cross between the Formosan sika deer [Cervus nippon taiouanus] and other deer species) that could potentially breed with the native Japanese sika deer (C. n. centralis). We used an existing genetic marker for the mitochondrial cytochrome b gene and two novel markers for nuclear DNA, developed using publicly available next‐generation sequencing data. We identified one mainland deer with a mitochondrial haplotype identical to that of the Formosan sika deer as well as nuclear heterozygous sequences identical to those of Formosan and Japanese sika deer. This suggests that the mainland deer is a hybrid offspring of the Okinoshima population and native deer. However, only Japanese sika deer sequences were found in the other 42 samples, indicating limited introgression. Nevertheless, hybridization pre‐ and postintroduction in the Okinoshima population could cause multispecies introgression among Japanese sika deer, negatively affecting genetic integrity. We developed a simple test based on polymerase chain reaction–restriction fragment length polymorphism to detect introgression in natural populations. Our method can accelerate genetic monitoring of Japanese sika deer in Kinki District. In conclusion, to prevent further introgression and maintain genetic integrity of Japanese sika deer, we recommend establishing fences around Okinoshima Island to limit migration, besides a continued genetic monitoring of the native deer.     

Browsed twig environmental DNA: diagnostic PCR to identify ungulate species

Ungulate browsing can have a strong effect on ecological processes by affecting plant community structure and composition, with cascading effects on nutrient cycling and animal communities. However, in the absence of direct observations of foraging, species‐specific foraging behaviours are difficult to quantify. We therefore know relatively little about foraging competition and species‐specific browsing patterns in systems with several browsers. However, during browsing, a small amount of saliva containing buccal cells is deposited at the bite site, providing a source of environmental DNA (eDNA) that can be used for species identification. Here, we describe extraction and PCR protocols for a browser species diagnostic kit. Species‐specific primers for mitochondrial DNA were optimized and validated using twigs browsed by captive animals. A time series showed that about 50% of the samples will amplify up to 12 weeks after the browsing event and that some samples amplify up to 24 weeks after browsing (12.5%). Applied to samples of natural browsing from an area where moose (Alces alces), roe deer (Capreolus capreolus), fallow deer (Cervus dama) and red deer (Cervus elaphus) are sympatric, amplification success reached 75%. This method promises to greatly improve our understanding of multispecies browsing systems without the need for direct observations.     

Prevalence of Neospora caninum and Toxoplasma gondii antibodies in wild ruminants from the countryside or captivity in the Czech Republic

In the Czech Republic, sera from 720 wild ruminants were examined for antibodies to Neospora caninum by screening competitive-inhibition enzyme-linked immunosorbent assay and confirmed by indirect fluorescence antibody test (IFAT); the same sera were also examined for antibodies to Toxoplasma gondii by IFAT. Neospora caninum antibodies were found in 14% (11 positive/79 tested) roe deer (Capreolus capreolus), 14% (2/14) sika deer (Cervus nippon), 6% (24/ 377) red deer (Cervus elaphus), 1% (2/143) fallow deer (Dama dama), 3% (3/105) mouflon (Ovis musimon), and none of 2 reindeer (Rangifer tarandus). Toxoplasma gondii antibodies were found in 50% (7/14) sika deer, 45% (169/377) red deer, 24% (19/79) roe deer, 17% (24/143) fallow deer, 9% (9/105) mouflon, and 1 of 2 reindeer. In 42 samples of wild ruminants that tested positive for N. caninum antibodies, 28 (67% of the positive N. caninum samples) reacted solely to N. caninum. This is the first evidence of N. caninum infection in mouflon, the first N. caninum seroprevalence study in farmed red deer, and the first survey of N. caninum in wild ruminants from the Czech Republic.     

Tracing the genetic roots of the sika deer Cervus nippon naturalized in Germany and Austria

To determine the geographical origin of the sika deer (Cervus nippon) naturalized in Germany and Austria, we sequenced the mitochondrial control region for 214 individuals. Adding these sequences to previously published data from native sika deer across its natural geographic range, the total comes to 245, extending what is already known about the geographical variation in this sequence in Cervus nippon. From these sequences, a neighbour-joining tree was constructed. This tree showed that the 49 different mitochondrial (mt)DNA types are grouped into three distinct phylogenetic clusters, which correspond to different geographic areas. Similarities between sequences of the naturalized sika deer and those described from native sika deer from both southern Honshu, Kyushu with associated islands, and northern Honshu suggest that the ancestors of the sika deer populations in Germany and Austria originated from the Japanese archipelago. In contrast, there is no evidence that female sika deer of Chinese, Taiwanese or north Vietnamese origin were involved in the ancestry of the present sika population in Germany and Austria.     

<Emphasis Type="Italic">Anaplasma phagocytophilum</Emphasis> infection in a multi-species deer community in the New Forest,England

The tick-transmitted Anaplasma phagocytophilum has been recorded in a range of mammal species and causes granulocytic ehrlichiosis in humans, horses, and companion animals as well as tick-borne fever in ruminants. Although deer and other ruminant species are known to be natural hosts, the distribution among sympatric deer populations is unexplored. Blood from 80 deer of four species were screened using an A. phagocytophilum-specific real-time polymerase chain reaction. Overall, 29% (19–40) of deer tested positive. Fallow deer (Dama dama), the most numerous species, had significantly lower prevalence (21%) than roe (Capreolus capreolus), red (Cervus elaphus), or sika (Cervus nippon) deer (average 50%). It is suggested that patterns of habitat use influence infection levels in different deer species. The role of deer as reservoirs of anaplasmosis remains unknown; however, prevalence in deer could be a useful index of local infection pressure and the risk of disease in domestic animals and humans.     

Estimating abundance of introduced Chinese muntjac Muntiacus reevesi and native roe deer Capreolus capreolus using portable thermal imaging equipment

• 1 Managing the conservation impacts of deer requires knowledge of their numbers. However, estimating densities in forested areas is problematic, with pellet‐group‐based methods subject to error and uncertainty in estimating defecation and decay rates in addition to sampling variance. Use of thermal imaging equipment allows direct census by distance sampling.
• 2 Densities of introduced Chinese muntjac Muntiacus reevesi and native roe deer Capreolus capreolus were estimated in 12.8 km² of conifer forest in eastern England by thermal imaging distance transects. Estimated density of introduced muntjac (±95% confidence intervals [CI]: 20 ± 8 km⁻²) exceeded that of native roe deer (16 ± 6 km⁻²); 95% CI of c. 40% were achieved in 10 days of fieldwork.
• 3 Density estimates were not sensitive to the number of width bands applied during analysis. Detectability functions differed, with narrower effective strip widths (ESW) for muntjac (74 m) than roe deer (123 m). Thus, it is important to discriminate between species when censusing mixed assemblages. Detectability and ESW also differed among plantation growth stages. Stratification by habitat may therefore improve accuracy of density estimates but would require additional survey effort.

     

Rumen Ciliates of White-tailed Deer (Odocoileus virginianus), Axis Deer (Axis axis), Sika Deer (Cervus nippon) and Fallow Deer (Dama dama) from Texas

Samples of rumen contents from 33 white-tailed deer (Odocoileus virginianus), 31 axis deer (Axis axis), 26 sika deer (Cervus nippon), and 25 fallow deer (Dama dama) were collected from four study areas in central Texas. The geometric mean concentration of total protozoa was 50.2 x 10(4) per ml, with no differences between species (P > 0.36). White-tailed deer had a higher percentage of Entodinium and lower percentage of Diplodiniinae (P < 0.01) than the other deer species, which were not different from each other. Occurrence of Epidinium, Isotricha, and Dasytricha was sporadic and did not differ among deer species. Numerous new host records of protozoan species were observed: white-tailed deer--four; axis deer--five; sika deer--five; fallow deer--four. This brings the total number of protozoan species identified in each deer species to: white-tailed--eight; axis--12; sika--15; fallow--16. For all species combined, protozoan concentration were 7.5 to 11-fold higher (P < 0.01) from Area 4, which differed from the other three areas by having a stream that allowed deer to have free access to water. Criteria used for identification of medium-size Eudiplodinium species were evaluated.     

Evidence of higher levels of testosterone during the velvet period in muntjac than in other cervids

Previous studies have shown that despite having a clear seasonal fluctuation in fecal testosterone concentration, the significantly lower testosterone levels found in velvet stags of the nonseasonal breeder muntjac (Muntiacus sp.) apparently did not stop their spermatogenesis as in other deer species. In the present study, in vitro cultivated Leydig cells isolated from adult stags of three native deer species of Taiwan were treated with androstenedione, with or without adding human chorionic gonadotropin. Results showed that, unlike the two seasonal breeders, sika deer (Cervus nippon) and sambar deer (Rusa unicolor), Leydig cells of velvet muntjac had no dramatic reduction in or even maintained the full capability of their testosterone productivity compared with the hard-antlered stage. The decrease in fecal testosterone level observed earlier in muntjac during the velvet period was probably due to a reduction of number of Leydig cells. These results support the hypothesis that testosterone production in muntjac during its velvet period might never be low enough to trigger the quiescent phase of the reproduction cycle.