Intraspecific Groups Research Articles

Intraspecific groups of Umbelopsis ramanniana inferred from nucleotide sequences of nuclear rDNA internal transcribed spacer regions and sporangiospore morphology

Umbelopsis ramanniana is a well-known species in this genus. A characteristic morphological feature of this fungus is the remarkable variation in the sporangiospore shape, which implies the genetic variations occur in the nucleotide sequences of the internal transcribed spacer (ITS) regions of the nuclear ribosomal DNA (nrDNA) in the U. ramanniana isolates. The relationship between the variations of the sequences of the nrDNA ITS regions and those of the sporangiospore morphology was investigated for 12 isolates of U. ramanniana collected in Europe. Neighbor-joining and parsimony analyses on the sequences suggested that these isolates split into three groups. Precise examination of the morphology showed that the isolates of those respective groups were different from each other in their sporangiospore shape. The present study implies at least three intraspecific groups exist in U. ramanniana and that the variations in the nucleotide sequences of the nrDNA ITS regions correlate well with those in the sporangiospore shape in these intraspecific groups.

Sequence-Based Typing of adeB as a Potential Tool To Identify Intraspecific Groups among Clinical Strains of Multidrug-Resistant Acinetobacter baumannii

Sequence analysis of an 850-bp fragment internal to the aspecific drug efflux gene ade B revealed 11 sequence types (STs) among a collection of 50 multidrug-resistant Acinetobacter baumannii (MDRAB) strains, including members of pan-European clones I, II, and III. The delineation of STs conformed with the intraspecific grouping of these strains previously determined by different DNA fingerprinting methods. Larger strain collections need to be screened to further explore the potential of sequence-based ade B typing as a universal tool for the monitoring of MDRAB clones.

Intraspecific groups of Claviceps purpurea associated with grass species in Willapa Bay, Washington, and the prospects for biological control of invasive Spartina alterniflora

Abstract Spartina alterniflora is a salt marsh halophyte introduced to the Pacific Coast of the United States that has become a noxious weed in Willapa Bay, Washington. A sap-feeding insect has been released as part of a biological control program, which has established at multiple sites. A useful complement to this program would be a biological agent that attacks seed, to reduce expansion of the infestation by seedling recruitment. One possibility is the floral-infecting, fungal pathogen Claviceps purpurea , which causes the ergot disease. This species is comprised of three intraspecific groups, of which one is specific to salt marsh habitats, G3. Based on random amplified polymorphic DNA markers, all three intraspecific groups of C. purpurea were found on grasses in Willapa Bay. The incidence of ergot on Spartina was very low over the three-year sampling period. Genetic diversity was low among G3 isolates, suggesting it may have been recently introduced to the region. Greenhouse tests showed S. alterniflora from Washington to be as susceptible to C. purpurea as S. alterniflora from the Atlantic Coast, where ergot has reached epidemic levels. Neighbor-joining analysis of amplified fragment length polymorphism markers suggests that G3 C. purpurea in Washington is most closely related to Southeastern USA G3 C. purpurea . Pairwise comparisons as part of AMOVA showed that Willapa Bay isolates are different from those of all other geographic regions except Argentina. The low intensity of disease in Washington may be due, in part, to a G3 ergot population that is not well adapted to conditions in this area.

Molecular characterisation of Beauveria bassiana isolates obtained from overwintering sites of Sunn Pests ( Eurygaster and Aelia species)

110 isolates of Beauveria (104 B. bassiana, 5 Beauveria spp., 1 B. brongniartii) were obtained from Sunn Pests (Eurygaster and Aelia species), litter, and other insect samples at overwintering sites in seven countries in the Middle East and West Asia. DNA was extracted from these isolates, and four techniques were used to characterize and to investigate genetic diversity at the molecular level: ITS-RFLP, ITS sequencing, ISSR-PCR, and AFLP. The ITS-RFLP and ITS sequences did not detect significant genetic variation among the isolates. However, both ISSR-PCR and AFLP analyses gave indications of intraspecific groupings correlated with geographical origin and relative genetic diversity among some isolates, but no obvious association with Sunn Pest hosts. There was no obvious genotypic grouping of B. bassiana isolates from E. integriceps, perhaps suggesting the overwintering populations were infected by generalist native isolates rather than by host-specific ones that might be more suitable for biocontrol purposes.

Morphological variation in the deep ocean-dwelling coccolithophore Florisphaera profunda (Haptophyta)

Detailed analysis of the morphology of Florisphaera profunda from plankton samples collected at three sites in the Atlantic and Pacific Oceans reveals wide variation in this deep ocean-dwelling coccolithophore. In addition to the two varieties described previously, we found a third distinctive form, Florisphaera profunda var. rhinocera var. nov. All three varieties occur at each of the sampling sites. The analysis of monthly samples from different levels in the lower photic zone (LPZ) (100–200 m) at the Hawaii Ocean Time series station suggests that the varieties have similar distributions, which are correlated to primary productivity and the availability of light. The analysis of coccolith and coccosphere size in F. profunda reveals the existence of several size modes in Florisphaera profunda var. profunda and F. profunda var. elongata. The biological significance of these modes, or morphotypes is not known. However, their co-occurrence in single samples from different oceanic areas suggests that they are not ecophenotypes. In the light of recent molecular genetic analyses of intraspecific groups within commonly occurring coccolithophores, the varieties and size morphotypes of F. profunda are of significant interest for the study of marine phytoplankton biodiversity. Coccolithophores inhabiting the LPZ may be adapted to the low light, high nutrient conditions of this layer and hold great potential as a means to reconstruct past oceanographic conditions such as the position of the nutricline. However, coccolithophore biodiversity in the LPZ is poorly documented and the number of species may be much higher than previously thought.

RAPD-PCR used to confirm that four pectic isozyme (zymogram) groups within the AustralianRhizoctonia solaniAG 8 population are true intraspecific groups

RAPD-PCRs were used to study 79 isolates of Rhizoctonia solani AG 8 representing four pectic isozyme groups [zymogram (ZG)] (ZG1-1, 1-2, 1-4 and 1-5) from various locations in southern Australia. RAPD-PCR was performed on all isolates using six primers and the relatedness of the isolates determined by generating a neighbour joining tree. All isolates were also grouped according to vegetatively compatible populations (VCPs). Within each ZG there were four to nine VCPs. These studies show that the AG 8 population contains four distinct groups that matched the four ZGs and support the concept that ZGs are distinct intraspecific groups.

Stock enhancement and conservation culture of sturgeons: problems and prospects

Stock enhancement is the main source of Acipenser gueldenstaedtii and A. stellatus recruitment in the Sea of Azov, where up to 30 million juveniles have been released in recent years. The hatchery production strategy aimed solely to produce and release the largest possible number of juveniles, utilizing only the most mature broodfish of the spring spawning run. Although monitoring of age, mass and physiological conditions of the broodstock during the period of hatchery breeding did not show significant changes, the spawning run was dramatically shortened from several months to just 15 days, and includes only fish with advanced gonadal maturity. Conservation of the Azov Sea species and their unique spawning ecotypes is currently supported by the Federal Living Gene Bank, which maintains over 9000 adults of eight endangered species. This paper summarizes the results of comparative analysis of biological characteristics such as growth, age of the first sexual maturation, relative fecundity, and morphological and physiological indices in wild and cultured specimens of different species and intraspecific groups of sturgeons. We conclude that there is a need for developing better hatchery technologies to maintain diversity of the stocks, through breeding protocols that maximize the genetic diversity of offspring based on evaluation of parentage and relatedness in farmed stocks by microsatellite loci.

Vocal communication in the bicoloured white-toothed shrewCrocidura leucodon

Vocal sounds of 15 individuals ofCrocidura leucodon (Hermann, 1780) emitted during agonistic and amicable interactions in male-male, female-female and male-female dyadic encounters, and intraspecific cage groups, were studied. An analysis of spectral properties, along with an examination of context and function, were performed. The sounds registered during agonistic interactions showed an increase, then a decrease in frequency, often followed a complex undulating curve. The dominant frequency (DF) was 10.7±0.05 kHz, and duration (DU) was 104.2±4.4 ms. The calls emitted by shrews at investigation and grooming often ended with chirping notes (DF=4.8±0.2 kHz, DU=23.5±1.1 ms). While clustering and huddling up to the partner, the animals produced calls consisting of short notes with a very low intensity (DF=1.0±0.07 kHz, DU=35.2±0.8 ms). Based on these finding, it can be assumed that threatening sounds, emitted in agonistic encounters, allow shrews to avoid conflicts, while those, emitted when clustering and huddling up to the partner, contribute to maintenance of group cohesiveness. The variability of frequency ranges and intensity of sounds probably reflects the territorial and gregarious behaviour ofC. leucodon and adaptation to communication in variable acoustic environments.

The Use of Reversible Inhibitors of Cholinesterases for Identification of Intraspecific Groups of the Comandor Squid Berryteuthis magister from Different Zones of the Northwestern Area of the Pacific Ocean

The Use of Reversible Inhibitors of Cholinesterases for Identification of Intraspecific Groups of the Comandor Squid Berryteuthis magister from Different Zones of the Northwestern Area of the Pacific Ocean

Molecular characterization of Aphanomyces species associated with legumes

The identification of plant-associated isolates of Aphanomyces spp. has been mainly based on morphological characters. These types of features, however, can be unreliable due to their high variation and degree of overlap between different taxa. In this work, strains of Aphanomyces, with plant pathogenic and non-pathogenic characteristics, derived mainly from the roots of several leguminous crops in Sweden, as well as a number of reference strains of A. euteiches, A. cladogamus and A. cochlioides were compared by morphology, AT-rich DNA RFLPs and sequence analysis of the total ITS/5.8S rRNA gene region. Parsimony analysis of the sequence data of the total ITS region of 21 strains separated the taxa at the specific level, while two intra-specific groups were also detected within A. euteiches. One comprised all pathogenic isolates of A. euteiches from Sweden, together with two isolates from France and the USA. These isolates formed a homogenous group with identical ITS regions and a single AT-rich DNA RFLP banding pattern. The second ITS subspecific group included reference strains of A. euteiches with preferential pathogenicity to bean and alfalfa, all of which originated from the USA. The bean and alfalfa pathotypes were further distinguished by their different AT-rich DNA RFLPs. The non-pathogenic isolates of Aphanomyces from Sweden associated with the roots of several legumes, formed a genotypically uniform group with an identical ITS sequence and a single AT-rich DNA RFLP pattern. The ITS sequence of this group was identical to that of reference strains of A. cladogamus, suggesting that the non-pathogenic isolates belonged to this species. Intra-specific AT-rich DNA banding profiles were also obtained for isolates of A. cladogamus and these patterns corresponded well to the original hosts.

Morphological and genetic variation in <i>Cicindela lusitanica</i> Mandl, 1935 (Coleoptera, Carabidae, Cicindelinae): implications for conservation

The establishment of taxonomic and geographical boundaries is a common problem when analysing clinal distributions. This is of particular concern when the assessment of intraspecific groupings is required for conservation management. The tiger beetle Cicindela lusitanica Mandl, 1935 (Coleoptera, Carabidae) is a typical case in which two recognised subspecies are distributed in a clinal latitudinal fashion in the dune systems along the Atlantic coast of Portugal. This habitat is increasingly under threat, and conservation measures are needed. We investigated the validity of the two named subspecies, based on a re-analysis of elytral and genitalic measurements using multivariate analysis. We also analysed variation in mitochondrial Cytochrome Oxidase I gene for a total of six populations along the cline. Multivariate analysis supported the idea of a morphological cline and revealed a clear distinction of the southernmost population and also some degree of distinctiveness of the most northern populations, partially supporting the recognised subspecific ranking. The mtDNA analysis identified two main groups corresponding to northern and southern populations. Both sets of markers showed that variation within the C. lusitanica assemblage is complex, with the boundaries between morphological and mtDNA groups not in agreement. However, populations at either end of the distributional range are clearly distinct from each other, and should be considered as provisional units for conservation programmes.

Fingerprinting the rice isolates of R. solani Kuhn using RAPD markers

The genetic differences underlying Rhizoctonia solani populations provide a useful means for examining the nature and spread of the population within the rice system. So far, no attempt has been made to define variability in relation to spatial distribution and no information is available on the amount of variability in R. solani within the field. Many anastomosis groups are subdivided on the basis of the cultural, virulence, molecular, biochemical, immunological, and other characteristics into intraspecific groups (ISGs) (Ogoshi 1987). The most convincing validation of AG and ISG concepts has come from molecular systematic studies (Vilgalys and Cubeta 1994). Our study was undertaken to (1) analyze the interfield variability within 46 Indian rice isolates of R. solani collected from two fields, one each at Seola-Kala, Dehradun District (hilly region, 24 isolates), and Nagina, Bijnore District (plain region, 22 isolates), for cultural and morphological characteristics, aggressiveness, anastomosis behavior, nuclear staining, and molecular characterization by RAPD analysis; (2) assess the agreement among five methods in differentiating the isolates; and 3) study the extent and possible factors responsible for intrafield variability in rice. This is the first attempt to define intrafield variability among R. solani isolates that cause sheath blight in rice.

Vigilance towards raptors by nuclear species in bird mixed flocks in a Brazilian savannah

A nuclear or leader species is the one around which foraging activity is organized. In the campo-cerrado (Brazilian savannah) up to four bird species (Saltator atricollis, Cypsnagra hirundinacea, Mimus saturninus, and Neothraupis fasciata) may function as nuclear or leader species in mixed species flocks. The aim of this study was to assess the features shown by these nuclear species. I quantified parameters of sociality, communication and alertness of nuclear bird species in mixed flocks with different composition. Parameters related to sociality (mean intraspecific group size) and communication (frequency of contact calls) were not correlated with the leadership. On the other hand, the most alert species was in the front of a given mixed flock most of the time. The leader species spent more time in vigilance and gave most alarm calls due to approaching raptors earlier. The results of this study strongly suggest that the alertness of a species is the major character of nuclear bird species in mixed flocks of the campo-cerrado.

DNA sequence and RFLP data reflect geographical spread and relationships of Amylostereum areolatum and its insect vectors.

The white rot fungus, Amylostereum areolatum (Basidiomycetes), is best known for its symbiotic relationship with various siricid wood wasp species. In this study, the relationship between isolates of A. areolatum associated with two wood wasp species, Sirex noctilio and S. juvencus, are considered to identify possible intraspecific groups. Isolates from the northern (native) and southern (exotic) hemispheres are included to determine patterns of geographical spread and origin of introductions into the southern hemisphere. The phylogenetic relationships of these isolates to authentic isolates of A. chailletii, A. laevigatum and A. ferreum were also investigated. Sequence and restriction fragment length polymorphism (RFLP) analyses of the variable nuc-IGS-rDNA region provided markers to distinguish intraspecific groups within A. areolatum. Isolates of A. areolatum associated with S. noctilio and S. juvencus contained four heterogenic sequences in the DNA region analysed. These sequences occurred in one of five combinations in each isolate. Some of these sequences were unique to isolates of A. areolatum from either wasp species, while others were present in both groups. This shows the ancient and specialized evolutionary relationship that exists between these insects and fungi. Isolates from the southern hemisphere all share the same sequence group. This supports previous hypotheses that S. noctilio has spread between countries and continents of this region. At the interspecific level, the IGS-rDNA sequence analysis showed that A. ferreum and A. laevigatum are closely related to each other, and they in turn are related to A. chailletii. Amylostereum areolatum was the most distinctly defined species in the genus. This can be attributed to the obligate relationship between A. areolatum and its insect vectors. Polymerase chain reaction-RFLP analysis was also shown to be an effective tool to distinguish between the different species of Amylostereum.

A review of the biology of the jumbo squid Dosidicus gigas (Cephalopoda: Ommastrephidae)

The taxonomy, functional morphology, evolutionary biology and ecology of the jumbo squid, Dosidicus gigas, were reviewed using the data from many Soviet/Russian expeditions and all available literature. D. gigas is one of the largest and most abundant of the nektonic squid in the epipelagic zone of the world Ocean. It occurs in the eastern Pacific with its species range limited by the isoline of phosphate concentration of 0.8 mg-at P-PO 4 3−/m 2 in the 0–100 m layer. Three intraspecific groups of D. gigas may be distinguished on the basis of the size of adult males and females: small (mantle length (ML) of adult males 130–260 mm, females 140–340 mm), medium-sized (240–420 and 280–600 mm, respectively) and large (>400–500 mm and 550–650 to 1000 mm and more, respectively). Growth is rapid. The life span of all three groups is about 1 year, with the biggest specimens of the large group probably living 2 years. D. gigas are monocyclic with the highest potential female fecundity among cephalopods; up to 32 million oocytes. Spawning takes place throughout the year, with a distinct peak during spring and summer in the southern hemisphere (October–January). D. gigas is an active predator. The most common prey among fish species are epipelagic lanternfish, and among squid species are ommastrephids, including D. gigas. Throughout the whole life cycle the prey sizes constitute 5–15% of the squid total length. Parasite fauna include 9–12 species of nematode, cestode and trematode, and the ciliate Chromidina. The total instantaneous stock of D. gigas within the limits of the species range was estimated at around 7–10 million tonnes, including around 2–4 million tonnes in the open ocean beyond the exclusive economic zones.

Spreading Disease through Social Groupings in Competition

Many animal populations live in social groups which avoid contact with other conspecific groups for at least part of the year. This may give rise to competition between groups for items such as shelter, land and mates. We couple intra-specific group competition with disease dynamics to investigate how infectious diseases may spread through population subgroups, particularly with reference to the contact rates between groups. Our model uses a nonlinear systems of ODEs for which steady-state analysis is carried out in the simplest two-group system. This indicates that coexistence of social groups is possible with the disease or that competitive exclusion occurs with one group dying out whilst the other retains disease. Moreover, we show that in certain circumstances the model can exhibit multistability and we discuss the ecological implications of this result in relation to contact between social groups.

Ontogenetic approach to studying natural avian populations

The asymmetry of digit folidosis and the correlation of exterior characteristics have been studied in 20 passerine species. The level of the characteristic asymmetry depends on the phylopatry level and regularly increases in the species disposed to annual change of the nesting site. We assume that the revealed variability reflects interpopulation flow of genes. Age-, sex-, and biotope-related changes associated with urbanization have been revealed in the correlation of characteristics. Older birds have more pronounced correlation of characteristics; it is also more specific for males than females. Correlation of characteristics is less pronounced in the urban avian populations. These differences are interpreted in terms of stabilizing selection within intraspecific groups.

Phenetic Analysis of Aboriginal and Introduced Populations of Sable (Martes zibellina) in Russia

Using standard and multivariate statistic methods, an epigenetic character—foramina in fossa condyloidei inferior(FFCI)—was studied in sable populations. This character was shown to be most frequent in southeastern populations of the species (Primorye and the Baikal region) while its distribution in the remaining part of the range was polyclinal. The expression of FFCI was directly associated with coat color and longitude, and inversely associated with skull size. This trend was broken by some western populations formed in the 1950s by introduction, which exhibited stable morphological differences with adjacent aboriginal sable populations. Most populations of the species exhibit differences in the manifestation of the studied characters. Frequency of the FFCI manifestation can be used as an additional population characteristic, an associative diagnostic character that shows high discriminating capability in detecting phenogenetic relationships of intraspecific groups.

Population diversity of the Vicia sativa agg. (Fabaceae) in the flora of the former USSR deduced from RAPD and seed protein analyses

The genetic diversity of 58 wild and weedy populations representing taxa within the V. sativa aggregate from the former USSR, 4 cultivars of V. sativa, 2 accessions of V. cordata and 3 accessions of V. macrocarpa from Mediterranean countries were analysed using randomly amplified DNA fragments (RAPDs) and seed protein electrophoresis (SDS-PAGE). Interspecific variation between taxa in the V. sativa aggregate could readily be detected using both techniques. RAPDs and seed protein patterns were found to be an effective means of identifying accessions that cannot be identified clearly by morphological criteria alone. RAPD and seed protein analysis revealed a clear relationship between observed genetic variation of populations and their geographical distribution. Populations from each region had their own gene pools. Geographical variation was detected in V. segetalis. The degree of genetic divergence between local populations was usually related to proximity. In several locations where wild and weedy populations of different V. sativa agg. taxa grow sympatrically, intermediate forms could be detected at the DNA and protein levels. Both RAPD and seed protein analysis support the view that the V. sativa aggregate consists of 8 taxa warranting recognition at the species level. Several species in this aggregate are evolving intra-specific groups which can readily be detected at the molecular level.

Using Genetics to Identify Intraspecific Conservation Units: a Critique of Current Methods

Genetic criteria have recently been proposed for identifying evolutionarily significant units (ESUs) and management units (MUs; Moritz 1994). Although this proposal has proved useful for focusing discussion about the intraspecific groupings of relevance to conservation, I am concerned that the criteria put forward have been accepted and applied without sufficient debate about their merit or limitations. My aim is to stimulate renewed debate on this subject by identifying some weaknesses in the proposed criteria. Although Moritz (1994) distinguished between the biological definitions of ESUs and MUs and the genetic criteria he proposed for recognizing such groups, many papers that cite his work erroneously refer to the recognition criteria as the definitions. An ESU is a group of organisms that has been isolated from other conspecific groups for a sufficient period of time to have undergone meaningful genetic divergence from those other groups (Ryder 1986). Moritz (1994) suggested that ESUs could be identified genetically as groups whose mtDNA lineages were reciprocally monophyletic, meaning that all lineages within each group share more-recent common ancestors than any lineage from one group shares with any lineage from the other group. In contrast, an MU is a group in which local population dynamics are determined primarily by birth and death rather than immigration and emigration (Moritz et al. 1995). Moritz (1994) suggested that MUs could be identified as populations with significant differences in allele distributions. An important point regarding both of these concepts is that they apply only when the populations under study are naturally divided into groups (Moritz et al. 1995). Of course, genetic study may also be of value in situations where populations are continuously distributed, but such populations cannot be subdivided into ESUs and MUs.