Molecular evolution study in China: progress and future promise

China has a large land area with highly diverse topography, climate and vegetation, and animal resources and is ranked eighth in the world and first in the Northern Hemisphere on richness of biodiversity. Even though little work on molecular evolution had

Evolution and management of the mukene (Rastrineobola argentea) fishery

Rastrineobola argentea locally known as mukene in Uganda, omena in Kenya and dagaa in Tanzania occurs in Lake Nabugabo, Lake Victoria, the Upper Victoria Nileand Lake Kyoga (Greenwood 1966). While its fishery is well established on Lakes Victoria and Kyoga, the species is not yet exploited on Lake Nabugabo. Generally such smaller sized fish species as R. argentea become important commercial species in lakes where they occur when catches of preferred largersized table fish start showing signs ofdecline mostly as a result of overexploitation. With the current trends of declining fish catches on Lake Nabugabo, human exploitation of mukene on this lake is therefore just a matter of time. The species is exploited both for direct human consumption and as the protein ingredient in the manufacture of animal feeds.

Implications of changes in trophic diversity and food webs on fisheries and the environment

Most of the earth's ecosystems are experiencing slight to catastrophic losses of biodiversity, caused by habitat destruction, alien species introduction, climate change and pollution (Wilcove et al., 1998). These human effects have led to the extinction of native fish species, the collapse of their populations and the loss of ecological integrity and ecosystem functioning (Ogutu-Ohwayo & Hecky, 1991; Witte et al. , 1992a; Mills et al., 1994; Vitousek et al., 1996). Food webs are macro-descriptors of community feeding interactions that can be used to map the flow of materials and nutrients in ecosystems (Jepsen & Winemiller, 2002). Comparative food web studies have been used to address theoretical questions such as 'does greater trophic connectivity increase stability?' (Cohen et al., 1990), and 'does the number of trophic levels increase with productivity?' (Briand & Cohen, 1987). Answers to such questions have obvious applications for natural resources management. From a multi-species fisheries standpoint, there is a need to understand consumer-resource dynamics within complex trophic networks.

Molecular phylogeny, recent radiation and evolution of gross morphology of the rhubarb genus Rheum (Polygonaceae) inferred from chloroplast DNA trnL-F sequences

Background and Aims Rheum, a highly diversified genus with about 60 species, is mainly confined to the mountainous and desert regions of the Qinghai-Tibetan plateau and adjacent areas. This genus represents a good example of the extensive diversification of the temperate genera in the Qinghai-Tibetan plateau, in which the forces to drive diversification remain unknown. To date, the infrageneric classification of Rheum has been mainly based on morphological characters. However, it may have been subject to convergent evolution under habitat pressure, and the systematic position of some sections are unclear, especially Sect. Globulosa, which has globular inflorescences, and Sect. Nobilia, which has semi-translucent bracts. Recent palynological research has found substantial contradictions between exine patterns and the current classification of Rheum. Two specific objectives of this research were (1) to evaluate possible relationships of some ambiguous sections with a unique morphology, and (2) to examine possible occurrence of the radiative speciation with low genetic divergence across the total genus and the correlation between the extensive diversification time of Rheum and past geographical events, especially the recent large-scale uplifts of the Qinghai-Tibetan Plateau.Methods The chloroplast DNA trnL-F region of 29 individuals representing 26 species of Rheum, belonging to seven out of eight sections, was sequenced and compared. The phylogenetic relationships were further constructed based on the sequences obtained.Key Results Despite the highly diversified morphology, the genetic variation in this DNA fragment is relatively low. The molecular phylogeny is highly inconsistent with gross morphology, pollen exine patterns and traditional classifications, except for identifying all samples of Sect. Palmata, three species of Sect. Spiciformia and a few species of Sect. Rheum as corresponding monophyletic groups. The monotypic Sect. Globulosa showed a tentative position within the clade comprising five species of Sect. Rheum. All of the analyses revealed the paraphyly of R. nobile and R. alexandrae, the only two species of Sect. Nobilia circumscribed by the possession of large bracts. The crude calibration of lineages based on trnL-F sequence differentiation implied an extensive diversification of Rheum within approx. 7 million years.Conclusions Based on these results, it is suggested that the rich geological and ecological diversity caused by the recent large-scale uplifts of the Qinghai-Tibetan Plateau since the late Tertiary, coupled with the oscillating climate of the Quaternary stage, might have promoted rapid speciation in small and isolated populations, as well as allowing the fixation of unique or rare morphological characters in Rheum. Such a rapid radiation, combined with introgressive hybridization and reticulate evolution, may have caused the transfer of cpDNA haplotypes between morphologically dissimilar species, and might account for the inconsistency between morphological classification and molecular phylogeny reported here.

The Effects of Geography, Environment and Phylogeny on Community Assembly and Gene Flow Dynamics

It is increasingly evident that evolutionary processes play a role in how ecological communities are assembled. However the extend to which evolution influences how plants respond to spatial and environmental gradients and interact with each other is less clear. In this dissertation I leverage evolutionary tools and thinking to understand how space and environment affect community composition and patterns of gene flow in a unique system of Atlantic rainforest and restinga (sandy coastal plains) habitats in Southeastern Brazil.

In chapter one I investigate how space and environment affect the population genetic structure and gene flow of Aechmea nudicaulis, a bromeliad species that co-occurs in forest and restinga habitats. I genotyped seven microsatellite loci and sequenced one chloroplast DNA region for individuals collected in 7 pairs of forest / restinga sites. Bayesian genetic clustering analyses show that populations of A. nudicaulis are geographically structured in northern and southern populations, a pattern consistent with broader scale phylogeographic dynamics of the Atlantic rainforest. On the other hand, explicit migration models based on the coalescent estimate that inter-habitat gene flow is less common than gene flow between populations in the same habitat type, despite their geographic discontinuity. I conclude that there is evidence for repeated colonization of the restingas from forest populations even though the steep environmental gradient between habitats is a stronger barrier to gene flow than geographic distance.

In chapter two I use data on 2800 individual plants finely mapped in a restinga plot and on first-year survival of 500 seedlings to understand the roles of phylogeny, functional traits and abiotic conditions in the spatial structuring of that community. I demonstrate that phylogeny is a poor predictor of functional traits in and that convergence in these traits is pervasive. In general, the community is not phylogenetically structured, with at best 14% of the plots deviating significantly from the null model. The functional traits SLA, leaf dry matter content (LDMC), and maximum height also showed no clear pattern of spatial structuring. On the other hand, leaf area is strongly overdispersed across all spatial scales. Although leaf area overdispersion would be generally taken as evidence of competition, I argue that interpretation is probably misleading. Finally, I show that seedling survival is dramatically increased when they grow shaded by an adult individual, suggesting that seedlings are being facilitated. Phylogenetic distance to their adult neighbor has no influence on rates of survival though. Taken together, these results indicate that phylogeny has very limited influence on the fine scale assembly of restinga communities.

Recovery of a biodiversity action plans species in northwest England: possible role of climate change, artificial habitat and water quality amelioration. Occasional Publication of the Marine Biological Association 16

The honeycomb reef worm Sabellaria alveolata is recognised as being an important component of intertidal communities. It is a priority habitat within the UK Biodiversity Action Plan and as a biogenic reef forming species is covered by Annex 1 of the EC habitats directive. S. alveolata has a lusitanean (southern) distribution, being largely restricted to the south and west coasts of England. A broad-scale survey of S. alveolata distribution along the north-west coasts was undertaken in 2003/2004. These records were then compared with previous distribution records, mainly those collected by Cunningham in 1984. More detailed mapping was carried out at Hilbre Island at the mouth of the River Dee, due to recent reports that S. alveolata had become re-established there after a long absence.

Regional climate change and harmful algal blooms in the northeast Atlantic

We investigated long-term spatial variability in a number of Harmful Algal Blooms (HABs) in the northeast Atlantic and North Sea using data from the Continuous Plankton Recorder. Over the last four decades, some dinoflagellate taxa showed pronounced variation in the south and east of the North Sea, with the most significant increases being restricted to the adjacent waters off Norway. There was also a general decrease along the eastern coast of the United Kingdom. The most prominent feature in the interannual bloom frequencies over the last four decades was the anomalously high values recorded in the late 1980s in the northern and central North Sea areas. The only mesoscale area in the northeast Atlantic to show a significant increase in bloom formation over the last decade was the Norwegian coastal region. The changing spatial patterns of HAB taxa and the frequency of bloom formation are discussed in relation to regional climate change, in particular, changes in temperature, salinity, and the North Atlantic Oscillation (NAO). Areas highly vulnerable to the effects of regional climate change on HABs are Norwegian coastal waters and the Skagerrak. Other vulnerable areas include Danish coastal waters, and to a lesser extent, the German and Dutch Bight and the northern Irish Sea. Quite apart from eutrophication, our results give a preview of what might happen to certain HAB genera under changing climatic conditions in temperate environments and their responses to variability of climate oscillations such as the NAO.

Marine biodiversity and climate change: assessing and predicting the influence of climatic change using intertidal rocky shore biota. Occasional Publication of the Marine Biological Association 20

In the last 60 years climate change has altered the distribution and abundance of many seashore species. Below is a summary of the findings of this project. The MarClim project was a four year multi-partner funded project created to investigate the effects of climatic warming on marine biodiversity. In particular the project aimed to use intertidal species, whose abundances had been shown to fluctuate with changes in climatic conditions, as indicator species of likely responses of species not only on rocky shores, but also those found offshore. The project used historic time series data, from in some cases the 1950s onwards, and contemporary data collected as part of the MarClim project (2001-2005), to provide evidence of changes in the abundance, range and population structure of intertidal species and relate these changes to recent rapid climatic warming. In particular quantitative counts of barnacles, limpets and trochids were made as well as semi-quantitative surveys of up to 56 intertidal taxa.Historic and contemporary data informed experiments to understand the mechanisms behind these changes and models to predict future species ranges and abundances.

Plankton and climate

Plankton has two roles with respect to climate: first as an indicator of climate change in present day populations and in the fossil record and second as a factor contributing to climate change through, for example, its role in the CO sub(2) cycle, in cloud formation via dimethylsulfide (DMS) production, and in altering the reflectivity of sea water as a component of suspended particulate matter. Current research on both the contribution of plankton to climate change and its role as an indicator of change are central to predicting potential scenarios that may occur in the future at a time when global mean temperatures are predicted to rise at an unprecedented rate by 1.5-6 degree C within the next 100 years.

Spatial, seasonal and long-term fluctuations of plankton in relation to hydroclimatic features in the English Channel, Celtic Sea and Bay of Biscay

Plankton collected by the Continuous Plankton Recorder (CPR) survey were investigated for the English Channel, Celtic Sea and Bay of Biscay from 1979 to 1995. The main goal was to study the relationship between climate and plankton and to understand the factors influencing it. In order to take into account the spatial and temporal structure of biological data, a three-mode principal component analysis (PCA) was developed. It not only identified 5 zones characterised by their similar biological composition and by the seasonal and inter-annual evolution of the plankton, it also made species associations based on their location and year-to-year change. The studied species have stronger year-to-year fluctuations in abundance over the English Channel and Celtic Sea than the species offshore in the Bay of Biscay. The changes in abundance of plankton in the English Channel are negatively related to inter-annual changes of climatic conditions from December to March (North Atlantic Oscillation [NAO] index and air temperature). Thus, the negative relationship shown by Fromentin and Planque (1996; Mar Ecol Prog Ser 134:111-118) between year-to-year changes of Calanus finmarchicus abundance in the northern North Atlantic and North Sea and NAO was also found for the most abundant copepods in the Channel. However, the hypothesis proposed to explain the plankton/NAO relationship is different for this region and a new hypothesis is proposed. In the Celtic Sea, a relationship between the planktonic assemblage and the air temperature was detected, but it is weaker than for the English Channel. No relationship was found for the Bay of Biscay. Thus, the local physical environment and the biological composition of these zones appear to modify the relationship between winter climatic conditions and the year-to-year fluctuations of the studied planktonic species. This shows, therefore, that the relationship between climate and plankton is difficult to generalise.

Plankton, fisheries and climate change - insights into ocean ecosystems

This paper examines long term changes in the plankton of the North Atlantic and northwest European shelf seas and discusses the forcing mechanisms behind some observed interannual, decadal and spatial patterns of variability with a focus on climate change. Evidence from the Continuous Plankton Records suggests that the plankton integrates hydrometeorological signals and may be used as a possible index of climate change. Changes evident in the plankton are likely to have important effects on the carrying capacity of fisheries and are of relvance to eutrophication issues and to the assessment of biodiversity. The scale of the changes seen over the past five decades emphasises the importance of maintaining existing, and establishing new, long term and wide scale monitoring programmes of the world's oceans in initiatives such as the Global Ocean Observing System (GOOS).

Climate effects and benthic-pelagic coupling in the North Sea

The North Sea is one of the most biologically productive ecosystems in the world and supports important fisheries. Climate-induced changes occurred in the pelagic ecosystems of the North Sea during the 1980s. These changes, which have been observed from phytoplankton to fish and among permanent (holoplankton) and temporary (meroplankton) plankton species, have resulted in alterations in plankton community composition and seasonality. Until now, the effects of climate-driven changes on biological linkages between pelagic and benthic ecosystems have not been examined. The present study indicates that changes in benthic organisms could have a profound effect on the trophodynamics of the pelagos. We demonstrate this by analyses of a long-term time series of North Sea plankton and sea surface temperature data. We discover that pronounced changes in the North Sea meroplankton, mainly related to an increased abundance and spatial distribution of the larvae of a benthic echinoderm, Echinocardium cordatum, result primarily from a stepwise increase in sea temperature after 1987 that has caused warmer conditions to occur earlier in the year than previously. Key stages of reproduction in E. cordatum, gametogenesis and spawning, appear to be influenced by winter and spring sea temperature and their larval development is affected by the quantity and quality of their phytoplankton food. Our analyses suggest that a new thermal regime in the North Sea in winter and spring may have benefited reproduction and survival in this benthic species. As a result, E. cordatum may be altering the trophodynamics of the summer pelagic ecosystem through competition between its larvae and holozooplankton taxa.