Mitochondrial DNA sequence variability in red-legged partridge, <Emphasis Type="Italic">Alectoris rufa</Emphasis>, Spanish populations and the origins of genetic contamination from <Emphasis Type="Italic">A. chukar</Emphasis>

The analysis of 135 mitochondrial D-loop sequences of the Iberian autochthonous red-legged partridge (Alectoris rufa) from wild population hunting bags from various locations and fowl runs in Spain yielded 37 different haplotypes. Among these, three haplotypes correspond to chukar partridges (Alectoris chukar), indicating genetic introgression from birds illegally introduced for restocking: three individuals carrying such haplotypes where found in natural populations, one appeared among those sampled on a mass reproduction farm and the remaining 10 in another fowl-run. The geographical origin of the contaminating chukar haplotypes could be assigned to the most easterly area of the chukar partridge geographical distribution in China. Molecular diversity parameters in the A. rufa samples indicate a considerable amount of genetic variation. Φ_ST showed significant differences among populations that are not explained by geographical distance alone. Particularly, one northern population (Palencia) shows a certain degree of genetic differentiation that could reflect a previously suggested subspecies division. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Genetic variability in the endemic <Emphasis Type="Italic">Leucojum valentinum</Emphasis>

The genetic variability of Leucojum valentinum Pau (Amaryllidaceae), a vulnerable endemic species restricted to a small area in the region of Valencia (Eastern Spain), has been studied using random amplified polymorphic DNA (RAPD) markers. A total of 197 individuals from eleven populations were studied using 13 RAPD primers. Our results show high variability for the species, low differentiation among populations and uncorrelated levels of genetic variability and population size. Four groups in which three populations (SAG, PUG and COL) are separated from all the others were found, but without connection to geographical location.     

Distinct electrophoretic polymorphism pattern at alcohol dehydrogenase (<Emphasis Type="Italic">Adh</Emphasis>) locus of <Emphasis Type="Italic">Drosophila melanogaster</Emphasis> natural populations from Turkey

Small number of Drosophila melanogaster populations from two distinct geographical regions of Turkey, Central Anatolia and Black Sea, were studied. Populations sampled were electrophoresed for a single locus, alcohol dehydrogenase (Adh) to assess population differentiation. Both the magnitude of genetic differentiation levels and the population structure based on hierarchical F-statistics allow populations to be grouped on two genetically divergent area, Central Anatolian and Black Sea. One ecological correlate, average yearly maximum rainfall, R _year, seems to track this Adh genetic variation pattern. The study also shows that a typical pattern of geographical Adh polymorphism can emerge with a handfull of populations sampled across a relatively small distance. The text was submitted by the author in English.     

Findings of Andriashevs eel cod <Emphasis Type="Italic">Muraenolepis andriashevi</Emphasis> (Gadiformes: Muraenolepididae) at Discovery Seamount (South Atlantic)

Findings of a rare fish, Andriashevs eel cod Muraenolepis andriashevi Balushkin et Prirodina, 2005 (Muraenolepididae), from Discovery Seamount (South Atlantic) are described. The new findings extend the geographical distribution area and the range of morphological variability of this species previously known only from two type-specimens from the Agulhas Bank (South Africa).     

Italian Peninsula preserves an evolutionary lineage of the fat dormouse Glis glis L. (Rodentia: Gliridae)

The present study examines the population genetic structure of fifty‐nine specimens of Glis glis (Linneaus, 1766) from thirteen localities in central Europe, sequencing a 400‐bp segment of the mitochondrial cytochrome b (cyt b) gene and a 673‐bp segment of the cytochrome c oxidase subunit I (COI) gene. The consensus tree obtained from Bayesian analysis revealed a robust dichotomy, showing two sister groups: one clade includes samples from a wide geographical area, extending from north‐central Europe to northern Italy (major branch sensu Bilton), and the other comprises samples collected in central and southern Italy and in Sicily (Italian branch). According to the Tajima–Nei model, the two phylogroups were separated by a sequence divergence of 0.8% (cyt b) – 2.6% (COI), showing the COI gene to be more informative than cyt b. On a smaller geographical scale, the Italian clade was further substructured, displaying geographical differentiation along the Peninsula. The gene pool in this area was patchy; whereas populations from Sicily Island demonstrated fixed cyt b and COI haplotypes, assuming processes of isolation and selection. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 11–21.     

Towards a ‘Sea‐Level Sensitive’ dynamic model: impact of island ontogeny and glacio‐eustasy on global patterns of marine island biogeography

A synthetic model is presented to enlarge the evolutionary framework of the General Dynamic Model (GDM) and the Glacial Sensitive Model (GSM) of oceanic island biogeography from the terrestrial to the marine realm. The proposed ‘Sea‐Level Sensitive’ dynamic model (SLS) of marine island biogeography integrates historical and ecological biogeography with patterns of glacio‐eustasy, merging concepts from areas as diverse as taxonomy, biogeography, marine biology, volcanology, sedimentology, stratigraphy, palaeontology, geochronology and geomorphology. Fundamental to the SLS model is the dynamic variation of the littoral area of volcanic oceanic islands (defined as the area between the intertidal and the 50‐m isobath) in response to sea‐level oscillations driven by glacial–interglacial cycles. The following questions are considered by means of this revision: (i) what was the impact of (global) glacio‐eustatic sea‐level oscillations, particularly those of the Pleistocene glacial–interglacial episodes, on the littoral marine fauna and flora of volcanic oceanic islands? (ii) What are the main factors that explain the present littoral marine biodiversity on volcanic oceanic islands? (iii) How can differences in historical and ecological biogeography be reconciled, from a marine point of view? These questions are addressed by compiling the bathymetry of 11 Atlantic archipelagos/islands to obtain quantitative data regarding changes in the littoral area based on Pleistocene sea‐level oscillations, from 150 thousand years ago (ka) to the present. Within the framework of a model sensitive to changing sea levels, we discuss the principal factors affecting the geographical range of marine species; the relationships between modes of larval development, dispersal strategies and geographical range; the relationships between times of speciation, modes of larval development, ecological zonation and geographical range; the influence of sea‐surface temperatures and latitude on littoral marine species diversity; the effect of eustatic sea‐level changes and their impact on the littoral marine biota; island marine species–area relationships; and finally, the physical effects of island ontogeny and its associated submarine topography and marine substrate on littoral biota. Based on the SLS dynamic model, we offer a number of predictions for tropical, subtropical and temperate volcanic oceanic islands on how rates of immigration, colonization, in‐situ speciation, local disappearance, and extinction interact and affect the marine biodiversity around islands during glacials and interglacials, thus allowing future testing of the theory.     

Nouvelle découverte dans le Nord-Ouest de Madagascar et répartition géographique des espèces du genre Palaeopropithecus

During the field-work of 2003 in the Narinda peninsula in the Province of Mahajanga (North-West of Madagascar), we found a Palaeopropithecus of large size in the new cave “Raulin Zohy”. This fossil differs in morphology and size from the remains coming from other sites of this area and belonging to a new yet undescribed species. This discovery proves that two species of this genus existed in the costal area of the Province of Mahajanga. This Palaeopropithecus attributed to maximus species allows a reconsideration of the geographical distribution of this subfossil lemur species, and asks an interesting question about the biogeography on the small new species.     

气候变化对柴胡与狭叶柴胡适生分布的影响

研究气候变化下物种适生区的分布格局与变迁,对于物种的保护和资源的可持续利用具有重要的理论和实践意义。选取柴胡(Bupleurum chinense)与狭叶柴胡(Bupleurum scorzonerifolium)在中国地域内的381个有效分布点和36个环境因子,利用MaxEnt模型模拟当前以及未来(2050和2070年)两种气候情景下(RCP4.5和RCP8.5)其适生区的分布格局,并分析了制约其适生区分布的主导环境因子。结果表明：(1)影响柴胡适生区分布的主导环境因子为最湿月份降水量、最干季度平均温度以及海拔。影响狭叶柴胡适生区分布的主导环境因子为最湿月份降水量、温度季节性变化标准差以及海拔;(2)当前气候条件下,柴胡适生区总面积为1.4755×10⁶km²,约占我国国土面积的15.37%,中、高度适生区主要分布在陕西南部、山西东部、甘肃东南部、山东中部、河北中西部等地;狭叶柴胡适生区总面积为1.8034×10⁶km²,约占我国国土面积的18.78%,中、高度适生区主要分布在黑龙江西部和东部、内...     

Genetic variation and clonal diversity of <Emphasis Type="Italic">Bromus ircutensis</Emphasis> Kom. in the Otingdag sandy land detected by <Emphasis Type="Italic">ISSR markers</Emphasis>

Genetic variation and clonal diversity of nine populations of Bromus ircutensis Kom. from the Otingdag sandy land were investigated using Inter Simple Sequence Repeat (ISSR) markers. A total of 102 bands were amplified by using 11 ISSR primers chosen for the study. Among those 99% were polymorphic indicating high level of genetic variation at the species level with a mean genetic diversity (H) of 0.292 and Shannon information index (I) of 0.450. Percentage of polymorphic loci (PPL) of nine populations was 76.48% on average, which provides more evidence of considerable genetic variation at the population level. AMOVA analysis revealed that total genetic variation was higher within populations (87.06%) than between populations (12.94%), which is mainly the result of the extensive gene flow (Nm = 1.682) among B. ircutensis populations. UPGMA cluster analysis divided the nine populations into two groups. There was significant or moderate negative correlations between genetic diversity parameters (PPL, H, I) and longitude or latitude. Mantel test also showed a significant correlation between geographical distance and genetic distance (r = 0.681, p = 0.002). Our findings indicated that distribution of B. ircutensis populations was influenced by geographical and ecological factors. Clonal diversity was also high with 108 individuals identified by 11 ISSR primers being all of different genets. Our results provide a molecular basis for sustainable management and conservation of B. ircutensis in the study area.     

Phylogeographic evidence for the postglacial colonization of the North and Baltic Sea coasts from inland glacial refugia by Triglochin maritima L.

We investigated the geographical distribution of genetic variation in 67 individuals of Triglochin maritima from 38 localities across Europe using AFLP markers. Analysis of genetic variation resulted in the recognition of two major genetic groups. Apart from few geographical outliers, these are distributed (1) along the Atlantic coasts of Portugal, Spain and France and (2) in the North Sea area, the Baltic Sea area, at central European inland localities, the northern Adriatic Sea coast and the Mediterranean coast of southwest France. Considering possible range shifts of T. maritima in reaction to Quaternary climatic changes as deduced from the present-day northern temperature limit of the species, Quaternary changes of coastline in the North Sea area and the very recent origin of the Baltic Sea, we conclude that the coastal populations of T. maritima in the North Sea and Baltic Sea areas originated from inland populations.     

气候变化情景下裸冠菊在中国的潜在适生区分布预测

外来入侵植物裸冠菊(Gymnocoronis spilanthoides)具有较强的入侵适应性能快速繁殖扩散,会对本土物种的生长繁殖及本地生态安全、景观格局等产生不良影响。基于265个有效分布点和7个环境变量,调整优化预测模型的调控倍频和特征组合参数,应用MaxEnt、ArcGIS、R软件预测当前和未来(2050s, 2070s)不同气候情景(SSP126, SSP245,SSP370, SSP585)下裸冠菊在中国的潜在地理分布,定量分析其适生区的空间变化及质心移动轨迹,最后采用受试者工作特征(ROC)曲线下面积(AUC)和测试遗漏率评估模型的精确性。未来气候模式选择中国国家气候中心开发的CMIP6中BCC-CSM2-MR。结果表明：(1)模型预测结果极准确,各组模型的AUC值均高于0.97;(2)最干季降水量(bio17)、最冷季度平均温(bio11)、温度季节性变化(bio4)和最暖季度平均降雨量(bio18)是影响裸冠菊地理分布的主导气候因子;(3)当前气候条件下,裸冠菊的总适生区面积达到191.18×10⁴km²,约占国土总面积的1...     

末次冰盛期以来香果树潜在地理分布格局变迁

香果树是中国特有的单种属孑遗树种,探讨末次冰盛期以来香果树在中国的潜在地理分布格局及其变化,对研究茜草科乃至中国亚热带植物区系的系统发育、古生态和古气候变迁等具有重要作用。研究基于最大熵MaxEnt模型与ArcGIS空间分析技术,利用香果树分布点位信息与气候数据,构建其在末次冰盛期(LGM)、全新世中期(MID)、当前(1960—1990年)以及未来(2061—2080年)的潜在地理分布格局,探明其分布格局的变化趋势,揭示引起其潜在地理分布格局改变的关键因子。结果表明,香果树当前适生区总面积约197.575×10⁴ km²,主要位于中国亚热带地区,其中高适生区集中分布于四川盆周山地、武陵山与武夷山地区,最干季度平均温、最湿月降水量、最冷季度降水量是限制其分布的主要气候因子。末次冰盛期时香果树广泛分布于中国亚热带地区,随后适生区开始缩减且向内陆退缩,全新世中期后适生区面积继续缩减并向高纬度地区迁移。随着全球气候变暖,在不同排放情景下香果树适宜生境面积均进一步缩减并向西与高纬度地区迁移。总体而言,从末次冰盛期至未来,香果树适生区呈现持续缩减并向西...     

mtDNA Diversity and genetic lineages of eighteen cattle breeds from <Emphasis Type="Italic">Bos taurus </Emphasis>and<Emphasis Type="Italic"> Bos indicus</Emphasis> in China

In order to clarify the origin and genetic diversity of indigenous cattle breeds in China, we carried out phylogenetic analysis of representatives of those breeds by employing mitochondrial gene polymorphism. Complete cyt b gene sequences, 1140 bp in length, were determined for a total of 136 individuals from 18 different breeds and these sequences were clustered into two distinct genetic lineages: taurine (Bos taurus) and zebu (Bos indicus). In analysis of the cyt b gene diversity, Chinese cattle showed higher nucleotide (0.00923) and haplotype diversity (0.848) than the reports from other studies, and the animals from the taurine lineage indicated higher nucleotide diversity (0.00330) and haplotype diversity (0.746) than the ones from the zebu lineage (0.00136; 0.661). The zebu mtDNA dominated in the southern breeds (63.3–100%), while the taurine dominated in the northern breeds (81.8–100%). Six cattle breeds from the central area of China exhibited intermediate frequencies of zebu mtDNA (25–71.4%). This polymorphism revealed a declining south-to-north gradient of female zebu introgression and a geographical hybrid zone of Bos taurus and Bos indicus in China.     

Significance of habitat type for the genetic population structure of <Emphasis Type="Italic">Panonychus citri</Emphasis> (Acari: Tetranychidae)

Restricted migration and habitat fragmentation promote genetic differentiation between populations: Because most of the hosts of Panonychus citri are woody plants, mainly citrus trees that are usually planted at intervals of several metres, this mite likely faces more risks (e.g., starvation) by dispersing between host plants, compared to other spider mite species that infest both herbaceous and woody plants, such as Tetranychus urticae. Such a limited gene flow between patches (host plants) can lead to differentiation of populations even within a small area. Therefore, we hypothesize that P. citri populations are genetically differentiated not only between distant populations but also within small areas, such as within a grove. To test this hypothesis, we investigated the divergence of P. citri populations in Japanese citrus groves according to a hierarchical arrangement of geographical distance, ranging from distant populations (10 groves distributed throughout different areas in two major Japanese islands; this level of analysis is referred to as ‘geographic’) to local populations (different trees in a specific grove; ‘local’). Three molecular markers were used an esterase locus, one microsatellite and a point mutation in the mitochondrial cytochrome oxidase subunit I. At a local level acaricide susceptibility tests were also performed using two acaricides: fenpyroximate (25 ppm) and etoxazole (3.33 ppm). At a broad geographic level the gene diversity decreased with decreasing area size and distance between populations. By contrast, at the local level, populations maintained a significant level of variation between trees within groves, and the divergence within groves was higher than between groves. Whereas no statistical difference of the mortalities was detected among groves for the two acaricides tested, the difference was statistically significant among trees within groves in fenpyroximate (ANOVA, p < 0.025) and marginal in etoxazole (0.1 < p < 0.05). We concluded that P. citri populations maintain a higher level of variation between trees (or patches of trees) within groves than between groves at the local level, though the gene diversity tended to be smaller with decreasing distance between populations at the geographical level. Results are discussed in relation to the dispersal behaviour of spider mites.     

Spatio‐temporal patterns of genetic variations in populations of yellowtail kingfish Seriola lalandi from the south‐eastern Pacific Ocean and potential implications for its fishery management

The genetic population structure and genetic diversity of yellowtail kingfish Seriola lalandi from the coastal south‐eastern Pacific Ocean (SEP) were evaluated at spatiotemporal scale in order to understand the ecology of this species. Between 2012 and 2015, temporal and spatial population genetic structure and a low genetic diversity were detected in S. lalandi from SEP. These results suggest that S. lalandi specimens arriving annually from offshore to the SEP coast could come from at least two genetically distinct populations, revealing a particular life strategy (i.e. reproductive or habitat segregation) for this fish species. Therefore, the SEP coast might constitute a point of population mixing for this species. Additionally, the low genetic diversity of S. lalandi in the SEP could be a result of a founder effect or overfishing. Regardless of the process explaining the genetic diversity and structure of S. lalandi in this geographical area, this new information should be considered in order to implement successful fishery management of this resource in the South Pacific.     

Comparative analysis on the diversity of <Emphasis Type="Italic">Auricularia auricula</Emphasis>-<Emphasis Type="Italic">judae</Emphasis> by physiological characteristics,somatic incompatibility and TRAP fingerprinting

Phenotypic traits (physiological characteristics and somatic incompatibility) and genotypic traits (target region amplification polymorphism TRAP) were used to study the diversity of 32 main cultivars of Auricularia auricula-judae in China. Twenty seven important and stable physiological indexes were evaluated; somatic incompatibility test (SIT) reaction was described from three aspects: type, pigment, and intensity; 16 pairs of TRAP primer combinations produced 535 unambiguous and reproducible DNA fragments, of these 524 (97.9%) were polymorphic. Dendrograms were constructed by Unweighted Pair-group Method with Arithmetic Averages (UPGMA) method, and the principal coordinate analysis (PCO) of the three methods (physiological characteristics, SIT intensity and TRAP) exhibited similar clustered patterns, revealing that all the tested strains could be divided into three distinct groups, each of which was correlated with different geographical regions. Most strains originated from the same area were with a narrow genetic basis and could possibly be domesticated from the local wild-type strains, some strains were suspected to be synonymous. The grouping information obtained in the present work provides significant information for further genetic improvement of A. auricula-judae.     

Comparative cytogenetic study of the forms of <Emphasis Type="Italic">Macleaya cordata</Emphasis> (Willd.) R. Br. From different localities

A comparative cytogenetic study of two introduced forms of Makleaya cordata (Willd.) R. Br. = syn. Bocconia cordata Willd. grown in different ecological and geographical regions (Moscow and Donetsk areas) was carried out. In the study, a complex of methods utilizing various chromosomal markers, i.e., C- and DAPI-banding technique, fluorescence in situ hybridization (FISH) with probes of 26S and 5S rDNA, as well as estimation of the total area of C-positive regions (C-HCH) in prophase nucleoli and meiosis analysis, was used. In the karyotypes (2n = 20), each chromosome was identified on the basis of C-banding and FISH patterns and the chromosome ideograms were built. Pericentrometric and telomeric C-positive bands in chromosomes of the Moscow form karyotype were found to be smaller and intercalary bands, larger than the corresponding bands in the M. cordata form grown in Donetsk. It was found that the content of C-HCH in prophase nucleoli in the form of M. cordata grown in Donetsk was higher than in the form grown in Moscow. In both forms sites of 26S rDNA and 5s rDNA were localized on satellite chromosome 1 and on chromosome 4 respectively but the signals were more intensive in the plant form grown in Donetsk. The results of this study enable selecting M. cordata forms for use in pharmacology and recommending them for cultivation in various ecological and geographical regions.     

A survey of genome‐wide single nucleotide polymorphisms through genome resequencing in the Périgord black truffle (Tuber melanosporum Vittad.)

The Périgord black truffle (Tuber melanosporum Vittad.), considered a gastronomic delicacy worldwide, is an ectomycorrhizal filamentous fungus that is ecologically important in Mediterranean French, Italian and Spanish woodlands. In this study, we developed a novel resource of single nucleotide polymorphisms (SNPs) for T. melanosporum using Illumina high‐throughput resequencing. The genome from six T. melanosporum geographical accessions was sequenced to a depth of approximately 20×. These geographical accessions were selected from different populations within the northern and southern regions of the geographical species distribution. Approximately 80% of the reads for each of the six resequenced geographical accessions mapped against the reference T. melanosporum genome assembly, estimating the core genome size of this organism to be approximately 110 Mbp. A total of 442 326 SNPs corresponding to 3540 SNPs/Mbps were identified as being included in all seven genomes. The SNPs occurred more frequently in repeated sequences (85%), although 4501 SNPs were also identified in the coding regions of 2587 genes. Using the ratio of nonsynonymous mutations per nonsynonymous site (pN) to synonymous mutations per synonymous site (pS) and Tajima's D index scanning the whole genome, we were able to identify genomic regions and genes potentially subjected to positive or purifying selection. The SNPs identified represent a valuable resource for future population genetics and genomics studies.     

Genome‐wide assessment of tandem repeat markers for biogeographical analyses of the corn smut fungus,Ustilago maydis

It has been postulated that the fungus Ustilago maydis followed its host maize around the world. In order to understand the biogeography of this fungus relative to its host, we used a bioinformatics approach to develop 86 tandem repeat markers useful for population studies of U. maydis. We characterized repeat motifs between two and 155 nucleotides using 36 isolates from USA, Mexico and South America. Our data suggested that (i) repeat motif length does not predict the number of alleles for that locus, and (ii) that the more polymorphic markers can resolve differences in a small geographical area.     

基于MaxEnt模型评估刺五加在东北地区的空间分布

研究刺五加(Acanthopanax senticosus)在东北地区的潜在分布区及生态适宜性,针对267个刺五加分布样点数据和17个环境因子数据,应用最大熵模型(Maximum Entropy Model,简称MaxEnt)和地理信息系统(Geographic Information System,GIS)评估刺五加的地理分布。结果表明:最大熵模型的AUC值为0.929,模型预测结果的准确性可信度高,可以用来预测刺五加的地理分布。刺五加生态适宜区主要集中在长白山山脉及小兴安岭东南地区,分布面积约为22.12万km~2,存在概率最高的区域主要在辽宁省东部、吉林省东南部以及黑龙江省中部。影响刺五加地理分布的主要环境因子依次为:年均降水量、森林类型、极端低温、生长季降水量及海拔。耦合了大尺度环境数据、植被群落类型数据与刺五加分布之间的关系,预测了东北地区刺五加的生态适宜区及主导环境因子,为其种群恢复与开发利用提供了科学依据。