Morphological and genetic relationships of the Crocidura monticola species complex (Soricidae: Crocidurinae) in Sundaland

Small Crocidurinae shrews (weight <8 g) from Southeast Asia have been poorly studied to date, mainly because of the difficulty to catch them and the concomitant paucity of reference specimens available in museums. Hence their systematics is still debated, and most small Crocidura shrews from Sundaland are assigned to the monticola species complex. Here, we report a study based on a survey of shrews caught with large pitfalls set on forest floors in Peninsular Malaysia. Morphometric analyses based on 14 skull measurements showed that these shrews tend to be larger with increasing altitude, but showed otherwise no consistent variation. When compared to museum specimens of the monticola species complex sampled in the Sundaland (total: 77 specimens), the Malay shrews tend also to be larger than those living on Kalimantan (Borneo) and Sumatra. All are, however, morphologically distinct from the other species, C. maxi, found in eastern Java and on the Lesser Sundas. Molecular analyses of a subset of these small shrews and based on a mitochondrial (cytochrome b) and a nuclear gene (Apolipoprotein B) suggest that samples from the central region of Peninsular Malaysia (Bukit Rengit and Ulu Gombak) genetically differ from other Malaysian populations (by about 7% K2P distance at the cyt b gene) and are more closely related to some samples from Sumatra and Borneo. These differences did not correlate with the altitudinal variation evidenced from the morphological analysis. Reference sequences from the terra typica of monticola and maxi (both species were originally described from Java) are however needed to determine if these unexpected genetic differences warrant additional taxonomic subdivision within the Sundaland.     

Population genetics of the mangrove salt marsh snake, <Emphasis Type="Italic">Nerodia clarkii compressicauda</Emphasis>, in a linear,fragmented habitat

The mangrove salt marsh snake (Nerodia clarkii compressicauda) occupies a unique and disappearing habitat in much of coastal southern Florida. Given extensive habitat fragmentation and high predation pressure in open spaces, it seems likely that populations of N. c. compressicauda consist of isolated groups of related individuals. To assess the degree of population subdivision in this species we genotyped a total of 125 individuals from seven locations along the Florida coast at four microsatellite loci. Overall heterozygosity was moderate (57.7%) and somewhat lower than that seen in other snake species. Population subdivision was particularly pronounced with 19 of 21 sample pair-wise Φ_ST values significantly different from zero and ranging from 0.064 to 0.343 (P ≤ 0.05). About 11 of 39 alleles were private alleles that also tended to be in high frequency in the populations where they occurred (average frequency ~27%). The correlation of genetic and geographic distances was highly significant and positive (r ² = 0.8733 and P < 0.001) with Φ_ST increasing by ~0.01 for every 10 km of separation. Overall, salt marsh snake populations appear to be fractured into isolated neighborhoods on the order of 50–80 km. In spite of its apparent local abundance, we believe that N. c. compressicauda is in need of conservation protection. The combination of extremely low dispersal, narrow habitat requirements, and most importantly, extensive habitat alteration resulting from coastal real estate development may mean that N. c. compressicauda is highly susceptible to population extirpation and potentially extinction.     

The genus Sorex (Mammalia, Soricidae)–distribution and evolutionary aspects of Eurasian species

There are about 60 species of shrews of the genus Sorex distributed over the Nearctic and Palaearctic regions; these are usually divided into the subgenera Sorex, Otisorex and Microsorex . The Old World species are listed and their phylogeny discussed, with special emphasis laid on the karyotypes. It is proposed that the Old World forms should be divided into the subgenera Homalurus, Sorex and Otisorex . It is also suggested that the subgenus Sorex could be divided into at least three taxonomic units.     

Nineteen new microsatellite DNA polymorphisms in pigtailed macaques (Macaca nemestrina)

Microsatellite loci known to be polymorphic in baboons (Papio hamadryas) and/or humans were tested in pigtailed macaques (Macaca nemestrina) from the Washington Regional Primate Research Center. Nineteen polymorphisms were identified in the macaques, with an average of 9.2 alleles per locus and an average heterozygosity of 0.76. Seven loci were analyzed using radiolabelled PCR primers and standard gel electrophoresis. Twelve loci were studied using fluorescently labelled primers and the Perkin-Elmer ABI 377 genotyping system. Of these 19 pigtailed macaque polymorphisms, 12 were used to perform paternity testing among captive animals. In a set of 15 infants, this panel of 12 genetic polymorphisms was sufficient to establish paternity in all cases. The number of alleles per locus in pigtailed macaques was compared with the number of alleles in a sample of baboons, and no significant correlation was observed. This indicates that population genetic processes such as genetic drift and recurrent mutation act rapidly enough on these loci to eliminate any relationship in levels of polymorphism across those two species. These 19 loci will be valuable for a range of genetic studies in pigtailed macaques, including paternity testing, analysis of population structure and differentiation among wild populations, and genetic linkage mapping.     

Parentage determination of mandarin fish (Siniperca chuatsi) based on microsatellite DNA markers

In this study, ten microsatellite loci were chosen to estimate the parentage of 260 progeny in five mandarin fish (Siniperca chuatsi) full-sib families. Simulation based on allele frequency date demonstrated the combined exclusion power would be over 97% if the number of loci was up to nine. Based on the information from these nine loci, 98% of progeny were unambiguously allocated to their putative parental pairs in the parentage analysis. The assignment success rate by the real data set was lower than that predicted by the simulations, with 94% of progeny assigned correctly. The discrepancies might be caused by a scoring error or allelic dropout caused by poor quality genomic DNA. Moreover, 69 progeny were selected randomly for the double-blind test, the result indicated that 95% of the progeny can be correctly assigned to their families. This study provided a microsatellite-based approach for parentage assignment in S. chuatsi, and that will be useful for investigation of genetic background and molecular marker-assisted selective breeding in this species.     

Isolation by distance, linguistic similarity, and the genetic structure on Bougainville Island

Previous research has revealed extensive genetic variation among villages on Bougainville, in the Solomon Islands. Using previously published gene frequency data for seven loci, the role of isolation by distance in structuring genetic variation on Bougainville was reanalyzed. Newer methods of kinship estimation show that earlier estimates of the isolation by distance parameters were low. The fit of the model is highly significant (R2 = 0.409; P less than 0.001), and the parameter estimates indicate high isolation: a = 0.0538, b = 0.1978, L = -0.0057. Several methods of residual analysis were applied in order to determine factors affecting the fit of the model. Linguistic similarity has a significant effect on genetic variation once the effects of geographic distance are taken into account. Population-specific deviations from the expected model may be explained, in part, in terms of population history. Compared to other human populations, Bougainville Island shows an even greater among-group variation than has been suggested previously.     

Population structure of North American beluga whales (Delphinapterus leucas) based on nuclear DNA microsatellite variation and contrasted with the population structure revealed by mitochondrial DNA variation

Beluga whales ( Delphinapterus leucas ) in North American waters migrate seasonally between wintering areas in broken pack ice and summering locations in estuaries and other open water areas in the Arctic and sub-Arctic. Results from our previous investigation of beluga whale mitochondrial DNA (mtDNA) revealed genetic heterogeneity among beluga from different summering locations that was interpreted as representing a high degree of summering site philopatry. However, mtDNA is maternally inherited and does not reflect mating that may occur among beluga from different summering locations in wintering areas or during annual migrations. To test the possibility that breeding occurs among beluga from different summering locations, genetic variability at five nuclear DNA (nDNA) microsatellite loci was examined in the same animals tested in the mtDNA study. Beluga samples ( n = 640) were collected between 1984 and 1994 from 24 sites across North America, mostly during the summer. Whales from the various sites were categorized into eight summering locations as identified by mtDNA analysis, as well as four hypothesized wintering areas: Bering Sea, Hudson Strait (Hudson Strait, Labrador Sea, southwest Davis Strait), Baffin Bay (North Water, east Davis Strait), and St Lawrence River. Microsatellite allele frequencies indicated genetic homogeneity among animals from summering sites believed to winter together but differentiation among whales from some of the wintering areas. In particular, beluga from western North America (Bering Sea) were clearly distinguished from beluga from eastern North America (Hudson Strait, Baffin Bay, and St Lawrence River). Based upon the combined data set, the population of North American beluga whales was divided into two evolutionarily significant units. However, the population may be further subdivided into management units to reflect distinct groups of beluga at summering locations.     

Population structure of North American beluga whales (Delphinapterus leucas) based on nuclear DNA microsatellite variation and contrasted with the population structure revealed by mitochondrial DNA variation

Beluga whales ( Delphinapterus leucas ) in North American waters migrate seasonally between wintering areas in broken pack ice and summering locations in estuaries and other open water areas in the Arctic and sub-Arctic. Results from our previous investigation of beluga whale mitochondrial DNA (mtDNA) revealed genetic heterogeneity among beluga from different summering locations that was interpreted as representing a high degree of summering site philopatry. However, mtDNA is maternally inherited and does not reflect mating that may occur among beluga from different summering locations in wintering areas or during annual migrations. To test the possibility that breeding occurs among beluga from different summering locations, genetic variability at five nuclear DNA (nDNA) microsatellite loci was examined in the same animals tested in the mtDNA study. Beluga samples ( n = 640) were collected between 1984 and 1994 from 24 sites across North America, mostly during the summer. Whales from the various sites were categorized into eight summering locations as identified by mtDNA analysis, as well as four hypothesized wintering areas: Bering Sea, Hudson Strait (Hudson Strait, Labrador Sea, southwest Davis Strait), Baffin Bay (North Water, east Davis Strait), and St Lawrence River. Microsatellite allele frequencies indicated genetic homogeneity among animals from summering sites believed to winter together but differentiation among whales from some of the wintering areas. In particular, beluga from western North America (Bering Sea) were clearly distinguished from beluga from eastern North America (Hudson Strait, Baffin Bay, and St Lawrence River). Based upon the combined data set, the population of North American beluga whales was divided into two evolutionarily significant units. However, the population may be further subdivided into management units to reflect distinct groups of beluga at summering locations.     

Population genetic structure of Japanese wild soybean (Glycine soja) based on microsatellite variation

The research objectives were to determine aspects of the population dynamics relevant to effective monitoring of gene flow in the soybean crop complex in Japan. Using 20 microsatellite primers, 616 individuals from 77 wild soybean (Glycine soja) populations were analysed. All samples were of small seed size (< 0.03 g), were directly collected in the field and came from all parts of Japan where wild soybeans grow, except Hokkaido. Japanese wild soybean showed significant reduction in observed heterozygosity, low outcrossing rate (mean 3.4%) and strong genetic differentiation among populations. However, the individual assignment test revealed evidence of rare long-distance seed dispersal (> 10 km) events among populations, and spatial autocorrelation analysis revealed that populations within a radius of 100 km showed a close genetic relationship to one another. When analysis of graphical ordination was applied to compare the microsatellite variation of wild soybean with that of 53 widely grown Japanese varieties of cultivated soybean (Glycine max), the primary factor of genetic differentiation was based on differences between wild and cultivated soybeans and the secondary factor was geographical differentiation of wild soybean populations. Admixture analysis revealed that 6.8% of individuals appear to show introgression from cultivated soybeans. These results indicated that population genetic structure of Japanese wild soybean is (i) strongly affected by the founder effect due to seed dispersal and inbreeding strategy, (ii) generally well differentiated from cultivated soybean, but (iii) introgression from cultivated soybean occurs. The implications of the results for the release of transgenic soybeans where wild soybeans grow are discussed.     

First record of Sorex (Drepanosorex) margaritodon (Mammalia, Soricidae) in Western Europe: biostratigraphy, biogeography and evolution of the species

The taxonomy of the extinct European subgenus Drepanosorex (Mammalia, Soricidae) has traditionally been problematic, but it seems to comprise five valid species from the Pleistocene: Sorex (Drepanosorex) praearaneus, S. (D.) savini, S. (D.) margaritodon, S. (D.) austriacus and S. (D.) rupestris. The first record of Sorex (Drepanosorex) margaritodon in Western Europe comes from the Lower Red Unit (levels TE7–14) of Sima del Elefante (Sierra de Atapuerca, Burgos, Spain), which is dated to ca. 1.1–1.5 Ma. Detailed morphological comparisons and morphometric analyses have allowed us to assign the items from Sima del Elefante indisputably to this taxon. Sorex (D.) margaritodon is now firmly dated to the Early Pleistocene of Central Europe and the north of the Iberian Peninsula, which makes it a very useful biochronological tool in the continental context. Sorex (D.) margaritodon and S. (D.) savini could have evolved in Central Europe from the more primitive S. (D.) praearaneus, which could also be the potential ancestor of the Caucasian Sorex (D.) rupestris. Sorex (D.) margaritodon, the Drepanosorex species with the westernmost distribution in Europe, may be regarded as the most probable ancestor of S. (D.) austriacus.     

Contrasting patterns of mitochondrial and microsatellite genetic structure among Western European populations of tawny owls (Strix aluco)

A recent study of mitochondrial phylogeography of tawny owls (Strix aluco) in western Europe suggested that this species survived the Pleistocene glaciations in three allopatric refugia located in Iberia, Italy, and the Balkans, and the latter was likely the predominant source of postglacial colonization of northern Europe. New data from seven microsatellite loci from 184 individual owls distributed among 14 populations were used to assess the genetic congruence between nuclear and mitochondrial DNA (mtDNA) markers. Microsatellites corroborated the major phylogeographical conclusions reached on the basis of the mtDNA sequences, but also showed important differences leading to novel inferences. Microsatellites corroborated the three major refugia and supported the Balkan origin of northern populations. When corrected for differences in effective population size, microsatellites and mtDNA yielded generally congruent overall estimates of population structure (N*ST=0.12 vs. RST=0.16); however, there was substantial heterogeneity in the RST among the seven nuclear loci that was not correlated with heterozygosity. Populations representing the Balkans postglacial expansion interact with populations from the other two refugia forming two clines near the Alps and the Pyrenees. In both cases, the apparent position of the contact zones differed substantially between markers due to the genetic composition of populations sampled in northern Italy and Madrid. Microsatellite data did not corroborate the lower genetic diversity of northern, recently populated regions as was found with mtDNA; this discrepancy was taken as evidence for a recent bottleneck recovery. Finally, this study suggests that congruence among genetic markers should be more likely in cases of range expansion into new areas than when populations interact across contact zones.     

Population structure and genetic variability of pearl oyster Pinctada mazatlanica along Pacific coasts from Mexico to Panama

Populations of the Calafia pearl oyster Pinctada mazatlanica ofthe American Pacific coasts have been considered endangeredbecause of overfishing and/or alteration to coastal areas. Weassessed genetic variability and the pattern of populationstructure among 9 samples collected from Mexico to Panama, usingmtDNA RFLP analysis of two genes: 12S rRNA and subunit one ofCytochrome oxydase (COI). Haplotype diversity varied from 0.000to 0.856. The Panama population appeared to be monomorphic, whilethe other samples exhibited a level of haplotypic variabilitysimilar to those reported in the literature for the same kind ofanalysis on other bivalves species. A test for the impact ofdemographic history on genetic diversity was applied on thesequence data, and the results were congruent with a recentdecline of population sizes. Genetic differentiation was shown tofollow a scheme of isolation by distance, with low levels ofdifferentiation at the scales of ten to one hundred kilometres,whereas stronger and significant genetic structure was detectedat a larger scale. Three significantly distinct groups could thenbe defined, which correspond to Northern Mexico, Southern Mexico,and Panama.     

Population genetic structure of the spotted seal Phoca largha along the Coast of Hokkaido,based on mitochondrial DNA sequences

Population genetic structure of the spotted seal, Phoca largha, along coastal regions of Hokkaido was investigated, using mitochondrial DNA (mtDNA) sequences. A 571-bp fragment of the mtDNA control region and adjacent threonine and proline transfer RNA genes was sequenced from 66 seals. We categorized all individuals into three groups considering sampling area and season: twenty-four seals from the Sea of Okhotsk in winter, 11 seals from the Sea of Okhotsk coast in fall, and 31 seals from the Sea of Japan coast in winter. From the 66 animals, 57 haplotypes were identified. Compared with the harbor seal sequence, all spotted seals examined shared two deletions in the control region, which distinguished between the two species. Forty-nine haplotypes were represented by a single individual, and haplotypes shared by more than two animals were generally restricted to same sampling-groups. Phylogenetic trees did not indicate clear geographic differences among the three groups. An Analysis of molecular variances (AMOVA) did not showed any significant population genetic structure in Hokkaido spotted seals (Phi(st )= -0.003). Our results showed a high level of diversity but no genetic structure, and did not deny the possibility that seals in the Okhotsk breeding concentration mainly stayed in the fall Okhotsk and also inhabited in the winter Sea of Japan.     

The microsatellite polymorphism and gene flow in the contact zone of four common shrew (Sorex araneus L., Mammalia) chromosome races

The variation of microsatellite loci in 130 individuals of four common shrew chromosome races (Moscow, Western Dvina, Seliger, and St. Petersburg) contacting on the Valdai Hills was studied. A low level of genetic differences between the chromosome races, which differ at three-five fixed diagnostic metacentric chromosomes, was found. The genetic differentiation within the races is more considerable as compared with that between the races. A high deficiency in heterozygotes was recorded; presumably, this is connected with regular variation in the population sizes. It is assumed that the fixation of centric chromosome fusions was supported by selection (drive) in the evolution of the common shrew against the background of a neutral evolution of the microsatellite loci.     

Population genetic structure of Penaeus merguiensis in Thailand based on nuclear DNA variation

Polymorphisms of nuclear DNA markers were used to study the genetic variation and differentiation among populations of Penaeus merguiensis in Thailand. The data consisted of three nuclear loci analysed for 163 individuals from five populations collected from the Gulf of Thailand (Trad, Surat Thani and Songkhla) and the Andaman Sea (Satun and Trang). The multilocus F_ST estimated at three nuclear loci revealed great and highly significant differentiation between the Gulf of Thailand and Andaman Sea (F_ST=0.203, P<0.001), mostly due to the polymorphism of locus PvAmy. In addition, significant population differentiation was also found within the Gulf of Thailand. These results were compared to that of a previous mitochondrial DNA survey spanning the same geographical range where two divergent mitochondrial clades were reported. The present study brings support to the fact that the existence of these two clades is not due to a mixture of cryptic species but reflects their phylogeographic origin. The strong genetic structure of P. merguiensis on each side of the Thailand peninsula for both mitochondrial and nuclear genes could thus be linked to the phylogeographic divide between Indian Ocean and Pacific forms on the west and east sides respectively.     

种群微卫星DNA分析中样本量对各种遗传多样性度量指标的影响

我们以中国飞蝗种群的微卫星遗传分析数据为例 ,评估了取样对种群遗传多样性指标的影响 ,结果显示 :样本大小与所观测到的每位点等位基因数、平均等位基因数及基因丰富度指数均呈显著正相关 ,而与期望杂合度无显著相关 ;微卫星位点多态性的高低直接影响所观测到的种群基因丰富度及其检测所需的样本量 ;对大多数种群遗传和分子生态学研究而言 ,30 - 5 0个个体是微卫星DNA分析所需要的最小样本量。基因丰富度经过稀疏法或多次随机抽样法校正后 ,可适用于瓶颈效应等种群历史数量变动的检测。另外 ,在研究中 ,还应避免采集时间的不同及样本的性比构成所可能造成的对种群遗传结构的影响     

Genetic effects of habitat fragmentation on blue sucker populations in the upper Missouri River (<Emphasis Type=Italic>Cycleptus elongatus</Emphasis> Lesueur, 1918)

The blue sucker, Cycleptus elongatus, is a large catostomid fish that occurs in main stem rivers throughout the Mississippi basin of North America. Although not federally listed as threatened or endangered, populations are not considered stable in any of 21 states where they occur. Included in the range is the Missouri River, which flows more than 3,200 km from Montana to St. Louis, Missouri. Historically, C. elongatus was distributed continuously throughout the main stem Missouri and its major tributaries, but from 1952 to 1963, six major impoundments were constructed on the upper Missouri by the US Army Corps of Engineers. The resulting reservoirs have inundated and fragmented large riverine habitat from Yankton, South Dakota to the headwaters. C. elongatus still occurs in remnant stretches between reservoirs; however, little is known of the impacts of the dams on these populations. In order to test for such effects, 231 individuals from nine sites were genotyped at 14 variable microsatellite loci. An additional 142 individuals from six sites in the Mississippi River were also genotyped for comparative purposes. In the Missouri, allelic richness was reduced in inter-reservoir sites relative to those in the free flowing lower river. In addition, significant isolation by distance occurs in the Missouri, a pattern not present in the unimpounded Mississippi. These results are consistent with reduced intradrainage gene flow in the Missouri River and are the first to indicate effects of impoundments on genetic structure in the system. This information will assist governing agencies in making informed decisions regarding conservation of C. elongatus in the Missouri River drainage and throughout the range.     

Hierarchical analyses of genetic differentiation in a hybrid zone of Sorex araneus (Insectivora: Soricidae)

Microsatellites are used to unravel the fine-scale genetic structure of a hybrid zone between chromosome races Valais and Cordon of the common shrew ( Sorex araneus ) located in the French Alps. A total of 269 individuals collected between 1992 and 1995 was typed for seven microsatellite loci. A modified version of the classical multiple correspondence analysis is carried out. This analysis clearly shows the dichotomy between the two races. Several approaches are used to study genetic structuring. Gene flow is clearly reduced between these chromosome races and is estimated at one migrant every two generations using R -statistics and one migrant per generation using F -statistics. Hierarchical F - and R -statistics are compared and their efficiency to detect inter- and intraracial patterns of divergence is discussed. Within-race genetic structuring is significant, but remains weak. F _ST displays similar values on both sides of the hybrid zone, although no environmental barriers are found on the Cordon side, whereas the Valais side is divided by several mountain rivers. We introduce the exact G -test to microsatellite data which proved to be a powerful test to detect genetic differentiation within as well as among races. The genetic background of karyotypic hybrids was compared with the genetic background of pure parental forms using a CRT–MCA. Our results indicate that, without knowledge of the karyotypes, we would not have been able to distinguish these hybrids from karyotypically pure samples.