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Lack of association between winter coat colour and genetic population structure in the Japanese hare, Lepus brachyurus (Lagomorpha: Leporidae)
Abstract
Seasonal changes in fur colour in some mammalian species have long attracted the attention of biologists, especially in species showing population variation in these seasonal changes. Genetic differences among populations that show differences in seasonal changes in coat colour have been poorly studied. Because the Japanese hare (Lepus brachyurus) has two allopatric morphotypes that show remarkably different coat colours in winter, we examined the population genetic structure of the species using partial sequences of the SRY gene and six autosomal genes: three coat colour-related genes (ASIP, TYR, and MC1R) and three putatively neutral genes (TSHB, APOB, and SPTBN1). The phylogenetic tree of SRY sequences exhibited two distinct lineages that diverged approsimately 1 Mya. Although the two lineages exhibited a clear allopatric distribution, it was not consistent with the distribution of morphotypes. In addition, six nuclear gene sequences failed to reveal genetic differences between morphotypes. Population network trees for 11 expedient populations divided the populations into four groups. Genetic structure analysis revealed an admixture of four genetic clusters in L. brachyurus, two of which showed large genetic differences. Our results suggest ancient vicariance in L. brachyurus, and we detected no genetic differences between the two morphotypes. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, ●●, ●●–●●.
... These studies suggest that frequent and massive introgressions of mtDNA among East Asian hares have led to confusion regarding their taxonomic and phylogenetic relationships. On the other hand, L. brachyurus, the hare species endemic to the Japanese Archipelago, is suggested to have a long independent history, beginning before the Middle Pleistocene (Nunome et al., 2010(Nunome et al., , 2014Yamada et al., 2002), despite the possibility of secondary contact and introgressive hybridization with L. timidus and other continental species across land bridges during glacial periods. Comparative genetic studies on continents and insular isolates are currently of fundamental importance to understand the geographical factors in evolutionary divergence and shaping biodiversity of a focal area (Patiño et al., 2017), while only a handful of phylogeographic studies have been conducted in East Asia including both sides of the archipelago and the continent (e.g., Aoki et al., 2018;Kinoshita et al., 2015;Sakka et al., 2010). ...
... In total, 97 tissue samples from four Lepus species-L. timidus (n = 42), L. mandshuricus (n = 14), L. coreanus (n = 10), and L. brachyurus (n = 31)-were obtained from road-killed or hunted animals that were collected for the present study and previous studies (Kinoshita et al., 2012;Nunome et al., 2010Nunome et al., , 2014. Sampling locations are shown in Fig. 1 and Supplementary Table 1. ...
... We amplified 7,088-bp fragments, representing the maximum total length of six autosomal gene loci (Mgf,Tg,Tshb,Sptbn1,Mc1r,and Asip), one X chromosomal locus (Phka2), one Y chromosomal locus (Sry), and one mitochondrial gene locus (Cytb). Polymerase chain reaction (PCR) analysis was performed following previously described methods (Kinoshita et al., 2012;Nunome et al., 2014). Sequences of the two nDNA loci (Mgf and Phka2) represented intron regions; the Mc1r sequence was from an exon region; and Tg, Tshb, Sptbn1, Asip, and Sry sequences included both intron and exon regions. ...
... Populations comprising both winter white and invariant winter brown colour morphs tend to associate with areas of low or unpredictable seasonal snow cover (Mills et al., 2018); e.g. Arctic fox (Hersteinsson, 1989), Japanese hare [Lepus brachyurus (Nunome et al., 2014)], or stoat (Hewson & Watson, 1979). ...
... Also, major dominant genes may determine the winter grey/blue morph in Swedish mountain hares [called 'heath-hares' (Fig. 2D) (Bergengren, 1969)] and the winter brown M. nivalis vulgaris morph in least weasels (Stolt, 1979), but particular gene mutations were not investigated. Nunome et al. (2014) found no differentiation between Japanese hare populations of winter white and winter brown morphs in three candidate genes (Agouti,TYR,Mc1r). Similarly, no association has been found between colour polymorphism and Mc1r and three other candidate genes (Tyr, Tyrp1, and Dct) in willow ptarmigan (Skoglund & Hoglund, 2010). ...
Animals that occupy temperate and polar regions have specialized traits that help them survive in harsh, highly seasonal environments. One particularly important adaptation is seasonal coat colour (SCC) moulting. Over 20 species of birds and mammals distributed across the northern hemisphere undergo complete, biannual colour change from brown in the summer to completely white in the winter. But as climate change decreases duration of snow cover, seasonally winter white species (including the snowshoe hare Lepus americanus, Arctic fox Vulpes lagopus and willow ptarmigan Lagopus lagopus) become highly contrasted against dark snowless backgrounds. The negative consequences of camouflage mismatch and adaptive potential is of high interest for conservation. Here we provide the first comprehensive review across birds and mammals of the adaptive value and mechanisms underpinning SCC moulting. We found that across species, the main function of SCC moults is seasonal camouflage against snow, and photoperiod is the main driver of the moult phenology. Next, although many underlying mechanisms remain unclear, mammalian species share similarities in some aspects of hair growth, neuroendocrine control, and the effects of intrinsic and extrinsic factors on moult phenology. The underlying basis of SCC moults in birds is less understood and differs from mammals in several aspects. Lastly, our synthesis suggests that due to limited plasticity in SCC moulting, evolutionary adaptation will be necessary to mediate future camouflage mismatch and a detailed understanding of the SCC moulting will be needed to manage populations effectively under climate change.
... Historic and ongoing introgressive hybridization in natural populations upon secondary contact together with shared ancestral polymorphism due to incomplete lineage sorting do complicate evolutionary and systematic inference of the genus Lepus. Moreover, phenotypic or morphological characters and molecular markers may or may not concordantly indicate evolutionary divergence between subspecies or species (e.g., Bonhomme, et al. [32] Palacios [3], Alves et al. [8,16], Melo-Ferreira et al. [10], for hares from the Iberian Peninsula; Palacios [4], Pierpaoli et al. [33], Riga et al. [34], for L. corsicanus and L. europaeus; Yom-Tov [35], Suchentrunk et al. [36], Ben Slimen et al. [37], for hares from Israel; Ben Slimen et al. [38,21], for hares from Tunisia; Palacios et al. [39], and Suchentrunk et al. [40,41], for cape hares from South Africa; Scandura et al. [42] and Canu et al. [43] for hares from Sardinia; Liu et al. [9,44] for hares from China; Nunome et al. [45], for Japanese hares). ...
... melainus" form from eastern Asia considered conspecific with L. mandshuricus [44,123]. Even certain alleles of single coat colour genes (TYR, MC1R) did not predict the two winter coat types in Japanese hares, L. brachyurus [45]. ...
For hares (Lepus spp., Leporidae, Lagomorpha, Mammalia) from Ethiopia no conclusive molecular phylogenetic data are available. To provide a first molecular phylogenetic model for the Abyssinian Hare (Lepus habessinicus), the Ethiopian Hare (L. fagani), and the Ethiopian Highland Hare (L. starcki) and their evolutionary relationships to hares from Africa, Eurasia, and North America, we phylogenetically analysed mitochondrial ATPase subunit 6 (ATP6; n = 153 / 416bp) and nuclear transferrin (TF; n = 155 / 434bp) sequences of phenotypically determined individuals. For the hares from Ethiopia, genotype composition at twelve microsatellite loci (n = 107) was used to explore both interspecific gene pool separation and levels of current hybridization, as has been observed in some other Lepus species. For phylogenetic analyses ATP6 and TF sequences of Lepus species from South and North Africa (L. capensis, L. saxatilis), the Anatolian peninsula and Europe (L. europaeus, L. timidus) were also produced and additional TF sequences of 18 Lepus species retrieved from GenBank were included as well. Median joining networks, neighbour joining, maximum likelihood analyses, as well as Bayesian inference resulted in similar models of evolution of the three species from Ethiopia for the ATP6 and TF sequences, respectively. The Ethiopian species are, however, not monophyletic, with signatures of contemporary uni- and bidirectional mitochondrial introgression and/ or shared ancestral polymorphism. Lepus habessinicus carries mtDNA distinct from South African L. capensis and North African L. capensis sensu lato; that finding is not in line with earlier suggestions of its conspecificity with L. capensis. Lepus starcki has mtDNA distinct from L. capensis and L. europaeus, which is not in line with earlier suggestions to include it either in L. capensis or L. europaeus. Lepus fagani shares mitochondrial haplotypes with the other two species from Ethiopia, despite its distinct phenotypic and microsatellite differences; moreover, it is not represented by a species-specific mitochondrial haplogroup, suggesting considerable mitochondrial capture by the other species from Ethiopia or species from other parts of Africa. Both mitochondrial and nuclear sequences indicate close phylogenetic relationships among all three Lepus species from Ethiopia, with L. fagani being surprisingly tightly connected to L. habessinicus. TF sequences suggest close evolutionary relationships between the three Ethiopian species and Cape hares from South and North Africa; they further suggest that hares from Ethiopia hold a position ancestral to many Eurasian and North American species.
... Such an inconsistent trend may be caused by evolutionarily optimizing the spatial niche of those species by preferentially fitting for the geographic space with the regional-specific environmental conditions, characterized by vegetation, terrain, and climates, strongly disturbed/influenced by the Asian winter monsoon. In fact, the plasticity specialized for snowfall has been found only in those two species; namely, while hares inhabiting northern Japan have obtained morphological plasticity for heavy snowfall (i.e., larger hind foot length [66] and whiter pelage during winters [67]), serows have been considered habitat and dietary specialists only for cool-temperate forests with snowfall [28,68]. In contrast, omnivorous mesocarnivores (i.e., raccoon dogs and martens) with the largest niche breadth posed constricted adaptability to the present-day geographic space (Fig. 3). ...
Background
Recent climate changes have produced extreme climate events. This study focused on extreme snowfall and intended to discuss the vulnerability of temperate mammals against it through interspecies comparisons of spatial niches in northern Japan. We constructed niche models for seven non-hibernating species through wide-scaled snow tracking on skis, whose total survey length was 1144 km.
Results
We detected a low correlation (rs < 0.4) between most pairs of species niches, indicating that most species possessed different overwintering tactics. A morphological advantage in locomotion cost on snow did not always expand niche breadth. In contrast, a spatial niche could respond to (1) drastic landscape change by a diminishing understory due to snow, possibly leading to changes in predator-prey interactions, and (2) the mass of cold air, affecting thermoregulatory cost and food accessibility. When extraordinary snowfall occurred, the nonarboreal species with larger body sizes could niche shift, whereas the smaller-sized or semi-arboreal mammals did not. In addition, compared to omnivores, herbivores were prone to severe restriction of niche breadth due to a reduction in food accessibility under extreme climates.
Conclusions
Dietary habits and body size could determine the redundancy of niche width, which may govern robustness/vulnerability to extreme snowfall events.
... However, we note that the present study was based only on mitochondrial DNA, which allows tracing of only the maternal lineage. Nuclear DNA analysis using multilocus data such as Y-chromosomal loci, microsatellites, or other SNPs would be needed to clarify male dispersal among locations in a future study since discordance in population structures between the mitochondrial and nuclear DNA has been well known (e.g., Yasuda et al. 2012;Nunome et al. 2014). ...
Nucleotide sequences of the mitochondrial D-loop region were examined in three wild rodents (Apodemus argenteus, Apodemus speciosus, and Myodes smithii) on the northern slope of Mt. Fuji, the highest mountain in Japan, to elucidate the past evolutionary and present anthropogenic processes shaping their genetic diversity. Nucleotide diversity, median-joining network, and mismatch distribution analyses suggested that A. argenteus has multiple divergent lineages, possibly due to multiple previous expansion events, whereas A. speciosus and M. smithii are younger lineages that could be derived from single expansion events. These findings indicate that Mt. Fuji plays an important role as a reservoir maintaining lineages through multiple past expansion events. Artificial infrastructure also affected the genetic diversity of the two Apodemus species, as populations of these species on the two sides of the Fuji Subaru Line roadway were genetically distinct. To construct a proper conservation strategy based on genetic diversity, we suggest that the past and present contributors to genetic diversity must be clarified. Such clarification is especially important for the Mt. Fuji environment, which harbors rich biodiversity but also incurs much human impact as a national park.
... This line is similar to that between the two major haplogroups of C. dsinezumi (Fig. 4) although the southern part of the line for C. dsinezumi is posited a little more eastward than that for U. talpoides. The border between the two haplogroups of cytb gene in the Japanese hare (Lepus brachyurus) is found in the west of the Kinki Region (Nunome et al. 2010) and the border between the two haplogroups of the Sry gene on Y chromosome is located in eastern Honshu (Nunome et al. 2014). Both demarcation lines of L. brachyurus are quite different from that of the two main haplogroups in C. dsinezumi and were estimated to have diverged before the Middle Pleistocene. ...
The Japanese white-toothed shrew (Crocidura dsinezumi) is a species endemic to Japan. For this species, only minimal phylogeographic investigations have been conducted. We obtained DNA sequences of mitochondrial cytochrome b and control region and nuclear ApoB genes for 191 individuals of C. dsinezumi from 107 locations collected throughout its known range. In the phylogenetic trees based on mitochondrial DNA sequences, two haplogroups (Eastern and Western Clades) were recognized, and the demarcation line between them was located in central Honshu without an overlapping area. The estimated divergence time between the two major clades indicated that they could have diverged prior to the final geologic division of Hondo and the Asian Continent (100–150 KYA). For the ApoB gene, Types A, G, and R (heterozygote) were recognized although there was a single site mutation. Type A mainly occurs in eastern and central Japan and Types G and R in central and western Japan. It was suggested in the present study that some shrews in Hokkaido were introduced recently from eastern Honshu (possibly the Tohoku Region) whereas others might have been distributed there naturally, and that population in Jeju (South Korea) was introduced recently from Kyushu.
... These two major clades were inferred to have diverged 1.2 MYA following the lineage-specific evolutionary rate of 1.4 %/lineage/myr (therefore, 2.8 % divergence rate) on the basis of the assumption that L. timidus and L. brachyurus diverged 3.6 MYA (Wu et al. 2005). Their recent study on the nuclear male-specific Sry gene also indicated a similar but a little younger divergence time between northern and southern lineages (1.07 MYA; Nunome et al. 2014). Nunome et al. (2010) also showed that the initial divergence in each northern and southern clade occurred 0.33 MYA and 0.38 MYA, respectively. ...
To elucidate the origins of the Japanese mammalian fauna from the perspectives of biogeography and community ecology, I reviewed molecular phylogenetic and phylogeographic studies for all non-volant terrestrial mammals indigenous to the Japanese Archipelago (63 species), with a particular focus on obtaining reliable chronological data. The results of this review demonstrate that geological vicariance events in the Tsugaru and Korea (Tsushima) Straits can explain the distribution of many Japanese mammals, in particular the Hokkaido-endemic species with Late Pleistocene origins and the Honshu–Shikoku–Kyushu-endemic species with Middle Pleistocene or earlier origins. Phylogenetic relatedness also contributed to the observed patterns of distribution through the processes of competitive exclusion and species assortment, and abiotic environmental filtering was another important factor. Later colonists of Honshu–Shikoku–Kyushu, from northern Hokkaido or the southern Tsushima Islands, were mostly excluded owing to the competitive dominance of earlier residents or environmental filtering. On the other hand, the fragmented distributions of some species with more ancient origins in both Hokkaido and Honshu–Shikoku–Kyushu may be a result of the competitive dominance of later migrants. Ecological coexistence can be achieved by phylogenetically dispersed species, supporting the principle of species assortment. Because almost all aspects of the mammalian faunal assembly in Japan can be explained by geological events or community ecological processes, the Japanese Archipelago may be an ideal model island system in which to study the mechanisms of faunal assembly.
The genetic basis of adaptive traits has rarely been used to predict future vulnerability of populations to climate change. We show that light versus dark seasonal pelage in white-tailed jackrabbits (Lepus townsendii) tracks snow cover and is primarily determined by genetic variation at endothelin receptor type B (EDNRB), corin serine peptidase (CORIN), and agouti signaling protein (ASIP). Winter color variation was associated with deeply divergent alleles at these genes, reflecting selection on both ancestral and introgressed variation. Forecasted reductions in snow cover are likely to induce widespread camouflage mismatch. However, simulated populations with variation for darker winter pelage are predicted to adapt rapidly, providing a trait-based genetic framework to facilitate evolutionary rescue. These discoveries demonstrate how the genetic basis of climate change adaptation can inform conservation.
Comparative studies of closely related species or populations in contrasting environments can potentially provide insights into adaptive mechanisms. We review the phylogeography and population diversity of brackish water species derived from marine species, Ulva prolifera Müller (Ulvophyceae) and Pyropia tenera (Kjellman) N. Kikuchi, M. Miyata, M.S. Hwang & H.G. Choi (Bangiophyceae). Brackish U. prolifera and marine Ulva linza L. have been resolved as closely related species based on phylogenetic analysis of moleclar markers, with U. linza apparently parental to U. prolifera. Our analyses of 5S rDNA spacer region in samples from an Ulvalean bloom in Qingdao, China, indicate that the species appear to be derived from Japanese U. prolifera. Hybridization tests suggest that U. linza and the Qingdao bloom samples are probably distinct species, but gene flow is possible between them. The threatened brackish water species, P. tenera, is morphologically and phylogenetically related to the coastal species, Pyropia yezoensis (Ueda) M.S. Hwang & H.G. Choi. One form,
P. yezoensis
Ueda f. narawaensis Miura (new combination “Pyropia yezoensis f. narawaensis” has not yet been proposed), is the largest aquaculture source of “Nori” in Japan. Hybridization between these species has been reported, especially between male P. tenera and female P. yezoensis. Sequences of the nrITS1 region and rbcL gene, and PCR-RFLP (ARP4 gene) analyses suggested that P. tenera is distributed across 15 prefectures from Kyushu to Tohoku in Japan; but is restricted to estuarine and brackish water habitats. Based on SSR analysis on the genetically identified P. tenera samples, we conclude that this species spread from Kyushu to Tohoku through the Kanto region.
Patterns of geographic variation in phenotype or genotype may provide evidence for natural selection. Here, we compare phenotypic variation in color, allele frequencies of a pigmentation gene (the melanocortin-1 receptor, Mc1r), and patterns of neutral mitochondrial DNA (mtDNA) variation in rock pocket mice (Chaetodipus intermedius) across a habitat gradient in southern Arizona. Pocket mice inhabiting volcanic lava have dark coats with unbanded, uniformly melanic hairs, whereas mice from nearby light-colored granitic rocks have light coats with banded hairs. This color polymorphism is a presumed adaptation to avoid predation. Previous work has demonstrated that two Mc1r alleles, D and d, differ by four amino acids, and are responsible for the color polymorphism: DD and Dd genotypes are melanic whereas dd genotypes are light colored. To determine the frequency of the two Mc1r allelic classes across the dark-colored lava and neighboring light-colored granite, we sequenced the Mc1r gene in 175 individuals from a 35-km transect in the Pinacate lava region. We also sequenced two neutral mtDNA genes, COIII and ND3, in the same individuals. We found a strong correlation between Mc1r allele frequency and habitat color and no correlation between mtDNA markers and habitat color. Using estimates of migration from mtDNA haplotypes between dark- and light-colored sampling sites and Mc1r allele frequencies at each site, we estimated selection coefficients against mismatched Mc1r alleles, assuming a simple model of migration-selection balance. Habitat-dependent selection appears strong but asymmetric: selection is stronger against light mice on dark rock than against melanic mice on light rock. Together these results suggest that natural selection acts to match pocket mouse coat color to substrate color, despite high levels of gene flow between light and melanic populations.
Identifying the genes underlying adaptation is a major challenge in evolutionary biology. Here, we describe the molecular changes underlying adaptive coat color variation in a natural population of rock pocket mice, Chaetodipus intermedius. Rock pocket mice are generally light-colored and live on light-colored rocks. However, populations of dark (melanic) mice are found on dark lava, and this concealing coloration provides protection from avian and mammalian predators. We conducted association studies by using markers in candidate pigmentation genes and discovered four mutations in the melanocortin-1-receptor gene, Mc1r, that seem to be responsible for adaptive melanism in one population of lava-dwelling pocket mice. Interestingly, another melanic population of these mice on a different lava flow shows no association with Mc1r mutations, indicating that adaptive dark color has evolved independently in this species through changes at different genes.
Most examples of seasonal mismatches in phenology span multiple trophic levels, with timing of animal reproduction, hibernation, or migration becoming detached from peak food supply. The consequences of such mismatches are difficult to link to specific future climate change scenarios because the responses across trophic levels have complex underlying climate drivers often confounded by other stressors. In contrast, seasonal coat color polyphenism creating camouflage against snow is a direct and potentially severe type of seasonal mismatch if crypsis becomes compromised by the animal being white when snow is absent. It is unknown whether plasticity in the initiation or rate of coat color change will be able to reduce mismatch between the seasonal coat color and an increasingly snow-free background. We find that natural populations of snowshoe hares exposed to 3 y of widely varying snowpack have plasticity in the rate of the spring white-to-brown molt, but not in either the initiation dates of color change or the rate of the fall brown-to-white molt. Using an ensemble of locally downscaled climate projections, we also show that annual average duration of snowpack is forecast to decrease by 29-35 d by midcentury and 40-69 d by the end of the century. Without evolution in coat color phenology, the reduced snow duration will increase the number of days that white hares will be mismatched on a snowless background by four- to eightfold by the end of the century. This novel and visually compelling climate change-induced stressor likely applies to >9 widely distributed mammals with seasonal coat color.
We examined the phylogenetic status and history of the mountain hare Lepus timidus in and around Hokkaido using mitochondrial cytochrome b (cyt b) sequences from 158 samples from Hokkaido and 14 from Sakhalin, as well as four samples from the Korean hare, L. coreanus. The phylogenetic analysis of the cyt b sequences generated in this study and obtained from DNA databases showed the clear genetic specificity of the Hokkaido lineage as a clade. The Hokkaido lineage was estimated to have diverged from the other conspecific and L. coreanus lineages 0.46 and 0.30 million years ago (Mya), respectively. These results suggest that the common ancestor of the mitochondrial lineage in Hokkaido and Korea inhabited Far East Asia before colonization by the present continental lineages of L. timidus, including the Sakhalin population. We estimated the time of the most recent common ancestor of the Hokkaido population to be 0.17 Mya, and found two distinct haplogroups within the island. One group had greater genetic diversity (mean number of pairwise differences: π = 0.0188 ± 0.0108) and appears to have expanded from the west to the entire island of Hokkaido. The other had lower genetic diversity (π = 0.0038 ± 0.0037) and its distribution was concentrated in the east. These contrasting west/east trends indicate that the Hokkaido population was fragmented in the past, and then subsequently expanded. Our study suggests that Hokkaido was an important refugium for boreal species in the far eastern region, and allowed the formation of various population genetic structures within the island.
A two-year field study of colour change in a population of Mountain hares showed that the rate of colour change was significantly faster in a warm spring than in a cold one. The same result was found in individually marked wild hares, indicating that the response is not due to differences in age or sex ratios. It is postulated that the white coat is for camouflage, and the duration for which it is worn is correlated with temperature because of the coat's thickness. Moulting is probably timed by daylength, and the rate of moult affected by temperature.
We present STRUCTURE HARVESTER (available at http://taylor0.biology.ucla.edu/structureHarvester/), a web-based program for collating results generated by the program STRUCTURE. The program provides a fast way to assess
and visualize likelihood values across multiple values of K and hundreds of iterations for easier detection of the number of genetic groups that best fit the data. In addition, STRUCTURE
HARVESTER will reformat data for use in downstream programs, such as CLUMPP.
KeywordsStructure–Population structure–Population genetics–Evanno method–Visualization–Clustering
To evaluate the intraspecific evolutionary history and local differentiation of the Japanese water shrew Chimarrogale platycephala (Temminck, 1842), we an a lyzed the mitochondrial cytochromeb (Cytb) sequence divergence for samples from 55 localities in the Japanese is lands of Honshu and Kyushu. According to phylogenetic
trees based on theCytb data, there were fourCytb haplotype lineages, which showed rough affinities with geographic areas, namely, Eastern/Central Honshu, the Kinki District
of Western Honshu, the Chugoku District of Western Honshu, and Kyushu. However, in the alpine areas of the boundary between
the Kinki and Chugoku Districts, complicated distribution patterns of theCytb haplotypes were revealed. Considering the present data and geological history in the Quaternary, we hypothesized the following
evolutionary scenario. First, differ entiation and division into four primary ancestral geographic colonies of the shrews
occurred in hypothetical refugia in the mid — late Pleistocene. Subsequently, rapid expansion occurred and caused the complicated
distribution patterns of theCytb haplotypes in the boundary areas owing to the complex topography during the late stage of the Quaternary.
Key words
Chimarrogale platycephala
-phylogeography-colonization history-cytochromeb gene
1.1.|Seasonal moult has major effects on coat insulation and solar heat gain in the three species of subarctic mammals that shift between white winter pelages and darker summer coats: Lepus americanus, Mustela erminea, and Phodopus sungorus.2.2.|At low wind speeds, coat thermal resistance is elevated 27% (Phodopus) to 87% (Lepus) in winter months compared to summer months.3.3.|In most cases, fractional solar heat gain to the skin is reduced in winter coats compared to summer coats.4.4.|The decrease in solar heat gain in winter coats is due largely to increased insulation and not to altered optical qualities. This is because the thermal effect of radiation penetrating more deeply into winter coats importantly counteracts the effects of these coat's higher reflectivity.
We previously revealed the presence of six genetically distinct matrilineal populations of the Japanese dormouse Glirulus japonicus in the distribution range of Honshu, Shikoku, and Kyushu islands. In this study, we extended this analysis using mitochondrial cytochrome b gene sequences (n = 96) and Y-chromosome-specific SRY gene sequences (n = 22) from individuals collected from Honshu, Shikoku, Kyushu, and Oki Dogo I. The cytochrome b sequence data allowed us to define precise geographic ranges of the six previously known and three newly found distinct matrilineal lineages: northeastern Honshu (I), east-central Honshu (II), west-central Honshu and the Kii Peninsula (III), the western part of Honshu (IV), Shikoku (V), westernmost Honshu and Kyushu (VI), the northern part of central Honshu (VII), the southern part of central Honshu (VIII), and Oki Dogo I. (IX). Our inference of geographic borders suggests that regions of lower and higher altitudes in the mountain systems played important roles in driving the hosting and separation of lineages, respectively. Six matrilineal lineages (I, II, V, VI, VIII, and XI) were shown to possess their own SRY haplotypes, while lineages III and IV shared one haplotype. These data together with our previous observation of nuclear ribosomal RNA gene variation indicate advanced populational subdivision in this species. It is thus evident that each of the populations, including those living at high latitudes and in limited geographic spaces, have survived for several million years. A specific ability to tolerate cold may have permitted G. japonicus to preserve anciently diverged lineages in each locality.
We examined nucleotide changes that underlie coat color variation in Black Rats (the Rattus rattus species complex), which show polymorphism in dorsal fur color, including either grayish brown (agouti) or black (melanistic) forms. We examined the full coding sequence of a gene known to produce melanism in other vertebrates-melanocortin-1-receptor gene Mc1r (954 bp) -using samples of both R. rattus (with 2n = 38) and its close relative Asian Black Rat (R. tanezumi; 2n = 42). We used 61 specimens from Japan with karyotype-known individuals and four samples from Pakistan. We found 11 allele sequences and constructed a network tree that shows two distinct clusters, with allelic segregation according to karyotype and by inference, representing the two species. We found that a nucleotide substitution from G to A at site 280, producing an amino acid change from glutamic acid to lysine, was associated with the dominant trait of the melanistic form of the coat color in R. rattus. Notably, the derived SNP 280A was found in a single allele, with the ancestral SNP 280G present in seven alleles. By contrast, all three alleles for R. tanezumi retain the ancestral SNP 280G. These results suggest a possible recent origin of melanism in R. rattus.
Interspecific hybridization may lead to the introgression of genes and genomes across species barriers and contribute to a reticulate evolutionary pattern and thus taxonomic uncertainties. Since several previous studies have demonstrated that introgressive hybridization has occurred among some species within Lepus, therefore it is possible that introgressive hybridization events also occur among Chinese Lepus species and contribute to the current taxonomic confusion.
Data from four mtDNA genes, from 116 individuals, and one nuclear gene, from 119 individuals, provides the first evidence of frequent introgression events via historical and recent interspecific hybridizations among six Chinese Lepus species. Remarkably, the mtDNA of L. mandshuricus was completely replaced by mtDNA from L. timidus and L. sinensis. Analysis of the nuclear DNA sequence revealed a high proportion of heterozygous genotypes containing alleles from two divergent clades and that several haplotypes were shared among species, suggesting repeated and recent introgression. Furthermore, results from the present analyses suggest that Chinese hares belong to eight species.
This study provides a framework for understanding the patterns of speciation and the taxonomy of this clade. The existence of morphological intermediates and atypical mitochondrial gene genealogies resulting from frequent hybridization events likely contribute to the current taxonomic confusion of Chinese hares. The present study also demonstrated that nuclear gene sequence could offer a powerful complementary data set with mtDNA in tracing a complete evolutionary history of recently diverged species.
We performed a phylogeographic analysis of the Japanese hare, Lepus brachyurus, using the mitochondrial cytochrome b gene (1140 bp). In total, 119 haplotypes were recovered from 197 samples isolated from 82 localities on three main islands of the Japanese archipelago: Honshu, Sikoku, Kyushu, Sado Island and the Oki Islands. Results showed two distinct clades at a genetic distance of 3.5%, equivalent to an estimated 1.2 million years. The two clades, encompassing seven subclades, showed an apparent geographic affinity to Kyushu, Shikoku and the nearby area of Honshu (southern group) by one clade, whereas the other clade covered the remaining area of Honshu (northern group). The landscape shape interpolation analysis exhibited a higher genetic diversity in the southern parts of central Honshu (northern group) and Shikoku and Kyushu regions (southern group), suggesting the existence of multiple geographical origins of population expansion in each clade. The Bayesian skyline plot analysis showed that lineage diversifications occurred about 0.35, 0.20 and 0.05 million years ago (Mya), which coincide closely with the glacial-interglacial cycles during the Pleistocene. Therefore, we suggest that the Japanese hare population once inhabited northern and southern refugia, and subsequently developed several populations through local demographic fluctuations. The present day demarcation in the northern and southern geographic groups is considered to be a temporal remnant of Pleistocene population dynamics and the geographic boundary between them could move or fade away in time.
Seasonal adaptation is widespread among mammals of temperate and polar latitudes. The changes in physiology, morphology and behaviour are controlled by the photoneuroendocrine system that, as a first step, translates day lengths into a hormonal signal (melatonin). Decoding of the humoral melatonin signal, i.e. responses on the cellular level to slight alterations in signal duration, represents the prerequisite for appropriate timing of winter acclimatization in photoperiodic animals. Corresponding to the diversity of affected traits, several hormone systems are involved in the regulation downstream of the neural integration of photoperiodic time measurement. Results from recent studies provide new insights into seasonal control of reproduction and energy balance. Most intriguingly, the availability of thyroid hormone within hypothalamic key regions, which is a crucial determinant of seasonal transitions, appears to be regulated by hormone secretion from the pars tuberalis of the pituitary gland. This proposed neuroendocrine pathway contradicts the common view of the pituitary as a gland that acts downstream of the hypothalamus. In the present overview of (neuro)endocrine mechanisms underlying seasonal acclimatization, we are focusing on the dwarf hamster Phodopus sungorus (long-day breeder) that is known for large amplitudes in seasonal changes. However, important findings in other mammalian species such as Syrian hamsters and sheep (short-day breeder) are considered as well.
Population variation in the degree of seasonal polymorphism is rare in birds, and the genetic basis of this phenomenon remains largely undescribed. Both sexes of Scandinavian and Scottish Willow grouse (Lagopus lagopus) display marked differences in their winter phenotypes, with Scottish grouse retaining a pigmented plumage year-round and Scandinavian Willow grouse molting to a white morph during winter. A widely studied pathway implicated in vertebrate pigmentation is the melanin system, for which functional variation has been characterised in many taxa.
We sequenced coding regions from four genes involved in melanin pigmentation (DCT, MC1R, TYR and TYRP1), and an additional control involved in the melanocortin pathway (AGRP), to investigate the genetic basis of winter plumage in Lagopus. Despite the well documented role of the melanin system in animal coloration, we found no plumage-associated polymorphism or evidence for selection in a total of approximately 2.6 kb analysed sequence.
Our results indicate that the genetic basis of alternating between pigmented and unpigmented seasonal phenotypes is more likely explained by regulatory changes controlling the expression of these or other loci in the physiological pathway leading to pigmentation.
The phylogenetic relationships within the horseshoe bats (genus Rhinolophus) are poorly resolved, particularly at deeper levels within the tree. We present a better-resolved phylogenetic hypothesis for 30 rhinolophid species based on parsimony and Bayesian analyses of the mitochondrial cytochrome b gene and three nuclear introns (TG, THY and PRKC1). Strong support was found for the existence of two geographic clades within the monophyletic Rhinolophidae: an African group and an Oriental assemblage. The relaxed Bayesian clock method indicated that the two rhinolophid clades diverged approximately 35 million years ago and results from Dispersal Vicariance (DIVA) analysis suggest that the horseshoe bats arose in Asia and subsequently dispersed into Europe and Africa.
Molecular phylogenetic analyses of combined mitochondrial DNA sequences (2814 bp; cytochrome b gene, displacement loop region, and NADH dehydrogenase subunit 2 gene) identified nine groups among 49 individual Japanese martens, Martes melampus, collected from several areas in Japan. The grouping was not correlated with winter coat color, but was consistent with geography. In particular, the monophyly of 29 Tsushima martens, M. m. tsuensis, was supported by strong clade support and topological tests. Haplotype and nucleotide diversities were much lower for the Tsushima population than for any population on the Japanese main islands. In addition, analyses of heterozygosity in nuclear growth hormone receptor gene sequences (654 bp) showed genetic homogeneity for the Tsushima population. This evidence supports the view that the Tsushima marten's long history of isolation on small islands is responsible for its genetic distinctiveness and uniformity, validating the Tsushima population as an evolutionarily significant unit.
Motivation: DnaSP is a software package for a comprehensive analysis of DNA polymorphism data. Version 5 implements a number of new features
and analytical methods allowing extensive DNA polymorphism analyses on large datasets. Among other features, the newly implemented
methods allow for: (i) analyses on multiple data files; (ii) haplotype phasing; (iii) analyses on insertion/deletion polymorphism
data; (iv) visualizing sliding window results integrated with available genome annotations in the UCSC browser.
Availability: Freely available to academic users from: http://www.ub.edu/dnasp
Contact: jrozas{at}ub.edu
Morphological diversity within closely related species is an essential aspect of evolution and adaptation. Mutations in the
Melanocortin 1 receptor (Mc1r) gene contribute to pigmentary diversity in natural populations of fish, birds, and many mammals. However, melanism in the
gray wolf, Canis lupus, is caused by a different melanocortin pathway component, the K locus, that encodes a beta-defensin protein that acts as an alternative ligand for Mc1r. We show that the melanistic K locus mutation in North American wolves derives from past hybridization with domestic dogs, has risen to high frequency in
forested habitats, and exhibits a molecular signature of positive selection. The same mutation also causes melanism in the
coyote, Canis latrans, and in Italian gray wolves, and hence our results demonstrate how traits selected in domesticated species can influence
the morphological diversity of their wild relatives.
Local thyroid hormone catabolism within the mediobasal hypothalamus (MBH) by thyroid hormone-activating (DIO2) and -inactivating (DIO3) enzymes regulates seasonal reproduction in birds and mammals. Recent functional genomics analysis in birds has shown that long days induce thyroid-stimulating hormone production in the pars tuberalis (PT) of the pituitary gland, which triggers DIO2 expression in the ependymal cells (EC) of the MBH. In mammals, nocturnal melatonin secretion provides an endocrine signal of the photoperiod to the PT that contains melatonin receptors in high density, but the interface between the melatonin signal perceived in the PT and the thyroid hormone levels in the MBH remains unclear. Here we provide evidence in mice that TSH participates in this photoperiodic signal transduction. Although most mouse strains are considered to be nonseasonal, a robust photoperiodic response comprising induced expression of TSHB (TSH β subunit), CGA (TSH α subunit), and DIO2, and reduced expression of DIO3, was observed in melatonin-proficient CBA/N mice. These responses could not be elicited in melatonin-deficient C57BL/6J, but treatment of C57BL/6J mice with exogenous melatonin elicited similar effects on the expression of the above-mentioned genes as observed in CBA/N after transfer to short-day conditions. The EC was found to express TSH receptor (TSHR), and ICV injection of TSH induced DIO2 expression. Finally, we show that melatonin administration did not affect the expression of TSHB, DIO2, and DIO3 in TSHR-null mice. Taken together, our findings suggest that melatonin-dependent regulation of thyroid hormone levels in the MBH appears to involve TSH in mammals.
• circadian rhythm
• melatonin
• pars tuberalis
• photoperiodism
• type 2 and 3 iodothyronine deiodinases
A critical seasonal event for anadromous Chinook salmon (Oncorhynchus tshawytscha) is the time at which adults migrate from the ocean to breed in freshwater. We investigated whether allelic variation at the circadian rhythm genes, OtsClock1a and OtsClock1b, underlies genetic control of migration timing among 42 populations in North America. We identified eight length variants of the functionally important polyglutamine repeat motif (PolyQ) of OtsClock1b while OtsClock1a PolyQ was highly conserved. We found evidence of a latitudinal cline in average allele length and frequency of the two most common OtsClock1b alleles. The shorter 335 bp allele increases in frequency with decreasing latitude while the longer 359 bp allele increases in frequency at higher latitudes. Comparison to 13 microsatellite loci showed that 335 and 359 bp deviate significantly from neutral expectations. Furthermore, a hierarchical gene diversity analysis based on OtsClock1b PolyQ variation revealed that run timing explains 40.9 per cent of the overall genetic variance among populations. By contrast, an analysis based on 13 microsatellite loci showed that run timing explains only 13.2 per cent of the overall genetic variance. Our findings suggest that length polymorphisms in OtsClock1b PolyQ may be maintained by selection and reflect an adaptation to ecological factors correlated with latitude, such as the seasonally changing day length.
The process of coat color change of the snow-shoe hare, Lepus brachyurus angustidens HOLLISTER which inhabits in the north-eastern part of the mainland of Japan was studied from September of 1963 to April of 1966. It was found that illumination length per day has much to do with the color change. The results of experiments were as the following. The color change from brown to white from autumn to winter was inhibited by the exposure of animals to artificial illumination of longer than 12 hours per day with fluorescent lamps which started from the middle of September. The color change from white to brown from winter to spring was almost stopped by exposure to the artificial illumination of 10 hours per day in a dark room which started at the middle of February. Longer exposure accelerated the change of browning in white winter animals. Colored lights and temperatures exerted no influence to the color changes. From these results, the day-length in nature is considered to be most important among the environmental factors controlling the coat color change of the snow-shoe hare. © 1967, JAPANESE SOCIETY OF APPLIED ENTOMOLOGY AND ZOOLOGY. All rights reserved.
We describe a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations. We assume a model in which there are K populations (where K may be unknown), each of which is characterized by a set of allele frequencies at each locus. Individuals in the sample are assigned (probabilistically) to populations, or jointly to two or more populations if their genotypes indicate that they are admixed. Our model does not assume a particular mutation process, and it can be applied to most of the commonly used genetic markers, provided that they are not closely linked. Applications of our method include demonstrating the presence of population structure, assigning individuals to populations, studying hybrid zones, and identifying migrants and admixed individuals. We show that the method can produce highly accurate assignments using modest numbers of loci—e.g., seven microsatellite loci in an example using genotype data from an endangered bird species. The software used for this article is available from http://www.stats.ox.ac.uk/~pritch/home.html.
Most microsatellites are very polymorphic. This makes them powerful markers for observing genetic differentiation between closely related populations. The population structure of the Greenlandic Arctic fox (Alopex lagopus) was studied genetically by analysing six polymorphic microsatellite loci of 75 foxes from four populations in different parts of Greenland. Genotypes were determined at the six loci for most of the individuals. Population differentiation was quantified in three different ways both within the total population and pairwise between all populations. The tests were Fisher's exact test, Rho estimates and Fst estimates, all of which supported a highly significant subdivision of the total population, and they showed significant differentiation in allele frequencies between all pairs of localities. It is concluded that the known long-distance migration of the Greenlandic Arctic fox has not resulted in complete genetic mixing of the populations. Fisher's exact test was also used to estimate levels of genetic differentiation between the two colour morphs: white and blue. No difference was found between allele frequencies of the two color morphs in any of the locations, and it was concluded that the white and blue morphs of the Greenlandic Arctic fox share the same habitat, at least during the mating season.
Tohoku hare, like other wild mammals, manifests periodical sexual activity according to the season. Minimal ovarian weight is observed during the season from November until January. Generally, gradual enlargement of size with increase in weight is seen from the end of Feburuary or from early March. During the breeding season, in spring and summer, the ovary is large in size and active. It undergoes rapid degeneration from September or sometimes from October. In the present experiment the effect of prolonged light exposure upon breeding was studied, with special reference to ovarian activity. From December 11, 1968, 25 mature females and 10 males in captivity were exposed daily to natural daylight from sunrise to 9a.m. and then artificial light was added until 9p.m. An increase in ovarian weight was observed from 50 days after the start of the experiment, namely from the end of January. However, a similar state of ovarian activity is not normally attained until late Feburuary or early March in the wild. Though the exposure experiment was ended on May 6, the ovary showed no signs of degeneration even on Apil 12. This year, the first pregnant female was captured in the wild on Feburuary 26 and one female gave birth to a litter of 3 on April 5. However, in the experiment a pregnant female was observed on January 30 and one female gave birth to a litter of one on Feburuary 22. The experimented animals continued to give birth until April 10. From April 11 to June 29 breeding seemed to be ceased but from June 30 it began again and continued until August 22. It is worthy to note that the ovaries, both of the wild animals or of the animals experimented, contained fully grown follicles at all seasons of the year. © 1971, JAPANESE SOCIETY OF APPLIED ENTOMOLOGY AND ZOOLOGY. All rights reserved.
A new method called the neighbor-joining method is proposed for reconstructing phylogenetic trees from evolutionary distance data. The principle of this method is to find pairs of operational taxonomic units (OTUs [= neighbors]) that minimize the total branch length at each stage of clustering of OTUs starting with a starlike tree. The branch lengths as well as the topology of a parsimonious tree can quickly be obtained by using this method. Using computer simulation, we studied the efficiency of this method in obtaining the correct unrooted tree in comparison with that of five other tree-making methods: the unweighted pair group method of analysis, Farris's method, Sattath and Tversky's method, Li's method, and Tateno et al.'s modified Farris method. The new, neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods.
A study on the inter- and intraspecies variation of MC1R gene was performed in Lepus species inhabiting the Mediterranean basin (L. granatansis, L. europaeus, L. corsicanus, L. castroviejoi and L. mediterraneus) and their neighboring species in Europe (L. timidus) and Africa (L. saxatilis, L. capensis), in order to infer micro- versus macroevolutionary adaptation. Eleven different sequences were isolated that corresponded to five amino acid sequences. Comparison of MC1R nucleotide phylogenetic tree with phylogenies resulting from mtDNA regions of the same species showed absence of congruence between these sets of markers. The Mediterranean area that offered refugia during last glaciation retains more MC1R genotypes compared with populations of North and Central Europe as a consequence of founder effects. L. corsicanus and L. castroviejoi bore identical alleles supportive of their conspecificity, as indicated by other molecular markers. Within L. europaeus, a group of Israeli hares were distinguished by a different MC1R functional allele; additional differences in coat colour and other genetic markers raise doubts about its taxonomic status. Finally, the present data reinforced the idea of bi-directional introgressive hybridization between L. europaeus and L. timidus in Switzerland.
— We studied sequence variation in 16S rDNA in 204 individuals from 37 populations of the land snail Candidula unifasciata (Poiret 1801) across the core species range in France, Switzerland, and Germany. Phylogeographic, nested clade, and coalescence analyses were used to elucidate the species evolutionary history. The study revealed the presence of two major evolutionary lineages that evolved in separate refuges in southeast France as result of previous fragmentation during the Pleistocene. Applying a recent extension of the nested clade analysis (Templeton 2001), we inferred that range expansions along river valleys in independent corridors to the north led eventually to a secondary contact zone of the major clades around the Geneva Basin. There is evidence supporting the idea that the formation of the secondary contact zone and the colonization of Germany might be postglacial events. The phylogeographic history inferred for C. unifasciata differs from general biogeographic patterns of postglacial colonization previously identified for other taxa, and it might represent a common model for species with restricted dispersal.
A number of the so-called Tohoku hare, Lepus brachyurus angustidens HOLLISTER were collected in the mountain of Yamagata Prefecture from May, 1962 to September, 1964 in order to determine the breeding season, litter size and ovarian weight. The observation was made on 136 specimens. The results are as follows: 1) The gestation period of the animal extended from February to July and the young were born between April and August, being more frequent in May and June than in the other months. The average litter size was larger in the month in which the highest rate of birth occurred than in the other months. 2) The female matured sexually in about ten months after birth. Therefore, the first breeding season came next year. 3) The average number of embryo found in the uterus was 1.85 in 12 pregnant females and the largest number was 3. The number of the young in one birth was ordinarily 1 or 2 but sometimes 3. 4) The average litter size observed from the number of the captured young in the field was 1.86 and the largest litter size was 4. The litter size was the largest in May, being 2.50. 5) The weight of the ovary of both sides in the same female was almost equal. There was no difference of the ovarian weight between the uterine side with the fetus and the side without fetus. 6) The ovarian weight increased suddenly to 400mg in February. The smallest ovarian weight of the pregnant female was 470 mg. © 1965, JAPANESE SOCIETY OF APPLIED ENTOMOLOGY AND ZOOLOGY. All rights reserved.
The seasonal colour changes of mountain hares (Lepus timidus) were studied by standardized field observations in Scotland. The rate of colour change in spring varied according to the climate, being retarded in very cold springs and hastened in mild springs. Hares at high altitudes turned white earlier and more completely than hares at low altitudes, and turned dark later in spring. The colour and moult of different individuals varied greatly. Late-born young turned white later in autumn than fully grown hares. Climate and light cycle are discussed in relation to these colour changes.
The mountain hare undergoes three annual moults. These are a spring moult from white to brown, an autumn moult from brown to brown, a winter moult from brown to white
Flat air‐dried skins were used to trace the course of the moults because new growth is clearly indicated by hair root marks on the flesh side of the skin
The pelage of the mountain hare consists of fur, pile hair and guard hair. The summer pelage is described
The autumn moult begins in June and ends in September. It begins about the end of the main breeding season. Some white hair is grown, particularly on the feet
The winter moult begins in October. Winter fur is longer, finer in texture and denser than that of summer or autumn. Projecting as “fine white hair” to the tips of the pile hair it is largely responsible for the hare's white colouring. Moulting on the body ceases in December; on the head not until January or early February
The spring moult begins in February, rather later than the beginning of the breeding season. Pelage is shed before replacement in this moult and in the autumn moult; in the winter moult the old hair is only shed when the new hair is almost or fully grown
No significant regional variations, owing to temperature, occur within England and Scotland. Variations in the progress of the moult, due to temperature, may occur
There is some blanching of winter pile and guard hairs and probably of whiskers
In season and duration the moults resemble those of the Scottish ptarmigan
The three annual moults and plumages of Scottish ptarmigan (Lagopus mutus) were studied from shot specimens but particularly from field observations. Cocks were ahead of hens in showing the grey autumn plumage but hens were ahead of cocks in turning white in winter. Although cocks were ahead in growing summer plumage, after late April the hens passed them. Ptarmigan on the same hill turned dark earlier in mild than in cold springs.
Abstract Several species of Arctic mammals have brown hair in the summer and molt into a white pelage in the winter. It is unknown whether characteristics other than color of the hair also change during the color transition between seasons. We borrowed guard hair samples from museums to represent summer and winter pelages of five species: Alopex lagopus (Arctic fox), Lepus americanus (snowshoe hare), Lepus Arcticus (Arctic hare), Mustela erminea (ermine) and Mustela nivalis (least weasel). Micro-structural differences exist between the brown and white hairs. In general, white winter hairs had larger upper shaft medullas comprising more air-filled cells and smaller lower shafts. These structural changes may function in conservation of heat or in increasing light reflection to whiten the fur and aid as camouflage. © 1997 Published by Elsevier Science Ltd on behalf of The Royal Swedish Academy of Sciences.
To test the association between temperate forest dynamics and glacial refugia for arboreal small mammals, we studied the phylogeography of the Japanese giant flying squirrel (Petaurista leucogenys) using complete mitochondrial cytochrome b gene sequences (1140 bp). This squirrel is endemic to three of Japan's main islands: Honshu, Shikoku, and Kyushu. We examined 58 specimens of P. leucogenys collected from 40 localities in Japan. Additionally, two individuals with unknown sampling localities were included in phylogenetic analyses. There were 54 haplotypes of P. leucogenys. We found five major phylogroups (Northern, Central, South-eastern, South-western, and Southern). These phylogroups may have originated from glacial refugia during the Late Pleistocene. After the last glaciation, the Northern phylogroup, widely distributed in eastern Japan, could have extensively expanded northward from its refugia. By contrast, in western Japan, population expansion was restricted to western Japan. All members of four phylogroups existed in western Japan during glaciations. The complicated phylogeographical pattern of P. leucogenys populations originating from western Japan may have resulted from the long history. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 98, 47–60.
Most microsatellites are very polymorphic. This makes them powerful markers for observing genetic differentiation between closely related populations. The population structure of the Greenlandic Arctic fox (Alopex lagopus) was studied genetically by analysing six polymorphic microsatellite loci of 75 foxes from four populations in different parts of Greenland. Genotypes were determined at the six loci for most of the individuals. Population differentiation was quantified in three different ways both within the total population and pairwise between all populations. The tests were Fisher's exact test, Rho estimates and Fst estimates, all of which supported a highly significant subdivision of the total population, and they showed significant differentiation in allele frequencies between all pairs of localities. It is concluded that the known long-distance migration of the Greenlandic Arctic fox has not resulted in complete genetic mixing of the populations. Fisher's exact test was also used to estimate levels of genetic differentiation between the two colour morphs: white and blue. No difference was found between allele frequencies of the two color morphs in any of the locations, and it was concluded that the white and blue morphs of the Greenlandic Arctic fox share the same habitat, at least during the mating season.
Lagomorph pelage coloration was matched to habitat type, geographical region, altitude and behaviour to explore the adaptive significance of coloration patterns in this little-studied order of mammals. Analyses were conducted with and without taking phylogeny into account. The former analyses were based on a weighted, phylogenetic supertree for all extant species of lagomorphs that we constructed using morphological and molecular data from 146 papers in the literature. Although our analyses represent an initial, somewhat crude investigation, several clear trends are evident. First, overall body coloration across lagomorphs tends to match the background as shown for pale and red coloration and perhaps seasonal pelage change. The case for countershading being a method of concealment is far less strong. Second, ear tips appear to have a communicative role since they are conspicuous in many different habitats. Third, hypotheses for tail tips having a communicative role, for extremities being dark for physiological reasons, and for Gloger's rule received only partial support. © 2003 The Linnean Society of London, Biological Journal of the Linnean Society, 2003, 79, 309–328.
To investigate genetic diversity among populations of the sika deer, Cervus nippon, nucleotide sequences (705–824 bases) of the mitochondrial D-loop regions were determined in animals from 13 localities in the Japanese islands. Phylogenetic trees constructed by the sequences indicated that the Japanese sika deer is separated into two distinct lineages: the northern Japan group (the Hokkaido island and most of the Honshu mainland) and the southern Japan group (a part of the southern Honshu mainland, the Kyushu island, and small islands around the Kyushu island). All sika deer examined in this study shared four to seven units of repetitive sequences (37 to 40 bases each) within the D-loop sequences. The number of tandem repeats was different among the populations, and it was specific to each population. Six or seven repeats occurred in populations of the northern Japan group, while four or five repeats occurred in populations of the southern Japan group. Each repeat unit included several nucleotide substitutions, compared with others, and 26 types were identified from 31 animals. Sequences of the first, second, and third units in arrays were clearly different between the northern and the southern groups. Based on these D-loop data, colonization and separation of the sika deer populations in the Japanese islands were estimated to have occurred less than 0.5 million years before present. Our results provide an invaluable insight into better understanding the evolutionary history, phylogeny, taxonomy, and population genetics of the sika deer.
Studies on hypophysectomized weasels indicate that the pituitary gland is necessary for normal pelage cycles. Animals hypophysectomized in both the winter and summer coats molted and regrew white hair, but intact weasels in the winter or summer coats molted to, or maintained, the brown pelage when held under an artificial photoperiod of 12 light and 12 dark hours.Hypophysectomized weasels treated with purified corticotropin or melanocyte-stimulating hormone regrew pigmented hair typical of the summer pelage after hair growth was initiated by plucking fur, whereas hypophysectomized controls regrew white hair after growth had been similarly induced. Hypophysectomized weasels treated with unfractionated ovine gonadotropin molted and regrew white hair, but hypophysectomized animals treated with corticotropin and unfractionated ovine gonadotropin molted and regrew brown hair. Hypophysectomized controls did not molt but regrew white hair after hair growth was initiated by plucking.Purified follicle-stimulating hormone, luteinizing hormone, thyroid-stimulating hormone, and hydrocortisone had no effect on the induction of molting and/or the growth of pigmented hair in hypophysectomized weasels.
We present here a new version of the Arlequin program available under three different forms: a Windows graphical version (Winarl35), a console version of Arlequin (arlecore), and a specific console version to compute summary statistics (arlsumstat). The command-line versions run under both Linux and Windows. The main innovations of the new version include enhanced outputs in XML format, the possibility to embed graphics displaying computation results directly into output files, and the implementation of a new method to detect loci under selection from genome scans. Command-line versions are designed to handle large series of files, and arlsumstat can be used to generate summary statistics from simulated data sets within an Approximate Bayesian Computation framework.
During adaptive radiations, animals colonize diverse environments, which requires adaptation in multiple phenotypic traits. Because hormones mediate the dynamic regulation of suites of phenotypic traits, evolutionary changes in hormonal signaling pathways might contribute to adaptation to new environments. Here we report changes in the thyroid hormone signaling pathway in stream-resident ecotypes of threespine stickleback fish (Gasterosteus aculeatus), which have repeatedly evolved from ancestral marine ecotypes. Stream-resident fish exhibit a lower plasma concentration of thyroid hormone and a lower metabolic rate, which is likely adaptive for permanent residency in small streams. The thyroid-stimulating hormone-β2 (TSHβ2) gene exhibited significantly lower mRNA expression in pituitary glands of stream-resident sticklebacks relative to marine sticklebacks. Some of the difference in TSHβ2 transcript levels can be explained by cis-regulatory differences at the TSHβ2 gene locus. Consistent with these expression differences, a strong signature of divergent natural selection was found at the TSHβ2 genomic locus. By contrast, there were no differences between the marine and stream-resident ecotypes in mRNA levels or genomic sequence in the paralogous TSHβ1 gene. Our data indicate that evolutionary changes in hormonal signaling have played an important role in the postglacial adaptive radiation of sticklebacks.
Bifurcating evolutionary trees are commonly used to describe genetic relationships between populations, but may not be appropriate for populations that did not evolve in a hierarchical manner. The degree to which bifurcating trees distort genetic relationships between populations can be quantified with R(2), the proportion the variation in a matrix of genetic distances between populations that is explained by a tree. Computer simulations were used to measure how well the unweighted pair group method with arithmetic mean (UPGMA) and neighbor-joining (NJ) trees depicted population structure for three evolutionary models: a hierarchical model of population fragmentation, a linear stepping-stone model of gene flow and a two-dimensional stepping-stone model of gene flow. These simulations showed that the UPGMA did an excellent job of describing population structure when populations had a bifurcating history of fragmentation, but severely distorted genetic relationships for the linear and two-dimensional stepping-stone models. The NJ algorithm worked well in a broader range of evolutionary histories, including the linear stepping-stone model. A computer program for performing the calculations described in this study is available for download at www.montana.edu/kalinowski.