Hokkaido Population Research Articles

Annual variation in recruitment rates for the sika deer (Cervus nippon) population in eastern Hokkaido, Japan

Annual variation in recruitment rates for the sika deer (<i>Cervus nippon</i>) population in eastern Hokkaido, Japan

Life history of different giant water bug, Appasus japonicus (Belostomatidae: Heteroptera), populations throughout the Japanese Archipelago

AbstractAs temperatures in the Japanese Archipelago vary, species widely distributed in Japan should have different active periods, ecologies, and life histories. Information on developmental zero and effective accumulated temperature is necessary to estimate life history. The giant water bug, Appasus japonicus, found in rice paddies, ponds, and other lentic waters, is distributed throughout Japan except for the Ryukyu Islands, and is a representative taxon in which the male cares for the eggs. In this study, we investigated the life history, including the length of the breeding season, of different A. japonicus populations from Hokkaido, Ibaraki, Hyogo, and Nagasaki. The developmental period, developmental zero, and effective accumulated temperature of the eggs and nymphs showed no significant differences among the populations. The life history for each population was estimated based on climate data. This showed that the Hokkaido population had a shorter and more extremely limited breeding season than the other populations. The estimated number of generations during one breeding season was approximately one in Hokkaido, two in Ibaraki and Hyogo, and three in Nagasaki. The estimated number of times males cared for eggs during the breeding season was less than one in Hokkaido, eight in Ibaraki and Hyogo, and twelve in Nagasaki. Although Belostomatidae may carry multiple egg masses during the breeding season, this study shows that the male of the Hokkaido population does not care for multiple egg masses.

Stable Isotope Analysis Reveals Intensive Exploitation of Pet Food by the Newly Established Oriental Magpie Pica serica Population in Hokkaido, Japan

Stable Isotope Analysis Reveals Intensive Exploitation of Pet Food by the Newly Established Oriental Magpie Pica serica Population in Hokkaido, Japan

A comparison of sex‐specific markers for two wild masu salmon populations in Hokkaido, Japan

AbstractWe evaluated the utility of three male‐specific molecular markers, sdY, sdY 227U and OtY2m, in two wild populations of masu salmon (Oncorhynchus masou) in southwestern Hokkaido, Japan. Male‐specific fragments amplified in all phenotypic males across the markers. Phenotypic females were genetically identified as males using sdY (57%) and sdY 227U (4%), but no phenotypic females were identified as males using OtY2m. We conclude that OtY2m was the most reliable sex marker, followed closely by sdY 227U, among those tested in our study populations. Additional research is warranted to test the applicability of these markers in other populations and Oncorhynchus species.

Possible Shifts in the Genetic Diversity of Red-crowned Cranes (Grus japonensis) in Hokkaido, Japan: Indications of Continental Gene Flow.

Red-crowned cranes (Grus japonensis) consist of two distinct groups: the continental population and the island population. The island population, localized in Hokkaido, Japan, exhibits very low genetic diversity due to its rapid recovery from the brink of extinction. Our previous research in 2018 highlighted a possible mating between a male from the continental population, with the Gj5 haplotype, and a female from the island population, with the Gj2 haplotype, at Hitominuma Sawmp shore in northern Hokkaido. The present study attempted to unravel the distribution of their offspring by examining the major histocompatibility complex (MHC) of this mixed breeding pair compared with samples collected from cranes in northern and southeastern Hokkaido between 2008 and 2022. The analysis identified 55 MHC types, including 10 known types in a dataset of 89 crane samples, based on amino acid sequences. A total of 58 MHC types were recognized, based on nucleotide sequences, as there were many cases in which the same amino acid sequence had different nucleotide sequences. The five DNA types of MHC in the Hitominuma Swamp male were predominantly identified in eight cranes from northern Hokkaido and one chick from southeastern Hokkaido. In addition, population genetic analysis, based on insertion/deletion (InDel) polymorphisms, indicates distinct population differentiation between the northern and southeastern regions of Hokkaido. These results suggest that genetic contributions from the continental red-crowned crane population have already been integrated into the Hokkaido populations, with a more pronounced influence in northern Hokkaido.

Computational Simulation Model to Predict Behavior Changes in Inflammatory Bowel Disease Patients during the COVID-19 Pandemic: Analysis of Two Regional Japanese Populations.

Managing inflammatory bowel disease (IBD) is a major challenge for physicians and patients during the COVID-19 pandemic. To understand the impact of the pandemic on patient behaviors and disruptions in medical care, we used a combination of population-based modeling, system dynamics simulation, and linear optimization. Synthetic IBD populations in Tokyo and Hokkaido were created by localizing an existing US-based synthetic IBD population using data from the Ministry of Health, Labor, and Welfare in Japan. A clinical pathway of IBD-specific disease progression was constructed and calibrated using longitudinal claims data from JMDC Inc for patients with IBD before and during the COVID-19 pandemic. Key points considered for disruptions in patient behavior (demand) and medical care (supply) were diagnosis of new patients, clinic visits for new patients seeking care and diagnosed patients receiving continuous care, number of procedures, and the interval between procedures or biologic prescriptions. COVID-19 had a large initial impact and subsequent smaller impacts on demand and supply despite higher infection rates. Our population model (Behavior Predictor) and patient treatment simulation model (Demand Simulator) represent the dynamics of clinical care demand among patients with IBD in Japan, both in recapitulating historical demand curves and simulating future demand during disruption scenarios, such as pandemic, earthquake, and economic crisis.

Complex host/symbiont integration of a multi-partner symbiotic system in the eusocial aphid Ceratovacuna japonica.

Some hemipteran insects rely on multiple endosymbionts for essential nutrients. However, the evolution of multi-partner symbiotic systems is not well-established. Here, we report a co-obligate symbiosis in the eusocial aphid, Ceratovacuna japonica. 16S rRNA amplicon sequencing unveiled co-infection with a novel Arsenophonus sp. symbiont and Buchnera aphidicola, a common obligate endosymbiont in aphids. Both symbionts were housed within distinct bacteriocytes and were maternally transmitted. The Buchnera and Arsenophonus symbionts had streamlined genomes of 432,286bp and 853,149bp, respectively, and exhibited metabolic complementarity in riboflavin and peptidoglycan synthesis pathways. These anatomical and genomic properties were similar to those of independently evolved multi-partner symbiotic systems, such as Buchnera-Serratia in Lachninae and Periphyllus aphids, representing remarkable parallelism. Furthermore, symbiont populations and bacteriome morphology differed between reproductive and soldier castes. Our study provides the first example of co-obligate symbiosis in Hormaphidinae and gives insight into the evolutionary genetics of this complex system.

Conventional Gel Electrophoresis-Resolvable Insertion/Deletion Markers for Individual Identification and Analysis of Population Genetics in Red-Crowned Cranes in Eastern Hokkaido, Japan.

Simple SummaryThe red-crowned crane is an endangered bird species in the Far East Eurasian continent and Hokkaido, Japan. Individual identification has been achieved with banding and installed transmitters in only a few cranes, though individual identification is essential for various assessments of cranes on their behavioral characteristics, for example. An insertion/deletion (InDel) mutation is a mutation ranging from 1 to 50 bp and is very useful for genetic studies. If primer sets across InDels (>20 bp) can be designed, an InDel polymorphism can be determined with conventional agarose gel electrophoresis, as reported in some plant species. We found a sufficient number of InDel primer sets to be used for individual identification and analysis of population genetics of red-crowned cranes in Hokkaido. The method has additional advantages, such as convenience and low cost, without sequencing and an expensive apparatus.Red-crowned crane Grus japonensis is an endangered species in two separate populations: the mainland population in the Eurasian continent and the island population in eastern Hokkaido, Japan. We found 11 insertion/deletion (InDel) markers in the genome of the red-crowned crane and designed primer sets across these InDels that can be analyzed with conventional agarose gel electrophoresis. Sixty-six samples of whole blood and skeletal muscle obtained from red-crowned cranes, including 12 families in eastern Hokkaido from 1994 to 2021, showed different patterns in gel images of 11 InDel PCR reactions except for two pairs. The combined non-exclusion probability of the 11 markers indicates that individuals can be determined with a probability of 99.9%. In 39 non-relative chicks, the expected heterozygosity (He) was 0.316, suggesting low genetic diversity. This might not be caused by high levels of inbreeding since the average FIS was not significantly different from zero (0.095, p = 0.075). The results suggest that the 11 InDel primer sets can be used for fairly accurate individual identification as well as genetic population analyses in red-crowned cranes in the island population.

Genetic relations among wild populations of Saccharina japonica in the western North Pacific

We performed microsatellite polymorphism analysis for wild populations of Saccharina japonica, a kelp species that is, among wild production areas, mainly produced in Hokkaido, is indispensable as an ingredient of Japanese food that differs in application and value depending on the origin (variety), growing in southern Sakhalin, Primorsky Krai, and Hokkaido to investigate the genetic relations among the populations. A total of 230 alleles (Polymorphic Information Content: 0.08–0.69) were detected from 18 loci. In the analysis by region, the differentiation index (Fst) and genetic distance (DS) were lower between the Sakhalin southwestern-end populations or the Sakhalin southern coast populations and the Hokkaido populations. However, gene structure analysis showed that the clusters dominant in the kelp in the Sakhalin or Hokkaido population group also existed in the other population group, suggesting that genes are exchanged between these regions. When analyses were performed by origin, one of the Sakhalin southwestern-end populations formed a clade with the Hokkaido populations in the phylogenetic tree, both having similar genetic structure, and the Fst and DS values were particularly low with the Hokkaido East populations (S. japonica var. diabolica. The Fst and DS values were also low between the five Sakhalin southern populations – a sister group with the Hokkaido East populations in the phylogenetic tree – and the North Hokkaido populations (S. japonica var. ochotensis), indicating that these Sakhalin southwestern-end and southern populations may be used as alternatives to Hokkaido populations for culinary purposes.

Origin of a pair of red-crowned cranes (Grus japonensis) found in Sarobetsu Wetland, northwestern Hokkaido, Japan: a possible crossbreeding between the island and the mainland population.

Red-crowned cranes Grus japonensis, which are an endangered species, have two separate populations, a mainland population in the Eurasian continent and an island population in eastern Hokkaido, Japan. Island cranes showed three haplotypes (Gj1, Gj2 and Gj13), whereas ten haplotypes (Gj3–Gj12) were confirmed in captive cranes and stray cranes. We found Gj5 haplotype in feathers of two cranes as well as four new haplotypes in seven wild crane feathers collected in South Korea. We also found feathers in the nest in Sarobetsu Wetland in northwestern Hokkaido. While the haplotype of female-derived feathers was Gj2, that of male-derived feathers was Gj5. The results suggest that there has been crossbreeding between cranes in the island population and cranes in the mainland population.

Demographic History of the Brown Bear (Ursus arctos) on Hokkaido Island, Japan, Based on Whole-Genomic Sequence Analysis

Previous studies of the brown bear (Ursus arctos) on Hokkaido Island, Japan, have detected three geographically distinct subpopulations representing different mitochondrial lineages and shown that gene flow between subpopulations has occurred due to male-biased dispersal. In this study, we determined whole-genomic sequences for six Hokkaido brown bears and analyzed these data along with previously published genomic sequences of 17 brown bears from other parts of the world. We found that the Hokkaido population is genetically distinct from the other populations, keeping genetic diversity higher than the endangered populations in western Europe but lower than most populations on the continents. A reconstruction of historical demography showed no increase in population size for the Hokkaido population during the Eemian interglacial period (130,000–114,000 years ago). In a phylogenetic analysis of the autosomal data, the Hokkaido population formed a clade distinct from North American and European populations, showing that it has maintained genetic diversity independently from continental populations following geographical isolation on the island. This autosomal genetic similarity contrasts with the geographically separate mitochondrial lineages on Hokkaido and indicates the occurrence of male-driven gene flow between subpopulations.

Corrigendum

Corrigendum

Genetic region responsible for the differences of starch properties in two glutinous rice cultivars in Hokkaido, Japan.

Starch properties are major determinants of grain quality and food characteristics in rice (Oryza sativa L.). Control of starch properties will lead to the development of rice cultivars with desirable characteristics. We performed quantitative trait locus analysis and detected a putative region on chromosome 2 associated with phenotypic variation of starch properties in two glutinous rice varieties developed in the Hokkaido region of Japan: ‘Kitayukimochi’, which has a low pasting temperature and creates soft rice cakes, and ‘Shirokumamochi’, which has a high pasting temperature and creates hard rice cakes. Starch branching enzyme IIb (SbeIIb) was identified as a candidate gene within the region. Sequence analysis of SbeIIb in parental lines identified two single-nucleotide polymorphisms (SNPs) with non-synonymous mutations in the coding region of the ‘Shirokumamochi’ genotype (SbeIIbsr). We genotyped over 100 rice cultivars, including 28 rice varieties in the Honshu region of Japan, using the CAPS marker, which was designed using one of the SNPs. However, SbeIIbsr was not found in rice cultivars in Honshu. Distribution analysis indicated that SbeIIbsr was introduced to the rice breeding population in Hokkaido from the American variety ‘Cody’ via the Hokkaido cultivar ‘Kitaake’. As a result, SbeIIbsr was distributed only in progenies of ‘Kitaake’.

Microtiter plate test using liquid medium is an alternative method for monitoring metyltetraprole sensitivity in Cercospora beticola.

BACKGROUNDMetyltetraprole is a new quinone outside inhibitor (QoI) fungicide showing potent activity against QoI‐resistant fungi that possess the G143A cytochrome b mutation, which confers resistance to existing QoIs such as trifloxystrobin. For its sustainable use, monitoring of metyltetraprole sensitivity is necessary and the establishment of appropriate methodology is important in each pathogen species.RESULTSIn Cercospora beticola, the causal agent of sugar beet leaf spot, some isolates were less sensitive to metyltetraprole (EC50 > 1 mg L–1, higher than the saturated concentration) using the common agar plate method, even with 100 mg L−1 salicylhydroxamic acid, an alternative oxidase inhibitor. However, microtiter tests (EC50 < 0.01 mg L−1), conidial germination tests (EC50 < 0.01 mg L−1) and in planta tests (>80% control at 75 mg L−1 run‐off spraying) confirmed that all tested isolates were highly sensitive to metyltetraprole. For trifloxystrobin, G143A mutants were clearly resistant upon microtiter plate tests (median EC50 > 2 mg L−1) and distinct from wild‐type isolates (median EC50 < 0.01 mg L−1). Notably, mycelium fragments were usable for the microtiter plate tests and the test was applicable for isolates that do not form sufficient conidia. Our monitoring study by microtiter plate tests did not indicate the presence of metyltetraprole‐resistant C. beticola isolates in populations in Hokkaido, Japan.CONCLUSIONThe microtiter tests were revealed to be useful for monitoring the sensitivity of C. beticola to metyltetraprole and trifloxystrobin. © 2020 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Ricker analysis of dynamics for two populations of walleye pollock in the Japan Sea

Recent changes in reproduction are considered for two populations of walleye pollock which spawn in the Japan Sea at the coasts of Primorye and Hokkaido. Interannual dynamics of reproduction for both populations corresponds to the stock-recruitment dependence described by Ricker curve that determines the maximum recruitment with an optimal value of stock equal to the carrying capacity of the biotope for the species and the lower recruitment if the stock is either lower or higher than this optimal value. However, instability of the Ricker curve parameters is noted, and their recent changes were unfavorable for reproduction of both populations and caused decreasing of their stocks, with sharp decline in the early 1990s. Basing on authors results and cited data, climate change in the Japan Sea region is determined as the reason of this decreasing, in particular weakening of winter monsoon. In spite of a common nature, mechanisms of the climate change influence on two studied populations are completely different: reproduction of the Hokkaido population worsened because of increasing transfer of its eggs and larvae out of the Japan Sea in conditions of the strengthening Tsushima Current, that was explained in the terms of Ricker curve as decreasing of population fecundity, but reproduction of the Primorye population worsened because of unfavorable for pollock reconstructions in the local ecosystem located in the south periphery of the Subarctic zone in conditions of increasing water temperature that was explained in the terms of Ricker curve as shrinkage of carrying capacity for pollock (from approximately 150 .103 t to almost zero level). Note that the carrying capacity did not shrink but slightly extended (to 500 .103 t) for the Hokkaido population located in the north periphery of the Subtropic zone. Features of climate warming influence onto subarctic and subtropic ecosystems are discussed.

Isolation and characterization of microsatellites from a cicada, Yezoterpnosia nigricosta (Hemiptera: Cicadidae), distributed in subarctic and cool temperate forests.

The cicada Yezoterpnosia nigricosta (Hemiptera: Cicadidae) is distributed in subarctic and cool temperate forests in Japan, China and the Russian Far East. Due to its limited and isolated distribution at higher altitudes in cool temperate forests on the main island of Japan, especially in the central and southern areas, this species is listed as a threatened or near-threatened species on the Red List of 12 prefectures in Japan. Moreover, there are concerns about the impacts of climate change on the species' distribution and population demography. In this study, seventeen microsatellite markers were developed for Y. nigricosta, and marker suitability was evaluated using 32 individuals from two populations in Nagano prefecture (central Japan) and Hokkaido, a northern island of Japan. The number of alleles, expected heterozygosity and fixation index at each locus were 1-15 (mean = 4.294), 0.000-0.914 (mean = 0.519) and -0.225-0.456 (mean = 0.108), respectively. Furthermore, there was moderate genetic differentiation between the two populations (FST = 0.111, F'ST = 0.237). These markers will be useful to evaluate the genetic structure and to infer population demographic history of Y. nigricosta populations, which can contribute to population genetics studies of this species.

Genetic markers on the distribution of ancient marine hunters in Priokhotye

Представлен обзор сведений о генетическом полиморфизме современного и древнего населения Севера Азии и Америки с целью реконструкции истории миграций древних морских охотников в Охотоморском регионе. Проанализированы данные о полиморфизме митохондриальной ДНК и распространенности «арктиче- ской» мутации – варианта rs80356779-A гена CPT1A. Известно, что «арктический» вариант гена CPT1A с высокой частотой распространен в современных популяциях эскимосов, чукчей, коряков и других народов Охотоморско- го региона, хозяйственный уклад которых связан с морским зверобойным промыслом. Согласно палеогеномным данным, самые ранние находки «арктического» варианта гена CPT1A обнаружены у гренландских и канадских па- леоэскимосов (4 тыс. лет назад), представителей токаревской культуры Северного Приохотья (3 тыс. лет назад) и носителей культуры позднего дзёмона острова Хоккайдо (3.5–3.8 тыс. лет назад). Результаты анализа позволили выявить несколько миграционных событий, связанных с распространением морских охотников в Охотоморском регионе. Самая поздняя миграция, оставившая следы у носителей культуры эпи-дзёмон (2.0–2.5 тыс. лет назад), привнесла с севера Приохотья на Хоккайдо и соседние территории Приамурья митохондриальную гаплогруппу G1b и «арктический» вариант гена CPT1A. Следы более ранней миграции, также привнесшей «арктическую» мута- цию, зарегистрированы у населения позднего дзёмона Хоккайдо (3.5–3.8 тыс. лет назад). Проведен филогенети- ческий анализ митохондриальных геномов, относящихся к редкой гаплогруппе C1a, встречающейся у населения Дальнего Востока и Японии, но в филогенетическом отношении родственной C1-гаплогруппам американских индейцев. Результаты показали, что дивергенция митохондриальных линий в пределах гаплогруппы C1a проис- ходила в диапазоне от 7.9 до 6.6 тыс. лет назад, а возраст японской ветви гаплогруппы C1a составляет ~5.2 тыс. лет. Пока неизвестно, связана ли эта миграция с распространением «арктического» варианта гена CPT1A или же присутствие C1a-гаплотипов у населения островов Японии маркирует собой еще один, более ранний, эпизод миграционной истории, связывающей население северо-западной Пацифики и Северной Америки.

Origins of Nonnative Populations of Bufo japonicus formosus (Amphibia: Bufonidae) in Hokkaido, Japan, as Inferred by a Molecular Approach

The Eastern-Japanese common toad, Bufo japonicus formosus, is distributed from southern Hokkaido to Kinki district of northeastern Honshu, Japan. However, Hokkaido populations are suspected to be nonnative and derived from relatively recent artificial introduction from Honshu. To clarify the origin of Hokkaido populations, we analyzed sequence variations of the mitochondrial cytochrome b gene in the toads from Hokkaido and compared the sequence data from previous studies. We obtained ten haplotypes from six sites on Hokkaido. Samples from the sites located along Ishikari river system, Asahikawa, Ebetsu, and Ishikari cities, had six haplotypes. Only one haplotype was obtained in Sapporo city and it was genetically far from Ishikari river's ones. Hakodate and Muroran cities samples had one and two haplotypes, respectively. All ten haplotypes from Hokkaido were genetically identical or close to haplotype data from Kanto district or Shizuoka Prefecture, mid-eastern Honshu, far from Hokkaido. Therefore, the toad populations of Hokkaido were considered to be nonnative and multiple introductions from eastern Honshu to Hokkaido were implied.

Geographical Gradients of Genetic Diversity and Differentiation among the Southernmost Marginal Populations of Abies sachalinensis Revealed by EST-SSR Polymorphism

Research Highlights: We detected the longitudinal gradients of genetic diversity parameters, such as the number of alleles, effective number of alleles, heterozygosity, and inbreeding coefficient, and found that these might be attributable to climatic conditions, such as temperature and snow depth. Background and Objectives: Genetic diversity among local populations of a plant species at its distributional margin has long been of interest in ecological genetics. Populations at the distribution center grow well in favorable conditions, but those at the range margins are exposed to unfavorable environments, and the environmental conditions at establishment sites might reflect the genetic diversity of local populations. This is known as the central-marginal hypothesis in which marginal populations show lower genetic variation and higher differentiation than in central populations. In addition, genetic variation in a local population is influenced by phylogenetic constraints and the population history of selection under environmental constraints. In this study, we investigated this hypothesis in relation to Abies sachalinensis, a major conifer species in Hokkaido. Materials and Methods: A total of 1189 trees from 25 natural populations were analyzed using 19 EST-SSR loci. Results: The eastern populations, namely, those in the species distribution center, showed greater genetic diversity than did the western peripheral populations. Another important finding is that the southwestern marginal populations were genetically differentiated from the other populations. Conclusions: These differences might be due to genetic drift in the small and isolated populations at the range margin. Therefore, our results indicated that the central-marginal hypothesis held true for the southernmost A. sachalinensis populations in Hokkaido.

Distribution of the mutant allele of the DMRT3 gene associated with ambling gaits in Japanese native horse populations.

There are currently eight native horse populations in Japan, namely, Hokkaido, Kiso, Noma, Taishu, Misaki, Tokara, Miyako, and Yonaguni horses. Since locomotion traits, including gaitedness, are important for riding and packing horses, the genetic properties associated with these traits could be informative for understanding the characteristics and history of these horses. In this study, we investigated the distribution of the mutant allele of DMRT3 gene (DMRT3:p.Ser301Ter) associated with ambling gaits in the Japanese native horse. We also examined haplotypes of SNPs in the 83-kb region including DMRT3 gene by genotyping four SNPs in this region. The results revealed the presence of DMRT3:p.Ser301Ter in the Hokkaido and Yonaguni populations at allele frequencies of 0.18 and 0.02, respectively, and the observed haplotype associated with DMRT3:p.Ser301Ter was estimated as the most common haplotype in the horses in the world. Since DMRT3:p.Ser301Ter has been hypothesized to spread across Eurasian continent from Medieval England after 850 to 900 CE, our findings of the presence of DMRT3:p.Ser301Ter with the common haplotype in the Japanese native horses will provide a new insight into the history of the Japanese native horse, such as considerable level of gene flow from Eurasian continent after 850 to 900 CE.