The genetic population structure of lacustrine sockeye salmon, <Emphasis Type="Italic">Oncorhynchus nerka,</Emphasis> in Japan as the endangered species

Lacustrine sockeye salmon (Oncorhynchus nerka) are listed as an endangered species in Japan despite little genetic information on their population structure. In order to clarify the genetic diversity and structure of Japanese populations for evaluating on the bottleneck effect and an endangered species, we analyzed the ND5 region of mitochondrial DNA (mtDNA) and 45 single nucleotide polymorphisms (SNPs) in 640 lacustrine sockeye salmon in Japan and 80 anadromous sockeye salmon in Iliamna Lake of Alaska. The genetic diversity of the Japanese population in both mtDNA and SNPs was significantly less than that of the Iliamna Lake population. Moreover, all Japanese populations had SNP loci deviating from the HWE. In spite of low genetic diversity, the SNP analyses resulted that the Japanese population was significantly divided into three groups. These suggest that Japanese sockeye salmon populations should be protected as an endangered species and genetically disturbed by the hatchery program and transplantations.     

Lacustrine growth of juvenile pink salmon and a comparison with sympatric sockeye salmon

The growth rates of naturally sympatric juvenile pink Oncorhynchus gorbuscha and sockeye Oncorhynchus nerka salmon were compared in a common lacustrine environment in south‐west Alsaka, an unusual opportunity given the normal disparity in freshwater residence time of these two species. Fork length ( L _F) frequency distributions of juvenile pink salmon caught in the lake during the summer in 1991 and 1999–2003 indicated a growth rate of 0·54 mm day⁻¹, 54% greater than the estimated growth rate of juvenile sockeye salmon sampled from 1958 to 2003 (0·35 mm day⁻¹). Examination of daily growth rings on otoliths indicated that pink salmon in Lake Aleknagik grew an average of 1·34 mm day⁻¹ in 2003 but sockeye salmon grew only 0·63 mm day⁻¹(average specific growth rates were 3·0 and 1·8% day⁻¹, respectively). Pink salmon increased from c . 32 mm L _F and 0·2 g at emergence to 78 mm L _F and 3·0 g within 3–4 weeks. After experiencing these rapid growth rates, the pink salmon appeared to leave the lake by late July in most years. The diets of pink and sockeye salmon in the littoral zone of the lake were very similar; >80% of the stomach contents consisted of adult and pupal insects and the remainder was zooplankton. This high degree of diet overlap suggested that the observed differences in growth rate were not attributable to variation in prey composition.     

Comparative anatomy of the dorsal hump in mature Pacific salmon

Mature male Pacific salmon (Genus Oncorhynchus ) demonstrate prominent morphological changes, such as the development of a dorsal hump. The degree of dorsal hump formation depends on the species in Pacific salmon. It is generally accepted that mature males of sockeye (O. nerka ) and pink (O. gorbuscha ) salmon develop most pronounced dorsal humps. The internal structure of the dorsal hump in pink salmon has been confirmed in detail. In this study, the dorsal hump morphologies were analyzed in four Pacific salmon species inhabiting Japan, masu (O. masou ), sockeye, chum (O. keta ), and pink salmon. The internal structure of the dorsal humps also depended on the species; sockeye and pink salmon showed conspicuous development of connective tissue and growth of bone tissues in the dorsal tissues. Masu and chum salmon exhibited less‐pronounced increases in connective tissues and bone growth. Hyaluronic acid was clearly detected in dorsal hump connective tissue by histochemistry, except for in masu salmon. The lipid content in dorsal hump connective tissue was richer in masu and chum salmon than in sockeye and pink salmon. These results revealed that the patterns of dorsal hump formation differed among species, and especially sockeye and pink salmon develop pronounced dorsal humps through both increases in the amount of connective tissue and the growth of bone tissues. In contrast, masu and chum salmon develop their dorsal humps by the growth of bone tissues, rather than the development of connective tissue.     

Salmonid olfactory system-specific protein (N24) exhibits glutathione S-transferase class pi-like structure

A salmonid olfactory system-specific protein (N24) that has been identified in lacustrine sockeye salmon (Oncorhynchus nerka) was characterized by biochemical and molecular biological techniques. N24 is a homodimer, and the intact molecular mass is estimated as approximately 43.3 kDa by gel filtration. Furthermore, N24 was located only in the cytosolic fraction of the olfactory tissues as determined by subcellular fractionation. cDNA encoding the lacustrine sockeye salmon N24 was isolated and sequenced. This cDNA contained a coding region encoding 216 amino acid residues and the molecular mass of this protein is calculated to be 242,224.77. The protein and nucleotide sequencing demonstrates the existence of a remarkable homology between N24 and glutathione S-transferase (GST; EC 2.5.1.18) class pi enzymes. Northern analysis showed that N24 mRNA with a length of 950 bases is expressed in lacustrine sockeye salmon olfactory epithelium. Olfactory receptor cells showed strong hybridization signals for N24 mRNA in the olfactory epithelium. N24 demonstrated glutathione binding activity in affinity-purified GST column experiments. The present study describes for the first time cDNA cloning of GST in fish olfactory epithelium.     

Prey selection and efficiency of naïve and experienced juvenile sockeye salmon

Prey selection and growth efficiency of juvenile sockeye salmon Oncorhynchus nerka switched between live prey and pelleted diets were investigated. First feeding sockeye salmon fry were placed into one of three dietary treatments for 7 months prior to assessing potential differences with a growth and a behavioural assay. Dietary treatments were (1) adult Artemia franciscana for 1 month, followed by pelleted feed for an additional 6 months ( Art − BD), (2) pelleted feed from first feeding for 7 months (BD) and (3) adult A. franciscana for 1 month, and a combination of pelleted feed and live adult A. franciscana for 6 months ( Art + BD). Equal numbers from each treatment group were then tagged, pooled into replicate 'common garden' tanks and fed novel live prey items ( Daphnia sp. and mosquito Culex pipiens larvae) for an additional 3 weeks. No significant differences in the growth efficiency of sockeye salmon were found during the 3 week feeding trial on the novel prey items. Additional sockeye salmon from each dietary treatment were used in a behavioural assay to determine if the treatments had an impact on foraging efficiency (prey selection or time to capture prey). No significant differences in prey selection were found among treatment groups in time to capture pellets, A. franciscana or mosquito larvae. Also, no significant differences were found within treatment groups in time to capture different food sources. No substantive benefits in foraging efficiency of sockeye salmon associated with prior exposure to live prey were demonstrated. This suggests that altering existing hatchery practices for juvenile sockeye salmon by offering live food prior to release is unlikely to influence post-hatchery feeding behaviour or increase post-release survival.     

Variation in smoltification age and its determinants in sockeye salmon of Lake Azabach’e

In this paper, we analyze scale samples of sexually mature sockeye salmon from Lake Azabach'e collected over many years and data on the abundance of zooplankton in this lake. For native juvenile sockeye salmon, the major limiting factor of growth and smoltification is food availability. During the observation period from 1977 to 1993, two-year-olds were the most numerous group among the downstream-migrating sockeye salmon. Short-term fluctuations in the proportion of one-year-old smolts during downstream migration are attributed to outbreaks of plankton due to the natural fertilization of the lake.     

Rapid Carbon Turnover During Growth of Atlantic Salmon (Salmo salar) Smolts in Sea Water, and Evidence for Reduced Food Consumption by Growth-Stunts

Wild Atlantic salmon smolts were captured during spring out-migration in the Northwest Miramichi River, New Brunswick, Canada, and placed on an isotopically distinct hatchery diet to determine the relative contributions of growth and metabolic turnover to isotopic change. As expected for an ectothermic species, growth explained a large amount of isotopic variation in changing stable carbon ratios of muscle tissue (average r ²= 0.46 ) for the 3 years of study. Turnover rates of muscle carbon in all 3 years in growing fish (0.24–0.66 month^–1) were higher than previously reported values for other ectothermic species, but there was little evidence for isotopic change in non-growers (average r ²= 0.041, p > 0.1). It is unlikely that non-growers had consumed any of the hatchery diet over a 2-month period, thus preventing them from acquiring the new carbon isotopic signature. This period of food deprivation resulted in nitrogen-15 enrichment in liver relative to muscle (p= 0.003). It is advised that future isotope studies of metabolic turnover rates in ectotherms be conducted on slow-growing animals over a long time period. This would serve to avoid the obscuring effects of growth on isotopic change, and provide stronger comparisons to endothermic tissue turnover rates.     

MOLECULAR GENETIC EVIDENCE FOR PARALLEL LIFE-HISTORY EVOLUTION WITHIN A PACIFIC SALMON (SOCKEYE SALMON AND KOKANEE,ONCORHYNCHUS NERKA)

The Pacific salmon Oncorhynchus nerka typically occurs as a sea-run form (sockeye salmon) or may reside permanently in lakes (kokanee) thoughout its native North Pacific. We tested whether such geographically extensive ecotypic variation resulted from parallel evolutionary divergence thoughout the North Pacific or whether the two forms are monophyletic groups by examining allelic variation between sockeye salmon and kokanee at two minisatellite DNA repeat loci and in mitochondrial DNA (mtDNA) Bgl II restriction sites. Our examination of over 750 fish from 24 populations, ranging from Kamchatka to the Columbia River, identified two major genetic groups of North Pacific O. nerka: a “northwestern” group consisting of fish from Kamchatka, western Alaska, and northwestern British Columbia, and a “southern” group consisting of sockeye salmon and kokanee populations from the Fraser and Columbia River systems. Maximum-likelihood analysis accompanied by bootstrapping provided strong support for these two genetic groups of O. nerka; the populations did not cluster by migratory form, but genetic affinities were organized more strongly by geographic proximity. The two major genetic groups resolved in our study probably stem from historical isolation and dispersal of O. nerka from two major Wisconsinan glacial refugia in the North Pacific. There were significant minisatellite DNA allele frequency differences between sockeye salmon and kokanee populations from different parts of the same watershed, between populations spawning in different tributaries of the same lake, and also between sympatric populations spawning in the same stream at the same time. MtDNA Bgl II restriction site variation was significant between sockeye salmon and kokanee spawning in different parts of the same major watershed but not between forms spawning in closer degrees of reproductive sympatry. Patterns of genetic affinity and allele sharing suggested that kokanee have arisen from sea-run sockeye salmon several times independently in the North Pacific. We conclude that sockeye salmon and kokanee are para- and polyphyletic, respectively, and that the present geographic distribution of the ecotypes results from parallel evolutionary origins of kokanee from sockeye (divergences between them) thoughout the North Pacific.     

Does among‐population variation in burst swimming performance of sockeye salmon Oncorhynchus nerka fry reflect early life migrations?

Using a fixed‐speed test, burst swimming performance was found to vary among nine populations of emergent sockeye salmon Oncorhynchus nerka fry reared in a common‐garden environment. No consistent relationship was, however, detected between difficulty of fry migration (upstream v. downstream) to rearing areas and total burst swimming duration or bursting rate.     

A wide window of migration phenology captures inter‐annual variability of favourable conditions: Results of a whole‐lake experiment with juvenile Pacific salmon

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Effects of surgically implanted acoustic transmitters >2% of body mass on the swimming performance, survival and growth of juvenile sockeye and Chinook salmon

The influence of surgical implantation of an acoustic transmitter on the swimming performance, growth and survival of juvenile sockeye salmon Oncorhynchus nerka and Chinook salmon Oncorhynchus tshawytscha was examined. The transmitter had a mass of 0·7 g in air while sockeye salmon had a mass of 7·0–16·0 g and Chinook salmon had a mass of 6·7–23·1 g (a transmitter burden of 4·5–10·3% for sockeye salmon and 3·1–10·7% for Chinook salmon). Mean critical swimming speeds (U_crit) for Chinook salmon ranged from 47·5 to 51·2 cm s^?1 [4·34–4·69 body lengths (fork length, L_F) s^?1] and did not differ among tagged, untagged and sham‐tagged groups. Tagged sockeye salmon, however, did have lower U_crit than control or sham fish. The mean U_crit for tagged sockeye salmon was 46·1 cm s^?1 (4·1 L_F s^?1), which was c. 5% less than the mean U_crit for control and sham fish (both groups were 48·6 cm s^?1 or 4·3 L_F s^?1). A laboratory evaluation determined that there was no difference in L_F or mass among treatments (control, sham or tag) either at the start or at the end of the test period, suggesting that implantation did not negatively influence the growth of either species. None of the sockeye salmon held under laboratory conditions died from the influence of surgical implantation of transmitters. In contrast, this study found that the 21 day survival differed between tagged and control groups of Chinook salmon, although this result may have been confounded by the poor health of Chinook salmon treatment groups.     

Countergradient variation in carotenoid use between sympatric morphs of sockeye salmon (Oncorhynchus nerka) exposes nonanadromous hybrids in the wild by their mismatched spawning colour

Understanding the mechanisms that decrease gene flow between diverging populations is critical to understanding speciation. Anadromous (sockeye) and nonanadromous (kokanee) morphs of the Pacific sockeye salmon Oncorhynchus nerka spawn sympatrically and interbreed, yet allele frequency differences at neutral loci indicate restricted gene flow. Disruptive natural selection associated with strong selective differences between anadromous and nonanadromous life histories is thought to maintain the genetic differentiation of the morphs. Recently, a putative third morph of O. nerka exhibiting green rather than red breeding colour has been found on the spawning grounds sympatric with sockeye and kokanee. We investigated the ancestry of these green fish in a 2‐year controlled breeding study by using previously documented heritable, countergradient variation in red breeding colour to distinguish pure and hybrid morphs. Stabilizing sexual selection for similar red breeding colour in sockeye and kokanee has led to adaptive differences in the efficiency of carotenoid uptake between the morphs given differences in carotenoid availability between marine and lacustrine habitats. On the same diet, offspring parented by the green fish were intermediate in colour and in the concentration of dietary carotenoid pigments in their flesh and skin to those parented by either sockeye or kokanee; they were most similar to those parented by known kokanee × sockeye hybrids. This countergradient variation in carotenoid use results in a genotype‐environment mismatch in nonanadromous hybrids that exposes them by their breeding colour on the spawning grounds. Given that red colour is important in mate choice, sexual selection will almost certainly reduce reproductive opportunities for these hybrids and promote sympatric divergence of these incipient species. © 2005 The Linnean Society of London, Biological Journal of the Linnean Society, 2005, 84 , 287–305.     

Climate effects on growth, phenology, and survival of sockeye salmon (Oncorhynchus nerka): a synthesis of the current state of knowledge and future research directions

Sockeye salmon (Oncorhynchus nerka) is one of the most iconic and valued species of Pacific salmon. Various studies have examined the potential effects of future climate change on sockeye salmon, but there is currently no synthesis of the documented effects of climate on this species. In this paper, we present a synthesis of 80 peer-reviewed publications in the English language evaluating the effects of climate on sockeye salmon growth, phenology, and survival. The great majority of studies examined have been conducted with stocks from North America (90?% of studies). Survival (55?%) has been the most frequently studied aspect of the sockeye salmon life history in relation to climate, followed by growth (45?%) and phenology (30?%), with temperature (83.4?%) being the climate-related variable most frequently examined in such studies. Across life stages, the effects of climate-related variables have been most frequently studied on fry (36.3?%) and least studied on spawners (7.5?%). Our synthesis revealed that associations between temperature and growth, phenology, or survival have been uncovered for all the life stages of sockeye salmon, whereas relationships with other climate-related variables have been sparse. There is substantial evidence that sockeye salmon are influenced by thermal conditions experienced at regional, rather than ocean- or continental-wide scales, and that responses to temperature vary among and within stocks. The mechanisms by which climate affect sockeye salmon during the early stages in freshwater and while at sea are still poorly understood and warrant future research. More research on the effects of non-temperature, climate-related variables (e.g. stream flow, ocean pH), inter-generational and carry-over effects of climate, interaction between climate and non-climate stressors, and adaptation to climate change are also needed. Such information will be critical to advance our understanding of how sockeye salmon stocks will fare with future climate change.     

Statistical analysis on otolith data of anadromous fishes

Stable oxygen and carbon isotope (δ¹⁸O and δ¹³C) analyses of otoliths are becoming increasingly common in fisheries science and management. However, little is known about the statistical properties of isotopic data and few attempts have been made to explore appropriate statistical methods that could be used for otolith data analysis. In this paper, we present a pilot study on δ¹⁸O and δ¹³C data from otoliths of two anadromous fish species, Atlantic salmon (Salmo salar) and Pacific sockeye salmon (Oncorhynchus nerka). The results indicated that the salmon otolith data were not normally distributed, so that linear discriminant function analysis and commonly-used statistical tests such as ANOVA and the t-test may not be appropriate. Using non-parametric k-sample nearest neighbor discriminant analysis, we were able to discriminate with high accuracy among five hatcheries for Atlantic salmon and the origins of wild and hatchery sockeye salmon. Analyses also indicated that the sample sizes required to estimate δ¹⁸O and δ¹³C means based on the different sources of variability (between group or within group) and precision levels (≤ ±5.0 %) were not large. These results and conclusions not only address the statistical considerations of isotopic data from otoliths, but also have practical importance for fisheries management as well.     

Genetic Diversity in a Small Population of Sockeye Salmon Oncorhynchus nerkaWalbaum from the Ola River (the Northern Coast of the Okhotsk Sea)

The genetic structure of a small sockeye salmon population from the Ola River (Tauyskaya Inlet, the Okhotsk Sea) was shown to exhibit high heterogeneity. Significant differences of LDH-B2*and ALAT-2*gene frequencies were detected not only among samples within the spawner and juvenile groups but also between spawners and juveniles as a whole. The average heterozygosity of sockeye salmon from the Ola River was considerably lower than the corresponding values for other Asian populations. The Ola sockeye salmon is genetically similar to the population from the Pakhach River of the northwestern Kamchatka Peninsula but different from other Kamchatka populations and the Okhota River population. A hypothesis explaining the genetic differentiation of Asian sockeye populations is advanced.     

Tendencies of Density Dynamics in Reophilic and Lacustrine Sockeye Salmon Oncorhynchus nerkain the Basin of Azabach'e Lake

Temporal series of density in the spawners of two sockeye salmon populations from Azabach'e Lake (Kamchatka River basin) were analyzed using periodic functions. It has been found that the quality of describing the density dynamics for sockeye salmon by such models is very high (R ²= 0.943 and R ²= 0.905 for early and late populations, respectively). The density (for early sockeye salmon) and total number (for late sockeye salmon) distributions of the reproductive fraction of the populations have been developed and analyzed.     

Salmon‐derived nutrients drive diatom beta‐diversity patterns

1. Pacific salmon are a textbook example of migratory animals that transfer nutrients between ecosystems, but little is known about how salmon‐derived nutrients (SDN) affect the biodiversity of recipient freshwater ecosystems. We examined paleolimnological records from six Alaskan lakes to define how changes in SDN from sockeye salmon (Oncorhynchus nerka) influenced sedimentary diatom community structure and beta‐diversity among lakes and through time. 2. Using an isotopic mixing model, we showed that SDN loading could account for >80% of the lake total nitrogen budgets and strongly regulated diatom community composition. Spatial dissimilarity in diatom communities was positively related to differences in SDN among lakes (r² = 0.69, P < 0.01, n = 10). Likewise, temporal dissimilarity in diatom communities was positively related to differences in SDN in a sediment core with substantial variation in salmon spawner dynamics between 1700 and 1950 AD (r² = 0.34, P < 0.01, n = 19). Finally, beta‐diversity metrics quantifying temporal turnover within each lake’s sediment record were also positively related to the variance in SDN loading among lakes (r² = 0.88, P < 0.05, n = 5). Mean SDN was only negatively correlated to temporal diatom beta‐diversity. 3. Spatially subsidised systems often receive temporally variable resource inputs, and thus, it is not surprising that, unlike previous studies, we found that resource variability was the key driver of community composition and beta‐diversity. In habitats that receive strongly fluctuating external nutrient loads, environment heterogeneity may overweigh stochastic community processes. In addition, freshwater diatoms are characterised by great dispersal capabilities and short life cycles and therefore may be a more sensitive indicator for evaluating the role of resource variability than previously used model organisms. These results suggest that productivity–diversity relationship vary with the nature of nutrient loading and the life history of the community studied. 4. Overall, our study highlights that the transport of nutrients by sockeye salmon across ecosystem boundaries is a significant driver of algal community and biodiversity in nursery lakes, mainly through changing the magnitude of nutrient variation. As such, freshwater species diversity in regions like the U.S. Pacific Northwest may become impoverished where there have been long‐term declines in salmon populations and decreases in nutrient variability among lakes.     

Evaluating Relationships between Wild Skeena River Sockeye Salmon Productivity and the Abundance of Spawning Channel Enhanced Sockeye Smolts

The enhancement of salmon populations has long been used to increase the abundance of salmon returning to spawn and/or to be captured in fisheries. However, in some instances enhancement can have adverse impacts on adjacent non-enhanced populations. In Canada''s Skeena watershed, smolt-to-adult survival of Babine Lake sockeye from 1962–2002 was inversely related to the abundance of sockeye smolts leaving Babine Lake. This relationship has led to the concern that Babine Lake smolt production, which is primarily enhanced by spawning channels, may depress wild Skeena (Babine and non-Babine) sockeye populations as a result of increased competition between wild and enhanced sockeye smolts as they leave their natal lakes and co-migrate to sea. To test this hypothesis we used data on Skeena sockeye populations and oceanographic conditions to statistically examine the relationship between Skeena sockeye productivity (adult salmon produced per spawner) and an index of Babine Lake enhanced smolt abundance while accounting for the potential influence of early marine conditions. While we had relatively high power to detect large effects, we did not find support for the hypothesis that the productivity of wild Skeena sockeye is inversely related to the abundance of enhanced sockeye smolts leaving Babine Lake in a given year. Importantly, life-time productivity of Skeena sockeye is only partially explained by marine survival, and likely is an unreliable measure of the influence of smolt abundance. Limitations to our analyses, which include: (1) the reliance upon adult salmon produced per spawner (rather than per smolt) as an index of marine survival, and (2) incomplete age structure for most of the populations considered, highlight uncertainties that should be addressed if understanding relationships between wild and enhanced sockeye is a priority in the Skeena.     

Sea louse infection of juvenile sockeye salmon in relation to marine salmon farms on Canada's west coast

Background

Pathogens are growing threats to wildlife. The rapid growth of marine salmon farms over the past two decades has increased host abundance for pathogenic sea lice in coastal waters, and wild juvenile salmon swimming past farms are frequently infected with lice. Here we report the first investigation of the potential role of salmon farms in transmitting sea lice to juvenile sockeye salmon (Oncorhynchus nerka).

Methodology/Principal Findings

We used genetic analyses to determine the origin of sockeye from Canada''s two most important salmon rivers, the Fraser and Skeena; Fraser sockeye migrate through a region with salmon farms, and Skeena sockeye do not. We compared lice levels between Fraser and Skeena juvenile sockeye, and within the salmon farm region we compared lice levels on wild fish either before or after migration past farms. We matched the latter data on wild juveniles with sea lice data concurrently gathered on farms. Fraser River sockeye migrating through a region with salmon farms hosted an order of magnitude more sea lice than Skeena River populations, where there are no farms. Lice abundances on juvenile sockeye in the salmon farm region were substantially higher downstream of farms than upstream of farms for the two common species of lice: Caligus clemensi and Lepeophtheirus salmonis, and changes in their proportions between two years matched changes on the fish farms. Mixed-effects models show that position relative to salmon farms best explained C. clemensi abundance on sockeye, while migration year combined with position relative to salmon farms and temperature was one of two top models to explain L. salmonis abundance.

Conclusions/Significance

This is the first study to demonstrate a potential role of salmon farms in sea lice transmission to juvenile sockeye salmon during their critical early marine migration. Moreover, it demonstrates a major migration corridor past farms for sockeye that originated in the Fraser River, a complex of populations that are the subject of conservation concern.     

Individual growth and phase differentiation of lacustrine masu salmon, Oncorhynchus masou, under artificial rearing conditions

 In lacustrine masu salmon, Oncorhynchus masou, originated from anadromous fish and inhabiting an artificial lake (Shumarinai Lake), we examined the relationship between individual growth during the juvenile stage and phase differentiation under artificial rearing conditions. In females, the mean fork length of potential (subsequent) 1+ smolts and potential 1+ parr (1+ parr show fish that neither smolted nor matured until 1+ autumn) always differed after their first summer (0+ summer), the former being larger. In males, the juveniles that grew faster during their first spring became 0+ mature male parr. After their first summer, potential 1+ smolts were always larger in body length than potential 1+ mature parr and potential 1+ parr. These results were similar to previous reports of anadromous masu salmon, suggesting that the lacustrine masu salmon studied seems to have maintained the phase differentiation as in the original fish, likely because only 60 years have passed since the formation of the lacustrine population.