Prevalence of Sarcocystis sp. in stranded Atlantic white-sided dolphins (Lagenorhynchus acutus)

In January 1998 and 1999, two mass strandings of dolphins occurred in Wellfleet, Massachusetts. The strandings were composed of 97 and 53 animals, respectively. Tissues from 35 Atlantic white-sided dolphins (Lagenorhynchus acutus) from the 1998 stranding and 52 from the 1999 stranding were examined histologically. In the 1998 stranding, unidentified protozoal tissue cysts were seen in skeletal muscle from 11 of 28 (39%) dolphins. In addition, two dolphins had a protozoal tissue cyst in cardiac muscle. In the 1999 stranding, nine of 23 (39%) dolphins had the same protozoal tissue cysts in skeletal muscle. The identification of these protozoal tissue cysts as Sarcocystis sp. was confirmed by light and transmission electron microscopy. The high prevalence of sarcocysts in these dolphins suggests that they are likely intermediate hosts for previously undescribed Sarcocystis spp. The ultrastructure of the sarcocyst walls suggests that more than one species of Sarcocystis are present in dolphins.     

A mass stranding of white-sided dolphins (Lagenorhynchus acutus) in Ireland: biological and pathological studies

We give details of the biological and pathological findings in a mass stranding of 19 white-sided dolphins on the west coast of Ireland. The pod consisted of adults and calves; no juveniles were present. The calf of a recently parturient female was not found. The presence of small foetuses suggested that mating took place in late August or early September. The largest and oldest male was severely diseased but the remainder of the pod were in good health although some minor lesions were found. The site where the animals came ashore was compatible with the geomagnetic theory of mass strandings.     

Phylogeography and population dynamics of the white-sided dolphin (Lagenorhynchus acutus) in the North Atlantic

Highly mobile species in the marine environment may be expected to show little differentiation at the population level, but this is often not the case. Instead cryptic population structure is common, and effective conservation will require an understanding of how these patterns evolve. Here we present an assessment from both sides of the North Atlantic of differentiation among populations of a dolphin species that inhabits mainly pelagic waters, the Atlantic white-sided dolphin. We compare eleven putative populations in the western and eastern North Atlantic at mtDNA and microsatellite DNA loci and find reduced nucleotide diversity and signals for historical bottlenecks and post-bottleneck expansions in all regions. We calculate expansion times to have occurred during the early Holocene, following the last glacial maximum (LGM). We find evidence for connectivity among populations from either side of the North Atlantic, and differentiation between putative populations in the far northeast compared with all other areas sampled. Some data suggest the possibility of separate refugia during the LGM explaining this pattern, although ongoing ecological processes may also be a factor. We discuss the implications for developing effective programs of conservation and management in the context of ongoing anthropogenic impact.     

Microbiological characterization of three Atlantic whiteside dolphins (Lagenorhynchus acutus) from stranding through captivity with subsequent rehabilitation and release of one animal

Three live Atlantic whiteside dolphins (Lagenorhynchus acutus) were found beach-stranded on Cape Cod in Massachusetts and were shipped to Mystic Marinelife Aquarium in Connecticut and held in captivity. Swab samples were collected routinely from the anus and blowhole of live animals and from internal organs at necropsy for microbial culture. Despite antibiotic therapy, one animal died on day 9 of captivity, and one died after 110 days. The survivor was released after 126 days of captivity. Klebsiella pneumoniae septicemia and staphylococcal pneumonia were likely responsible for the two deaths. A total of 26 different organisms (or groups of organisms) were recovered from the three dolphins, including several (e.g., Pseudomonas spp, Streptococcus faecalis Candida albicans, Proteus-Morganella spp, Vibrio spp) that, in addition to the above organisms, could be potentially pathogenic for debilitated animals. Newly rescued marine mammals should be segregated from healthy animals if possible.     

Intraspecific variation in the dolphins Lagenorhynchus albirostris and L. acutus (Mammalia: Cetacea) in metrical and non-metrical skull characters, with remarks on occurrence

Intraspecific multivariate data analyses of 27 metrical and 20 non-metrical characters were performed on skulls of L. albirostris (Gray, 1846) and L. acutus (Gray, 1826) to distinguish between possible populations from the eastern and the western North Atlantic.
The results from principal component (PC) analysis and partial least square (PLS) analysis suggest that the skulls of L. albirostris were taken from separate populations, whereas those of L. acutus were not.
A difference in the occurrence-patterns of the two species was found, indicating that the degree of intraspecific variation may be linked to the water-depth related distribution.     

Origin and genetic diversity of Spartina anglica (Poaceae) using nuclear DNA markers

Spartina alterniflora, introduced into the UK in the 1800s, was the seed parent in an interspecific hybridization with S. maritima. The sterile F1 hybrid S. ×townsendii gave rise to the fertile allopolyploid S. anglica by chromosomal doubling. Previous chromosome, isozyme, and cpDNA surveys did not reveal notable genetic variation within either the parental or the hybrid species. We used nuclear DNA markers (random amplified polymorphic DNA ([RAPD]) and inter-simple sequence repeats (ISSR) to further explore the origin, diversity, and parentage of S. anglica. We found DNA fragments in S. ×townsendii were the aggregate of diagnostic DNA fragments from S. maritima and S. alterniflora, thus confirming its hybrid origin. The S. ×townsendii genotype was identical to most of the S. anglica individuals analyzed, establishing the genetic concordance of these two taxa. We found widespread genetic variation within S. anglica. This could indicate that S. anglica arose several times, from different S. maritima sires. Alternatively, alleles could have been lost through recombination and/or through loss of entire chromosomes in S. anglica. Finally, all but one S. anglica individual had a S. alterniflora component that was indistinguishable from a S. alterniflora plant extant in Marchwood, UK, leaving open the possibility that this plant is the actual seed parent of S. anglica.     

Phylogeny of Cidaroida (Echinodermata: Echinoidea) based on mitochondrial and nuclear markers

We present the first molecular phylogeny of Cidaroida, one of the most problematic groups within the echinoids. Two genes??the nuclear ribosomal gene 28?S rRNA and the mitochondrial protein-encoding gene COI??were obtained from 21 specimens representing 17 genera and 20 species, among which 13 species belong to Cidaroida. Phylogenetic analyses of the combined molecular data using parsimony and maximum likelihood optimality criteria resulted in a well-resolved phylogeny. Our results are broadly compatible (with the notable exception of Cidaris cidaris) with previous results obtained from morphological data. We find that Cidaroida represent a monophyletic group sister to the non-cidaroid Echinoidea. The family Cidaridae sensu Mortensen (1928) and Fell (1966) is paraphyletic because of the placement of Psychocidaris ohshimai as sister-group to Histocidaris elegans. Inside the Stylocidarina, we show that the two Atlantic species Stylocidaris affinis and Stylocidaris lineata constitute a well-supported clade. However, these two taxa could also represent two morphotypes within a single species showing high morphological variation.     

Phylogenetic relationships within the Phyllopoda (Crustacea,Branchiopoda) based on mitochondrial and nuclear markers

For several decades the relationships within the Branchiopoda (Anostraca + Phyllopoda) have been a matter of controversy. Interpretations of plesiomorphic or apomorphic character states are a difficult venture, in particular in the Phyllopoda. We explore the relationships within the Phyllopoda at the level of nucleotid comparisons of the two genes 12S rDNA (mitochondrial) and EF1alpha (nuclear), and at a higher molecular level based on introns found in the gene EF1alpha. Within the Phyllopoda our explorations show further evidence for a non-monophyletic Conchostraca (Spinicaudata + Cyclestherida + Laevicaudata). The monotypic Cyclestherida is more closely related to the Cladocera, both together forming the Cladoceromorpha. The Spinicaudata (Leptestheriidae, Limnadiidae, and Cyzicidae) is well supported. Spinicaudata and Cladoceromorpha form a monophylum. The position of the Laevicaudata remains unclear but we find neither support for a sister group relationship to the Spinicaudata nor for a close relationship of Laevicaudata and Cladocera. Within the Cladocera, we favour the Gymnomera concept with the monotypic Haplopoda being the sister group to the monophyletic Onychopoda. The Ctenopoda seems to be the sister group to the Gymnomera, which contradicts the common view of a more basal position of the Ctenopoda.     

Investigation of the genetic diversity of an invasive whitefly (Bemisia tabaci) in China using both mitochondrial and nuclear DNA markers

It is often considered that reduced genetic variation due to bottlenecks and founder effects limits the capacity for species to establish in new environments and subsequently spread. The recent invasion (during the past five years) of an alien whitefly, one member of Bemisia tabaci cryptic species complex, referred to as Mediterranean (herein referred to as Q-type) in Shandong Province, China, provides an ideal opportunity to study the changes in genetic variation between its home range in the Mediterranean region and its invasion range. Using both the mitochondrial cytochrome oxidase I (mtCOI) and nuclear (microsatellite) DNA, we show that Q in Shandong likely originated in the western Mediterranean. We also found that the haplotype diversity was low compared with its presumed geographic origin, whereas microsatellite allele diversity showed no such decline. A key factor in invasions is the establishment of females and so bottleneck and founder events can lead to a very rapid and considerable loss of mitochondrial diversity. The lack of haplotype diversity in Shandong supports the interpretation that, at one or more points between the western Mediterranean and China, the invading Q lost haplotype diversity, most probably through the serial process of establishment and redistribution through trade in ornamental plants. However, the loss in haplotype diversity does not necessarily mean that nuclear allelic diversity should also decline. Provided females can mate freely with whichever males are available, allelic diversity can be maintained or even increased relative to the origin of the invader. Our findings may offer some explanation to the apparent paradox between the concept of reduced genetic variation limiting adaptation to new environments and the observed low diversity in successful invaders.     

Insights into the mating habits of the tiger salamander (Ambystoma tigrinum tigrinum) as revealed by genetic parentage analyses

Among urodeles, ambystomatid salamanders are particularly amenable to genetic parentage analyses because they are explosive aggregate breeders that typically have large progeny arrays. Such analyses can lead to direct inferences about otherwise cryptic aspects of salamander natural history, including the rate of multiple mating, individual reproductive success, and the spatial distribution of clutches. In 2002, we collected eastern tiger salamander (Ambystoma tigrinum tigrinum) egg masses (> 1000 embryos) from a approximately 80 m linear transect in Indiana, USA. Embryos were genotyped at four variable microsatellite loci and the resulting progeny array data were used to reconstruct multilocus genotypes of the parental dams and sires for each egg mass. UPGMA analysis of genetic distances among embryos resolved four instances of egg mass admixture, where two or more females had oviposited at exactly the same site resulting in the mixing of independent cohorts. In total, 41 discrete egg masses were available for parentage analyses. Twenty-three egg masses (56%) consisted exclusively of full-siblings (i.e. were singly sired) and 18 (44%) were multiply sired (mean 2.6 males/clutch). Parentage could be genetically assigned to one of 17 distinct parent pairs involving at least 15 females and 14 different males. Reproductive skew was evident among males who sired multiply sired clutches. Additional evidence of the effects of sexual selection on male reproductive success was apparent via significant positive correlations between male mating and reproductive success. Females frequently partitioned their clutches into multiple discrete egg masses that were separated from one another by as many as 43 m. Collectively, these data provide the first direct evidence for polygynandry in a wild population of tiger salamanders.     

Preliminary study of the genetic diversity of eastern Assamese macaques (Macaca assamensis assamensis) in Thailand based on mitochondrial DNA and microsatellite markers

Human overpopulation, deforestation, invasion of agricultural areas, and livestock are the primary causes for population fragmentation of wildlife. The distribution range of species of the genus Macaca is constantly decreasing and becoming increasingly fragmented due to forest deterioration. Assamese macaques (M. assamensis) are classified as near threatened in the International Union for Conservation of Nature (IUCN) Red List of Threatened Animals (2008) and have been declared a protected wildlife animal according to Wildlife Preservation and Protection Act, B.E.2535 (1992) of Thailand. As studies of the population history and genetic diversity of Assamese macaques in Thailand are currently lacking, we aimed at a first investigation of their genetic diversity based on mitochondrial DNA [hypervariable regions 1 and 2 (HV1, HV2) and cytochrome B (CYTB) regions], as well as 15 microsatellite markers of five sampling sites distributed across Thailand. Our results indicate that Assamese macaques in Thailand are diverse, with eight maternal haplotypes and a low inbreeding coefficient in the Phu Khieo Wildlife Sanctuary (PKWS) population. Moreover, our phylogenetic and median-joining network analysis based on mitochondrial (mt)DNA suggests a population distribution in accordance with the evolutionary scenario proposed for M. sinica. Today, the population of Assamese macaques is fragmented, and conservation strategies are needed to ensure the maintenance of genetic diversity of this primate species.     

Molecular phylogeny of the tribe Sphodrini (Coleoptera: Carabidae) based on mitochondrial and nuclear markers

A phylogenetic analysis of 6.4 kb of nucleotide sequence data from seven genes (mitochondrial cox1-cox2 and tRNA(leu), and nuclear Ef-1alpha C0, Ef-1alpha C1, 28S, and 18S) was done to reconstruct the phylogenetic relationships of the ground-beetle tribe Sphodrini. Gene regions of variable nucleotide length were aligned using both a secondary structure model, Clustal W, and a combination of the two. Sensitivity analysis was performed in order to explore the effect of alignment methods. The ribosomal and protein-coding genes were largely congruent based on the ILD test and partitioned Bremer support measures. MtDNA analysis provided high resolution and high support for most clades. The tribe Sphodrini and the related tribes Platynini, Pterostichini and Zabrini made up monophyletic clades, but the relationship between them was weakly resolved and sensitive to alignment strategy. Previously suggested relationships between subtribes of Sphodrini were not corroborated, and only the subtribe Atranopsina revealed high support as the sister clade to the other subtribes. The analyses clearly demonstrated the importance of exploring effects of alignment methods that may become particularly important in resolving polytomies and nodes with low support.     

Uncovering cryptic diversity in Aspidomorphus (Serpentes: Elapidae): Evidence from mitochondrial and nuclear markers

The Papuan region, comprising New Guinea and nearby islands, has a complex geological history that has fostered high levels of biodiversity and endemism. Unfortunately, much of this diversity remains undocumented. We examine the evolutionary relationships of the venomous snake genus Aspidomorphus (Elapidae: Hydrophiinae), a Papuan endemic, and document extensive cryptic lineage diversification. Between Aspidomorphus species we find 22.2–27.9% corrected cyt-b sequence divergence. Within species we find 17.7–23.7% maximum sequence divergence. These high levels of genetic divergence may have complicated previous phylogenetic studies, which have had difficulty placing Aspidomorphus within the subfamily Hydrophiinae. Compared to previous studies, we increase sampling within Hydrophiinae to include all currently recognized species of Aspidomorphus and increase species representation for the genera Demansia and Toxicocalamus. We confirm monophyly of Aspidomorphus and resolve placement of the genus utilizing a set of seven molecular markers (12S, 16S, cyt-b, ND4, c-mos, MyHC-2, and RAG-1); we find strong support for a sister-group relationship between Aspidomorphus and a Demansia/Toxicocalamus preussi clade. We also use one mitochondrial (cyt-b) and one nuclear marker (SPTBN1) to document deep genetic divergence within all currently recognized species of Aspidomorphus and discuss the Solomon Island Arc as a potential center of divergence in this species. Lastly, we find high levels of concordance between the mtDNA and nuDNA markers used for inter-species phylogenetic reconstruction.     

The first genetic map of pigeon pea based on diversity arrays technology (DArT) markers

With an objective to develop a genetic map in pigeon pea (Cajanus spp.), a total of 554 diversity arrays technology (DArT) markers showed polymorphism in a pigeon pea F₂ mapping population of 72 progenies derived from an interspecific cross of ICP 28 (Cajanus cajan) and ICPW 94 (Cajanus scarabaeoides). Approximately 13% of markers did not conform to expected segregation ratio. The total number of DArT marker loci segregating in Mendelian manner was 405 with 73.1% (P > 0.001) of DArT markers having unique segregation patterns. Two groups of genetic maps were generated using DArT markers. While the maternal genetic linkage map had 122 unique DArT maternal marker loci, the paternal genetic linkage map has a total of 172 unique DArT paternal marker loci. The length of these two maps covered 270.0 cM and 451.6 cM, respectively. These are the first genetic linkage maps developed for pigeon pea, and this is the first report of genetic mapping in any grain legume using diversity arrays technology.     

Association analysis,genetic diversity and structure analysis of tobacco based on AFLP markers

Knowledge in the area of genetic diversity could aid in providing useful information in the selection of material for breeding such as hybridization programs and quantitative trait loci mapping. To this end, 50 Nicotiana tabacum genotypes were genotyped with 21 primer combination of amplified fragment length polymorphism (AFLP). A total of 480 unambiguous DNA fragments and 373 polymorphic bands were produced with an average of 17.76 per primer combination. Also, the results revealed high polymorphic rate varing from 52.63 to 92.59 %, demonstrating that AFLP technique utilized in this research can be a powerful and valuable tool in the breeding program of N. tabacum. Cluster analysis based on complete linkage method using Jaccard’s genetic distance, grouped the 50 tobacco genotypes into eight clusters including three relatively big clusters, one cluster including Golden gift, Burly 7022 and Burly Kreuzung, one cluster consisting of two individuals (Pereg234, R9) and three single-member clusters (Pennbel69, Coker176 and Budisher Burley E), Recent genotypes showed high genetic distance from other genotypes belonging to cluster I and II. Association analysis between seven important traits and AFLP markers were performed using four statistical models. The results revealed the model containing both the factors, population structure (Q) and general similarity in genetic background arising from shared kinship (K), reduces false positive associations between markers and phenotype. According to the results nine markers were determined that could be considered to be the most interesting candidates for further studies.     

基于线粒体DNA的中国亚洲象种群遗传多样性及种群遗传结构

亚洲象是我国国家一级保护动物.本文利用非损伤性取样法,以亚洲象粪便中脱落的肠道上皮细胞为DNA来源,选用线粒体DNA作为分子标记,对分布于我国境内的亚洲象种群的遗传结构和种群遗传多样性进行研究.本研究得到mtDNA序列片段长度为556 bp,经对178个个体进行扩增结果分析,共得到24个单倍型.在5个地理种群中,除南滚河种群外,其他4个种群中的114个个体共享同一单倍型,南滚河种群与其他种群间未观察到共享单倍型.系统发生分析,观察到中国境内现有亚洲象种群在进化上分为两大分支,α和β.其中分支α中包含除南滚河种群外的4个地理种群,分支β仅含有南滚河种群,表明南滚河种群与其他4个地理种群间存在明显分化.遗传多样性分析结果表明,中国境内的亚洲象种群的遗传多样性水平较低,分析原因认为是栖息地破碎化阻断了种群间有效的基因交流.     

Insights into the phylogenetic and taxonomy of philasterid ciliates (Protozoa, Ciliophora, Scuticociliatia) based on analyses of multiple molecular markers

Scuticociliates are a rich assemblage of species with mostly unresolved phylogenetic relationships, especially in the order Philasterida. In the present work, 48 new sequences for three linked genes are characterized and phylogenetic trees are constructed to assess the inter- and intra-generic relationships of philasterids. Results reveal the following: (1) the combined three-gene tree provides more resolution in nodes than in the SSU-rDNA topologies; (2) the family Orchitophryidae is non-monophyletic as it is split into two parts and Paranophrys magna, Metanophrys sp. and Metanophrys sinensis are designated incertae sedis at the familial level; (3) Uronematidae is non-monophyletic and Homalogastra setosa is designated incertae sedis; (4) Parauronematidae becomes a junior synonym of Uronematidae and the clade containing A. haemophila, Miamiensis avidus, and Glauconema trihymene might stand for a new family; (5) Parauronema being a junior synonym of Uronema is supported and P. longum should be removed from the genus Parauronema; (6) Uronema is not monophyletic and molecular analyses reveal that Uronema sp. QD shares a more recent common ancestor with Uronemella species than with other Uronema species; (7) Metanophrys is polyphyletic; (8) multiple samples of two highly controversial species, viz., Mesanophrys pugettensis and M. chesapeakensis have identical ITS1-5.8S-ITS2 region sequence and we propose they should be synonymous with M. carcini, and (9) there may be cryptic species in M. carcini and M. avidus.     

Molecular phylogeny of Old World swifts (Aves: Apodiformes, Apodidae, Apus and Tachymarptis) based on mitochondrial and nuclear markers

We provide a molecular phylogeny for Old World swifts of genera Apus and Tachymarptis (tribe Apodini) based on a taxon-complete sampling at the species level. Phylogenetic reconstructions were based on two mitochondrial (cytochrome b, 12S rRNA) and three nuclear markers (introns of fibrinogen and glyceraldehyde 3-phosphate dehydrogenase plus anonymous marker 12884) while the myoglobin intron 2 did not show any intergeneric variation or phylogenetic signal among the target taxa at all. In contrast to previous hypotheses, the two genera Apus and Tachymarptis were shown as reciprocally monophyletic in all reconstructions. Apus was consistently divided into three major clades: (1) East Asian clade of A. pacificus and A. acuticauda, (2) African-Asian clade of A. caffer, A. batesi, A. horus, A. affinis and A. nipalensis, (3) African-Palearctic clade of eight currently accepted species among which sequences of A. apus and A. pallidus clustered in a terminal crown clade. Phylogenetic signal of all four nuclear markers was extremely shallow within and among species of tribe Apodini and even among genera, such that intra- and intergeneric relationships of Apus, Tachymarptis and Cypsiurus were poorly resolved by nuclear data alone. Four species, A. pacificus, A. barbatus, A. affinis and A. caffer were consistently found to be paraphyletic with respect to their closest relatives and possible taxonomic consequences are discussed without giving particular recommendations due to limitations of sampling. Incomplete mitochondrial lineage sorting with cytochrome-b haplotypes shared among species and across large geographic distances was observed in two species pairs: A. affinis/A. nipalensis and A. apus/A. pallidus. Mitochondrial introgression caused by extant or past gene flow was ruled out as an explanation for the low interspecific differentiation in these two cases because all nuclear markers appeared to be highly unsorted among Apus species, too. Apparently, the two extant species pairs originated from very recent dispersal and/or speciation events. The currently accepted superspecies classification within Apus was not supported by our results.     

Molecular phylogeny of the western South Atlantic Sciaenidae based on mitochondrial and nuclear data

Fragments of mitochondrial (COI and rRNA 16S) and nuclear (Tmo-4C4) genes were sequenced to evaluate the phylogenetic relationships among 15 genera of the western South Atlantic Sciaenidae, two freshwater genera and the northwest Pacific Larimichthys crocea.Our results suggest a great diversification for the western Atlantic assemblage; the monophyly of Macrodon, Menticirrhus and Plagioscion genera; the distinctiveness of Bardiella, Stellifer and Ophioscion as belonging to the same clade; the possible existence of two distinct groups in Stellifer; the closer relationship between Lonchurus and Paralonchurus; the non-monophyly of Cynoscion; and the remarkable diversification of Larimus breviceps populations in the Brazilian coast. This is the most comprehensive study evaluating the phylogenetic relationships of the western Atlantic sciaenid and provides a guide for future studies within this family.