Genetic diversity of mango accessions (Mangifera indica) using new microsatellite markers and morphological descriptors.

Genetic diversity estimates based on morphological and molecular data can provide different information on the relationship between cultivars of a species. This study aimed to develop new microsatellite markers as additional tools in genetic studies on mangoes (Mangifera indica L.), and to analyze the genetic variability of 20 mango cultivars based on morphological descriptors and microsatellite markers. We aimed to better understand the cultivars enhanced breeding histories and to support crossbreeding planning. Positive clones were selected from a DNA library enriched for microsatellite regions for sequencing and primer design. Four plants of each of the 20 accessions were used for observations, based on 48 morphological descriptors. Twenty accessions were analyzed using 27 microsatellite markers, of which 16 were developed during this study. The clusters, based on the morphological descriptors by Ward - MLM strategy and the microsatellite markers, suggested that Brazilian mango cultivars have extensive genetic diversity and are related to cultivars with different provenances, demonstrating their different enhanced breeding histories.

Molecular data extend Australian Cricotopus midge (Chironomidae) species diversity, and provide a phylogenetic hypothesis for biogeography and freshwater monitoring

Resolving species relationships and confirming diagnostic morphological characters for insect clades that are highly plastic, and/or include morphologically cryptic species, is crucial for both academic and applied reasons. Within the true fly (Diptera) family Chironomidae, a most ubiquitous freshwater insect group, the genera CricotopusWulp, 1874 and ParatrichocladiusSantos-Abreu, 1918 have long been taxonomically confusing. Indeed, until recently the Australian fauna had been examined in just two unpublished theses: most species were known by informal manuscript names only, with no concept of relationships. Understanding species limits, and the associated ecology and evolution, is essential to address taxonomic sufficiency in biomonitoring surveys. Immature stages are collected routinely, but tolerance is generalized at the genus level, despite marked variation among species. Here, we explored this issue using a multilocus molecular phylogenetic approach, including the standard mitochondrial barcode region, and tested explicitly for phylogenetic signal in ecological tolerance of species. Additionally, we addressed biogeographical patterns by conducting Bayesian divergence time estimation. We sampled all but one of the now recognized Australian Cricotopus species and tested monophyly using representatives from other austral and Asian locations. Cricotopus is revealed as paraphyletic by the inclusion of a nested monophyletic Paratrichocladius, with in-group diversification beginning in the Eocene. Previous morphological species concepts are largely corroborated, but some additional cryptic diversity is revealed. No significant relationship was observed between the phylogenetic position of a species and its ecology, implying either that tolerance to deleterious environmental impacts is a convergent trait among many Cricotopus species or that sensitive and restricted taxa have diversified into more narrow niches from a widely tolerant ancestor.

Assessment and rationalization of genetic diversity of Papua New Guinea taro (Colocasia esculenta) using SSR DNA fingerprinting

Taro (Colocasia esculenta) accessions were collected from 15 provinces of Papua New Guinea (PNG). The collection, totalling 859 accessions was collated for characterization and a core collection of 81 accessions (10%) was established on the basis of characterization data generated on 30 agro-morphological descriptors, and DNA fingerprinting using seven SSR primers. The selection of accessions was based on cluster analysis of the morphological data enabling initial selection of 20% accessions. The 20% sample was then reduced and rationalized to 10% based on molecular data generated by SSR primers. This represents the first national core collection of any species established in PNG based on molecular markers. The core has been integrated with core from other Pacific Island countries, contributing to a Pacific regional core collection, which is conserved in vitro in the South Pacific Regional Germplasm Centre at Fiji. The core collection is a valuable resource for food security of the South Pacific region and is currently being utilized by the breeding programmes of small Pacific Island countries to broaden the genetic base of the crop.

Phylogenetics, taxon delimitation and phylogenetic diversity

Throughout the history of Linnean taxonomy, species have been described with varying degrees of justification. Many descriptions have been based on only a few ambiguous morphological characters. Moreover, species have been considered natural, well-defined units whereas higher taxa have been treated as disparate, non-existent creations. In the present thesis a few such cases were studied in detail. Often the species-level descriptions were based on only a few specimens and the variation previously thought to be interspecific was found to be intraspecific. In some cases morphological characters were sufficient to resolve the evolutionary relationships between the taxa, but generally more resolution was gained by the addition of molecular evidence. However, both morphological and molecular data were found to be deceptive in some cases. The DNA sequences of morphologically similar specimens were found to differ distinctly in some cases, whereas in other closely related species the morphology of specimens with identical DNA sequences differed substantially. This study counsels caution when evolutionary relationships are being studied utilizing only one source of evidence or a very limited number of characters (e.g. barcoding). Moreover, it emphasizes the importance of high quality data as well as the utilization of proper methods when making scientific inferences. Properly conducted analyses produce robust results that can be utilized in numerous interesting ways. The present thesis considered two such extensions of systematics. A novel hypothesis on the origin of bioluminescence in Elateriformia beetles is presented, tying it to the development of the clicking mechanism in the ancestors of these animals. An entirely different type of extension of systematics is the proposed high value of the white sand forests in maintaining the diversity of beetles in the Peruvian Amazon. White sand forests are under growing pressure from human activities that lead to deforestation. They were found to harbor an extremely diverse beetle fauna and many taxa were specialists living only in this unique habitat. In comparison to the predominant clay soil forests, considerably more elateroid beetles belonging to all studied taxonomic levels (species, genus, tribus, and subfamily) were collected in white sand forests. This evolutionary diversity is hypothesized to be due to a combination of factors: (1) the forest structure, which favors the fungus-plant interactions important for the elateroid beetles, (2) the old age of the forest type favoring survival of many evolutionary lineages and (3) the widespread distribution and fragmentation of the forests in the Miocene, favoring speciation.

Behavioural and morphological dimorphism of the sexes: an account of two primitively eusocial wasps

In social Hymenoptera, foraging, nest building, brood care and all other colony maintenance functions are carried out by the females while males function solely as reproductives. This asymmetry in social roles of the two sexes has led social insect researchers to focus almost exclusively on the females whereas males have remained relatively neglected. We studied two sympatric, primitively eusocial wasps, Ropalidia marginata and Ropalidia cyathiformis, and compared the morphological and behavioural profiles of males and females. Males of both species are smaller in size and weigh less compared to females. Males of the two species live in the nest for different durations. Borrowing from the ecological literature we use novel methods to compute and compare behavioural diversity and behavioural richness and show that females of both species are behaviourally richer and more diverse than the males.

Coalescent Method in Conjunction with Niche Modeling Reveals Cryptic Diversity among Centipedes in the Western Ghats of South India

Background: There has been growing interest in integrative taxonomy that uses data from multiple disciplines for species delimitation. Typically, in such studies, monophyly is taken as a proxy for taxonomic distinctiveness and these units are treated as potential species. However, monophyly could arise due to stochastic processes. Thus here, we have employed a recently developed tool based on coalescent approach to ascertain the taxonomic distinctiveness of various monophyletic units. Subsequently, the species status of these taxonomic units was further tested using corroborative evidence from morphology and ecology. This inter-disciplinary approach was implemented on endemic centipedes of the genus Digitipes (Attems 1930) from the Western Ghats (WG) biodiversity hotspot of India. The species of the genus Digitipes are morphologically conserved, despite their ancient late Cretaceous origin. Principal Findings: Our coalescent analysis based on mitochondrial dataset indicated the presence of nine putative species. The integrative approach, which includes nuclear, morphology, and climate datasets supported distinctiveness of eight putative species, of which three represent described species and five were new species. Among the five new species, three were morphologically cryptic species, emphasizing the effectiveness of this approach in discovering cryptic diversity in less explored areas of the tropics like the WG. In addition, species pairs showed variable divergence along the molecular, morphological and climate axes. Conclusions: A multidisciplinary approach illustrated here is successful in discovering cryptic diversity with an indication that the current estimates of invertebrate species richness for the WG might have been underestimated. Additionally, the importance of measuring multiple secondary properties of species while defining species boundaries was highlighted given variable divergence of each species pair across the disciplines.

Population diversity studies of pharaoh cuttlefish (Sepia pharaonis) in the Persian Gulf and the Gulf of Oman

The pharaoh Cuttlefish (Sepia Pharaonis) is the most abundant species in the persian gulf and oman sea. The stock patterns of this species was studied conserning biological, morphological and electrophoretical aspects. In addition to measuring the biological patterns; 21 quantitative and qualitative factors were measured or counted. There tissues namely muscle, eye and liver were also used for further polyacrylamide electrophoresis analysis (SDS-Page method). The densitograms of protein bands of each tissue were prepared by Gel-Scanner and also the amount of bands' areas were estimated. The results of LSD test showed that tentacle length (TL), Tentacle club length (TCL) and TCL were indicative factors which they showed significant difference between male TL and female specimen of Bushehr and Balouchestan regions. Regarding to length and weight frequencies data the results indicated that males are always bigger than females and also, the cuttlefishes of the gulf of oman are bigger than persian gulf's samples. There were found a significant sample correlation (95%) between different quantitative parameters and the most correlation (0.963) was found to be between TL and TCL; whereas the less correlation (0.384) was observed between GL and LA3. However the gill length factor illustrated the less correlation with the other factors. The results of Cluster analysis for both sexes showed that the cuttlefishes of both studied regions belongs to seperate stocks. The electrophoretic experiments of proteins showed that the protein bands of the sample tissue of muscle and eye from both sampling areas revealed significant differences; whereas the tissue of liver wasn't recognized as an indicative tissue for population studies. Taking into consideration the findings of the present study including: (1) difference in spawning season, (2) results of dendrograms, (3) observed Significant differences in one-way analysis of variance (ANOVA) for morphometric measurements, (4) differences in body length and weight, (5) ecological variations of the persian gulf and oman sea, (6) as well as the results of electrophoresis of proteins have indicatend that: "The Pharaoh cuttlefishes of Bushehr and Balouchestan waters belong to two seperate stocks. Also, it is believed that each region has propably two different populations and more studies are needed to approve this result.

Molecular and morphological analysis of endangered species Gymnodiptychus integrigymnatus (Teleostei: Cyprinidae)

Gymnodiptychus integrigymnatus is a critically endangered species endemic to the Gaoligongshan Mountains. It was thought to be only distributed in several headwater-streams of the Longchuanjiang River (west slope of the Gaoligongshan Mountains, belonging to the Irrawaddy River drainage). In recent years, dozens of G. integrigymnatus specimens have been collected in some streams on the east slope of the Gaoligongshan Mountains (the Salween drainage). We performed a morphological and genetic analyses (based on cytochrome b and D-loop) of the newly discovered populations of G. integrigymnatus to determine whether the degree of separation of these populations warrants species status. Our analysis from the cytochrome b gene revealed that nine individuals from the Irrawaddy drainage area and seven individuals from the Salween drainage area each have only one unique haplotype. The genetic distance between the two haplotypes is 1.97%. Our phylogenetic analysis revealed that G. integrigymnatus is closely related to highly specialized schizothoracine fishes. Analysis from the mitochondrial control region revealed that G. integrigymnatus has relatively high genetic diversity (pi was 0.00891 and h was 0.8714), and individuals from different river drainages do not share the same haplotypes. The AMOVA results indicated 87.27% genetic variability between the Salween and Irrawaddy populations. Phylogenetic trees show two major geographic groups corresponding to the river systems. We recommend that G. integrigymnatus should be considered as a high priority for protected species status in the Gaoligongshan Mountains National Nature Reserve, and that the area of the Gaoligongshan Mountains National Nature Reserve should be expanded to cover the entire distribution of G. integrigymnatus. Populations of G. integrigymnatus from different river systems should be treated as evolutionarily significant units.

Genetic status of selected fish taxa in relation to conservation of genetic and species diversity in the Victoria and Kyoga Lake basins

Cichlids are known for their explosive radiation especially in the African Great Lakes marked with a high level of lake endemism. These fishes have been characterized mainly along trophic and habitat differences, by variation in morphological structures such as teeth and jaws and by differences in body shape and coloration. Cichlids are important as a microcosm of macroevolution. The explosive radiation, young evolutionary scale, and the isolation of groups characterized with high levels of endemism and presence of living fossils makes the group important for evolutionary and genetic studies. Lake Victoria region cichlids which are isolated and relatively more recent in evolution were the last to be appreciated in their diversity. Recently Ole Seehausen has found scores of rock fishes in Lake Victoria which were up to then thought to be absent from the Lake and only known to occur in Lakes Malawi and Tanganyika. Greenwood put together the species groups of Lake Victoria, and later in the early 1980's revised the classification of haplochromine species to reflect the phyletic origin and interrelationship of the various groups in Lake Victoria region. Melan Stiassny has been interested in early evolution of cichlids while the likes of Paul Fuerst and Lees Kaufman and Axel Meyer have been interested and are working to explain the speciation mechanisms responsible for the explosive radiation and evolution of cichlids. Locally S.B Wandera and his student Getrude Narnulemo are spearheading the biodiversity and taxonomic studies of cichlids in Lake Victoria region

A new species of Amolops (Anura : Ranidae) from Yunnan, China, with a discussion of karyological diversity in Amolops

We describe a new species, Amolops tuberodepressus, from the mountainous regions of Jingdong County, Yunnan Province, China. This species differs from all other congeners in a combination of both karyological and morphological characteristics. Morphologically, the new species resembles A. mantzorum, A. kangtingensis, A. jinjiangensis, and A. liangshanensis occurring in southern Sichuan and northern Yunnan and may easily be confused with those species. However, Amolops tuberodepressus differs from those species by the presence of a distinct tympanum, flatter supratympanic fold, flatter tubercles on the flanks, and absence of a dorsolateral Fold. Karyological evidence also strongly supports the distinctness of the new species. A consideration of one Karyological character demonstrates that species of Amolops in southwestern China all share secondary constrictions on chromosome pair six. In view of the morphological similarity among species df Amolops in southwestern China, these species may have only recently diverged from a common ancestral species.

Ulva diversity in the Yellow Sea during the large-scale green algal blooms in 2008-2009

P>In the Yellow Sea of China, large-scale green tides have broken out for three consecutive years from 2007 to 2009. As part of the efforts to localize the algal source, two cruises were conducted in the early stage and the outbreak stage of the bloom in 2009. We analyzed the morphological and genetic diversity of drifting Ulva specimens and culture-derived isolates from seawater sampled in different localities. For phylogenetic analyses, the nuclear encoded ribosomal DNA internal transcribed spacer region (ITS nrDNA) and the plastid encoded large subunit of ribulose-1, 5-bisphosphate carboxylase/oxgenase gene (rbcL) were used. Our molecular and morphological data indicate that the dominant free-floating Ulva species in 2008 and 2009 possibly belonged to a single strain of the U. linza-procera-prolifera (LPP) clade. The ITS sequences from bloom-forming algal samples with dense branches were identical to those from U. linza-like specimens without branches derived from the Yellow Sea. Microscopic individuals of the dominant Ulva strain were detected in eight stations, revealing that spore dispersal in the water helped to enlarge biomass in the water during the outbreak stage of green tide in the Yellow Sea.

Origin of mitochondrial DNA diversity of domestic yaks

Background: The domestication of plants and animals was extremely important anthropologically. Previous studies have revealed a general tendency for populations of livestock species to include deeply divergent maternal lineages, indicating that they were domesticated in multiple, independent events from genetically discrete wild populations. However, in water buffalo, there are suggestions that a similar deep maternal bifurcation may have originated from a single population. These hypotheses have rarely been rigorously tested because of a lack of sufficient wild samples. To investigate the origin of the domestic yak (Poephagus grunnies), we analyzed 637 bp of maternal inherited mtDNA from 13 wild yaks (including eight wild yaks from a small population in west Qinghai) and 250 domesticated yaks from major herding regions.Results: The domestic yak populations had two deeply divergent phylogenetic groups with a divergence time of > 100,000 yrs BP. We here show that haplotypes clustering with two deeply divergent maternal lineages in domesticated yaks occur in a single, small, wild population. This finding suggests that all domestic yaks are derived from a single wild gene pool. However, there is no clear correlation of the mtDNA phylogenetic clades and the 10 morphological types of sampled yaks indicating that the latter diversified recently. Relatively high diversity was found in Qinghai and Tibet around the current wild distribution, in accordance with previous suggestions that the earliest domestications occurred in this region. Conventional molecular clock estimation led to an unrealistic early dating of the start of the domestication. However, Bayesian estimation of the coalescence time allowing a relaxation of the mutation rateConclusion: The information gathered here and the previous studies of other animals show that the demographic histories of domestication of livestock species were highly diverse despite the common general feature of deeply divergent maternal lineages. The results further suggest that domestication of local wild prey ungulate animals was a common occurrence during the development of human civilization following the postglacial colonization in different locations of the world, including the high, arid Qinghai-Tibetan Plateau.

Morphological and genetic variation in the north Atlantic copepod, Centropages typicus

This study describes phenotypic and genotypic variations in the planktonic copepod, Centropages typicus (Copepoda: Calanoida) that indicate differentiation between geographical samples. We found consistent differences in the morphology of the chela of the sexually modified fifth pereiopod (P5) of male C. typicus between samples from the Mediterranean, western North Atlantic and eastern North Atlantic. A 560 base pairs (bp) region of the C. typicus mitochondrial cytochrome c oxidase subunit I (COI) and a 462 bp fragment of the nuclear rDNA internal transcribed spacer (ITS) tandem array were analysed to determine whether these morphological variations reflect population genetic differentiation. Mitochondrial haplotype diversity was found to be high with 100 unique COI haplotypes among 116 individuals. Analysis of mtCOI variation suggested differentiation between the Mediterranean and Atlantic populations but no separation was detected within the Atlantic. Intragenomic variation in the ITS array suggested genetic differentiation between samples from the western North Atlantic and those from the eastern North Atlantic and Mediterranean. Breeding experiments would be required to elucidate the extent of genetic isolation between C. typicus from the different population centres.

Diversity of functional groups in the vegetation sandy seashore of the Grande, Anclitas and Caguamas Cays (Jardines de la Reina Archipelago, Cuba)

Sandy shores are known to be extreme ecosystems where the vegetation has evolved many morphological and physiological adaptations for its survival. With the aim of identify possible relationships between the vegetation´s functional diversity with abiotic factors and its corresponding quantification, we collected data on the abundance and richness of the sandy coast vegetation complex in Grande, Anclitas and Caguamas keys. Its flora is largely characterized by the dominance of hemicryptophytes and chamaephytes plants with nanophyllous leaves and displaying dispersal syndromes such as zoochory and anemochory. However, the functional groups´ richness, in the present study, varies from one key to another. Functional diversity is similar between the wet and dry seasons, and its spatial variation is influenced by the interplay of the set of abiotic factors herein studied.

Analysis of genetic diversity in Portuguese Ceratonia siliqua L. cultivars using RAPD and AFLP markers

Although carob (Ceratonia siliqua L.) is of great economic importance little is still known about the pattern of genetic variation within this species. Morphological characteristics based on 31 fruit and seeds of continuous characters determinant for agro-industrial uses, were compared with RAPD and AFLP markers for assessing genetic distances in 68 accessions of carob trees, from different cultivars, varieties and eco-geographic regions of Algarve. Eighteen selected RAPD primers applied to the 68 accessions produced a total of 235 fragments ranging from 200 to 2000 bp, of which 93 (40%) were polymorphic. Four AFLP selective primer combinations generated a total of 346 amplification fragments of which 110 were polymorphic. The average level of polymorphism based on four primer combinations was 31.8%. The phenetic trees based on RAPD and AFLP analyses gave high co-phenetic correlation values, and were found to be consistent in general with the analysis of morphological data, carried out on the same accessions. A number of RAPD and AFLP markers were found to be diagnostic for ‘Canela’ cultivar and 13 wild ungrafted trees.