Molecular phylogeny of three subfamilies of the Neanuridae (Insecta, Collembola) and the position of the antarctic species Friesea grisea Schäffer.

The nuclear 28S rRNA and the mitochondrial COII gene were used to establish phylogenetic relationships among species of the family Neanuridae, with special emphasis on species of the subfamily Neanurinae. Phylogenetic analysis was conducted using genetic distances, parsimony and likelihood methods. The D3-D5 fragment of the rRNA gene was very conserved, both in sequence and in secondary structure features. This fragment supplied little information on relationships at this level. The phylogenetic reconstruction based on 1st and 2nd codon positions of the COII gene was partly in accordance with morphological data, but it was discordant for the placement of some species. Relationships among the subfamilies Frieseinae, represented by the Antarctic species Friesea grisea, Pseudachorutinae and Neanurinae were uncertain. The subfamily Neanurinae and its tribes Neanurini and Paleonurini were shown as monophyletic taxa. Relationships between three species of the genus Bilobella were in accordance with morphological and biochemical data. Relationships between genera within the Neanurini were more controversial. In accordance with morphological hypotheses, a basal position of Thaumanura was suggested, but the molecular data placed Neanura muscorum in a derived position, in sharp contrast with morphological evidence. A close relationship was suggested between Deutonura conjuncta, Cansilianura malatestai and Lathriopyga longiseta. The disagreement between molecular and morphological data suggests that one or both data sets might be affected by a certain degree of homoplasy and that these data should be interpreted with caution in phylogenetic reconstructions.     

Hedysarum phylogeny mediated by RFLP analysis of nuclear ribosomal DNA – RFLP and Hedysarum phylogeny

The RFLP technique has been employed to investigate phylogenetic relationships between species of the Hedysarum genus. Homologous DNA probes were used to generate patterns from a set of the Mediterranean group. The degree of band sharing was used to estimate genetic distances between species and to draw phylogenetic trees. These are in good agreement with phylogeny based on morphological and isozyme markers, but contain novel insights. The results are discussed in the context of current work in molecular biosystematics in Hedysarum complex. Attempts made in this approach to access the extent of variability at the DNA level occurring with the domestication process have been investigated. With the availability of the tested probes, it has been assumed that the genetic structure is not affected by the domestication process.     

Two major evolutionary lineages revealed by molecular phylogeny in the parthenogenetic collembola species Folsomia candida

In order to measure the genetic variability and determine the evolutionary relationships among strains of the parthenogenetic “standard” springtail Folsomia candida, we used Random Amplified Polymorphic DNA (RAPD-PCR) markers and determined the nucleotide sequence of the 18S and 28S rDNA genes. Both types of molecular characters were found to be polymorphic. We obtained phylogenetic trees using Direct Optimization in the dynamic homology paradigm. The trees were polarized with Isotoma viridis as an outgroup. All the trees based on one or the other type of molecular characters or based on all characters pooled together, support the hypothesis of an early divergence of two distinct lineages among the 11 strains of F. candida under study. Our results also suggest that these lineages differ in their rate of evolution and mode of diversification. The geographical origin of the studied strains was examined but we found no clear relation between the phylogenetic relationships and probable geographical origins. The early divergence of several lineages in this species should be taken into account when comparing studies on genetically different strains of this model organism. RAPD-PCR typing is an easy and efficient tool for doing such a task.     

Micromorphology of a “welded” Sangamonian to Wisconsinan age paleosol in southwestern Wisconsin

Micromorphological characteristics indicate that in southwestern Wisconsin pedogenesis transgressed the Sangamonian-Wisconsinan chronostratigraphic boundary in conjunction with colluvial and eolian sedimentation. The use of micromorphology helps to distinguish between pedological, colluvial, and eolian components in the paleosol horizon sequence, which can be difficult to resolve and interpret solely from field investigations and from other laboratory analyses. Results show that a basal loess “mixed zone” within the welded paleosol profile contains features that are the products of colluvial reworking processes. We present micromorphology data which support stratigraphic relationships suggesting that colluvial processes were important in the formation of basal loess “mixed zones” in addition to other possible mixing processes such as pedoturbation and bioturbation.     

Molecular markers for promoting agro-biodiversity conservation: a case study from Italy. How cowpea landraces were saved from extinction

Landraces (LRs) are crop populations that are locally grown by farmers; they have a strategic role to play in rebuilding healthy and complex agro-ecosystems, but are at risk of extinction. This paper outlines how some LRs were rescued with the support of modern techniques such as molecular markers. Cowpea LRs from Umbria, Italy, were initially characterized for morphological, organoleptic and genetic traits and reintroduced among farmers. These activities led to an expansion of the area under LR based cowpea cultivation and increased farmers’ income. To encourage further LR cultivation a request for the Protected Designation of Origin (PDO) status has been promoted. Investigations were carried out to determine if it is possible to certify that the product actually belongs to the traditional agricultural and cultural context of the cultivation area. The genetic diversity and phylogenetic relationships among local LRs, other LRs, commercial varieties, and other taxa were investigated with five AFLP markers. Although genetic diversity is limited, genetic analysis showed that Umbrian cowpea LRs can be distinguished from commercial varieties, LRs from abroad and other taxa. There is a tight phylogenetic connection among Umbrian LRs. These data confirmed the available historical and sociological data and were included in the PDO specification. AFLP markers can be used to monitor the origin of seed lots that are on the market; this protects the rights of both consumers and farmers. This case study could be a resource for planning activities for the future on-farm conservation of other LRs in different countries.     

A simple molecular approach for identifying a rare Acronychia (Rutaceae) provides new insights on its multiple hybrid origins

Hybridization plays an important role in the evolution of plant diversity. Nonetheless, it is often difficult to clearly ascertain hybrid origin by assessing morphological characters alone. Acronychia littoralis (Rutaceae) is a recently described rare tree from littoral rainforests in eastern Australia. Two forms have been tentatively distinguished on the basis of different leaf morphology however, because of the variability of the discriminatory characters across populations (and in some cases across single individuals), compiling data on the exact distribution of each form has been a difficult process. To further complicate matters, some of these distinguishing morphological characters are intermediate between those of closely related, sympatric species. As a result, simple molecular techniques were developed to assist the development of adequate conservation and management strategies for A. littoralis and to better understand its evolutionary history. Sequence data from the ITS2 region were obtained and haplotype specific primers that distinguished the two forms and the related taxa were developed. Sequence data suggest that the two forms of A. littoralis are each of hybrid origin but both involve different parental taxa. The findings provide a perspective on the evolutionary dynamics of the local rainforest flora and highlight the need for phylogenetic evaluation of rare taxa where there is taxonomic ambiguity.     

Delimitation of Amaranthus cruentus L. and Amaranthus caudatus L. using micromorphology and AFLP analysis: an application in germplasm identification

The ‘Morelos’ accessions of Amaranthus from Mexico demonstrate taxonomic ambiguity at the basic morphologic level. The main cause is the enormous morphological and genetic variation exhibited by the species in the genus. Although basic morphological criteria can be applied to herbarium specimens or germplasm collections for quick taxonomic identification, the morphological data alone can be misleading. To ascertain the taxonomic identity of the ‘Morelos’ accessions and their hypothesized species affiliation to Amaranthus caudatus or Amaranthus cruentus, we conducted a comparative analysis of phylogenetic relationships among these taxa/accessions using amplified fragment length polymorphism (AFLP) and micromorphology methods. Based on AFLP data, all the controversial ‘Morelos’ accessions can be consistently placed into a single A. cruentus species clade, which is clearly separated from the A. caudatus species clade. The AFLP-based phylogenetic relationship of ‘Morelos’ and delimitation of A. cruentus and A. caudatus are further supported by micromorphology, showing that the combination of these techniques can provide more reliable data for germplasm identification than each method used alone.     

The impact of fossils on the Evolutionary Distinctiveness and conservation status of the Australian lungfish

The recognition of phylogenetic information for evaluating conservation priorities has stressed the importance of basal taxa. The “Evolutionary Distinctiveness” index (ED) is a species-specific index that includes branch length expressed as an absolute value measured in millions of years that can be applied to a single terminal taxon in a phylogeny. The ED depends on the tree pattern, i.e. of a cladogram included into a time-scale. When calculated for the Australian lungfish (Neoceratodusforsteri), a threatened dipnoan that occurs naturally only in southeast Queensland, the ED index shows variable value according to the chosen tree. On the basis of a recently proposed phylogeny including a new fossil find from the Early Cretaceous of Thailand, the ED value reaches the highest value for piscine sarcopterygians, and for all vertebrates, and thus reinforces the “originality” of this fish. This example points out the importance of fossils in the resolution of phylogenies and beyond, in the calculation of indexes supporting conservation decisions.     

Molecular phylogeny of the apterygotan insects based on nuclear and mitochondrial genes

Basal hexapodan orders (Apterygota) are traditionally divided in two well defined taxonomic groups, Entognatha and Ectognatha. Entognathy (the enclosed mouthparts condition) is considered the most distinctive character joining the Ellipura (Protura+ Collembola) with the order Diplura, whereas the presence of exposed mouthparts (ectognathy) is the feature shared by Microcoryphia and Zygentoma with the pterygote insects. In spite of the growing interest for the evolutionary history of the Apterygota, there is no complete agreement among the general phylogenetic hypotheses based on the study of morphological characters. In this study we analyzed the DNA sequence of segments of the nuclear Elongation Factor-1α(EF-1α) and of the mitochondrial 12S rRNA genes, and used different methods of phylogenetic reconstruction. The 12S gene seems to be more suited than the EF-1α to resolve some of the most outstanding systematic disputes, whereas the lack of resolution at the deeper nodes does not allow to assess the phylogenetic relationships within Microcoryphia and between ectognathan orders. We have obtained a fairly high support for the monophyly of the orders Diplura and Zygentoma. In the 12S analysis, the Ellipura and the Entognatha form monophyletic assemblages. In addition, the study of the distribution of introns in the EF-1α suggests a relationship between Collembola and Diplura.     

Speciation in the parthenogenetic oribatid mite genus Tectocepheus (Acari, Oribatida) as indicated by molecular phylogeny

Despite the lack of universal concepts for species and speciation, both sexual and asexual organisms are expected to diversify into discrete genotypic and morphological clusters. Species-rich clusters of parthenogenetic oribatid mites likely evolved in the absence of sexual reproduction. We used nucleotide sequences of the large and small rDNA genes (18S and 28S) and the coding genes for heat shock protein 82 (hsp82) and elongation factor-1 alpha (ef-1α) for phylogenetic analyses of three morphotypes of the parthenogenetic oribatid mite genus Tectocepheus. DNA sequence divergences of the different morphotypes were similar to those of sexual species in other organisms. Maximum likelihood analyses of single genes and combined data sets were largely congruent in reconstructing the phylogeny of the Tectocepheus species. The results suggest that the different morphotypes of Tectocepheus indeed evolved in the absence of sexual reproduction, and that Tectocepheus minor, Tectocepheus velatus and Tectocepheus sarekensis are best considered distinct species. Further, the results suggest that 18S rDNA, hsp82 and ef-1α are powerful markers for resolving phylogenetic relationships of oribatid mites. Saturation plots indicated that the D3-region of 28S is much more saturated than all other examined genes. This indicates that the D3-region is unsuitable for resolving ancient splits in oribatid mites.     

Comparison of the efficiency of A–PAGE and SDS–PAGE,ISSRs and RAPDs in resolving genetic relationships among <Emphasis Type="Italic">Triticum</Emphasis> and <Emphasis Type="Italic">Aegilops</Emphasis> species

Species that belong to the genus Triticum L. and the genetically related Aegilops L. genus are important genetic and economic resources because they have an evolutionary relationship with the two main agricultural crops T. aestivum (bread wheat) and T. durum (durum wheat). Therefore, it is important to understand the genetic relationships among the cultivated wheat species and their wild relatives. The latter have a great role in the improvement of cultivated wheat. Molecular markers are the best choice and most reliable means to study these relationships accurately. In this study, we compared the efficiency of the biochemical methods A–PAGE and SDS–PAGE on seed storage proteins and the molecular methods RAPDs and ISSRs to explore the genetic relationships among seven species of Triticum and 20 Aegilops species. Three phylogenetic trees obtained in this study were compared with available classifications and phylogenetic trees constructed earlier for these species. It was noted that the tree based on ISSRs data was the most congruent with those classification and trees. This may be attributed to the fact that ISSRs is more specific, and therefore more reliable. This study is the first to study genetic relationships among all species studied here using biochemical and molecular techniques.     

Species diversity versus phylogenetic diversity: A practical study in the taxonomically difficult genus Dactylorhiza (Orchidaceae)

Setting conservation priorities in taxonomically complex groups such as the orchid genus Dactylorhiza is a difficult task. As an alternative to taxonomic diversity, we used here a molecular phylogenetic analysis and the results of a genetic investigation using plastid microsatellites with an extensive geographic sampling to assess in a more objective way the patterns of diversity within this genus. Although western Europe is thought to be the main diversity centre for the genus due to the large number of species found there, we found higher phylogenetic and genetic diversity as well as higher endemicity in the Caucasus and the Mediterranean Basin, two biodiversity hotspots. Species number seems to be correlated with taxonomic effort, tentatively estimated here by the number of herbaria, and is thus biased and not an appropriate measure of diversity. Our results show that phylogenetic analyses and genetic data obtained with molecular tools can offer an alternative measure of biodiversity that is not sensitive to taxonomic inflation. Conservation of allotetraploid taxa is also discussed, and it is recommended that sites in which polyploids are formed should be conserved rather than any specific allotetraploid taxon.     

Phylogenetic relationships within <Emphasis Type="Italic">Lactuca</Emphasis> L. (Asteraceae), including African species,based on chloroplast DNA sequence comparisons

Lettuce (Lactuca sativa L.) belongs to the genus Lactuca L. and is an important vegetable worldwide. Over the past decades, there have been many controversies about the phylogeny of Lactuca species due to their complex and diverse morphological characters and insufficient molecular sampling. In this study we provide the most extensive molecular phylogenetic reconstruction of Lactuca, including African wild species, using two chloroplast genes (ndhF and trnL-F). The sampling covers nearly 40 % of the total endemic African Lactuca species and 34 % of the total Lactuca species. DNA sequences from all the subfamilies of Asteraceae in Genebank and those generated from Lactuca herbarium samples were used to establish the affiliation of Lactuca within Asteracaeae. Based on the subfamily tree, we selected 33 ndhF sequences from 30 species and 79 trnL-F sequences from 48 species to infer relationships within the genus Lactuca using randomized axelerated maximum likelihood and Bayesian inference analyses. Biogeographical, chromosomal and morphological character states were reconstructed over the Bayesian tree topology. We conclude that Lactuca contains two distinct phylogenetic clades—the crop clade and the Pterocypsela clade. Other North American, Asian and widespread species either form smaller clades or mix with the Melanoseris species. The newly sampled African endemic species probably should be treated as a new genus.     

Multiple diversity measures to identify complementary conservation areas for the Baja California peninsular cacti

The Baja California Peninsula is home to 85 species of cacti, of which 54 are endemic, highlighting its importance as a cactus diverse region within Mexico. Many species are under threat due to collection pressure and habitat loss, but ensuring maximal protection of cacti species requires a better understanding of diversity patterns. We assessed species richness, endemism, and phylogenetic and morphological diversity using herbarium records and a molecular phylogeny for 82 species of cacti found in the peninsula. The four diversity measures were estimated for the existing nature reserve network and for 314 hexagrids of 726 km². Using the hexagrid data, we surveyed our results for areas that best complement the current protected cacti diversity in the Baja California Peninsula. Currently, the natural reserve network in Baja shelters an important amount of the cacti diversity (74% of the species, 85.9% of the phylogenetic diversity, 76% of endemics and all the growth forms). While species richness produced several solutions to complement the diversity protected, by identifying priority species (endemic species with high contribution to overall PD) one best solution is reported. Three areas (San Matías, Magdalena and Margarita Islands and El Triunfo), selected using species richness, PD and endemism, best complement the diversity currently protected, increasing species richness to 89%, PD to 94% and endemism to 89%, and should be considered in future conservation plans. Two of these areas could be included within nature reserves already established.     

Phylogenetic position of the disjunct species <Emphasis Type="Italic">Musa ornata</Emphasis> (Musaceae): first approach to understand its distribution

Musa L. commonly known as the banana group is one of the most important and oldest food crops of humankind. Among the wild relatives with ornamental interest in the genus, Musa ornata Roxb. shows a disjunct distribution between Asia and North America (Mexico). The wild occurrence of this species in Mexico has led to speculation about the evolutionary relationships with its Asian relatives. This study examined the phylogenetic relationships between intercontinental specimens of this species and, based on registered evidence, explored the more likely hypothesis about the origins of its distribution. The phylogeny of intercontinental specimens, along with other representatives of the same genus, was carried out using three molecular markers (ITS, trnL-F, and atpB-rbcL) and applying three phylogenetic reconstruction methods: maximum parsimony, maximum likelihood, and Bayesian inference. The genetic analysis of the combined dataset grouped together all the Mexican and most Asian specimens, but the monophyly of the species was not supported. The relationships suggest that Mexican populations may have originated from an Asian invasion. However, several studies and historical documents suggest the presence of Musa in America long before the arrival of Europeans. Based on its current distribution, phylogenetic evidence, and fossil record, this species’ disjunct distribution could be explained in terms of an ancestral distribution range that encompassed America and Asia, followed by its subsequent restriction to the Old World and a secondary dispersal by humans. However, further studies are necessary to shed more light on the origins of this disjunct distribution.     

Boundary conditions of morphodynamic processes in the Mura River in Slovenia

Many alpine gravel-bed rivers have been altered in the past due to human interventions. A typical transboundary alpine river in Central Europe flowing over Austria, Slovenia, Croatia and Hungary is the Mura River (length: 465 km, catchment area: 14,304 km²). The main problem of the river before leaving Austria is bed degradation (average 0.5 m from 1970 to 2000) as a combined consequence of river regulation works and the reduced sediment supply from the upstream reaches due to the construction of hydro power plants. River restoration measures for the river reach on the border between Austria and Slovenia (SLO–A Mura reach) were proposed in 2000 to support both ecological and flood protection purposes that apply the concept “of self-restoration”. In order to apply similar process-oriented restoration strategies in the Mura River downstream in Slovenia, we consider the potentials for self-forming river processes. We have analysed the sediment granulometry and morphology of the Mura River in Slovenia, and discussed morphodynamic processes to detect potential for the Mura River recovery into a more diverse morphological structure. The cross section area increased by 8% between 1979 and 2005 on average, mainly due to riverbed degradation. On average, the thalweg of the Mura riverbed in Slovenia had degraded by 0.28 m in the 1979–2007 period, with the highest degradation of 2.28 m in one cross section and some cross sections being stable. The high river degradation trend from the SLO–A Mura reach is slowly shifting to the downstream direction into the Mura River in Slovenia. Nevertheless, the clear downstream coarsening of river sediments turns into the normal trend of sediment fining in the Mura River reach in Slovenia. The “self-restoration” potential in the Mura River reach in Slovenia is larger than on the SLO–A Mura reach due to still active morphological fluvial processes. These processes can be enhanced by the inflow of fresh coarse sediments from the SLO–A Mura reach, where active measures for re-establishing sediment transport are under way. In the long term, this will not work as proposed, if no sediment inflow is re-established from the Mura headwaters in Austria.     

Spatial and taxonomic correlates of species and species trait assemblages in soil invertebrate communities

Whether dispersal limitation and phylogenetic conservatism influence soil species assemblages is still a debated question. We hypothesized that spatial and phylogenetic patterns influence communities in a hump-backed fashion, maximizing their impact at intermediate spatial and phylogenetic distances. Species–environment relationships are blurred by dispersal limitation and restricted habitat choice at long and short spatial distances, respectively (Hypothesis 1). Co-occurrence of species/traits is limited by divergent evolution of species/traits and competitive exclusion at long and short phylogenetic distances, respectively (Hypothesis 2). Springtails were sampled over a wide array of environmental gradients, between-sample distance varying from a few cm to several km. We compared communities using species composition, habitat features, and geo-localization. We compared species using co-occurrence, habitat preference, traits and phylogeny. Mantel tests identified which factors contributed the best to species/traits assemblages. Within the studied area, species composition was influenced by habitat more than space. Traits displayed a strong phylogenetic signal, but they contributed less than habitat preferences to species co-occurrence. Species–environment relationships were better displayed within a 200 m distance, supporting Hypothesis 1. Occurrence-habitat preference relationships were better displayed at family level, supporting Hypothesis 2.     

The classification, distribution, and extent of soils with a xeric moisture regime in the United States

Soils with cool, moist winters and relatively warm, dry summers, a Mediterranean climate, are recognized as having a xeric moisture regime in Soil Taxonomy. These soils are classified mostly in taxa that use the formative element “xer” in the name. Soil series with either a xeric moisture regime or an aridic regime bordering on a xeric moisture regime make up more than 48,640,000 hectares in the western part of the United States. They are classified in the orders of Mollisols (20,080,000 ha), Aridisols (11,200,000 ha), Alfisols (5,320,000 ha), Inceptisols (4,800,000 ha), Entisols (4,400,000 ha), Vertisols (1,520,000 ha), Andisols (960,000 ha), and Ultisols (960,000 ha).