Japanese Sika Research Articles

Characterization and arbovirus susceptibility of cultured CERNI cells derived from sika deer (Cervus nippon).

Cervus nippon (sika deer) are widely distributed throughout eastern Asia. Deer possess a variety of antibodies against several zoonotic pathogens, indicating that they act as reservoir of zoonoses. In this study, we reported the characterization of cultured cells derived from sika deer and evaluated their susceptibility to arthropod-borne viruses to clarify their usefulness in virological studies. Cells derived from testicular tissue in Dulbecco's modified eagle medium with 16% fetal bovine serum started growing as primary cultured cells. The diploid cells consisted of 68 chromosomes, consistent with those of Japanese sika deer previously reported. The phylogenetic analysis showed the cells formed a robust clade with Japanese population of C. nippon, indicating that the cultured cells established in this study were originated from the Japanese sika deer. The cells immortalized by the simian virus 40 T-antigen were predominantly spindle-shaped cells exhibiting adhesive properties, and cultivated at 37°C and 5% CO2, which are common culture conditions for many mammalian cell lines. Western blotting analysis indicated that the cultured cells were multiple types of cells that coexist, including at least epithelial, fibroblast, and also Leydig cells. We confirmed that the cells have susceptibility to several arboviruses distributed in Japan: Getah virus, Japanese encephalitis virus, Oz virus, and severe fever with thrombocytopenia syndrome virus, but not to Tarumiz tick virus. From these results, the cells contribute to clarify the role of sika deer as a reservoir of zoonoses in nature and deer-associated experimental research at the cellular and molecular levels.

Soil erosion under forest hampers beech growth: Impacts of understory vegetation degradation by sika deer

The overpopulation of large herbivorous mammals degrades understory vegetation and hence promotes soil erosion in some northern hemisphere forests. Topsoil removal via erosion reduces soil water and nitrogen (N) content as well as exposes tree roots. However, whether topsoil removal inhibits tree growth through water and N uptake limitations has not been examined. This study aimed to measure the vertical length from exposed roots surface to the soil surface (exposed root height; ERH) under degraded forest understory vegetation and to evaluate its influence on tree growth. Specifically, we examined the relationships between ERH and beech growth and identified the timing of growth reduction based on annual tree-ring analysis at the individual scale. Furthermore, we discussed the effects of water and N limitations on beech growth reduction. We studied 12 Japanese beech trees on Mt. Sanpo, southern Kyushu Island, Japan, where understory vegetation was degraded and lost due to herbivory by Japanese sika deer from 1980 to 2003. Lower amounts of leaf production and relative growth rates of stem basal area increment (BAI) were observed in beech trees with higher ERH. Segmented regression analysis, which detects the changing time of a temporal trend (i.e., break-point), revealed that the BAI has resulted in a decreasing trend after 1997.6 ± 9.0 (yr), which coincided with the field observations on understory degradation in the study site. After the break-point of the BAI, the BAI of each study tree was negatively related to intrinsic water use efficiency, an integrated index of water limitation. These results suggest that soil erosion after the degradation of understory vegetation reduced beech growth, possibly because of the water limitations associated with root exposure. Reduced beech growth will reduce the supply of the litter layer that prevents topsoil erosion, which may enhance further soil erosion and tree growth reduction.

A historic religious sanctuary may have preserved ancestral genetics of Japanese sika deer (Cervus nippon).

Deer have been a major resource for human populations for thousands of years. Anthropogenic activities, such as hunting, have influenced the genetic structure and distribution of deer populations. In Japan, wild Japanese sika deer (Cervus nippon) have been hunted since ancient times but have also been historically protected as sacred animals in several sanctuaries. Sika deer have been protected for over a thousand years in the religious sanctuary around the Kasuga Taisha Shrine on the Kii Peninsula, located in the center of Japan. Here, we used short sequence repeats (SSR) and mitochondrial DNA (mtDNA) to investigate the genetic diversity, population structure, and demography of Japanese sika deer inhabiting the Kii Peninsula, Japan, and discuss possible anthropogenic influences. Using SSR, three distinct genetic groups were distinguished on the Kii Peninsula: an Eastern genetic group, a Western genetic group, and an isolated genetic group with individuals in the religious sanctuary of Kasuga Taisha Shrine in Nara city. The isolated genetic sanctuary group had only the mtDNA haplotype S4. The SSR genotype data suggested a newer divergence time of the genetic groups of the religious sanctuary than would have occurred as a result of Late Quaternary climate change. This time scale coincided with the establishment of the sanctuary with Kasuga Taisha Shrine. Thus, the religious protection conserved genetic variation over a thousand years.

Distribution, prevalence, and intensity of Sarcocystis infections in sika deer (Cervus nippon) of free-ranging populations in Germany and Austria.

Sika deer (Cervus nippon), which are native to the Japanese islands and the adjacent mainland of eastern Asia, have been introduced into Europe and established free-ranging populations in several countries. Various Sarcocystis species have been identified recently from farmed "mainland sika" deer in Lithuania and native "Japanese sika" deer in Japan. To study the distribution, prevalence and intensity of Sarcocystis infection in free-ranging sika deer outside of their natural range heart and/or diaphragm samples of 311 animals from nine populations in Germany and Austria were examined by histology.Overall, sarcocysts were detected in either heart or diaphragm of 107/311 deer (34.4%) with prevalence ranging roughly from 5 to 50% among the populations. Considering the 263 animals with both heart and diaphragm available, prevalence varied significantly (p < 0.0001) among calves (20.2%), yearlings (40.3%), and adult deer (49.1%) but did not differ between male and female deer (48.3% vs. 43.7%; p = 0.6483). Occurrence of sarcocysts in heart vs. diaphragm indicated a marginal difference (27.8% vs. 20.9%; p = 0.0839). Intensity of infection in all but one heart positive and all diaphragm positive animals was low (< 10 sarcocysts per square centimeter muscle cut). While heart sarcocyst counts of yearlings and adult deer were higher than those of calves and were higher in male compared to female sika deer, diaphragm sarcocyst counts did not differ significantly between age groups and sexes. Sarcocystis infection was demonstrated at variable prevalence in sika deer in all populations but intensity is apparently low. Further studies are needed to identify the species of Sarcocystis infecting sika deer naturalized outside their natural range.

Discrimination between two chromatic colors in sika deer

To clarify animal vision, biochemical, anatomical–histological, neurophysiological and behavioral research using horses, cows, sheep, pigs, and deer have been conducted. Japanese sika deer (Cervus nippon) have caused severe problems in Japan and many devices and repellents that use visual, auditory, and olfactory senses became commercially available to scare away deer from agricultural fields or rail tracks. Development of effective damage mitigation strategies needs more understanding of the senses of deer, especially visual. Ungulates, including sika deer, are dichromatic, with both S- and M-cones; however, the color vision of deer has not been thoroughly investigated. The present study was undertaken to understand the color vision characteristics of sika deer. We evaluated their ability to distinguish between various color combinations. Three captive sika deer were trained in a color discrimination experiment using a two-choice discrimination apparatus. The positive stimulus was always 5B6/8 (blue), and the following six colors were used as negative stimuli: white, 5Y6/8 (yellow), 10G6/8 (green), 10BG6/8 (blue–green), 5RP6/8 (red–purple), and 5BP6/8 (blue–purple) based on the dichromatic color vision confused colors chart. All deer could distinguish blue from white, yellow, and green. No deer could distinguish between blue and red–purple or blue–purple. Some deer could distinguish blue from blue–green, depending on the individual. Humans with protanopia confuse blue with red–purple or blue–purple, so these results suggest that the color vision characteristics of sika deer are similar to those of humans with protanopia. This is the first report discussing the findings of color combinations that are easily visible to deer.

Admixture mapping reveals loci for carcass mass in red deer x sika hybrids in Kintyre, Scotland.

We deployed admixture mapping on a sample of 386 deer from a hybrid swarm between native red deer (Cervus elaphus) and introduced Japanese sika (Cervus nippon) sampled in Kintyre, Scotland to search for quantitative trait loci (QTLs) underpinning phenotypic differences between the species. These two species are highly diverged genetically [Fst between pure species, based on 50K single nucleotide polymorphism (SNPs) = 0.532] and phenotypically: pure red have on average twice the carcass mass of pure sika in our sample (38.7 kg vs 19.1 kg). After controlling for sex, age, and population genetic structure, we found 10 autosomal genomic locations with QTL for carcass mass. Effect sizes ranged from 0.191 to 1.839 kg and as expected, in all cases the allele derived from sika conferred lower carcass mass. The sika population was fixed for all small carcass mass alleles, whereas the red deer population was typically polymorphic. GO term analysis of genes lying in the QTL regions are associated with oxygen transport. Although body mass is a likely target of selection, none of the SNPs marking QTL are introgressing faster or slower than expected in either direction.

Genetic Analysis of a Newly Established Deer Population Expanding in the Sasebo Area in Nagasaki Prefecture, Japan Reveals No Evidence of Genetic Disturbance by Formosan Sika Deer

Native sika deer (Cervus nippon) had not been observed in and around Sasebo City, Nagasaki Prefecture, Kyushu, Japan. However, deer have recently been confirmed in this area, and the number of individuals and the range have been expanding, causing damage to forestry and natural vegetation. Although the origin of these deer is unknown, it may be derived from Formosan sika deer (C. n. taiouanus), which is listed as an invasive alien species in Japan. There is concern about hybridization between this subspecies and the native Japanese sika deer. In the present study, we used genetic methods to assess the current status of the deer in the Sasebo area of Nagasaki Prefecture, particularly its origin and hybridization. Our study showed that the deer did not originate from Formosan sika deer, and we found no evidence of hybridization. The deer in the Sasebo area were found to have a haplotype included in the southern Japanese sika deer lineage. The current study was unable to identify the specific origin of the deer due to limitations in PCR-RFLP and mitochondrial DNA sequencing analysis.

A Microsatellite Genotyping-Based Genetic Study of Interspecific Hybridization between the Red and Sika Deer in the Western Czech Republic.

Simple SummaryThe sika deer is a very flexible invasive species, capable of living dynamically in both large forests and mixed environment characterized by a prevalence of agricultural land. The Japanese sika deer was introduced to the Czech Republic at the end of the 19th century. The success of an introduced alien species may consist in their hybridizing with closely related taxa. Where few barriers to gene flow exist, rapid introgression of genetic traits from one species into another frequently occurs. The current Czech sika populations embody the most abundant and expanding group in continental Europe. In western Bohemia, we confirmed the interspecific hybridization with the native red deer. In this context, the red deer gene pool is endangered. The animals proliferate steadily in all directions and will most probably spread all over the Czech Republic if no major, timely changes in game management are adopted.Although inter-species hybrids between the red and sika deer can be phenotypically determined only exceptionally, there is the eventuality of identification via molecular genetic analysis. We used bi-parentally inherited microsatellite markers and a Bayesian statistical framework to re-examine the proportion of hybrids in the Czech red and sika deer populations. In total, 123 samples were collected, and the nuclear dataset consisted of 2668 allelic values. The number of alleles per locus ranged from 10 (BM1818) to 22 (BM888 and T193), yielding the mean of 16 alleles per locus across the deer. The mean allelic diversity of the red deer markedly exceeded that of the Japanese sika deer. Interspecific hybrids were detected, enabling us to confirm the genetic introgression of the sika deer into the red deer populations and vice versa in western Bohemia. The mean hybrid score equaled 10.6%, with 14.3% of the hybrids being among red deer–like individuals and 6.7% among sika-like ones. At two western Bohemian locations, namely, Doupovské hory and Slavkovský les, the total percentages of hybrid animals equaled 18.8 and 8.9, respectively. No red deer alleles were detected in the sika populations of the subregions of Kladská, Žlutice, and Lány. The NeighborNet network clearly separated the seven red and sika deer sampling populations according to the geography. The knowledge gained from the evaluated data is applicable in hunting management to reduce hybridization with the European deer.

捕獲圧のない地域におけるヤクシカ密度指標の 18年間の増減：屋久島世界遺産地域・照葉樹林の事例

捕獲圧のない地域におけるヤクシカ密度指標の 18年間の増減：屋久島世界遺産地域・照葉樹林の事例

Lipoptena fortisetosa as a vector of Bartonella bacteria in Japanese sika deer (Cervus nippon)

BackgroundTwo species of deer ked (Lipoptena cervi and L. mazamae) have been identified as vectors of Bartonella bacteria in cervids in Europe and the USA. In an earlier study we showed that Japanese sika deer (Cervus nippon) harbor three Bartonella species, namely B. capreoli (lineage A) and two novel Bartonella species (lineages B and C); however, there is currently no information on the vector of Bartonella bacteria in sika deer. The aim of this study was to clarify potential vectors of Bartonella in Japanese sika deer.MethodsThirty-eight wingless deer keds (L. fortisetosa) and 36 ticks (Haemaphysalis and Ixodes species) were collected from sika deer. The prevalence of Bartonella in the arthropods was evaluated by real-time PCR targeting the 16S−23S internal transcribed spacer (ITS) and by culture of the organisms. The total number of Bartonella bacteria were quantified using real-time PCR. The distribution of Bartonella bacteria in deer ked organs was examined by immunofluorescence analysis. The relationship of Bartonella strains isolated from sika deer and arthropods were examined by a phylogenetic analysis based on concatenated sequences of the gltA, rpoB, ftsZ, and ribC genes, followed by a BLAST search for gltA and rpoB.ResultsBartonella prevalence in deer keds was 87.9% by real-time PCR and 51.5% in culture and that in the ticks was 8.3% by real-time PCR and 2.8% in culture. The mean number of Bartonella bacteria per ked was calculated to be 9.2 × 105 cells. Bartonella aggregates were localized in the midgut of the keds. The phylogenetic analysis and BLAST search showed that both the host deer and the keds harbored two Bartonella species (lineages B and C), while B. capreoli (lineage A) was not detected in the keds. Two novel Bartonella species (lineages D and E) were isolated from one ked.ConclusionsLipoptena fortisetosa likely serves as a vector of at least two Bartonella species (lineages B and C), whereas ticks do not seem to play a significant role in the transmission of Bartonella between sika deer based on the lower detection rates of Bartonella in ticks compared to keds. Bartonella species in lineages D and E appear to be L. fortisetosa-specific strains.Graphical

The origins and genetic composition of an expanding population of Japanese sika deer in southern Aizu, Fukushima Prefecture

The origins and genetic composition of an expanding population of Japanese sika deer in southern Aizu, Fukushima Prefecture

Establishment of a Novel Molecular Detection Method for Sarcocystis in Venison.

Recently, horse meat (basashi) contaminated with Sarcocystis spp. caused food poisoning in Japan. An official detection method provided by the Ministry of Health, Labour and Welfare (MHLW), Japan, was designed to detect Sarcocystis fayeri to diagnose and control outbreaks of basashi food poisoning. In 2011, Sarcocystis-contaminated venison also caused food poisoning. However, the official MHLW detection method was not adequate for detecting Sarcocystis spp. in venison. In this study, we established a novel PCR-based detection method that amplifies 18S rRNA gene based on the conserved region of the sequence in 32 species of Sarcocystis for screening and quantification. Fifty venison samples from three areas in Hokkaido were examined by the MHLW method and the novel detection method. All samples were Sarcocystis spp.-positive. A sequence analysis indicated the presence of a species of Sarcocystis specific to sika deer (Cervus nippon), and not to horses. Another primer pair was designed for a quantitative real-time PCR assay to determine the copy number of the Sarcocystis-18S rRNA gene in parasitized venison. The melting curve analysis revealed high specificity of this assay. The calculated curve demonstrated that this quantitative PCR assay showed R2 value of 0.993 with 10-106 copies. Using this quantitative real-time PCR assay, the gene copy numbers were determined in 50 venison samples. The copy numbers of each sample ranged from 104 to 107 per gram. The copy numbers differed according to the area in Hokkaido. This indicates that the density of Sarcocystis spp. that infect Sika deer in Hokkaido is affected by the area. The novel screening and quantitative PCR method for Sarcocystis in venison was useful for collecting epidemiological information on Sarcocystis in wild Japanese sika deer, which will contribute to improve the safety of venison products in Japan.

Genetic Variation in Y-Chromosome Genes of Sika Deer (Cervus nippon) in Japan.

Sika deer (Cervus nippon) in Japan are classified into southern and northern groups. However, previous studies primarily relied on maternally inherited mitochondrial DNA (mtDNA). The paternally inherited Y-chromosome is useful for analyzing the contribution of males to the population genetic history of sika deer. In total, approximately 16 kb of partial sequences of four Y-chromosomal genes, Y-linked, sex-determining region Y, DEAD-box helicase 3 Y-linked, and Zinc finger protein Y-linked, were sequenced to investigate intraspecific variation. As a result, we identified nine intronic single nucleotide polymorphisms (SNPs) in 478 sika deer samples collected over the entire Japanese archipelago from Hokkaido to Kyushu. SNP genotyping revealed 10 distinct haplotypes (SYH1-SYH10). The most common haplotype (SYH1) was present in all populations and was the most abundant haplotype, identified in 80.3% of the sampled individuals. The remaining haplotypes were unique to a single locality. SYH1 was also central to all other haplotypes that diverged by a SNP, resulting in this haplotype being the core of a star-like cluster topography. We found that contrary to mtDNA patterns, there was no clear differentiation of Y-chromosome markers between the southern and the northern populations. Due to the female philopatry of sika deer, mtDNA may provide a highly structured differentiation of populations. On the other hand, the male-biased gene flow may provide a reduced differentiation of populations. Our findings revealed that the genetic structure of the Japanese sika deer is more complex than previously thought based on mtDNA-based phylogeographic studies.

Presence of Sarcocystis sybillensis in Japanese sika deer (Cervus nippon) captured in its native territory and its phylogenetic relationship with Sarcocystis nipponi.

The first study reporting the morphological characterization of Sarcocystis sybillensis was performed in 1983; however, without any molecular analysis. Sarcocystis nipponi has been recently described as a species synonymic to S. sybillensis. We reconfirmed the presence of S. sybillensis in Japanese sika deer (Cervus nippon) captured in its native territory; and performed its molecular and phylogenetic characterization. The morphological characteristics of the sarcocysts were consistent with those of S. nipponi and S. sybillensis described in the first report. However, the nucleotide sequence of 18S rRNA gene of S. sybillensis showed only 91.9% identity to that of S. nipponi, suggesting low homology among the concerned Sarcocystis spp. Accordingly, S. sybillensis was found to occupy a clade distinct from that of S. nipponi in a phylogenetic tree of Sarcocystis. Therefore, the present study provides essential information on 18S rRNA-based molecular characterization of S. sybillensis and disproves the existing notion of morphology-based species synonymity of S. sibillensis and S. nipponi. These results also suggest that S. sybillensis belongs to type 2 Sarcocystis.

Bi-Directional Movement of Deer between Tomogashima Islands and the Western Part of the Kii Peninsula, Japan, with Special Reference to Hybridization between the Japanese Sika Deer (Cervus nippon centralis) and the Introduced Exotic Deer

Deer have been artificially introduced into many countries that are not within their native range. In some cases, they have disturbed the natural ecosystem in the invaded area. On Okinoshima Island in Wakayama Prefecture, Japan, exotic deer were introduced from Taiwan in 1955 and have since bred in the wild, raising concerns about their invasion into the habitats of, and hybridization with, the native Japanese sika deer. To determine the extent of gene introgression, we investigated the population structure of deer on Okinoshima Island and the surrounding areas, including the islands of Awajishima and Jinoshima, and the mainland area in the western Kii Peninsula. Genetic analyses using microsatellite and mitochondrial DNA markers revealed that both exotic deer and Japanese sika deer inhabited Jinoshima Island. On the other hand, one of the individuals captured on the mainland was a first-generation hybrid between the exotic and native deer. These results suggest the bi-directional movement of the exotic and native deer between the islands and the mainland, with the potential for hybridization.

Increased genetic marker density reveals high levels of admixture between red deer and introduced Japanese sika in Kintyre, Scotland.

Hybridization is a natural process at species range boundaries, but increasing numbers of species are hybridizing due to direct or indirect human activities. In such cases of anthropogenic hybridization, subsequent introgression can threaten the survival of native species. To date, many such systems have been studied with too few genetic markers to assess the level of threat resulting from advanced backcrossing. Here, we use 44,999 single nucleotide polymorphisms (SNPs) and the ADMIXTURE program to study two areas of Scotland where a panel of 22 diagnostic microsatellites previously identified introgression between native red deer (Cervus elaphus) and introduced Japanese sika (Cervus nippon). In Kintyre, we reclassify 26% of deer from the pure species categories to the hybrid category whereas in the NW Highlands we only reclassify 2%. As expected, the reclassified individuals are mostly advanced backcrosses. We also investigate the ability of marker panels selected on different posterior allele frequency criteria to find hybrids assigned by the full marker set and show that in our data, ancestry informative markers (i.e. those that are highly differentiated between the species, but not fixed) are better than diagnostic markers (those markers that are fixed between the species) because they are more evenly distributed in the genome. Diagnostic loci are concentrated on the X chromosome to the detriment of autosomal coverage.

Non-Invasive Age Estimation by Cranial Suture Closure in Japanese Sika Deer (Cervus nippon)

Although counting cementum annuli of lower incisor is a reliable method for age estimation in cervids, it inevitably involves the destruction of specimens. Here we studied the relationship between cranial suture closure patterns and age to test the possibility of cranial suture closure as a non-destructive age indicator in sika deer (Cervus nippon) specimens from Kinkazan Island, Japan, for which extensive life records were available. A strong positive relationship between the sum of suture closure level scores and age was found. We found that this relationship was even stronger than the relationship between age and the crown height of the first molar, which is frequently used for non-destructive age determination. Our study highlights the potential of cranial suture closure as an alternative valid tool for age estimation.

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.

Population Structure, Admixture, and Migration Patterns of Japanese Sika Deer (Cervus nippon) Inhabiting Toyama Prefecture in Japan.

Rapid expansion of sika deer, in both number and distribution, in the Japanese Archipelago has resulted in serious ecological disturbance. In the present study, the population structure and migration patterns of sika deer (Cervus nippon) among Toyama and adjacent Prefectures were investigated using 11 polymorphic microsatellite loci. Deviation from Hardy-Weinberg equilibrium was detected in both total and individual regional sika deer samples from Toyama Prefecture. Results of pairwise FST results, factorial correspondence analysis, and STRUCTURE analysis indicated that sika deer in Toyama are not genetically distinct from those in adjacent Prefectures. Bayesian STRUCTURE results suggested the existence of two distinct clusters. However, multiple lines of genetic structure and high admixture were detected across the populations located in the central region of Toyama Prefecture. Both contemporary and historical migration analyses showed that dispersal into Toyama Prefecture from neighboring prefectures was high, especially migration from the prefecture on the east into Toyama Prefecture, and bidirectional dispersion between Toyama Prefecture and the prefecture to the south. Knowledge of such genetic structures and population dynamics is required for appropriate management and conservation of sika deer populations in the Japanese Archipelago.

Estimating range expansion of wildlife in heterogeneous landscapes: A spatially explicit state-space matrix model coupled with an improved numerical integration technique.

Dispersal as well as population growth is a key demographic process that determines population dynamics. However, determining the effects of environmental covariates on dispersal from spatial‐temporal abundance proxy data is challenging owing to the complexity of model specification for directional dispersal permeability and the extremely high computational loads for numerical integration. In this paper, we present a case study estimating how environmental covariates affect the dispersal of Japanese sika deer by developing a spatially explicit state‐space matrix model coupled with an improved numerical integration technique (Markov chain Monte Carlo with particle filters). In particular, we explored the environmental drivers of inhomogeneous range expansion, characteristic of animals with short dispersal. Our model framework successfully reproduced the complex population dynamics of sika deer, including rapid changes in densely populated areas and distribution fronts within a decade. Furthermore, our results revealed that the inhomogeneous range expansion of sika deer seemed to be primarily caused by the dispersal process (i.e., movement barriers in fragmented forests) rather than population growth. Our state‐space matrix model enables the inference of population dynamics for a broad range of organisms, even those with low dispersal ability, in heterogeneous landscapes, and could address many pressing issues in conservation biology and ecosystem management.