Phylogenetic stability, tree shape, and character compatibility: a case study using early tetrapods

Phylogenetic tree shape varies as the evolutionary processes affecting a clade change over time. In this study, we examined an empirical phylogeny of fossil tetrapods during several time intervals, and studied how temporal constraints manifested in patterns of tree imbalance and character change. The results indicate that the impact of temporal constraints on tree shape is minimal and highlights the stability through time of the reference tetrapod phylogeny. Unexpected values of imbalance for Mississippian and Pennsylvanian time slices strongly support the hypothesis that the Carboniferous was a period of explosive tetrapod radiation. Several significant diversification shifts take place in the Mississippian and underpin increased terrestrialization among the earliest limbed vertebrates. Character incompatibility is relatively high at the beginning of tetrapod history, but quickly decreases to a relatively stable lower level, relative to a null distribution based on constant rates of character change. This implies that basal tetrapods had high, but declining, rates of homoplasy early in their evolutionary history, although the origin of Lissamphibia is an exception to this trend. The time slice approach is a powerful method of phylogenetic analysis and a useful tool for assessing the impact of combining extinct and extant taxa in phylogenetic analyses of large and speciose clades

The efficacy and potential risks of controlling sprouting in Finnish birches (Betula spp.) with the fungal decomposer Chondrostereum purpureum

Sprouting of fast-growing broad-leaved trees causes problems in young coniferous stands, under power transmission lines and along roads and railways. Public opinion and the Finnish Forest Certification System oppose the use of chemical herbicides to control sprouting, which means that most areas with problems rely on mechanical cutting. However, cutting is a poor control method for many broad-leaved species because the removal of leaders can stimulate the sprouting of side branches and cut stumps quickly re-sprout. In order to be effective, cutting must be carried out frequently but each cut increases the costs, making this control method increasingly difficult and expensive once begun. As such, alternative methods for sprout control that are both effective and environmentally sound represent a continuing challenge to managers and research biologists. Using biological control agents to prevent sprouting has been given serious consideration recently. Dutch and Canadian researchers have demonstrated the potential of the white-rot fungus Chondrostereum purpureum (Pers. ex Fr.) Pouzar as a control agent of stump sprouting in many hardwoods. These findings have focused the attention of the Finnish forestry community on the utilization of C. purpureum for biocontrol purposes. Primarily, this study sought determines the efficacy of native C. purpureum as an inhibitor of birch stump sprouting in Finland and to clarify its mode of action. Additionally, genotypic variation in Finnish C. purpureum was examined and the environmental risks posed by a biocontrol program using this fungus were assessed. Experimental results of the study demonstrated that C. purpureum clearly affects the sprouting of birch: both the frequency of living stumps and the number of living sprouts per stump were effectively reduced by the treatment. However, the treatment had no effect on the maximum height of new sprouts. There were clear differences among fungal isolates in preventing sprouting and those that possessed high oxidative activities as measured in the laboratory inhibited sprouting most efficiently in the field. The most effective treatment time during the growing season was in early and mid summer (May July). Genetic diversity in Nordic and Baltic populations of C. purpureum was found to be high at the regional scale but locally homogeneous. This natural distribution of diversity means that using local genotypes in biocontrol programs would effectively prevent the introduction of novel genes or genotypes. While a biocontrol program using local strains of C. purpureum would be environmentally neutral, pruned birches that are close to the treatment site would have a high susceptibility to infect by the fungus during the early spring.Lehtipuiden nopea kasvu ja vesominen ovat ongelmana monilla kohteilla, kuten havupuutaimikoissa, voimajohtojen alla ja tienvarsilla. Tehokkaita kemiallisia vesakontorjunta-aineita käytettiin runsaasti vielä 1980-luvulla, mutta niiden käytöstä on lähes kokonaan luovuttu haitallisten ympäristövaikutusten vuoksi. Nykyään vallitseva vesakontorjuntamenetelmä on mekaaninen vesakontorjunta raivaussahan tai -koneiden avulla. Ongelmana on, että lehtipuut kasvattavat nopeasti uusia vesoja katkaistujen tilalle ja raivaus joudutaan suorittamaan uudelleen muutaman vuoden välein. Niinpä uusien tehokkaampien ja ympäristölle ystävällisten vesakontorjuntamenetelmien kehittäminen on tulevaisuuden haaste. Biologisen vesakontorjunnan mahdollisuuksia on tutkittu 1980-luvulta lähtien mm. Hollannissa ja Kanadassa. Biologiseen vesakontorjuntaan on käytetty purppuranahakka (Chondrostereum purpureum) -nimistä lahottajasientä, jonka rihmastoa on ruiskutettu vastakatkaistuille kantopinnoille. Sienen on todettu olevan varteenotettava vaihtoehto eri lehtipuulajien vesakontorjunnassa ja sen hyödyntämisestä on kiinnostuttu viime vuosina myös Suomessa. Tutkimuksen tarkoituksena oli selvittää, soveltuuko purppuranahakka koivun biologiseen vesakontorjuntaan Suomen olosuhteissa ja tutkia sienen vaikutusmekanismeja vesomisen estäjänä kannossa. Lisäksi selvitettiin menetelmän käytöstä mahdollisesti aiheutuvia ympäristövaikutuksia. Tulokset osoittivat, että purppuranahakkakäsittely vähensi selvästi koivun vesomista: sekä kuolleiden kantojen määrä että elävien vesojen määrä per kanto väheni käsittelyn seurauksena. Käsittelyllä ei kuitenkaan ollut vaikutusta elävien vesojen pituuskasvuun. Eri sieniyksilöiden välillä oli selviä eroja tehokkuudessa estää vesojen muodostumista: sieniyksilöt, jotka tuottivat paljon ligninolyyttisiä entsyymejä, näyttivät estävän vesojen muodostumista tehokkaimmin. Käsittelyajankohdalla oli vaikutusta purppuranahakkakäsittelyn tehoon: tehokkain aika suorittaa käsittely oli touko-heinäkuussa. Pohjoismaisten ja baltialaisten purppuranahakkapopulaatioiden geneettisen monimuotoisuuden sisäinen vaihtelu oli suurta, mutta alueellisia eroja ei havaittu. Näin ollen mitä tahansa paikallista purppuranahakkakantaa voidaan käyttää vesakontorjunnassa ilman riskiä, että siirrettäisiin harvinaisia perimätyyppejä uusille alueille. Tulokset kuitenkin osoittivat, että käsitellyn alueen läheisyydessä karsituilla koivuilla voi olla suurentunut riski saada purppuranahakkatartunta keväällä. Näin ollen koivujen karsimista käsitellyn alueen läheisyydessä tulisi välttää keväällä muutama vuosi käsittelyn jälkeen

A cause for consilience: Utilizing multiple genomic data types to resolve problematic nodes within Arthropoda and Ecdysozoa

A major turning point in the study of metazoan evolution was the recognition of the existence of the Ecdysozoa in 1997. This is a group of eight animal phyla (Nematoda, Nematomorpha, Loricifera, Kinorhyncha, Priapulida, Tardigrada, Onychophora and Arthropoda). Ecdysozoa is the most specious clade of animals to ever exist and the relationships among its eight phyla are still heatedly debated. Similarly also the relationships among the three sub-phyla (Chelicerata, Pancrustacea and Myriapoda) within the most important ecdysozoan phylum (the Arthropoda) are still debated. Indeed, the two major problems in ecdysozoan phylogeny refer to the relationships of Myriapoda within Arthropoda, and of Tardigrada within Ecdysozoa. Difficulties in ecdysozoan relationships resides in lineages characterized by rapid, deep divergences and subsequently long periods of divergent evolution. Phylogenetic signal to resolve the relationships of these lineages is diluted, increasing the likelihood of recovery of phylogenetic artifacts. In an attempt to resolve the relationships within Ecdysozoa, consilience of three independent phylogenetic data sets was investigated. EST and rRNA and microRNA (miRNA) data were sampled across all major ecdysozoan phyla. In particular, a major contribution of this thesis is the first time sequencing of miRNAs for all the panarthropod phyla. MicroRNAs are genome regulatory elements that recently emerged as a source of useful phylogenetic data (Sempere et al. 2006) because of their low homoplasy levels. The considered data sets were analysed under phylogenetic methods and models, implemented to minimize the occurrence of phylogenetic reconstruction artifacts to understand the evolution of Ecdysozoa. Analyses of independent data types recovered well supported and corroborating evidence for the monophyly of Panarthropoda (Arthropoda, Onychophora and Tardigrada), a sister group relationships between Myriapoda and Pancrustacea within Arthropoda, and the paraphyly of Cycloneuralia (Nematoda, Nematomorpha, Loricifera, Kinorhyncha and Priapulida).

A cause for consilience: Utilizing multiple genomic data types to resolve problematic nodes within Arthropoda and Ecdysozoa

A major turning point in the study of metazoan evolution was the recognition of the existence of the Ecdysozoa in 1997. This is a group of eight animal phyla (Nematoda, Nematomorpha, Loricifera, Kinorhyncha, Priapulida, Tardigrada, Onychophora and Arthropoda). Ecdysozoa is the most specious clade of animals to ever exist and the relationships among its eight phyla are still heatedly debated. Similarly also the relationships among the three sub-phyla (Chelicerata, Pancrustacea and Myriapoda) within the most important ecdysozoan phylum (the Arthropoda) are still debated. Indeed, the two major problems in ecdysozoan phylogeny refer to the relationships of Myriapoda within Arthropoda, and of Tardigrada within Ecdysozoa. Difficulties in ecdysozoan relationships resides in lineages characterized by rapid, deep divergences and subsequently long periods of divergent evolution. Phylogenetic signal to resolve the relationships of these lineages is diluted, increasing the likelihood of recovery of phylogenetic artifacts. In an attempt to resolve the relationships within Ecdysozoa, consilience of three independent phylogenetic data sets was investigated. EST and rRNA and microRNA (miRNA) data were sampled across all major ecdysozoan phyla. In particular, a major contribution of this thesis is the first time sequencing of miRNAs for all the panarthropod phyla. MicroRNAs are genome regulatory elements that recently emerged as a source of useful phylogenetic data (Sempere et al. 2006) because of their low homoplasy levels. The considered data sets were analysed under phylogenetic methods and models, implemented to minimize the occurrence of phylogenetic reconstruction artifacts to understand the evolution of Ecdysozoa. Analyses of independent data types recovered well supported and corroborating evidence for the monophyly of Panarthropoda (Arthropoda, Onychophora and Tardigrada), a sister group relationships between Myriapoda and Pancrustacea within Arthropoda, and the paraphyly of Cycloneuralia (Nematoda, Nematomorpha, Loricifera, Kinorhyncha and Priapulida).

Factors Influencing Sustainable Cocoa Production in Northern Haiti

Given the environmental concerns on the one hand, especially soil erosion and deforestation, and the hope that the global cocoa market offers on the other hand, cocoa production is a potential candidate to simultaneously guarantee a competitive return to investment for farmers in northern Haiti and mitigate the negative environmental impact of farming practices. It becomes crucial for policy makers and investors to know and understand the key elements of the decision to produce cocoa. Though there has been substantial effort to improve the cocoa sector in Haiti, cocoa production systems in Haiti lag behind in the area of sustainability. To address the lack of information on key criteria farmers rely upon to produce cocoa sustainably, this study identifies factors influencing the sustainable cocoa production adoption decision. The act of adopting sustainable cocoa production in this study is defined by the rehabilitation of old cocoa farms and the establishment of new cocoa plantings that fit into agroforestry management systems. This study also is a first attempt at describing the current state of sustainable cocoa production in Haiti. A qualitative method was used to conduct this research. The approach used was focus groups. Fourteen focus groups and seven individual interviews provided data used to answer the research question. Additionally, a SWOT analysis was conducted on the cocoa sector. Results of the investigation indicate that farm gate price, farm size, property ownership, land configuration and rural infrastructures, networking, and animal feeding practices were key determinants of sustainable cocoa production in northern Haiti. In addition to these factors influencing sustainable cocoa production in northern Haiti, the SWOT analysis identified key elements that constrained or might help with expansion and growth of the cocoa sector. Weaknesses include lack of maintenance and rehabilitation of farms. One of the best opportunities lies in physical proximity to the U.S. market and special trade agreements with favorable buyers from the European Union who are looking for the fine cocoa flavor of the Criollo variety. Black pods, drought and climate change, low producer price and corruption within farmer cooperatives pose the greatest threats

The 1990 progress report and future plans

This document describes the progress and plans of the Artificial Intelligence Research Branch (RIA) at ARC in 1990. Activities span a range from basic scientific research to engineering development and to fielded NASA applications, particularly those applications that are enabled by basic research carried out at RIA. Work is conducted in-house and through collaborative partners in academia and industry. Our major focus is on a limited number of research themes with a dual commitment to technical excellence and proven applicability to NASA short, medium, and long-term problems. RIA acts as the Agency's lead organization for research aspects of artificial intelligence, working closely with a second research laboratory at JPL and AI applications groups at all NASA centers

Determinants of poverty in Mozambique (1996-97)

This report presents an analysis of the structural determinants of living standards and poverty in Mozambique, which is based on nationally-representative data from the first national household living standards survey since the end of the civil war: Poverty in Mozambique is predominantly a rural phenomenon and is pervasive, with over two-thirds of the population falling below the poverty line. The degree of regional variation of poverty within the country is striking. The policy simulations that illustrate the impact that changes in the levels of determinants of poverty have on poverty levels allow us to identify six possible elements of a prospective poverty alleviation strategy for Mozambique. These include (1) increased investment in education, (2) sustained economic growth, (3) a sectoral pattern of growth favoring faster growth in the industrial and services sectors, (4) measures to raise agricultural productivity, (5) improved rural infrastructure, and (6) reducing fertility and dependency load within households. In conclusion, any meaningful poverty reduction strategy in Mozambique must give the highest priority to rural areas and must address these macro-level and household-level determinants of poverty in its policy formulations.Economic development. ,Agricultural policies. ,Education Economic aspects. ,Living standards Mozambique. ,Poverty Mozambique. ,