Loss of Genetic Diversity Means Loss of Geological Information: The Endangered Japanese Crayfish Exhibits Remarkable Historical Footprints

Intra-specific genetic diversity is important not only because it influences population persistence and evolutionary potential, but also because it contains past geological, climatic and environmental information. In this paper, we show unusually clear genetic structure of the endangered Japanese crayfish that, as a sedentary species, provides many insights into lesser-known past environments in northern Japan. Over the native range, most populations consisted of unique 16S mtDNA haplotypes, resulting in significant genetic divergence (overall FST = 0.96). Owing to the simple and clear structure, a new graphic approach unraveled a detailed evolutionary history; regional crayfish populations were comprised of two distinct lineages that had experienced contrasting demographic processes (i.e. rapid expansion vs. slow stepwise range expansion) following differential drainage topologies and past climate events. Nuclear DNA sequences also showed deep separation between the lineages. Current ocean barriers to dispersal did not significantly affect the genetic structure of the freshwater crayfish, indicating the formation of relatively recent land bridges. This study provides one of the best examples of how phylogeographic analysis can unravel a detailed evolutionary history of a species and how this history contributes to the understanding of the past environment in the region. Ongoing local extinctions of the crayfish lead not only to loss of biodiversity but also to the loss of a significant information regarding past geological and climatic events

Lineage-level distribution models lead to more realistic climate change predictions for a threatened crayfish

Aim As climate change presents a major threat to biodiversity in the next decades, it is critical to assess its impact on species habitat suitability to inform biodiversity conservation. Species distribution models (SDMs) are a widely used tool to assess climate change impacts on species' geographical distributions. As the name of these models suggests, the species level is the most commonly used taxonomic unit in SDMs. However, recently it has been demonstrated that SDMs considering taxonomic resolution below (or above) the species level can make more reliable predictions of biodiversity change when different populations exhibit local adaptation. Here, we tested this idea using the Japanese crayfish (Cambaroides japonicus), a threatened species encompassing two geographically structured and phylogenetically distinct genetic lineages. Location Northern Japan. Methods We first estimated niche differentiation between the two lineages of C. japonicus using n-dimensional hypervolumes and then made climate change predictions of habitat suitability using SDMs constructed at two phylogenetic levels: species and intraspecific lineage. Results Our results showed only intermediate niche overlap, demonstrating measurable niche differences between the two lineages. The species-level SDM made future predictions that predicted much broader and severe impacts of climate change. However, the lineage-level SDMs led to reduced climate change impacts overall and also suggested that the eastern lineage may be more resilient to climate change than the western one. Main conclusions The two lineages of C. japonicus occupy different niche spaces. Compared with lineage-level models, species-level models can overestimate climate change impacts. These results not only have important implications for designing future conservation strategies for this threatened species, but also highlight the need for incorporating genetic information into SDMs to obtain realistic predictions of biodiversity change.Peer reviewe

Relative importance of host-dependent versus physical environmental characteristics affecting the distribution of an ectoparasitic copepod infecting the mouth cavity of stream salmonid

Understanding parasite distributional patterns is fundamental for elucidating host-parasite relationships. The genus Salmincola is an ectoparasitic copepod group specifically infecting freshwater salmonids. Considering their strong association with their hosts, we can predict that the distribution and prevalence (analogs to abundance) of Salmincola reflect host salmonids. An alternative hypothesis is that their distribution will be strongly affected by environmental factors like stream drift because they have a free-living stage with low swimming ability. If this is the case, we predict a longitudinal gradient with higher occurrence or infection levels in downstream areas. To estimate the relative strength among factors affecting infection levels, we investigated the distribution pattern of Salmincola sp. on wild white-spotted charr Salvelinus leucomaenis in a southern Hokkaido river system. Based on data from 19 sites across three seasons, we found that host density and flow velocity affected the prevalence of Salmincola. On the other hand, no longitudinal gradient was observed and the prevalence was extremely low in some fragmented habitats (i.e., above dams and waterfalls). This indicates some compensation mechanisms against unidirectional downstream dispersal. We found that parasite prevalence and intensity were much higher in large migratory (anadromous) fish and, therefore, hypothesize that long-distance upstream migration helps the redistribution and population persistence of parasites in upstream areas

Early maturation of rosyface dace, Tribolodon sachalinensis (Cyprinidae, Cypriniformes), in a small isolated population

Age at maturity is one of the key parameters of life-history. Whereas large variations in adult body size have been reported in Tribolodon sachalinensis (Nikolsky, 1889), age and size at first maturity have rarely been examined. Here, we report early maturation (+1 male) and sexual difference in age at maturity in an isolated population in Hokkaido, northern Japan, which is different from a previous study

Socially induced reproductive synchrony in a salmonid: an approximate Bayesian computation approach

Reproductive synchrony is a widespread phenomenon found in many taxa, including plants and corals. However, compared with synchrony caused by environmental cues, knowledge of socially induced reproductive synchrony is limited, partly due to the difficulty of experimentally manipulating and/or making detailed behavioral observations of populations in the wild. In this study, we developed a novel modeling framework combining an individual-based model, a hierarchical Bayesian model, and an approximate Bayesian computation (ABC) to elucidate socially induced reproductive synchrony. This method was applied to time-series redd (i.e., spawning nests) count data in 30 wild populations of stream-dwelling Dolly Varden charr. The model with reproductive synchrony explained all the redd count data, whereas the null model, which did not include the synchrony, failed to reproduce the observed data in several populations. In addition, our models suggest that Dolly Varden should be able to adjust spawning by up to a week following other females to produce synchrony. No significant correlation was observed between reproductive timing and environmental factors, suggesting that the major cue for the synchrony was social rather than environmental. The presence of reproductive synchrony within but not among local populations suggests that predator satiation is not the main driver of the synchrony; rather, other mechanisms must exist in the Dolly Varden, such as induced monogamy or polygamy, or avoidance of nest superimposition. This study has demonstrated the effectiveness of using individual-based and hierarchical modeling together with an ABC parameter estimation method in behavioral ecological studies

Potential resource competition between an invasive mammal and native birds: overlap in tree cavity preferences of feral raccoons and Ural owls

Invasive mammals include good tree climbers that use tree cavities for resting and nesting. Tree cavities are important but limited resources in most forests; thus, some invasive mammals can be serious competitors for native cavity-using species, especially cavity-nesting birds. Despite the potential impact, such inter-class competition has rarely been considered. We examined the possibility of resource competition for tree cavities between the invasive raccoon Procyon lotor and the native Ural owl Strix uralensis. Both species are nocturnal and use tree cavities during daytime. We assessed an overlap in cavity use for both species as an indication of potential competition by monitoring 341 cavities during their breeding season in a natural park in Hokkaido, Japan. Of 341 potentially available cavities, raccoons and Ural owls used 37 and 32, respectively. The characteristics of 58 cavities used by raccoons or owls were compared to 49 random cavities to determine if they selected cavities with certain characteristics. As predicted from a large amount of tree cavities and a low raccoon density in this managed forest, we did not find direct evidence of competition, such as physical interaction, intrusion to cavities, or habitat segregation. Cavity types used by both species overlapped considerably in terms of height, entrance size, depth, and other characteristics: their habitats were widely overlapped. Further, in four cavities, one species was replaced by the other. Given the similar habitat requirements, the invasive raccoon could be a potential competitor for Ural owl when raccoon density increases and/or cavity availability decreases, which is the case for many forests in Japan. This study suggests that potential threats of resource competition among not only closely but also distantly related taxa should be taken into consideration when studying the impacts of invasive species

Data from: Does nest predation risk affect the frequency of extra-pair paternity in a socially monogamous passerine?

While considerable variations in both the frequency of extra-pair paternity (EPP) and the behavioral events that produce it are recognized among species, populations, individuals, and breeding attempts, the determinants of these variations are surprisingly difficult to establish. Nest predation may be one such determinant, since it is the most important source of reproductive failure, and past studies have suggested a variety of reproductive flexibilities under nest predation risk. However, despite its potentially significant effect on mating behaviors, nest predation risk has rarely been discussed in association with variations in intraspecific EPP patterns. Here, we examined the effect of naturally occurring nest predation, which varied between sites, years, and breeding attempts, on patterns of EPP in 92 broods (132 adults and 710 nestlings) of the Japanese great tit Parus major minor. We found that the frequency of extra-pair offspring was positively correlated with the nest predation rate, along with a correlation to breeding attempts in a season, but not with other factors such as individual quality or breeding density. Under high nest-predation risk, it may be adaptive for males to search for additional extra-pair copulation to spread the risk of losing all offspring and to invest less in mate-guarding, which also enables females to seek additional extra-mating. The results of this study suggest that nest predation risk, among other factors, may significantly influence paternity allocation in birds

Hybridization between native white-spotted charr and nonnative brook trout in the upper Sorachi River, Hokkaido, Japan

Invasion status and impacts of nonnative brook trout (Salvelinus fontinalis) in a Hokkaido stream were investigated with field surveys and genetic analyses. Nonnative brook trout was detected in nine (41 %) of the 22 sampled reaches in three tributaries of the Sorachi River, Hokkaido, Japan. Based on the external pigmentation, twelve putative hybrids between brook trout and native white-spotted charr (Salvelinus leucomaenis) were collected in two reaches. Microsatellite and mitochondrial DNA data established that 58% of these hybrids were firstgeneration (F1) progenies between male brook trout and female white-spotted charr. Our results suggest potential negative impacts of nonnative brook trout on native charr populations in Hokkaido through interspecific interactions

Different habitat salinity between genetically divergent groups of a worm-like goby Luciogobius guttatus: an indication of cryptic species

Gobies of the genus Luciogobius have unusual morphological adaptations to interstitial rocky coastal habitats in far eastern Asia; an elongated scale-less body, the loss the first dorsal fin, and a drastically increased number of vertebrae. Convergent evolution makes the species distinction difficult and the existence of many cryptic species has been postulated. Two divergent lineages of L. guttatus had been reported with the possibility of niche differentiation between marine and brackish habitats. Here, we quantitatively assessed the water salinity of the habitats used by the two lineages in Hokkaido, Japan, as well as their morphology. One lineage occurred exclusively in high-salinity habitats in intertidal zones (> 25 aEuro degrees) and the other occurred mostly, but not exclusively, in low-salinity habitats near river mouths (< 5 aEuro degrees). This result, together with mtDNA molecular phylogeny, suggests that the brackish type might have originated from a marine ancestor. Two lineages occurred sympatrically on some shores. No apparent difference was observed in the external morphology between the lineages, whereas the number of vertebrae was significantly different. Our results support the preposition that the divergent lineages within L. guttatus represent cryptic species