Mitochondrial DNA variation in natural populations of the mushroom Agaricus bisporus

We investigated the patterns of mitochondrial DNA variation in the global population of the commercial mushroom Agaricus bisporus . Through the analysis of RFLP's among 441 isolates from nine countries in North America and Eurasia, we found a total of 140 mtDNA haplotypes. Based on population genetic analysis, there are four genetically distinct natural populations in this species, found in coastal California, desert California, France and Alberta (Canada). While 134 of the 140 mtDNA haplotypes were unique to single geographical regions, two mtDNA haplotypes, mt001 and mt002, were found in almost every population surveyed. These two mtDNA haplotypes also predominate among cultivars used throughout the world for at least the last two decades. These two mtDNA haplotypes are more similar to the cosmopolitan groups of mtDNA haplotypes than to the indigeneous clusters of mtDNA haplotypes from the two Californian regions.     

Consequences of a catadromous life-strategy for levels of mitochondrial DNA differentiation among populations of the Australian bass, Macquaria novemaculeata

The influence of a catadromous life-strategy on levels of spatial genetic structuring in fish is poorly understood. In an effort to gain a better appreciation of how this specialized life-strategy determines population genetic structuring, we assessed variation in the mitochondrial DNA (mtDNA) control region in a catadromous perciform, the Australian bass Macquaria novemaculeata . Nineteen putative haplotypes were resolved using temperature gradient gel electrophoresis from 10 geographically distinct populations. Significant heterogeneity was revealed in haplotype frequencies and their spatial distributions among many locales. Gene partitioning statistics ( AMOVA ) for both raw haplotype frequency data and frequency data with sequence divergences were concordant, indicating that M. novemaculeata populations were moderately genetically structured (Φ_ST = 0.05, 0.06; P < 0.001, respectively). Isolation by distance seems to be a strong structuring force in M. novemaculeata , culminating in no detectable phylogeographic structuring among haplotypes. Low sequence divergences were observed among many haplotypes and it is suggested that these are the result of pruning of maternal lineages by cyclical variations in female reproductive success. This study highlights the importance of life-history patterns and, in particular, spawning locality, in determining spatial structuring of mtDNA variation in catadromous species.     

Phylogeography and connectivity of molluscan parasites: Perkinsus spp. in Panama and beyond

Panama is a major hub for commercial shipping between two oceans, making it an ideal location to examine parasite biogeography, potential invasions, and the spread of infectious agents. Our goals were to (i) characterise the diversity and genetic connectivity of Perkinsus spp. haplotypes across the Panamanian Isthmus and (ii) combine these data with sequences from around the world to evaluate the current phylogeography and genetic connectivity of these widespread molluscan parasites. We collected 752 bivalves from 12 locations along the coast of Panama including locations around the Bocas del Toro archipelago and the Caribbean and Pacific entrances to the Panama Canal, from December 2012 to February 2013. We used molecular genetic methods to screen for Perkinsus spp. and obtained internal transcribed spacer region (ITS) ribosomal DNA (rDNA) sequences for all positive samples. Our sequence data were used to evaluate regional haplotype diversity and distribution across both coasts of Panama, and were then combined with publicly available sequences to create global haplotype networks. We found 26 ITS haplotypes from four Perkinsus spp. (1–12 haplotypes per species) in Panama. Perkinsus beihaiensis haplotypes had the highest genetic diversity, were the most regionally widespread, and were associated with the greatest number of hosts. On a global scale, network analyses demonstrated that some haplotypes found in Panama were cosmopolitan (Perkinsus chesapeaki, Perkinsus marinus), while others were more geographically restricted (Perkinsus olseni, P. beihaiensis), indicating different levels of genetic connectivity and dispersal. We found some Perkinsus haplotypes were shared across the Isthmus of Panama and several regions around the world, including across ocean basins. We also found that haplotype diversity is currently underestimated and directly related to the number of sequences. Nevertheless, our results demonstrate long-range dispersal and global connectivity for many haplotypes, suggesting that dispersal through shipping probably contributes to these biogeographical patterns.     

mtDNA affinities of the peoples of North-Central Mexico

mtDNA haplotypes of representatives of the cosmopolitan peoples of north-central Mexico were studied. Two hundred twenty-three samples from individuals residing in vicinities of two localities in north-central Mexico were analyzed. A combination of strategies was employed to identify the origin of each haplotype, including length variation analysis of the COII and tRNALYS intergenic region, nucleotide sequence analysis of control region hypervariable segment 1, and RFLP analysis of PCR products spanning diagnostic sites. Analysis of these data revealed that the majority of the mtDNA haplotypes were of Native American origin, belonging to one of four primary Native American haplogroups. Others were of European or African origin, and the frequency of African haplotypes was equivalent to that of haplotypes of European derivation. These results provide diagnostic, discrete character, molecular genetic evidence that, together with results of previous studies of classical genetic systems, is informative with regard to both the magnitude of African admixture and the relative maternal contribution of African, European, and Native American peoples to the genetic heritage of Mexico. Phylogenetic analysis revealed that African sequences formed a basal, paraphyletic group.     

Genetic structure of the star sea squirt, Botryllus schlosseri, introduced in southern European harbours

The introduction of new genetic variants or species is often caused by maritime transport between harbours. Botryllus schlosseri is a cosmopolitan ascidian species that is found in both harbours and open shore habitats. In order to determine the influence of ship traffic on the genetic structure and phylogeography of B. schlosseri in southern Europe, we analyzed the variability of a fragment of the mitochondrial gene cytochrome c oxidase subunit I (COI). We sampled seven Atlanto-Mediterranean harbour populations and three open-shore populations. In addition, we sequenced some colonies from the US-Atlantic coast and from other Mediterranean localities to perform phylogenetic analyses. Although the number of polymorphic sites recorded (25.8%) was within the range observed in other population studies based on ascidian COI sequences, the haplotypic diversity (16 haplotypes out of 181 sequences) was much lower. Moreover, a lack of intermediate haplotypes was observed. This pattern of high nucleotide diversity and low haplotype diversity was consistent with introduction events of a few divergent haplotypes. We found a strong genetic structure in the study populations. Gene flow was only appreciable between some harbour populations. Harbour- and open-shore populations were well differentiated, although there was no evidence for isolation by distance. A nested clade analysis pointed to long-distance colonization, possibly coupled with subsequent fragmentation, as the underlying process. Our results suggest that B. schlosseri entered the study area via harbour-hopping, possibly through recurrent introduction events. The haplotypes from North America and most of the European ones were grouped in the same phylogenetic clade. This suggests occasional gene flow between both continents, probably through ship transport.     

Complete mitochondrial DNA sequences of two haplotypes of the smallmouth bass, <Emphasis Type="Italic">Micropterus dolomieu</Emphasis>, collected from nonindigenous populations in Japan

We determined the complete mitochondrial genome sequences of two haplotypes of the smallmouth bass, Micropterus dolomieu; individuals used in the analysis were collected from nonindigenous populations in Japan. Both genomes comprised 16,488 bp, with genome contents and gene orders being identical to those of other teleost fishes. A previous study revealed that the Japanese smallmouth bass had only two haplotypes, and the present study revealed that the complete mitochondrial DNA (mtDNA) sequences of the haplotypes differed in only one nucleotide difference. The low genetic diversity in the mtDNA of the smallmouth bass individuals in our study and the results of the mtDNA sequence comparison between the Japanese and the North American individuals suggested that the fish had been transplanted from a fish farm with a low-diversity stock.     

A genetic analysis of the Italian Salernitano horse

Salernitano (SAL) is an ancient Italian horse breed developed over the course of the ages together with Napoletano and, during the 20th century, by crossing with Thoroughbred horse lines. Excellent in hurdle jumping, this breed is currently facing a concrete risk of extinction due to the lack of appropriate management strategies. This research is the first SAL genetic characterization that aims to set up the basic knowledge for a conservation plan. A representative sample of 61 SALs was analyzed by means of a set of 16 microsatellites markers (short tandem repeats (STRs)). The sequence of hypervariable D-loop mtDNA region was also performed on a subset of 24 mares in order to study the maternal diversity and obtain a complete picture of the internal genetic variation. All the molecular data were analyzed together with those obtained from three Sicilian horse breeds investigated in a previous research (Siciliano, Sanfratellano and Sicilian Oriental Purebred). STRs markers revealed a moderate level of genetic diversity in SAL (alleles/locus 5.1, He 0.67) and confirmed the hunch of genetic erosion. Autosomal variability highlighted a very light deficit of homozygotes (FIS=−0.067). Experimental D-loop sequences were compared by multiple alignments with those retrieved from biological databases and revealed two unreported haplotypes. The phylogenetic network, which was built on mtDNA sequences, included various cosmopolitan and European horses and showed SAL haplotypes distributed among different mtDNA lineages.     

Single-nucleotide polymorphisms and haplotype analysis in beta-defensin genes in different ethnic populations

Beta-defensins are cationic antimicrobial peptides expressed by epithelial cells and exhibit antibacterial, antifungal, and antiviral properties. The defensins are part of the innate host defense network and may have a significant protective role in the oral cavity and other mucosa. Defects or alteration in expression of the beta-defensins may be associated with susceptibility to infection and mucosal disorders. We examined the occurrence of single-nucleotide polymorphisms (SNPs) in the human beta-defensin genes DEFB1 and DEFB2 encoding human beta-defensin-1 and -2 (hBD-1, hBD-2), respectively, in five ethnic populations and defined haplotypes in these populations. Fifteen SNPs were identified in both DEFB1 and DEFB2. Coding region SNPs were found in very low frequency in both genes. One nonsynonymous DEFB1 SNP, G1654A (Val --> Ile), and one nonsynonymous DEFB2 SNP, T2312A (Leu --> His), were identified. Seven sites in each gene exhibited statistically significant differences in frequency between ethnic groups, with the greatest variation in the promoter and in the 5'-untranslated region of DEFB1. DEFB1 displayed 10 common haplotypes, including one cosmopolitan haplotype. Eight common haplotypes were found in DEFB2, including one cosmopolitan haplotype shared among all five ethnic groups. Our results show that genotypic variability among ethnic groups will need to be addressed when performing associative genetic studies of innate defense mechanisms and susceptibility to disease.     

Positive relationships between genetic diversity and abundance in fishes

Molecular markers, such as mitochondrial DNA and microsatellite loci, are widely studied to assess population genetics and phylogeography; however, the selective neutrality of these markers is increasingly being questioned. Given the importance of molecular markers in fisheries science and conservation, we evaluated the neutrality of both mtDNA and microsatellite loci through their associations with population size. We surveyed mtDNA and microsatellite data from the primary literature and determined whether genetic diversity increased with abundance across a total of 105 marine and freshwater fishes, with both global fisheries catch data and body size as proxies for abundance (with an additional 57 species for which only body size data were assessed). We found that microsatellite data generally yielded higher associations with abundance than mtDNA data, and within mtDNA analyses, number of haplotypes and haplotype diversity were more strongly associated with abundance than nucleotide diversity, particularly for freshwater fishes. We compared genetic diversity between freshwater and marine fishes and found that marine fishes had higher values of all measures of genetic diversity than freshwater fishes. Results for both mtDNA and microsatellites generally conformed to neutral expectations, although weaker relationships were often found between mtDNA nucleotide diversity and ‘abundance’ compared to any other genetic statistic. We speculate that this is because of historical events unrelated to natural selection, although a role for selection cannot be ruled out.     

Revealing the non-overlapping characteristics between original centers and genetic diversity of Purpureocillium lilacinum

Purpureocillium lilacinum is a free-living, multitrophic, cosmopolitan fungus. This study estimated the genetic diversity of P. lilacinum and its geographic distribution pattern based on a global ITS dataset. At the intercontinental levels, the highest genetic diversity was in Asia. Divergence time estimation indicated that Hap 5, Hap 9, Hap 31, and Hap 32 from the Hainan, Guangdong, Jiangxi, and Fujian regions of China in Asia were the earliest divergence haplotypes. The neutrality test indicated that P. lilacinum is undergoing population expansion. These results support that the southeastern coastal region of China is the original center of P. lilacinum, while the East Asian region adjacent to this origin is the center of the genetic diversity of P. lilacinum. The geographical distribution pattern of P. lilacinum showed that only one haplotype (Hap 1) was globally distributed and that most haplotypes were distributed in Asia, while the few remaining haplotypes were scattered on other continents. The results provide valuable information to elucidate the origin, genetic diversity, and evolution of fungi.     

Genetic variation and recent population history of the tropical gar Atractosteus tropicus Gill (Pisces: Lepisosteidae)

The tropical gar Atractosteus tropicus belongs to one of the few extant lineages of early bony fishes. The genetic variation detected both within and among 11 natural populations of A. tropicus in Mesoamerica along with the implications for their recent history are presented. Sequences from cytochrome b (307 bp) and cytochrome oxidase subunit II (607 bp) were used as data sources. Apparently, the populations of this fish have decreased in size because of anthropogenic pressures, such as habitat degradation and destruction. The observed values for nucleotide diversity (0·0016 ± 0·0018) and haplotype diversity (0·477 ± 0·302) suggest low levels of genetic variation. Nonetheless, most of the populations studied are currently in a period of genetic stasis. Recent isolation by distance, reduced gene flow and translocation were inferred as the processes maintaining this stasis. Phylogenetic analyses showed reciprocal monophyly between the haplotypes from Guatemala and the other populations. This, together with the observed genetic variation, suggests that the Guatemalan haplotypes might represent a new species. The haplotypes, other than those from Guatemala, exhibited a geographic pattern consistent with two main reproductive populations, one from the Pacific and the other from the Gulf of Mexico–Caribbean slope of Mesoamerica. Pleistocene glacial and interglacial periods might be responsible for moulding the heterogeneity in the genetic structure observed during this study.     

The phylogeography of the Placozoa suggests a taxon‐rich phylum in tropical and subtropical waters

Placozoa has been a key phylum for understanding early metazoan evolution. Yet this phylum is officially monotypic and with respect to its general biology and ecology has remained widely unknown. Worldwide sampling and sequencing of the mitochondrial large ribosomal subunit (16S) reveals a cosmopolitan distribution in tropical and subtropical waters of genetically different clades. We sampled a total of 39 tropical and subtropical locations worldwide and found 23 positive sites for placozoans. The number of genetically characterized sites was thereby increased from 15 to 37. The new sampling identified the first genotypes from two new oceanographic regions, the Eastern Atlantic and the Indian Ocean. We found seven out of 11 previously known haplotypes as well as five new haplotypes. One haplotype resembles a new genetic clade, increasing the number of clades from six to seven. Some of these clades seem to be cosmopolitan whereas others appear to be endemic. The phylogeography also shows that different clades occupy different ecological niches and identifies several euryoecious haplotypes with a cosmopolitic distribution as well as some stenoecious haplotypes with an endemic distribution. Haplotypes of different clades differ substantially in their phylogeographic distribution according to latitude. The genetic data also suggest deep phylogenetic branching patterns between clades.     

Development of cytochrome b primers for mitotyping of barbels (Barbus spp.)

Primers were developed that allow for rapid, reliable and inexpensive screening of cytochrome b by analysis of single-stranded conformational polymorphisms. Twenty different haplotypes were identified from six species of Iberian Barbus. These primers proved useful for population and species level studies, and could also be valuable in population genetic and phylogenetic studies of other cyprinin fishes.     

Population and colony genetic structure of the primitive termite Mastotermes darwiniensis

The termite Mastotermes darwiniensis is the sole extant member of its family and occupies the basal position in the phylogeny of the eusocial order Isoptera. In this study, we investigated the micro- and macrogeographic genetic structure of M. darwiniensis in its native range in Australia. A total of 1591 workers were sampled from 136 infested trees in 24 locales. Each locale was separated by 2-350 km, and these locales were found within two broader geographic regions approximately 1500 km apart. The multilocus genotypes of all termites were assayed at six polymorphic microsatellite loci. The genetic data indicated that colonies typically fed on multiple trees within locales and extended over linear distances of up to 320 m. Single colonies were frequently headed by multiple reproductives. Workers were highly related (r = 0.40) and substantially inbred (f = 0.10). Thus, M. darwiniensis colonies are characterized by the input of alleles from multiple reproductives, which sometimes engage in consanguineous matings. Our analyses of population genetic structure above the level of the colony indicated that locales and regions were significantly differentiated (theta(locale) = 0.50, theta(region) = 0.37). Moreover, locales showed a pattern of genetic isolation by distance within regions. Thus, M. darwiniensis populations display restricted gene flow over moderate geographic distances. We suggest that the genetic patterns displayed by M. darwiniensis result primarily from selective pressures acting to maintain high relatedness among colonymates while allowing colonies to grow rapidly and dominate local habitats.     

福建东张水库陆封型香鱼的遗传变异

测定了福建东张水库18尾陆封型香鱼的ND4-tRNA^Ser基因533 bp序列,发现2个可变位点和2个简约信息位点,共检测到4种单倍型。基于Kimura 2-parameter模型的遗传距离在0.001 9～0.003 9之间,在NJ系统树上无明显谱系结构;单倍型多样性(Hd)和核苷酸多样性(Pi)分别为0.627和0.001 37,平均核苷酸差异数为0.732,远低于两侧洄游型日本香鱼指名亚种(Hd为0.793,Pi为0.002 94),与被列为IUCN濒危物种名录的日本琉球香鱼亚种(Hd=0.519,Pi=0.001 11)相当。东张水库香鱼遗传多样性如此贫乏到底是历史原因还是近期陆封的结果,仍需进一步研究。目前亟待采取有效措施保护东张水库陆封香鱼。     

周公河齐口裂腹鱼种群的遗传多样性和遗传结构

为探讨周公河中齐口裂腹鱼(Schizothorax prenanti)的遗传多样性和遗传结构, 沿周公河连续设定6个采样点进行齐口裂腹鱼采集, 在进行基因组DNA提取后以线粒体控制区(D-loop)为分子标记进行种群遗传多样性和遗传结构的评估。结果从63尾齐口裂腹鱼中共检测到32个单倍型, 核苷酸多样性(π)为0.013, 单倍型多样性(h)为0.966。遗传多样性最高的为张家湾种群(PopF, π=0.018, h=1.000), 核苷酸多样性最低的为罗坝种群(PopC, π=0.010, h=0.970), 单倍型多样性最低的为瓦屋山大坝下游种群(PopB, π=0.015, h=0.867)。种群间共享13个单倍型, 多数齐口裂腹鱼种群间的遗传分化水平中等或较低, 仅Pop C和Pop F (F_st=0.195, P<0.01), 种群Pop A 和PopE (F_st=0.158, P<0.01)分化程度较高, 显示各种群间较密切的遗传关系。周公河不同河段齐口裂腹鱼群体的遗传多样性处于较高的水平, 各种群间具有较近的遗传关系。     

Comparative phylogeography of two bitterlings, Tanakia lanceolata and T. limbata (Teleostei, Cyprinidae), in Kyushu and adjacent districts of western Japan, based on mitochondrial DNA analysis

To understand the geographical patterns of genetic variation in freshwater fishes in western Japan, the genetic structures of populations of Tanakia lanceolata and T. limbata (Teleostei, Cyprinidae) in this area were investigated using mitochondrial DNA (mtDNA) cytb sequences. Neighbor-joining trees of mtDNA haplotypes revealed four and three genetically divergent groups in T. lanceolata and T. limbata, respectively. Each group was restricted to one or the other of the geographical regions in the area studied. The patterns of geographical divergence in the two species showed some similarities, which seem to reflect common historical events experienced by freshwater fishes distributed in western Japan. On the other hand, dissimilarities were also found in the patterns, indicating that species-specific historical processes also occurred. Within one region, T. lanceolata was less differentiated than T. limbata, suggesting a difference in the dispersal abilities of the two bitterlings. In addition, several individuals in Kunichika River on Shikoku island were morphologically identified as T. lanceolata but had mtDNA haplotypes of T. limbata. We tentatively suggest that these individuals are hybrids of the two species, but further studies employing nuclear markers are necessary to validate this hypothesis.     

The role of natural selection in genetic differentiation of worldwide populations of Drosophila ananassae

The main evolutionary forces leading to genetic differentiation between populations are generally considered to be natural selection, random genetic drift, and limited migration. However, little empirical evidence exists to help explain the extent, mechanism, and relative role of these forces. In this study, we make use of the differential migration behavior of genes located in regions of low and high recombination to infer the role and demographic distribution of natural selection in Drosophila ananassae. Sequence data were obtained from 13 populations, representing almost the entire range of cosmopolitan D. ananassae. The pattern of variation at a 5.1-kb fragment of the furrowed gene, located in a region of very low recombination, appears strikingly different from that of 10 noncoding DNA fragments (introns) in regions of normal to high recombination. Most interestingly, two main haplotypes are present at furrowed, one being fixed in northern populations and the other being fixed or in high frequency in more southern populations. A cline in the frequency of one of these haplotypes occurs in parallel latitudinal transects. Taken together, significant clinal variation and a test against alternative models of natural selection provide evidence of two independent selective sweeps restricted to specific regions of the species range.     

Genetic structuring and migration patterns of Atlantic bigeye tuna, <Emphasis Type="Italic">Thunnus obesus</Emphasis>(Lowe, 1839)

Background  

Large pelagic fishes are generally thought to have little population genetic structuring based on their cosmopolitan distribution, large population sizes and high dispersal capacities. However, gene flow can be influenced by ecological (e.g. homing behaviour) and physical (e.g. present-day ocean currents, past changes in sea temperature and levels) factors. In this regard, Atlantic bigeye tuna shows an interesting genetic structuring pattern with two highly divergent mitochondrial clades (Clades I and II), which are assumed to have been originated during the last Pleistocene glacial maxima. We assess genetic structure patterns of Atlantic bigeye tuna at the nuclear level, and compare them with mitochondrial evidence.     

Phylogeography of the cosmopolitan marine parasite Kudoa thyrsites (Myxozoa: Myxosporea)

Kudoa thyrsites (Myxozoa: Multivalvulida) is a cosmopolitan marine parasite of fishes associated with post-mortem tissue degradation. Financial losses incurred as a result of these infections are of concern to commercial fisheries. There is conflicting evidence whether K. thyrsites represents a cryptic species complex. Myxospore morphology is very similar for K. thyrsites across its range, but preliminary genetic analyses show some differences. Kudoa thyrsites and the morphologically similar Kudoa histolytica were examined from hosts in British Columbia, Canada, Oregon, USA, Chile, England, South Africa, Australia, and Japan. We compared myxospore morphology and DNA sequences of heat shock protein 70 and the small subunit, large subunit, and internal transcribed spacer 1 of the ribosomal DNA. There was some morphological variation between regional representatives, inconsistent with genetic analyses. Phylogenetically, major separations correlated to four broad geographic regions: Japan, Australia, eastern Pacific, and eastern Atlantic. Within these regions there was little additional genetic structure. These data are evidence for regional subdivision of K. thyrsites suggesting global transplantation of fishes has yet to homogenize these distinctions. Within regions, parasite gene flow appears to be high between host species, suggesting little host specificity and minimal cryptic speciation. Our data also indicate that K. histolytica is not a valid species, as it was morphologically and genetically indistinguishable from K. thyrsites.