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ABSTRACT: BACKGROUND: Animals co-evolve with their gut microbiota; the latter can perform complex metabolic reactions that cannot be done independently by the host. Although the importance of gut microbiota has been well demonstrated, there is a paucity of research regarding its role in foliage-foraging mammals with a specialized digestive system. RESULTS: In this study, a 16S rRNA gene survey and metagenomic sequencing were used to characterize genetic diversity and functional capability of cecal microbiota of the folivorous flying squirrel (Petaurista alborufus lena). Phylogenetic compositions of the cecal microbiota derived from 3 flying squirrels were dominated by Firmicutes. Based on end-sequences of fosmid clones from 1 flying squirrel, we inferred that microbial metabolism greatly contributed to intestinal functions, including degradation of carbohydrates, metabolism of proteins, and synthesis of vitamins. Moreover, 33 polysaccharide-degrading enzymes and 2 large genomic fragments containing a series of carbohydrate-associated genes were identified. CONCLUSIONS: Cecal microbiota of the leaf-eating flying squirrel have great metabolic potential for converting diverse plant materials into absorbable nutrients. The present study should serve as the basis for future investigations, using metagenomic approaches to elucidate the intricate mechanisms and interactions between host and gut microbiota of the flying squirrel digestive system, as well as other mammals with similar adaptations.
BMC Genomics 09/2012; 13(1):466. · 4.07 Impact Factor
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ABSTRACT: The objective was to apply a novel modification of a genome-wide, comparative cytogenetic technique (comparative genomic hybridization, comparative genomic hybridization (CGH)), to study species belonging to the myrmecophagous (ant/termite eating) mammalian orders/superorders (Pholidota, Tubulidentata, Carnivora, and Xenarthra), as a model for other applications in mammalian systematics and conservation biology. In this study, CGH was applied to high-quality metaphase spreads of pangolin (Pholidota), using probes of sloth and canine (Xenarthra and Carnivora, respectively) genomic DNA labeled with different fluorophores, thereby facilitating analysis of the visible color spectrum on pangolin karyotypes. Our results posited that pholidotes are closer to carnivores than to xenarthrans, which confirmed the current consensus that myrmecophagy in these mammalian lineages was more likely because of homoplasy (convergent evolution) than being an ancestral character. Since the modified CGH technique used is genome-wide, has chromosome-level resolution, and does not need full genome sequencing, it has considerable potential in systematics and other fields.
Theriogenology 12/2011; 77(8):1615-23. · 1.96 Impact Factor
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Shiao-Wei Huang,
You-Yu Lin,
En-Min You,
Tze-Tze Liu,
Hung-Yu Shu,
Keh-Ming Wu,
Shih-Feng Tsai,
Chu-Fang Lo,
Guang-Hsiung Kou,
Gwo-Chin Ma,
Ming Chen,
Dongying Wu,
Takashi Aoki,
Ikuo Hirono, Hon-Tsen Yu
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ABSTRACT: The black tiger shrimp (Penaeus monodon) is one of the most important aquaculture species in the world, representing the crustacean lineage which possesses the greatest species diversity among marine invertebrates. Yet, we barely know anything about their genomic structure. To understand the organization and evolution of the P. monodon genome, a fosmid library consisting of 288,000 colonies and was constructed, equivalent to 5.3-fold coverage of the 2.17 Gb genome. Approximately 11.1 Mb of fosmid end sequences (FESs) from 20,926 non-redundant reads representing 0.45% of the P. monodon genome were obtained for repetitive and protein-coding sequence analyses.
We found that microsatellite sequences were highly abundant in the P. monodon genome, comprising 8.3% of the total length. The density and the average length of microsatellites were evidently higher in comparison to those of other taxa. AT-rich microsatellite motifs, especially poly (AT) and poly (AAT), were the most abundant. High abundance of microsatellite sequences were also found in the transcribed regions. Furthermore, via self-BlastN analysis we identified 103 novel repetitive element families which were categorized into four groups, i.e., 33 WSSV-like repeats, 14 retrotransposons, 5 gene-like repeats, and 51 unannotated repeats. Overall, various types of repeats comprise 51.18% of the P. monodon genome in length. Approximately 7.4% of the FESs contained protein-coding sequences, and the Inhibitor of Apoptosis Protein (IAP) gene and the Innexin 3 gene homologues appear to be present in high abundance in the P. monodon genome.
The redundancy of various repeat types in the P. monodon genome illustrates its highly repetitive nature. In particular, long and dense microsatellite sequences as well as abundant WSSV-like sequences highlight the uniqueness of genome organization of penaeid shrimp from those of other taxa. These results provide substantial improvement to our current knowledge not only for shrimp but also for marine crustaceans of large genome size.
BMC Genomics 05/2011; 12:242. · 4.07 Impact Factor
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ABSTRACT: The systematic status of Pholidota has been a matter of debate, particularly regarding the apparent inconsistency between morphological and molecular studies. The Sry gene, a master regulator of male sex determination in eutherian mammals, has not yet been used for phylogenetic analyses of extant mammals. The objective of the present study was to clone and characterize the complete gene (1300 base pairs; bp) and amino acid sequences (229 residues) of Sry from the Formosan pangolin (Manis pentadactyla pentadactyla), a member of Pholidota. The Sry amino acid identity between pangolin and other reported species ranged from 42.5% (mouse, Mus musculus) to 84.1% (European hare, Lepus europaeus). Sequence conservation was primarily in the high motility group (HMG) box (234 bp), whereas homology outside the HMG box was low. The cloned Sry was mapped to the pangolin Y chromosome by fluorescence in situ hybridization (FISH); this was confirmed to be the first Y-borne molecular marker identified in Pholidota. Based on Bayesian phylogenetic analysis for Sry HMG sequences from 36 representative taxa, including the Formosan pangolin, Pholidota was more closely related to Carnivora than to Xenarthra, consistent with the emerging molecular tree inferred from markers not located on the Y chromosome. In conclusion, this study characterized the gene structure of Sry of the Formosan pangolin and provided insights into the phylogenetic position of Pholidota.
Theriogenology 01/2011; 75(1):55-64. · 1.96 Impact Factor
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Hon-Tsen Yu
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ABSTRACT: We analyzed population subdivision and gene flow of the Southeast Asian house mouse (Mus musculus castaneus) in Taiwan by using six microsatellite DNA markers. Seven populations of the house mouse (187 individuals), including one from Fukien Province in southeastern China, which is separated from Taiwan by the Taiwan Strait, were analyzed in this study. The overall polymorphic level at the six loci was high (He=0.76) although individual populations varied in their levels of heterozygosity (He=0.35–0.83). For the populations within Taiwan, there was no evidence of isolation by distance and the level of gene flow was not (inversely) correlated to geographic distances. Gene flow was estimated to be higher across the Taiwan Strait than within the island of Taiwan. These observations of gene flow cannot be understood unless in the context of the historical human settlements and agricultural expansion, and the commensal habits of the species. We also discussed the causes of population subdivision and genetic variation among populations in terms of ecological characteristics of the house mouse in Taiwan.
ZOOLOGICAL SCIENCE 07/2009; · 0.95 Impact Factor
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ABSTRACT: Insulin genes in mouse and rat compose a two-gene system in which Ins1 was retroposed from the partially processed mRNA of Ins2. When Ins1 originated and how it was retained in genomes still remain interesting problems. In this study, we used genomic approaches to detect insulin gene copy number variation in rodent species and investigated evolutionary forces acting on both Ins1 and Ins2. We characterized the phylogenetic distribution of the new insulin gene (Ins1) by Southern analyses and confirmed by sequencing insulin genes in the rodent genomes. The results demonstrate that Ins1 originated right before the mouse-rat split ( approximately 20 MYA), and both Ins1 and Ins2 are under strong functional constraints in these murine species. Interestingly, by examining a range of nucleotide polymorphisms, we detected positive selection acting on both Ins2 and Ins1 gene regions in the Mus musculus domesticus populations. Furthermore, three amino acid sites were also identified as having evolved under positive selection in two insulin peptides: two are in the signal peptide and one is in the C-peptide. Our data suggest an adaptive divergence in the mouse insulin two-gene system, which may result from the response to environmental change caused by the rise of agricultural civilization, as proposed by the thrifty-genotype hypothesis.
Genetics 04/2008; 178(3):1683-91. · 4.01 Impact Factor
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ABSTRACT: Recent literature demonstrates that retrogenes tend to leave the X chromosome and integrate onto the autosomes and evolve male-biased expression patterns. Several selection-based evolutionary mechanisms have been proposed to explain this observation. Testing these selection-based models requires examining the evolutionary history and functional properties of new retrogenes, particularly those that show evidence of directional movement between the X and the autosomes (X-related retrogenes). This includes autosomal retrogenes with parental paralogs on the X chromosome (X-derived autosomal retrogenes) and those retrogenes integrated onto the X chromosomes (X-linked retrogenes). In order to understand why retrogenes tend to move nonrandomly in genomes, we examined the expression patterns and evolutionary mechanisms concerning gene pairs having young retrogenes--originating less than 20 MYA (after mouse-rat split). We demonstrate that these X-derived autosomal retrogenes evolved a more restricted male-biased expression pattern: they are expressed exclusively or predominantly in the testis, in particular, during the late stages of spermatogenesis. In contrast, the parental counterparts have relatively broad expression patterns in various tissues and spermatogenetic stages. We further observed that positive selection is targeting these X-derived autosomal retrogenes with novel male-biased expression patterns. This suggests that such retrogenes evolved new male germ-line functions that may be complementary to the functions of the parental paralogs, which themselves contribute little during spermatogenesis. Such evolutionary changes may be beneficial to the populations. Furthermore, most identified X-related retrogenes have recruited novel adjacent sequences as their untranslated regions (UTRs), suggesting that these UTRs, acquired de novo, may play an important role in establishing new regulatory mechanisms to carry out the new male germ-line functions.
Molecular Biology and Evolution 11/2007; 24(10):2242-53. · 5.55 Impact Factor
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ABSTRACT: To determine the genetic relationship between different colour morphs (orange and black morphs) of Clark's anemonefish (Amphiprion clarkii) in Taiwan, we isolated eight polymorphic microsatellite loci. A large number of alleles (range, 6–30), and high levels of observed heterozygosity (range, 0.1231–0.8358) were resolved in 71 individuals from two populations, indicating that these markers should be useful in assessing the relationship between the two colour morphs of A. clarkii.
Molecular Ecology Notes 10/2007; 7(6):1169 - 1171. · 2.38 Impact Factor
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ABSTRACT: Chinese species of the genus Niviventer, predominantly distributed in the southeastern Tibetan Plateau and in Taiwan, are a diverse group and have not yet received a thorough molecular phylogenetic analysis. Here, we reconstructed the phylogenetic relationships of 32 specimens representing nine Chinese species of Niviventer, based on sequences of the complete mitochondrial cytochrome b gene. Maximum parsimony, maximum likelihood and Bayesian analysis resulted in three consistent trees, each supported by high bootstrap values. The results showed that the Niviventer species included here are monophyletic. The nine species were classified into three distinct clades: clade A with Niviventer brahma, N. confucianus, N. coxingi, N. culturatus, N. eha and N. fulvescens; clade B with N. andersoni and N. excelsior; clade C with N. cremoriventer. Our results also suggested that N. culturatus should be a valid species rather than a subspecies of N. confucianus. Divergence times among species were calibrated according to the middle-late Pleistocene (1.2-0.13 Mya) fossil records of N. confucianus. The results demonstrated that the first radiation event of the genus Niviventer occurred in early Pleistocene (about 1.66 Mya), followed by the divergence of clades A and B at about 1.46 Mya. Most of the extant Niviventer species appeared during early to middle Pleistocene (about 1.29-0.67 Mya). These divergence times are coincidental with the last uplift events of the Tibetan Plateau, Kun-Huang movement, Pleistocene glaciations and the vicariant formation of Taiwan Strait. Consequently geographical events and Pleistocene glaciations have played a great role in the diversification of Niviventer.
Molecular Phylogenetics and Evolution 09/2007; 44(2):521-9. · 3.61 Impact Factor
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ABSTRACT: Field observations were conducted on egg attendance in Chirixalus eiffingeri from April to August 2003. Parental attendance during embryonic development was performed exclusively by males. The frequency of egg attendance was low (27%), but it had a distinct diel pattern in which males were observed to attend eggs more frequently at night than during the day. Attendance frequency significantly decreased with increasing developmental stage of the embryos, but it was not statistically significantly related to clutch size. Field observations confirmed that male frogs actively moisten egg clutches using their ventral surfaces, presumably to prevent desiccation of egg clutches. The non-significant relationship between hatching success and frequency of egg attendance suggests that embryonic survival of C. eiffingeri is more than a function of egg attendance, and ecological and environmental factors, such as climate and characteristics of microhabitats, may also influence the survivorship of the embryos.
ZOOLOGICAL SCIENCE 06/2007; 24(5):434-40. · 0.95 Impact Factor
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ABSTRACT: Morphological and amplified fragment length polymorphism (AFLP) analyses were used to examine the evolutionary relationships among Asian common minnows (Zacco spp.) in Taiwan, where four morphotypes were recently reported. Congruent results from the two sets of analyses indicate that the four morphotypes represent four separate morphometric clades with distinct AFLPs. Consequently, we conclude that four species exist in Taiwan and the systematics of Zacco should be revised accordingly. We also discuss conservation implications and offer a key to the four proposed Zacco species.
Zoologica Scripta 06/2006; 35(4):341 - 351. · 2.91 Impact Factor
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ABSTRACT: Chirixalus eiffingeri is an arboreal breeding rhacophorid frog with unique parental care behaviours. We developed 11 polymorphic microsatellites as genetic makers for parentage analysis to resolve the ecology of parental care. The numbers of alleles per locus ranged from two to 17. The observed and expected heterozygosities averaged 0.433 and 0.656, respectively. Total exclusionary probability of these loci is 0.984 when no parental genotypes are known, and is 0.999 when one of the parental genotypes is known. The results indicate that the 11 markers should provide sufficient resolution for inferring genetic parentage in C. eiffingeri.
Molecular Ecology Notes 05/2005; 5(2):430 - 432. · 2.38 Impact Factor
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ABSTRACT: The identification of different clones is fundamental to the study of population structure among organisms with mixed reproductive
modes such as cnidarians. However, due to the low genetic variation of coral mtDNA and contamination by zooxanthellate DNA,
very few molecular markers are available for studying the clonal structure of cnidarians. Herein we used four polymorphic
loci of microsatellite DNA isolated from a zooxanthellae-free octocoral, Junceella juncea, to study its clonal structure in seven populations collected from three localities in Taiwan. In total, 40 multilocus genotypes
were found among 152 colonies, and the number of genotypes (clones) identified in the seven populations ranged from 2 to 16.
Each of the 40 multilocus genotypes was restricted to a single population, even where adjacent populations were only 100m
distant. The ratio of observed to expected genotypic diversity (Go:Ge) ranged from 0.217 to 0.650, and Go showed a significant departure from Ge (p<0.05) at each site indicating that asexual fragmentation may play a major role in the maintenance of established populations.
Mean relatedness (R) values showed that genotypes within reefs were more closely related than those between regions. The results indicate that
microsatellites are useful for discerning the clonal structures among and within populations at different spatial scales.
Coral Reefs 01/2005; 24(3):352-358. · 3.88 Impact Factor
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ABSTRACT: Distinct Taura syndrome virus (TSV) isolates were found in Metapenaeus ensis (isolate Tw2KMeTSV), Penaeus monodon (isolate Tw2KPmTSV) and Litopenaeus vannamei (isolate Tw02LvTSV). Nucleotide sequence analysis of these three isolates revealed differences in the TSV structural protein (capsid protein precursor) gene orf2. TSV ORF2 amino acid sequence comparison and phylogenetic analysis suggested a comparatively close relationship between these three Taiwanese isolates and the Hawaiian isolate HI94TSV. In P. monodon specimens that were naturally and experimentally infected with the Tw2KPmTSV isolate, the virus was contained and shrimps showed no clinical signs of infection. However, when P. monodon was challenged with the Tw2KMeTSV isolate, the virus replicated freely. The ORF2 amino acid sequence of the Tw2KMeTSV isolate differed from that of isolate Tw2KPmTSV in four positions and these differences may account for their phenotypic differences, at least in terms of their ability to replicate in specific hosts.
Journal of General Virology 11/2004; 85(Pt 10):2963-8. · 3.36 Impact Factor
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ABSTRACT: The tiger shrimp (Penaeus monodon) is an important marine crustacean in terms of biological diversity and aquaculture resource. The shrimp is widespread across the Indo-Pacific region and shows apparent genetic differentiation among geographical populations. It is common practice to transport female brooders between different countries to seed the shrimp farms, posing potential problems of unwanted population admixture. We developed 23 polymorphic microsatellites for P. monodon (average HE = 0.936) and these microsatellites were applicable for studying population differentiation, identifying valid stocks and tagging nonindigenous farmed shrimps.
Molecular Ecology Notes 08/2004; 4(3):345 - 347. · 2.38 Impact Factor
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Jennifer A Floyd,
David A Gold,
Dorothy Concepcion,
Tiffany H Poon,
Xiaobo Wang,
Elizabeth Keithley,
Dan Chen,
Erica J Ward,
Steven B Chinn,
Rick A Friedman, Hon-Tsen Yu,
Kazuo Moriwaki,
Toshihiko Shiroishi,
Bruce A Hamilton
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ABSTRACT: Endogenous retroviruses have shaped the evolution of mammalian genomes. Host genes that control the effects of retrovirus insertions are therefore of great interest. The modifier-of-vibrator-1 locus (Mvb1) controls levels of correctly processed mRNA from genes mutated by endogenous retrovirus insertions into introns, including the Pitpn(vb) tremor mutation and the Eya1(BOR) model of human branchiootorenal syndrome. Positional complementation cloning identifies Mvb1 as the nuclear export factor Nxf1, providing an unexpected link between the mRNA export receptor and pre-mRNA processing. Population structure of the suppressive allele in wild Mus musculus castaneus suggests selective advantage. A congenic Mvb1(CAST) allele is a useful tool for modifying gene expression from existing mutations and could be used to manipulate engineered mutations containing retroviral elements.
Nature Genetics 12/2003; 35(3):221-8. · 35.53 Impact Factor
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ABSTRACT: Major histocompatibility complex (MHC) genes are the most polymorphic loci known for vertebrates. Here we employed five microsatellite loci closely linked to the MHC region in an attempt to study the amount of genetic variation in 19 populations of the southeast Asian house mouse (Mus musculus castaneus) in Taiwan. The overall polymorphism at the five loci was high (He = 0.713), and the level of polymorphism varied from locus to locus. Furthermore, in order to investigate if selection is operating on MHC genes in natural mouse populations, we compared the extent and pattern of genetic variation for the MHC-linked microsatellite loci (the MHC loci) with those for the microsatellite loci located outside the MHC region (the non-MHC loci). The number of alleles and the logarithm of variance in repeat number were significantly higher for the MHC loci than for the non-MHC loci, presumably reflecting linkage to a locus under balancing selection. Although three statistical tests used do not provide support for selection, their lack of support may be due to low statistical power of the tests, to weakness of selection, or to a profound effect of genetic drift reducing the signature of balancing selection. Our results also suggested that the populations in the central and the southwestern regions of Taiwan might be one part of a metapopulation structure.
Genetica 11/2003; 119(2):201-18. · 2.15 Impact Factor
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ABSTRACT: We analyzed the population structure of the Japanese anchovy (Engraulis japonicus), a small pelagic fish, using 6 microsatellite DNA loci. The anchovy is known to have 2 separate spawning populations, one near northeastern Taiwan in the Pacific Ocean and the other near southwestern Taiwan in the Taiwan Strait. The planktonic larvae then drifted north to the feeding grounds in the East China Sea to advance in their life history. Three populations of the anchovy were analyzed, including 2 temporal population from the northeastern spawning ground (I-Lan 1999 and I-Lan 2000) and one population from the southwestern spawning ground (Peng-Hu 2000). The genetic variability of the 6 loci was high for all the populations. The average numbers of alleles per population ranged from 25.5 to 32.3, and the average observed heterozygosity ranged from 0.559 to 0.650. A significant population differentiation was found between geographic populations but not between the temporal populations. However, the level of geographic differentiation was weak, average FST 0.0088. The significant geographic population structure indicated that the populations of 2 spawning grounds belonged to separate stocks. Moreover, 16 of the 18 population-locus cases showed significant departure from Hardy-Weinberg equilibrium, implying that each spawning population in turn consisted of mixed native stocks. Finally, we posed 3 population models to be evaluated against the genetic data disclosed with the microsatellite markers.
Marine Biotechnology 11/2002; 4(5):471-9. · 3.43 Impact Factor
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Li-Li Chen,
Han-Ching Wang,
Chiu-Jung Huang,
Shao-En Peng,
Yen-Gu Chen,
Shin-Jen Lin,
Wei-Yu Chen,
Chang-Feng Dai, Hon-Tsen Yu,
Chung-Hsiung Wang,
Chu-Fang Lo,
Guang-Hsiung Kou
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ABSTRACT: The white spot syndrome virus DNA polymerase (DNA pol) gene (WSSV dnapol) has already been tentatively identified based on the presence of highly conserved motifs, but it shows low overall homology with other DNA pols and is also much larger (2351 amino acid residues vs 913-1244 aa). In the present study we perform a transcriptional analysis of the WSSV dnapol gene using the total RNA isolated from WSSV-infected shrimp at different times after infection. Northern blot analysis with a WSSV dnapol-specific riboprobe found a major transcript of 7.5 kb. 5'-RACE revealed that the major transcription start point is located 27 nucleotides downstream of the TATA box, at the nucleotide residue A within a CAGT motif, one of the initiator (Inr) motifs of arthropods. In a temporal expression analysis using differential RT-PCR, WSSV dnapol transcripts were detected at low levels at 2-4 h.p.i., increased at 6 h.p.i., and remained fairly constant thereafter. This is similar to the previously reported transcription patterns for genes encoding the key enzyme of nucleotide metabolism, ribonucleotide reductase. Phylogenetic analysis showed that the DNA pols from three different WSSV isolates form an extremely tight cluster. In addition, similar to an earlier phylogenetic analysis of WSSV protein kinase, the phylogenetic tree of viral DNA pols further supports the suggestion that WSSV is a distinct virus (likely at the family level) that does not belong to any of the virus families that are currently recognized.
Virology 10/2002; 301(1):136-47. · 3.35 Impact Factor
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ABSTRACT: We analyzed population subdivision and gene flow of the Southeast Asian house mouse (Mus musculus castaneus) in Taiwan by using six microsatellite DNA markers. Seven populations of the house mouse (187 individuals), including one from Fukien Province in southeastern China, which is separated from Taiwan by the Taiwan Strait, were analyzed in this study. The overall polymorphic level at the six loci was high (He = 0.76) although individual populations varied in their levels of heterozygosity (He = 0.35-0.83). For the populations within Taiwan, there was no evidence of isolation by distance and the level of gene flow was not (inversely) correlated to geographic distances. Gene flow was estimated to be higher across the Taiwan Strait than within the island of Taiwan. These observations of gene flow cannot be understood unless in the context of the historical human settlements and agricultural expansion, and the commensal habits of the species. We also discussed the causes of population subdivision and genetic variation among populations in terms of ecological characteristics of the house mouse in Taiwan.
ZOOLOGICAL SCIENCE 05/2002; 19(4):475-83. · 0.95 Impact Factor
