http://hdl.handle.net/2005/2 2013-04-29T20:35:07Z 2013-04-29T20:35:07Z Ghara, Mahua http://hdl.handle.net/2005/1875 2012-12-14T07:02:51Z 2012-12-13T18:30:00Z

Title: Divided They Stay : Species Coexistence In A Community Of Mutualists And Exploiters Authors: Ghara, Mahua Abstract: The fig–fig wasp interaction is a classic example of obligate mutualism and coevolution. It is also a nursery pollination mutualism and supports a diversity of exploiter/parasite/non-pollinating fig wasp species. Mutualists and exploiters comprise the fig wasp community. All the wasp community members are obligately dependent on the fig syconium (a globular closed structure comprising of hundreds to thousands of uniovulate florets) for completing their life cycle. The fig florets can be sessile (without a stalk) or pedicellate (stalked) and can support a community comprising 3–30 wasp species. Fig wasps can access the floral resources for oviposition directly by entering into the syconium (internal oviposition) or by penetration of the syconium surface (external oviposition). Most studies on the fig–fig wasp interaction have investigated the stability of the interaction, pollination biology, pollen dispersal, co-evolution or the effect of exploiters on this mutualism. However, studies dealing with community ecology and species coexistence mechanisms in these communities are rare. Factors contributing to coexistence of mutualists and exploiters in a fig wasp community were studied using a reasonably speciose fig wasp community associated with Ficus racemosa in south India. The wasp community of Ficus racemosa comprises a single species of pollinator and six species of exploiters; together they represent three genera of fig wasp species. The community members show differences in their feeding habit; they could be 1) gallers (feed on floral tissue after pollination and/or after inducing abnormal tissue development of the floret that is also called the gall), 2) inquilines (feed on gall tissue but cannot induce galling; survive by feeding on gall tissue and starving the host larva to death), or 3) parasitoids (lay eggs in or on developing offspring of a galler or inquiline species; develop by feeding on host tissue). Resource partitioning across temporal and spatial axes on this fig wasp community have been quantified. Ovipositor traits of each community member were also investigated since variation in ovipositor traits might facilitate resource partitioning. Finally, the role of life-history traits in species coexistence in this community was also explored. Temporal resource partitioning among members of the fig wasp community was studied (1) across the resource phenology, i.e. over the development phases of the fig syconium, and (2) on a diel scale. The seven members of the wasp community were found to partition their oviposition periods across fig syconium development phenology; some species used very young syconia (soft and smaller in size) for oviposition whereas others used mature (hard and bigger in size) syconia for oviposition. The first species to colonise the syconia were gallers and these were followed by parasitoids in a definite oviposition sequence. Pollinators arrived concurrently with an exploiter galler species and had the shortest oviposition window in terms of days. Although fig wasps are known to be largely diurnal, night oviposition in several fig wasp species was documented for the first time. Wasp species showed a peak in their activity period across the diel cycle and phenology. This is probably the first study to simultaneously investigate temporal partitioning across the syconium phenology as well as the diel scale in a fig wasp community. Partitioning of syconium space was investigated by quantifying the quality (type of floret—sessile or pedicellate) of floral resources. The number of individuals of each species developing in a syconium was quantified along with host accessibility during oviposition by each wasp species. The association between community members developing within a syconium was also tested. The differential occupancy of florets by each species based on their distance from the base of the syconium was evaluated. For the first time the relative distribution of males and females of the entire fig wasp community was quantified. The wasp community members used similar types of florets for oviposition. Seeds were found mostly in sessile florets and wasps were present in large numbers in pedicellate florets. Except for one wasp species, all others occurred uniformly within the syconium with respect to the distance from the base of the syconium. Species distribution models revealed higher prediction ability for the location of mutualists (seed and pollinator) within the syconium compared to exploiters. Within a syconium, all species pairs exhibited positive associations indicating either an absence of or low competitive exclusion. Some florets were modified by their gall occupants such that they were longer in length indicating the possibility of creation of an enemy-free zone by the gall occupant. Yet, most florets were accessible to ovipositing wasps based on ovipositor lengths and flexibility. The probability of finding a male decreased with increase in floret length when all wasp species were grouped together; however, this trend did not hold true when males and females of species were tested individually. Based on these results, the fig wasps of F. racemosa could be grouped into—(1) Early-arriving galler species which used immature florets, inducing large galls that protruded into the cavity, and with fewer individuals per syconium, (2) Galler species arriving concurrently with the pollinator, inducing galls that were morphologically indistinguishable from those of the pollinator, and with many individuals developing per fig syconium, and (3) Parasitoids and/or inquilines of the galler species, with variable abundance per syconium. Thus, these results show that the wasp species do not clearly partition floral resources between syconia and within syconium but they can modify their oviposition sites and also differ in the proportion of florets within a syconium used for oviposition. Oviposition sites of the fig wasps can be reached only by using their ovipositor. The resources for oviposition are hidden and hence might require tools for resource location and utilisation. The frequency and diversity of sensilla on the ovipositor, as well as ovipositor structure (morphology and sclerotisation of the tip) was documented for the entire wasp community. The internally-ovipositing pollinator had the simplest ovipositor, negligible sclerotisation and only one type of sensillum on its ovipositor; the externally ovipositing exploiter species had teeth on their ovipositors, sclerotisation and various types of ovipositor sensilla. Ovipositor sclerotisation and lateness of arrival for oviposition in syconium development were positively correlated. Ovipositor teeth height increased from gallers to parasitoids. Presence of different types of sensilla was noted which included mechano- and chemosensilla, as well as combined mechano-chemosensilla. Chemosensilla were most concentrated at ovipositor tips while mechanoreceptors were more widely distributed. Ovipositor traits of one putative parasitoid/inquiline species differed from those of its syntopic galler congeners and clustered with those of parasitoids within a different wasp subfamily. Thus ovipositor tools show lability based on adaptive necessity, and are not constrained by phylogeny. Life-history traits such as fecundity, pre-adult and adult lifespan were studied for each wasp member of the community. Trade-offs in life-history traits were also investigated. Interspecific variation in life-history traits was observed. Gallers were pro-ovigenic (all eggs were mature upon adult emergence) whereas parasitoids were synovigenic (eggs matured progressively during adult lifespan). Initial egg load was correlated with body size for some species, and there was a trade-off between egg number and egg size across all species. Although all species completed their development and left the syconium concurrently, they differed in their adult and preadult lifespans. Providing sucrose solutions increased parasitoid lifespan but had no effect on the longevity of some galler species. While feeding regimes and body size affected longevity in most species, an interaction effect between these variables was detected for only one species. Life-history traits of wasp species exhibited a continuum in relation to their arrival sequence at syconia for oviposition during syconium development, and therefore reflected their ecology. The largest number of eggs, smallest egg sizes, and shortest longevities were characteristic of the earliest-arriving galling wasps at the smallest, immature syconia; the converse characterised the later-arriving parasitoids at the larger, already exploited syconia. Thus life-history is an important correlate of community resource partitioning and can be used to understand community structure. The comparative approach revealed constraints and flexibility in trait evolution. This is probably the first comprehensive study of life-history traits in a fig wasp community.

2012-12-13T18:30:00Z Bansal, Rohini http://hdl.handle.net/2005/1936 2013-02-25T09:38:19Z 2013-02-24T18:30:00Z

Title: Phylogeny And Biogeography Of Hemidactylus Oken, 1817 Geckos Of The Indian Subcontinent Authors: Bansal, Rohini Abstract: Geckos of the genus Hemidactylus Oken, 1817 are one of the most widely distributed and species-rich groups of gekkonids. With approximately 90 species, the genus Hemidactylus accounts for 10% of the total number of species in the family Gekkonidae (Carranza and Arnold, 2006). They are found in a range of ecological conditions from wet tropical forest to arid deserts. Their wide distribution is believed to have been facilitated not only naturally, but also through human mediated transport. Indian subcontinent houses 31 species of these geckos, 23 of which are endemic to the subcontinent. The aim of this study was to understand the phylogeny and biogeography of Hemidactylus geckos of the Indian subcontinent. In order to arrive at the conclusions regarding the biogeographic history of this widely distributed taxon on the Indian subcontinent, an integrative approach was followed. First the phylogenetic reconstruction of Indian species was undertaken. The ancestral areas of distribution were reconstructed on the phylogeny and the divergence dates of the species were also estimated. Finally, the biogeographic events were inferred in accordance with the geological events with respect to the divergent times for these radiations. Results indicated that Hemidactylus geckos of the Indian subcontinent belong to three geographical clades: Southeast Asian clade, West-Asian arid clade and a ‘unique Indian radiation’ which consisted majority of the species distributed in India that are largely confined to the Indian subcontinent. Additionally, the three widely distributed, commensal species (H. brookii, H. frenatus and H. flaviviridis) were nested within the Indian radiation suggesting their Indian origin. It was also seen that the endemic Hemidactylus geckos of Sri Lanka have been derived from India through multiple independent dispersal events spread across the Oligocene-Miocene. These dispersals were both geo dispersal as well as transmarine dispersal events. However, the species distributed both in India and Sri Lanka appear to have undergone recent dispersals into Sri Lanka and probably back into India, primarily through human agency. Thus, it was inferred that the Indian subcontinent has served as an important arena for diversification among the Hemidactylus geckos and their spread. In addition, it was discovered that H. anamallensis, a species endemic to Southern Western Ghats of peninsular India was probably genetically distinct from Hemidactylus, indicating that it could not be Hemidactylus at all. Thus, the phylogenetic position of H. anamallensis within the subfamily Gekkoninae was also investigated and its genetic distinctiveness from that of Hemidactylus was also tested. Results showed that H. anamallensis lineage was indeed distinct from Hemidactylus group, as well as from other closely related genera (Cyrtodactylus and Geckoella) in both nuclear and mitochondrial markers. Divergence estimates supported a scenario wherein H. anamallensis dispersed across marine barrier to the drifting peninsular Indian plate in the late Cretaceous, whereas Hemidactylus arrived on the peninsular India after the Indian plate collided with the Eurasian plate. Based on these molecular evidence and biogeographical scenario it was proposed that genus Dravidogecko should be resurrected.

2013-02-24T18:30:00Z Kommireddy, Vasu http://hdl.handle.net/2005/1957 2013-03-27T07:36:41Z 2013-03-26T18:30:00Z

Title: Evolutionary Design Of Active Site Plasticity In R.KpnI For Promiscuity In Metal Ion Utilization And Substrate Recognition Authors: Kommireddy, Vasu Abstract: Restriction modification (R-M) systems are important components of the prokaryotic arsenal against invading genomes. R-M systems directly target the foreign DNA and are often considered as primitive immune systems in bacteria. The defense system comprises of two contrasting enzymatic activities – a restriction endonuclease (REase) and a methyltransferase (MTase). Functionally, REases cleave a specific DNA sequence endonucleolytically at the phosphodiester bonds generating 5' or 3' overhangs or blunt ends. MTases catalyze the transfer of a methyl group from S-adenosyl-Lmethionine to adenine or cytosine. Four types of R–M systems are found in bacteria, viz., Types I, II, III and IV. Type II R-M systems, comprising of a separate REase and MTase, are the most abundant and well-studied enzymes. Type II REases recognize and cleave DNA within or near their recognition sequences. Surprisingly, these enzymes share little or no sequence homology amongst them. All the enzymes identified so far can be grouped into conventional PD-(D/E)XK, ββα-Me, GIY-YIG, phospholipase-derived and half-pipe endonucleases according to their folds and active site structures. Owing to their high specificity and defined cleavage pattern, they have become indispensable tools in molecular biology and have been widely exploited for studying protein–DNA interactions. The work presented in this thesis deals with R.KpnI, which belongs to the HNH superfamily of nucleases and is characterized by the presence of a ββα-Me finger motif. The REase isolated from Klebsiella pneumoniae recognizes the palindromic DNA sequence GGTAC/C and cleaves DNA as indicated. The enzyme is unique in exhibiting promiscuous DNA cleavage in the presence of Mg2+, a natural co-factor for a vast majority of REases. Surprisingly, Ca2+ and Zn2+ completely suppress the Mg2+ mediated promiscuous activity and induce high fidelity cleavage. These unusual features of R.KpnI led to the functional characterization of the ββα-Me finger active site motif. In addition, the studies were aimed at understanding the mechanism and the biological significance of substrate and co-factor promiscuity exhibited by the enzyme. The salient aspects of the thesis are summarized below. A general introduction and overview of the literature on structure-function studies, mechanism of recognition and catalysis by REases with special emphasis on Type II enzymes is presented in the Chapter 1. An account of co-factor specificity in REases, role of metal ions in DNA binding as well as in phosphodiester bond hydrolysis is provided. The various aspects of R-M systems that target the invading DNA elements and counter strategies employed by the foreign genomes to evade the restriction are also covered. The new developments that provide insights in understanding the diversity of R-M systems and additional biological roles that could increase the fitness of the host organism harboring them are described. The features of substrate and metal ion specificity in REases and the efforts undertaken to alter the specificity have been dealt at the end of the chapter. From the structures of the several ββα-Me finger nucleases, the α-helix has been implicated in providing a structural scaffold for the correct juxtapositioning of the catalytic residues. However, no mutagenesis data exists to delineate its role. Homology modeling studies of R.KpnI suggested a crossover structure for the α-helix of the ββαMe finger active site motif, which could possibly form dimeric interface and/or structural scaffold for the active site. Chapter 2 describes the computational modeling and mutational analysis performed to understand the role of the residues present in this α-helix in intersubunit interactions and/or stabilization of the active site. Mutation of the residues present in the α-helix lead to the loss of the enzyme activity, but not dimerization ability. Subsequent biophysical experiments showed that the α-helix of the ββα-Me finger of R.KpnI plays an important role for the stability of the protein–DNA complex needed for its function. In Chapter 3, unusual co-factor flexibility for R.KpnI is shown by using a battery of divalent metal co-factors differing in ionic radii and coordination geometries. A number of alkaline earth and transition group metal ions function as co-factors for DNA cleavage. The metal ions replaced each other readily from the enzyme’s active site revealing the active site plasticity. Mutation of the invariant His residue of the HNH motif caused abolition of the enzyme activity with all the co-factors indicating that the enzyme follows single metal ion mechanism for DNA cleavage. The indispensability of the invariant His in nucleophile activation together with the broad co-factor tolerance of the enzyme indicated the role of metal ions in electrostatic stabilization during catalysis. At higher concentrations, Mg2+, Mn2+ or Co2+ stimulate promiscuous cleavage while Cd2+, Ni2+ or Zn2+ inhibit phosphodiester bond hydrolysis. The underlying molecular mechanisms for the modulation of the enzyme activity by the metal ion binding to the second site are presented. Regulation of the endonuclease activity and fidelity by a second metal ion binding is a unique feature of R.KpnI among REases and HNH nucleases. The identification of additional metal ion binding residues would help in engineering REase variants with enhanced activity and/or specificity. Chapter 4 describes the generation of an R.KpnI variant with altered co-factor specificity by exploiting the active site plasticity of the enzyme. The mutant enzyme is a Mn2+ -dependent endonuclease defective in DNA cleavage with Mg2+ and other divalent metal ions. In the engineered mutant, only Mn2+ is selectively bound at the active site, imparting in vitro activity while being dormant in vivo. In addition to the Mn2+ selectivity, the mutant is impaired in concerted double-stranded DNA cleavage leading to the accumulation of nicked intermediates. The nicking activity of the mutant enzyme is further enhanced by altering the reaction conditions. Thus, a single point mutation in the active site of R.KpnI generates a Mn2+ -dependent REase and a sequence specific nicking endonuclease. The potential applications of such enzymes engineered for selective metal ion dependent activities have been discussed. R.KpnI is peculiar in retaining robust promiscuous cleavage despite being a typical Type II REase in all other characteristics. Chapter 5 presents results of the growth properties and phage titer analysis carried out with R.KpnI and its high fidelity variant to understand the biological significance of promiscuous activity. The enzyme isolated from the K. pneumoniae exhibited biochemical properties similar to that of R.KpnI overexpressed in E.coli. It was observed that the wild type but not the high fidelity variant could effectively restrict bacteriophages methylated at GGTACC. These results show that the REase exhibits promiscuous activity in vivo, which would be advantageous for the organism to better target the incoming foreign DNA. The promiscuous behavior of the R.KpnI could be one of the counter strategies employed by the bacteria against the constantly evolving phages in the co-evolutionary arms race. In conclusion, the work described in this thesis provides new insights about structure, function and biology of REases in general and R.KpnI in particular. The co-factor and substrate promiscuity of R.KpnI may indicate its evolutionarily intermediate form that is yet to attain a high degree of specificity. Alternatively, it is possible that this unique feature is retained during the evolution of the HNH REases serving some unknown function(s) in the cell, in addition to having an edge in countering the phage infections.

2013-03-26T18:30:00Z Ranganathan, Yuvaraj http://hdl.handle.net/2005/1959 2013-04-01T07:20:53Z 2013-03-31T18:30:00Z

Title: Ants, Figs, Fig Wasps : The Chemical Ecology Of A Multitrophic System Authors: Ranganathan, Yuvaraj Abstract: Plant–animal interaction systems are complex food webs where the members—plants, pollinators, herbivores, parasites and predators of the pollinators/herbivores—interact with each other in ways which maximize their own fitness. Based on the net outcome, such interactions could be mutually beneficial to the interacting members (mutualism) or beneficial to only one of the interacting members at the cost of the other interacting members (herbivory, predation, parasitism). It is possible that such outcomes are actually a continuum and could swing in either direction from beneficial to detrimental and vice versa. Such transitions happen not only over long time scales, but could also happen within shorter time scales based on conditionalities. Conditional outcomes are those in which the outcome of an interaction between two partners is conditional on the involvement of a third partner. Thus, studying such outcomes necessitates taking into account systems beyond the classical two-partner interactions. In such complex multitrophic plant–animal interaction systems in which there are direct and indirect interactions between species, comprehending the dynamics of these multiple partners is very important for an understanding of how the system is structured. In Chapter 2 we investigate Ficus racemosa and its community of obligatory mutualistic and parasitic fig wasps that develop within the fig inflorescence or syconium, as well as their interaction with opportunistic ants. We focus on temporal resource partitioning among members of the fig wasp community over the development cycle of the fig syconia during which wasp oviposition and development occur and we study the activity rhythm of the ants associated with this community. We found that the members of the wasp community partitioned their oviposition across fig syconium development phenology and showed interspecific variation in activity across the diel cycle. The wasps presented a distinct sequence in their arrival at fig syconia for oviposition. We documented night oviposition in several fig wasp species for the first time. Ant activity on the fig syconia was correlated with wasp activity and was dependent on whether the ants were predatory or trophobiont-tending species; only numbers of predatory ants increased during peak arrivals of the wasps. In Chapter 3, we found that predatory ants (Oecophylla smaragdina) patrolling F. racemosa trees were attracted to the odour from fig syconia at different developmental phases, as well as to the odours of fig wasps, whereas other predatory ants (Technomyrmex albipes) responded only to odours of syconia from which fig wasps were dispersing and to fig wasp odour. However, trophobiont-tending ants (Myrmicaria brunnea) patrolling the same trees and exposed to the same volatiles were unresponsive to fig or fig wasp odours. The predatory ants demonstrated a concentration-dependent response towards volatiles from figs receptive to pollinators and those from which wasps were dispersing while the trophobiont-tending ants were unresponsive to such odours at all concentrations. Naıve predatory ants failed to respond to the volatiles to which the experienced predatory ants responded, indicating that the response to fig-related odours is learned. In Chapter 4 we characterise the dynamics of the volatile bouquet of the fig syconium from the initiation through pre-receptive, receptive, and late inter-floral stages which act as signals/ cues for different fig wasp species. We were also interested in diel patterns of volatile emission as some fig wasp species were strictly diurnal (the pollinator, Ceratosolen fusciceps) whereas other fig wasps such as Apocryptophagus fusca were observed ovipositing even during the nocturnal hours. We identified volatiles that were specific to syconium development phase as well as to the time of day in this bouquet. α-muurolene was identified as the sesquiterpene specific to receptive-phase as well as being present only during the day thus coinciding with the diurnal pollinator arrival pattern. Volatiles such as (E)-β-ocimene were present in increasing levels across the developmental stages of the fig and thus could act as background volatiles providing suitable information to fig wasps about host plants and their phases. Chapter 5 examines the responses of predatory and trophobiont-tending ant species to the cuticular hydrocarbon (CHC) extracts of four galler and two parasitoid fig wasp species associated with F. racemosa. Interestingly, the antennation response of both experienced and na¨ıve ants to these wasp extracts was identical indicating that prior exposure to such compounds is not necessary for eliciting such response. We also characterised these cuticular hydrocarbon extracts to find potential compounds which could as short-range cues for predatory ants. Ants were more responsive to the cuticular extracts of parasitoids rather than to those of galler wasps, implying that the CHC profile of carnivorous prey may contain more elicitors of aggressive behaviour in ants compared to herbivorous prey whose profiles may be more similar to those of their plant resources. We also find congruency between the cuticular profiles of parasitoids and their hosts suggesting that parasitoids could sequester compounds from their diet. Important findings and conclusions of the thesis are presented in Chapter 6. The first two parts of the appendices section discuss work carried out on alternative ways of analysing multivariate data sets such as plant volatiles and insect cuticular hydrocarbons. Appendix A details the use of Random Forests, an algorithm-based method of analysing complex data sets where there are more variables than samples, a situation akin to microarray data sets. This work illustrates the use of such techniques in chemical ecology, highlighting the potential pitfalls of classical multivariate tests and the advantages of newer more robust methods. Appendix B, an invited article following the publication of the earlier work, compares different data transformation procedures currently employed in such multivariate analysis. Appendix C details sex-specific differences in cuticular hydrocarbons of fig wasps, using the pollinator C. fusciceps as a case study.

2013-03-31T18:30:00Z