A molecular assessment of northeast Pacific Alaria species (Laminariales, Phaeophyceae) with reference to the utility of DNA barcoding

Despite their relatively complex morphologies, species in the genus Alaria Greville are notoriously difficult to identify with certainty. Morphological characters, often influenced by environmental factors, make individuals in similar habitats artificially appear related. Species identification would, therefore, benefit greatly from the application of molecular tools. We applied DNA barcoding, using the 5' end of the cytochrome c oxidase I (coxI-5') gene from the mitochondrial genome, to define species limits and relationships in northeast Pacific populations of Alaria. This emerging technique is being employed to catalogue species diversity worldwide, particularly among animals, and it has been shown to be sensitive enough to discriminate between closely related species. However, the utility of this marker for identifying or categorizing the majority of life remains unclear. We compared the resolution obtained with this marker to two other molecular systems commonly used in algal research: the nuclear internal transcribed spacer (ITS) of the ribosomal cistron, and the plastid Rubisco operon spacer (rbcSp). In agreement with previous results, Alaria fistulosa Postels & Ruprecht, with its distinct morphological, ecological and molecular features, stands apart from the other species in the genus and we establish Druehlia gen. nov. to accommodate it. For the remaining isolates, distinct mitochondrial haplotypes resolved with the barcode data indicate a period of genetic isolation for at least three incipient species in the northeast Pacific, whereas unexpected levels and patterns of ITS variation, as well as the extreme morphological plasticity found among these isolates, have most probably resulted from a recent collapse in species barriers. The cloning of ITS amplicons revealed multiple ITS copies in several individuals, further supporting this hypothesis.     

A new and highly divergent mitochondrial lineage in the Small Five-toed Jerboa,Allactaga elater,from Iran (Mammalia: Rodentia)

The Small Five-toed Jerboa, Allactaga elater, is a small rodent adapted to desert and semi-arid habitats with a widespread distribution around the Caucasus. Previous studies have suggested the occurrence of subspecific variation within the species but, except for a recent phylogeny of the genus Allactaga, most of the work done on the taxonomy of the group relies on morphological data only. To contribute to the current understanding of patterns of genetic diversity of A. elater we analysed one mitochondrial locus, cytochrome b, from 13 Iranian specimens. Comparing to a recent phylogeny, our results suggest the existence of two additional mitochondrial lineages, one that clusters within previously described lineages and a new and highly divergent one. The two novel mitochondrial lineages occur in the north and form two highly divergent monophyletic groups (Dxy = 14%), which likely separated during the Pleistocene.     

Phylogeny of the highly divergent zoanthid family Microzoanthidae (Anthozoa,Hexacorallia) from the Pacific

Fujii, T. & Reimer, J. D. (2011). Phylogeny of the highly divergent zoanthid family Microzoanthidae (Anthozoa, Hexacorallia) from the Pacific. —Zoologica Scripta, 40, 418–431. In this study, one new family, one new genus and two new species of zoanthids from rubble zones spanning the temperate, subtropical and tropical Pacific Ocean are described. Two new species are described, Microzoanthus occultus sp. n. and Microzoanthus kagerou sp. n., both belonging to the new genus Microzoanthus and new family Microzoanthidae, and they can be clearly distinguished both morphologically and genetically from each other and other zoanthids by their very small size, reduced or absent stolon, habitat usually on the bottom side of rubble zone rocks, and divergent and distinct DNA (cytochrome oxidase subunit I, mitochondrial 16S ribosomal DNA, internal transcribed spacer region of ribosomal DNA) sequences. The phylogenetic analyses clearly show Microzoanthidae fam. n. to be genetically far different from all other hexacorallians at the order level, but the macrocnemic arrangement of mesenteries and other morphological characters (colonial specimens with narrow stolons, two rows of tentacles sand encrustation) clearly place these specimens within the order Zoantharia. This study demonstrates how it is highly likely the existence of many marine invertebrate taxa remains overlooked, and that widely distributed groups such as Microzoanthidae fam. n. remain to be discovered.     

Mitochondrial DNA polymorphism among alpine populations of Gammarus lacustris (Crustacea, Amphipoda)

1. Mitochondrial DNA sequence analysis was used to investigate the phylogeographic structure among populations of the amphipod Gammarus lacustris isolated in high altitude lakes from the Northern to the Southern Alps, and to investigate the historical and demographic events that may have accompanied this differentiation.
2. The comparison of a 376‐base segment of the mitochondrial cytochrome c oxidase I gene in fifty‐four specimens from nine different populations reveals no variation within populations. However, northern populations appear divergent from those from the Southern Alps. A particular population, located at the limit between the Northern and Southern Alps shows an intermediate haplotype related to the southern lineage.
3. Consideration of the different mitochondrial lineages, together with geographical differences among populations, suggests a scenario for the post‐glacial colonization of G. lacustris in the alpine lakes.     

DNA barcoding the geometrid fauna of Bavaria (Lepidoptera): successes, surprises, and questions

Background

The State of Bavaria is involved in a research program that will lead to the construction of a DNA barcode library for all animal species within its territorial boundaries. The present study provides a comprehensive DNA barcode library for the Geometridae, one of the most diverse of insect families.

Methodology/Principal Findings

This study reports DNA barcodes for 400 Bavarian geometrid species, 98 per cent of the known fauna, and approximately one per cent of all Bavarian animal species. Although 98.5% of these species possess diagnostic barcode sequences in Bavaria, records from neighbouring countries suggest that species-level resolution may be compromised in up to 3.5% of cases. All taxa which apparently share barcodes are discussed in detail. One case of modest divergence (1.4%) revealed a species overlooked by the current taxonomic system: Eupithecia goossensiata Mabille, 1869 stat.n. is raised from synonymy with Eupithecia absinthiata (Clerck, 1759) to species rank. Deep intraspecific sequence divergences (>2%) were detected in 20 traditionally recognized species.

Conclusions/Significance

The study emphasizes the effectiveness of DNA barcoding as a tool for monitoring biodiversity. Open access is provided to a data set that includes records for 1,395 geometrid specimens (331 species) from Bavaria, with 69 additional species from neighbouring regions. Taxa with deep intraspecific sequence divergences are undergoing more detailed analysis to ascertain if they represent cases of cryptic diversity.     

DNA barcoding confirms polyphagy in a generalist moth,Homona mermerodes (Lepidoptera: Tortricidae)

Recent DNA barcoding of generalist insect herbivores has revealed complexes of cryptic species within named species. We evaluated the species concept for a common generalist moth occurring in New Guinea and Australia, Homona mermerodes, in light of host plant records and mitochondrial cytochrome c oxidase I haplotype diversity. Genetic divergence among H. mermerodes moths feeding on different host tree species was much lower than among several Homona species. Genetic divergence between haplotypes from New Guinea and Australia was also less than interspecific divergence. Whereas molecular species identification methods may reveal cryptic species in some generalist herbivores, these same methods may confirm polyphagy when identical haplotypes are reared from multiple host plant families. A lectotype for the species is designated, and a summarized bibliography and illustrations including male genitalia are provided for the first time.     

Coalescent-based hypothesis testing supports multiple Pleistocene refugia in the Pacific Northwest for the Pacific giant salamander (Dicamptodon tenebrosus)

Phylogeographic patterns of many taxa are explained by Pleistocene glaciation. The temperate rainforests within the Pacific Northwest of North America provide an excellent example of this phenomenon, and competing phylogenetic hypotheses exist regarding the number of Pleistocene refugia influencing genetic variation of endemic organisms. One such endemic is the Pacific giant salamander, Dicamptodon tenebrosus. In this study, we estimate this species' phylogeny and use a coalescent modeling approach to test five hypotheses concerning the number, location and divergence times of purported Pleistocene refugia. Single refugium hypotheses include: a northern refugium in the Columbia River Valley and a southern refugium in the Klamath-Siskiyou Mountains. Dual refugia hypotheses include these same refugia but separated at varying times: last glacial maximum (20,000 years ago), mid-Pleistocene (800,000 years ago) and early Pleistocene (1.7 million years ago). Phylogenetic analyses and inferences from nested clade analysis reveal distinct northern and southern lineages expanding from the Columbia River Valley and the Klamath-Siskiyou Mountains, respectively. Results of coalescent simulations reject both single refugium hypotheses and the hypothesis of dual refugia with a separation date in the late Pleistocene but not hypotheses predicting dual refugia with separation in early or mid-Pleistocene. Estimates of time since divergence between northern and southern lineages also indicate separation since early to mid-Pleistocene. Tests for expanding populations using mismatch distributions and 'g' distributions reveal demographic growth in the northern and southern lineages. The combination of these results provides strong evidence that this species was restricted into, and subsequently expanded from, at least two Pleistocene refugia in the Pacific Northwest.     

The variation in chum salmon Oncorhynchus keta (Walbaum) mitochondrial DNA and its connection with the paleogeographic events in the Northwest Pacific

The results of examining mtDNA variation in populations of chum salmon Oncorhynchus keta from the rivers of the basins of the seas of Japan and Okhotsk and in the chum salmon seasonal races of the Amur River are presented. A significant level of polymorphism between the majority of the populations studied was detected. The groups of chum salmon from the Japan and Okhotsk Seas displayed the most pronounced differences. Analysis of genetic variation demonstrated that periodic paleontologic and climatic changes in the past of this region were the most probable factor that caused the divergence of these populations. The advances and retreats of glaciers and the accompanying regressions and transgressions of the ocean level caused isolation of chum salmon in the refugia belonging hypothetically to the paleo-Suifun and paleo-Amur regions. These population groups diverged presumably 350-450 thousand years ago. Differences between the seasonal races of the Amur chum salmon are insignificant, and their emergence dates back to the period of the last Wisconsin glaciation. Probably, the main isolation factor now is the genetically determined time of spawning.     

Intraspecific variation in nuclear DNA content among world populations of a mosquito,Aedes albopictus (Skuse)

Summary Aedes albopictus is commonly distributed in most parts of the Oriental region and on many islands in the Indian and the Pacific Oceans. The species was recently introduced into the United States and Brazil. Feulgen cytophotometric quantitation of haploid nuclear DNA content was carried out for 37 populations of Ae. albopictus to determine the extent of intraspecific variation in nuclear DNA content and whether the range expansion of the species has coincided with an increase in DNA content. The haploid nuclear DNA content varied nearly three-fold. The minimum DNA content was 0.62 pg in Koh Samui from Thailand, and the maximum DNA content was 1.66 pg in Houston-61 from the United States. Statistical comparisons of populations revealed significant differences in DNA contents. No geographic clustering of populations was noted with respect to DNA content. In general, populations from the United States and Brazil had higher DNA contents, but there was no indication that the range expansion had occurred hand in hand with an increase in DNA content. Each population had a specific amount of DNA that is probably imposed by the microenvironment.     

Environmental calcium and mitochondrial DNA polymorphism among local populations of Gammarus fossarum (Crustacea, Amphipoda)

Mitochondrial DNA sequence analysis was used to investigate genetic diversity and phylogeographic population structure among geographically isolated alpine populations of the amphipod Gammarus fossarum. This study was performed across a region with an important glacial history and substantial geographical variations in calcium levels, in order to evaluate the relative impact on the genetic diversity of the population history and this environmental factor known to be associated with local adaptation and population growth. Analysis of the nucleotide sequences for a 376-bp segment of the cytochrome c oxidase I gene in 84 specimens from seven different populations revealed 20 different haplotypes distributed into five major lineages that are not geographically structured. Analysis of molecular variance indicates that the populations from the crystalline massif are less diverse than those living on limestone, suggesting a global correlation between genetic diversity and calcium concentration of the water. However, the role of this environmental factor appears to be indirect, with smaller population size leading to lower genetic diversity.     

Assessment of loci for DNA barcoding in the genus Thrips (Thysanoptera:Thripidae)

Identification of the juveniles of economically important thrips species on imports by morphology alone can be challenging and culturing is usually required. In the case of EU quarantine species such as Thrips palmi, rapid and accurate identification is essential. DNA barcoding using the Cytochrome oxidase I (COI) gene has become a popular technique for species identification; however, in some invertebrate genera COI has been shown to provide insufficient variability for species discrimination. This study presents a comparison of five different loci to investigate their ability to discriminate a small number of Thrips species. All five loci discriminated the species by neighbour-joining tree and varying degrees of discrimination were determined upon further investigation of the intraspecific and interspecific distances. Two distinct COI clades were observed for T. Palmi and judged to be COI haplotypes when data from the other four additional loci and geographical collection data were taken into consideration. COI was shown to provide sufficient variation to be used in future DNA barcoding efforts within the genus Thrips.     

Population genetics of Howellia aquatilis (Campanulaceae) in disjunct locations throughout the Pacific Northwest

Howellia aquatilis A.Gray (water howellia) is a federally-listed threatened aquatic plant species with limited distribution in four states: California, Idaho, Montana, and Washington. Previous studies have shown a lack of genetic variation within the species; these studies, however, have excluded samples from one or more states. There have been no published studies on the population biology or genetics of the six known California populations or their evolutionary relationship to the other Pacific Northwest populations. We used Amplified Fragment Length Polymorphisms to identify genetic variation within and among the California populations, and to compare the California populations to the Idaho, Montana, and Washington populations. Analysis of molecular variance of 92 individuals from the six California populations show that 83.8% of genetic variation is found within populations and 16.2% among populations (P < 0.001). All sampled populations from all states provide 83.7% variation within and 16.3% variation among populations (P < 0.001). A UPGMA analysis confirms there is no clear clustering of Howellia aquatilis populations within California, that the Montana populations cluster within the California populations, and, although with limited population sample sizes, the Idaho and Washington populations are distantly related to all other populations. Waterfowl migration patterns support a hypothesis for avian dispersal as a primary factor in gene flow in Howellia aquatilis.     

Predators associated with the hemlock woolly adelgid (Hemiptera: Adelgidae) in the Pacific Northwest

The hemlock woolly adelgid, Adelges tsugae Annand (Hemiptera: Adelgidae), is causing widespread mortality of eastern hemlock, Tsuga canadensis L. Carrière, in the eastern United States. In western North America, feeding by A. tsugae results in negligible damage to western hemlock, Tsuga heterophylla (Raf.) Sargent. Host tolerance and presence of endemic predators may be contributing to the relatively low levels of injury to T. heterophylla caused by A. tsugae. Field surveys of the predator community associated with A. tsugae infestations on 116 T. heterophylla at 16 sites in Oregon and Washington were conducted every 4-6 wk from March 2005 through November 2006. Fourteen uninfested T. heterophylla were also surveyed across 5 of the 16 sites. Each sample tree was assigned an A. tsugae population score ranging from 0 to 3. Predators collected from A. tsugae-infested T. heterophylla represent 55 species in 14 families, listed in order of abundance: Derodontidae, Chamaemyiidae, Hemerobiidae, Coccinellidae, Cantharidae, Reduviidae, Miridae, Syrphidae, Chrysopidae, Coniopterygidae, Staphylinidae, Anthocoridae, Nabidae, and Raphidiidae. Laricobius nigrinus Fender (Coleoptera: Derodontidae), Leucopis argenticollis Zetterstedt (Diptera: Chamaemyiidae), and Leucopis atrifacies (Aldrich) (Chamaemyiidae) were the most abundant predators; together comprising 59% of predator specimens recovered. Relationships among predators and A. tsugae were determined through community structure analysis. The abundances of Laricobius spp. larvae, L. nigrinus adults, Leucopis spp. larvae, and L. argenticollis adults were found to be positively correlated to A. tsugae population score. Predators were most abundant when the two generations of A. tsugae eggs were present. L. argenticollis and L. atrifacies were reared on A. tsugae in the laboratory, and host records show them to feed exclusively on Adelgidae.     

Chagas Disease in 2 Geriatric Rhesus Macaques (Macaca mulatta) Housed in the Pacific Northwest

Chagas disease (American trypanosomiasis) is caused by the protozoan parasite Trypanosoma cruzi. It is endemic in Latin America but also is found in the southern United States, particularly Texas and along the Gulf Coast. Typical clinical manifestations of Chagas disease are not well-characterized in rhesus macaques, but conduction abnormalities, myocarditis, and encephalitis and megaesophagus have been described. Here we report 2 cases of Chagas disease in rhesus macaques housed in the northwestern United States. The first case involved a geriatric male macaque with cardiomegaly, diagnosed as dilated cardiomyopathy on ultrasonographic examination. Postmortem findings included myocarditis as well as ganglioneuritis in the esophagus, stomach, and colon. The second case affected a geriatric female macaque experimentally infected with SIV. She was euthanized for a protocol-related time point. Microscopic examination revealed chronic myocarditis with amastigotes present in the cardiomyocytes, ganglioneuritis, and opportunistic infections attributed to her immunocompromised status. Banked serum samples from both macaques had positive titers for T. cruzi. T. cruzi DNA was amplified by conventional PCR from multiple tissues from both animals. Review of their histories revealed that both animals had been obtained from facilities in South Texas more than 12 y earlier. Given the long period of clinical latency, Chagas disease may be more prevalent in rhesus macaques than typically has been reported. T. cruzi infection should be considered for animals with unexplained cardiac or gastrointestinal pathology and that originated from areas known to have a high risk for disease transmission.Abbreviations: DCM, dilated cardiomyopathy; CMV, cytomegalovirus; NHP, nonhuman primateChagas disease is caused by the hemoflagellate protozoan parasite Trypanosoma cruzi. The disease is endemic in many regions of South and Central America, and its range extends to the southern United States. In the United States, there is evidence that the parasite has established a domestic transmission cycle with canine reservoirs,¹⁹ and there are numerous wildlife reservoirs, most importantly armadillos, raccoons, rodents, and opossums.⁶ The main mode of transmission is via arthropod vectors, primarily triatomine species (kissing bugs or cone-nosed bugs), which serve as intermediate hosts. Vector species are present in the southern half of the United States.² Infection has been reported sporadically in domestic nonhuman primate (NHP) colonies.¹² Autochthonous insect vector-mediated transmission in humans in the United States has been reported rarely.³³ Transmission of T. cruzi to NHP is thought to occur mainly through insect vectors, specifically by contamination of the oral mucous membranes with parasite-containing feces during consumption of the bug. The infection may remain subclinical for years and, similar to that in people, affects the nervous system, digestive system, and heart. Clinical findings in NHP are infrequent but can include subcutaneous edema, fever, anorexia, lethargy, heart failure, and sudden death.^4,5 As in humans, the disease in NHP consists of an acute phase, with a paucity of clinical manifestations, and a chronic phase, characterized by irreversible cardiomyopathy leading to cardiac dysfunction and death. Chronically infected NHP in the indeterminate form of the chronic phase can exhibit subclinical conduction and echocardiographic abnormalities.⁸T. cruzi infections have been reported in a number of NHP species housed in Texas, Louisiana, and Georgia. Species affected include rhesus macaques (Macaca mulatta),^12,17 cynomolgus macaques (M. fascicularis),^29,42 yellow baboons (Papio cynocephalus), olive baboons (P. anubis),^12,14,41 pig-tailed macaques (M. nemestrina),^12,35 squirrel monkeys (Saimiri sciureus),¹³ ring-tailed lemurs (Lemur catta),^15,30 black-eyed lemurs (Eulemur macaco flavifrons), black and white ruffed lemurs (Varecia variegata variegate),¹⁵ pileated gibbon (Hylobates pileatus),³⁶ a lion-tailed macaque (M. silenus),³⁰ a Celebes crested black macaque (M. nigra),²⁷ and a chimpanzee (Pan troglodytes).⁴ Here we report on 2 cases of Chagas disease in rhesus macaques housed in the northwestern United States but that originated from South Texas.     

Identification of molecular markers for DNA barcoding in the Aphidiinae (Hym. Braconidae)

Reliable identification of Aphidiinae species (Braconidae) is a prerequisite for conducting studies on aphid–parasitoid interactions at the community level. However, morphological identification of Aphidiinae species remains problematic even for specialists and is almost impossible with larval stages. Here, we compared the efficiency of two molecular markers [mitochondrial cytochrome c oxydase I (COI) and nuclear long wavelength rhodopsin (LWRh)] that could be used to accurately identify about 50 species of Aphidiinae that commonly occur in aphid–parasitoid networks in northwestern Europe. We first identified species on a morphological basis and then assessed the consistency of genetic and morphological data. Probably because of mitochondrial introgression, Aphidius ervi and A. microlophii were indistinguishable on the basis of their COI sequences, whereas LWRh sequences discriminated these species. Conversely, because of its lower variability, LWRh failed to discriminate two pairs of species (Aphidius aquilus, Aphidius salicis, Lysiphlebus confusus and Lysiphlebus fabarum). Our study showed that no unique locus but a combination of two genes should be used to accurately identify members of Aphidiinae.     

Phylogeography of the false smooth snakes, Macroprotodon (Serpentes, Colubridae): mitochondrial DNA sequences show European populations arrived recently from Northwest Africa

Mitochondrial DNA (1075 bp: cytochrome b, 300 bp; 12S rRNA, 393 bp; and 16S rRNA, 382 bp) corroborates the monophyly of the genus Macroprotodon and of the species M. mauritanicus, M. abubakeri, and M. brevis. The subspecies M. brevis ibericus is also monophyletic. The mtDNA tree presented here indicates that M. cucullatus consists of at least two separate units and may possibly represent a primitive morphology rather than a species in its own right. However, this hypothesis is tentative since it is only reflects the history of a single evolutionary unit (mtDNA). A definitive understanding of the evolution of M. cucullatus will not be possible until informative nuclear markers are added to the mitochondrial data. Macroprotodon appears to have originated in the Maghreb region of NW Africa and speciated there around 4-5.5 million years ago around the end of the Miocene period, after which its three main lineages may each have expanded north into more mesic conditions. The group also spread eastwards into coastal areas of Libya quite recently and on to Egypt and Israel. Later still, M. b. ibericus from extreme north Morocco reached the Iberian Peninsula, and M. mauritanicus from Tunisia or Algeria colonised the Balearic Islands of Menorca and Mallorca. Both these range extensions may result from very recent natural colonisations or even from accidental human introduction. Recency of origin of Iberian and Balearic populations is indicated by uniformity of their mtDNA even across large distances, and its great similarity to that of populations in source regions. Isolated populations assigned to M. cucullatus in the Hoggar mountains (southern Algeria) and Western Sahara are probably relicts from quite recent periods of climatic amelioration in the North African desert.     

Variation in Hypericins from wild populations ofHypericum perforatum L. in the Pacific Northwest of the U.S.A.

Representatives from eight wild populations ofHypericum perforatum L. were collected from Montana and Northern California at flowering, and subsequently analyzed for hypericin and pseudohypericin using HPLC analysis. Total individual plant concentrations in these wild populations were from 0.0003–0.1250% dry weight (DW) hypericin and 0.0019–0.8458% DW pseudohypericin. In general, hypericin concentrations were highest in the plant’s reproductive (flower and bud) tissues, followed by leaf and stem tissues, respectively. Hypericin and pseudohypericin concentrations were positively correlated in all samples, although the relative ratio of hypericin to pseudohypericin varied with site location.     

Drilling by Octopus vulgaris(Mollusca: Cephalopoda) in the Mediterranean

Octopus vulgaris drills holes in the shells of a variety of molluscs. The walls of the cavities drilled exhibit dissolution of mineral and organic material. The features which characterize the cavities have been described. The composition and structure of the shell itself is important in determining the size, shape and form of the cavity drilled, and not the size of the octopus. Capture, drilling the shell, and eating the occupant may take less than one hour.