Quantifying the roles of competing static gears: comparative selectivity of longlines and monofilament gill nets in a multi-species fishery of the Algarve (southern Portugal)

Fishing trials with monofilament gill nets and longlines using small hooks were carried out in Algarve waters (southern Portugal) over a one-year period. Four hook sizes of "Mustad" brand, round bent, flatted sea hooks (Quality 2316 DT, numbers 15, 13, 12 and 11) and four mesh sizes of 25, 30, 35 and 40 mm (bar length) monofilament gill nets were used. Commercially valuable sea breams dominated the longline catches while small pelagics were relatively more important in the gill nets. Significant differences in the catch size frequency distributions of the two gears were found for all the most important species caught by both gears (Boops boops, Diplodus bellottii, Diplodus vulgaris, Pagellus acarne, Pagellus erythrinus, Spondyiosoma cantharus, Scomber japonicus and Scorpaena notata), with longlines catching larger fish and a wider size range than nets. Whereas longline catch size frequency distributions for most species for the different hook sizes were generally highly overlapped, suggesting little or no differences in size selectivity, gill net catch size frequency distributions clearly showed size selection. A variety of models were fitted to the gill net and hook data using the SELECT method, while the parameters of the logistic model were estimated by maximum likelihood for the longline data. The bi-normal model gave the best fits for most of the species caught with gill nets, while the logistic model adequately described hook selectivity. The results of this study show that the two static gears compete for many of the same species and have different impacts in terms of catch composition and size selectivity. This information will I;e useful for the improved management of these small-scale fisheries in which many different gears compete for scarce resources.

Female Reproductive Biology and Spawning Periodicity of Two Species of King Prawns, Penaeus longistylus Kubo and Penaeus latisulcatus Kishinouye, from Queensland's East Coast Fishery

In the coastal region of central Queensland female red-spot king prawns, P. longistylus, and the western or blue-leg king prawns, P. latisulcatus, had high mean ovary weights and high proportions of advanced ovary development during the winter months of July and August of 1985 and 1986. On the basis of insemination, both species began copulating at the size of 26-27 mm CL, but P. longistylus matured and spawned at a smaller size than P. latisulcatus. Abundance of P. longistylus was generally three to four times greater than that of P. latisulcatus but the latter was subject to greater variation in abundance. Low mean ovary weight and low proportions of females with advanced ovaries were associated with the maximum mean bottom sea-water temperature (28.5ºC) for both species. Population fecundity indices indicated that peaks in yolk or egg production (a) displayed a similar pattern for both species, (b) varied in timing from year to year for both species and (c) were strongly influenced by abundance. Generally, sample estimates of abundance and commercial catch rates (CPUE) showed similar trends. Differences between the two may have been due to changes in targeted commercial effort in this multi-species fishery.

The cast net fishery, Kainji Lake, Nigeria 1970-1997

This study was carried out to establish trends in the cast net fishery of Kainji Lake, Nigeria. The cast net fishery was second in importance to the gillnet fishery in the early years after impoundment of the lake and still continues to be an important component of the fishery. Some of the economically important species such as Citharinus spp, Tilapia spp, Labeo spp, Alestes spp and Synodontis spp are exploited by cast nets. The study has not revealed any drastic perturbation in the species diversity, catch composition, and any real ecosystem overfishing. On the other hand, both the catfish, Auchenoglanis spp and the predator Hydrocynus spp appear to have increased in the catch in recent years. Never-the-less there is a decline in the mean weight of the major exploited fish species due to the capture of under sized fishes without allowing them to grow to 'legally' marketable sizes. The use of small meshed cast net and also fishing in the shallow waters of the lake can give rise to this situation. Thus, there are signs of growth overfishing in the fish stocks. It must also be acknowledged that the situation is complicated by the fact that in a multi-gear fishery as on Kainji Lake, the cast net fishery could not be managed in isolation without due regard to the other competing gears. The catch per unit of effort (CPUE) has declined in the cast net fishery possibly due to the increase in effort by the major fishing gears over the years. The ongoing extension campaigns by the KLFPP appears to be having the desired effect, as there was reduction in the number of the major fishing gears on the Lake in 1997. It can be anticipated that if this trend continues, the CPUE will recover in the long run. Yields observed from the mesh selectivity study revealed that for major species in the cast net fishery, both by number and weight, were maximal at 2.5 inch mesh, which contrasts with the fact that current minimum allowable mesh in the Fisheries Edict for the Lake is 2.0 inch. The adoption of 2.5 inch as the minimum allowable mesh in the cast net fishery is recommended to be included in future revision of existing regulations. It is also recommended that for this control to have a desired effect, the casting of the net from the shore should be prohibited so as to reduce the incidence of juvenile mortality in the nursery areas. (PDF contains 28 pages)

Nocturnal fish movement and trophic flow across habitat boundaries in a coral reef ecosystem (SW Puerto Rico)

Few studies have quantified the extent of nocturnal cross-habitat movements for fish, or the influence of habitat adjacencies on nutrient flows and trophodynamics. To investigate the patterns of nocturnal cross-boundary movements of fish and quantify trophic connectivity, fish were sampled at night with gillnets set along the boundaries between dominant habitat types (coral reef/seagrass and mangrove/seagrass) in southwestern Puerto Rico. Fish movement across adjacent boundary patches were equivalent at both coral reefs and mangroves. Prey biomass transfer was greater from seagrass to coral reefs (0.016 kg/km) and from mangroves to seagrass (0.006 kg/km) but not statistically significant, indicating a balance of flow between adjacent habitats. Pelagic species (jacks, sharks, rays) accounted for 37% of prey biomass transport at coral reef/seagrass and 46% at mangrove/seagrass while grunts and snappers accounted for 7% and 15%, respectively. This study indicated that coral reefs and mangroves serve as a feeding area for a wide range of multi-habitat fish species. Crabs were the most frequent prey item in fish leaving coral reefs while molluscs were observed slightly more frequently than crabs in fish entering coral reefs. For most prey types, biomass exported from mangroves was greater than biomass imported. The information on direction of fish movement together with analysis of prey data provided strong evidence of ecological linkages between distinct adjacent habitat types and highlighted the need for greater inclusion of a mosaic of multiple habitats when attempting to understand ecosystem function including the spatial transfer of energy across the seascape.

The declining state of the gillnet fishery in Lake Victoria, Uganda

Lake Victoria had a multi-species fishery dominated until the 1970s by the tilapiine and the haplochromine cichlids (Kudhongania and Cordone, 1974). From about 1930 to 1960, the fisheries of Lake Victoria were managed by controlling the mesh size of gill nets. Gill nets of stretched mesh sizes less than 127 mm (5 inches) were prohibited as they cropped immature Oreochromis esculentus (Ngege), the most important commercial species on the lake (Graham, 1929). The catch per night in the legal 127 mm mesh nets was over 30 fish of O. esculentus prior to 1921 but dropped to 6 and 1.5 fish in 1928 and 1954, respectively, (Beauchamp, 1955), indicating overfishing of the stocks. The overall aim of the survey was to determine the available fish stocks being harvested by the gill net fishery. The specific objectives included the determination of the species composition and catch levels. Gill nets of mesh sizes from 25.4 mm (1 inch) to 228.6 mm (9 inches) were used.

Discards of the Algarve (southern Portugal) crustacean trawl fishery

The crustacean trawl fishery off the Algarve coast (southern Portugal) takes place on the lower continental shelf and upper continental slope at depths between 150 and 600 m. This is a multi-species fishery targeting the shrimps Parapenaeus longirostris and Aristeus antennatus and the Norway lobster Nephrops norvegicus, with the latter two species the most important in the landings. The fishery is characterised by significant by-catch and discarding of a large number of species. As part of a study on the fate of trawl fishery discards, this component of the study focused on the quantification of the by-catch and discards of crustacean trawlers. Sampling took place on board seven commercial trawlers from June 1998 to October 1999. Data was collected from 48 tows in 22 fishing trips. The observers collected all of the catch that was discarded by the crew during the sorting operation and samples were taken to the laboratory for identification, weighing and measuring. The quantities of target species were recorded along with the presence of retained by-catch. Commercially valuable species that were retained included Plesiopenaeus edwardsianus, Aristeomorpha foliacea, Plesionika sp., and the fishes Lophius piscatorius and Merluccius merluccius. However, most of the species had no or little commercial value and were almost always discarded to the sea (90%). A total of 91 species were identified, 47 vertebrates and 44 invertebrates corresponding to 65 families. The Teleostei (78% and 68%) were the dominant group, both in number and weight. The species Micromesistius poutassou (34%), Gadiculus argenteus (10%) and Hoplostethus mediterraneus (8%) were the most important in weight. Ten species represented more than 82% of all discards in weight. Gadiculus argenteus (29%), Hoplostethus mediterraneus (21%) and Nezumia sclerorhynchus (10%) accounted for 60% of all discards in numbers. Data on the landed species composition is also presented.

Networks cities and ecological habitats

As the world’s rural populations continue to migrate from farmland to sprawling cities, transport networks form an impenetrable maze within which monocultures of urban form erupt from the spaces in‐between. These urban monocultures are as problematic to human activity in cities as cropping monocultures are to ecosystems in regional landscapes. In China, the speed of urbanisation is exacerbating the production of mono‐functional private and public spaces. Edges are tightly controlled. Barriers and management practices at these boundaries are discouraging the formation of new synergistic relationships, critical in the long‐term stability of ecosystems that host urban habitats. Some urban planners, engineers, urban designers, architects and landscape architects have recognised these shortcomings in contemporary Chinese cities. The ideology of sustainability, while critically debated, is bringing together thinking people in these and other professions under the umbrella of an ecological ethic. This essay aims to apply landscape ecology theory, a conceptual framework used by many professionals involved in land development processes, to a concept being developed by BAU International called Networks Cities: a city with its various land uses arranged in nets of continuity, adjacency, and superposition. It will consider six lesser‐known concepts in relation to creating enhanced human activity along (un)structured edges between proposed nets and suggest new frontiers that might be challenged in an eco‐city. Ecological theory suggests that sustaining biodiversity in regions and landscapes depends on habitat distribution patterns. Flora and fauna biologists have long studied edge habitats and have been confounded by the paradox that maximising the breadth of edges is detrimental to specialist species but favourable to generalist species. Generalist species of plants and animals tolerate frequent change in the landscape, frequenting two or more habitats for their survival. Specialist species are less tolerant of change, having specific habitat requirements during their life cycle. Protecting species richness then may be at odds with increasing mixed habitats or mixed‐use zones that are dynamic places where diverse activities occur. Forman (1995) in his book Land Mosaics however argues that these two objectives of land use management are entirely compatible. He postulates that an edge may be comprised of many small patches, corridors or convoluting boundaries of large patches. Many ecocentrists now consider humans to be just another species inhabiting the ecological environments of our cities. Hence habitat distribution theory may be useful in planning and designing better human habitats in a rapidly urbanising context like China. In less‐constructed environments, boundaries and edges provide important opportunities for the movement of multi‐habitat species into, along and from adjacent land use areas. For instance, invasive plants may escape into a national park from domestic gardens while wildlife may forage on garden plants in adjoining residential areas. It is at these interfaces that human interactions too flow backward and forward between land types. Spray applications of substances by farmers on cropland may disturb neighbouring homeowners while suburban residents may help themselves to farm produce on neighbouring orchards. Edge environments are some of the most dynamic and contested spaces in the landscape. Since most of us require access to at least two or three habitats diurnally, weekly, monthly or seasonally, their proximity to each other becomes critical in our attempts to improve the sustainability of our cities.

The past, present and projected scenarios in the Lake AIbert and Albert Nile fisheries: implications for sustainable management

Lake Albert is one of the largest lakes in Uganda that still supports a multi-species fishery which as a result of variable adult sizes of the species, causes management challenges especially in relation to gear mesh size enforcement. Prior to the 1980s, commercial species were 17 largesized fishes especially Citharinus citharinus, Distichodus niloticus and Lates spp. that were confmed to inshore habitats of the lake and were thus rapidly over fished. Frame and catch assessment surveys conducted in this study revealed a >80% dominance of small size fish species (Neobola bredoi and Brycinus nurse) and a 40 -60% decrease in the contribution of the large commercial species. Sustainability of small size fish species is uncertain due to seasonal fluctuations and low beach value. At about 150,000 tons of fish recorded from Lake Albert and Albert Nile, the beach value was estimated at 55.3 million USD. Despite the noted decline in catches of the large sized fishes their contribution was more than 50% of total beach value. Therefore, management measures should couple value addition for the small sized species and maintain effort regulation targeting recovery of the large previously important commercial species

Composition, biomass, distribution and population structure of the fish stocks

Until the 1970s, Lake Victoria had a multi-species fishery dominated by the tilapiine and haplochromine cichlids. There were important subsidiary fisheries for more than 20 genera of non-cichlid fishes, including catfishes (Bagrus docmak, Clarias gariepinus, Synodontis spp and Schilbe intermedius), the lungfish (Protopterus aethiopicus) and Labeo victorianus) (Kudhongania and Cordone 1974). Stocks of most of these species declined and others disappeared following the introduction of four tilapiines (Oreochromis niloticus, Oreochromis leucostictus, Tilapia rendalli and Tilapia zillit) and Nile perch (Lates niloticus) during the 1950s. Since then the commercial fishery in the Uganda portion of Lake Victoria has been dominated by the Nile perch, Nile tilapia (Oreochromis niloticus) and the native cyprinid species, Rastrineobola argentea (Mukene).

Fish species diversity, and the biology and ecology of common fish species in Lake Albert

Lake Albert contributes about 10% to the national fish production. It supports a multi-species fishery based on endemic species. To local fishermen, Lake Albert is a lifeline providing food and income.

The increased fishing pressure and the future of the fish stocks of Lake Victoria, Uganda

The Uganda sector of Lake Victoria occupies 29,580 km2 (43%). The lake used to boast of a multi-species fishery but presently relies on three major species Lates niloticus, Oreochromis niloticus and Rastrineobola argentea. During the past decade the total fish production on the Ugandan sector increased drastically from 17,000 tonnes in 1981 to about 13,000 tonnes 1991, indicating a healthy state of the fishery. This was contributed by a combination of factors including the explosive establishment of the introduced L. niloticus which contributed 60.8% in 1991 and the increase in the number of fishing canoes from 3470 in 1988 to 8000 in 1990. Isolated fishery resources studies carried out in different areas of the lake since 1971 seem, however, to indicate contrary trends in the available stocks and, therefore, the status of the fishery. In the experimental fishery, continued decline in catch rates have been recorded. Similarly, in the commercial fishery catch per unit of effort has been considerably poor (33 kg per canoe during January - March 1992) and the average size of individual fish laRded continued to decline, obviously pointing at possible over-fishing. This, therefore, calls for further urgent research on the available stocks for proper management strategies to be formulated.

The future prospects of the fish stocks of Lake Victoria, Uganda

Experimental trawling during the period 1981/86 and analysis of past commercial catch landings, mainly in the northern portion of Lake Victoria have indicated that the standing stocks and therefore, the estimates of sustainable yields of the most important fish species have unquestionably changed since the 1969/71 comprehensive lake-wide stock assessment survey. Lake Victoria which was originally a multi-species fishery now relies on two introduced species (Lates niloticus and Oreochromis niloticus) and one indigenous cyprinid (Rastrineobola argentea). Most of the traditional fish species, including the once dominant haplochromines, have either declined or disappeared. The catch rates in the experimental trawl catches declined from 797 kg/hr in 1969/71 to 575 kg/hr in 1981 and 166 kg/hr in 1985. The contribution of L. niloticus in the trawl catch increased from 0.9% in 1981 to 95.6% in 1985 while the contribution of the haplochromines decreased from about 91% to about 1% over the same period. The mean size of the individual fish caught (particularly the Nile perch) was also on the decline. Similar trends were also observed in the commercial fishery. However, recent observations in the Lake Kyoga commercial fishery that O. niloticus has now surpassed L.niloticus in importance may create more uncertainty regarding the future trends of the fish stocks of Lake Victoria. Inspite of the above situation, developments to increasingly exploit the fish stocks of the lake for export continue to take place. A number of fish processing and/or handling plants have been established in the Jinja, Kampala and Entebbe areas of the lake. Each of these plants is capable of handling upwards of 10 tons of fish a day, the target fish being L. niloticus and O. niloticus.

Influence of tree hollow characteristics on the diversity of saproxylic insect guilds in Iberian Mediterranean woodlands

Saproxylic diversity assessment is a major goal for conservation strategies in woodlands and it should consider woodland composition and configuration at site and tree level as key modelling factors. However, in Mediterranean woodlands little is known about the relation with the environmental factors that structure their assemblages, especially those linked to tree hollow microhabitats. We assessed the diversity of Syrphidae (Diptera) and Coleoptera saproxylic guilds that co-occurred in tree hollows located in three different Iberian Mediterranean woodlands in the Cabañeros National Park (Spain). Furthermore, we evaluated how differences in tree hollow microenvironmental variables (understood as the physical and biotic characteristics of a hollow and tree individual) influenced saproxylic guild diversity both within and among woodland sites. We found that woodland sites that provided greater heterogeneity of trees and hollow microhabitats determined higher saproxylic guild diversity. Nevertheless, certain species or even complete guilds can be favoured in woodlands where some hollow microhabitats predominate as a consequence of historical tree management. In general, hollow volume was the main determining factor for saproxylic guild richness and abundance in woodland sites, and large hollow volume was usually related to higher diversity, which highlighted the importance of multi-habitat hollow trees. Moreover, saproxylic guilds also responded to other different microenvironmental variables, which indicated different ecological preferences among guilds. The conservation of saproxylic insects in Iberian Mediterranean areas must be addressed to protect woodland sites that provide high diversity and large numbers of tree hollow microhabitats, and practices to enhance microhabitat heterogeneity should even be encouraged.

Assembly processes of invertebrate communities in springs across different spatial scales

Il presente lavoro ha lo scopo di comprendere i processi sottesi ai pattern di coesistenza tra le specie di invertebrati sorgentizi, distinguendo tra dinamiche stocastiche e deterministiche. Le sorgenti sono ecosistemi complessi e alcune loro caratteristiche (ad esempio l’insularità, la stabilità termica, la struttura ecotonale “a mosaico”, la frequente presenza di specie rare ed endemiche, o l’elevata diversità in taxa) le rendono laboratori naturali utili allo studio dei processi ecologici, tra cui i processi di assembly. Al fine di studiare queste dinamiche è necessario un approccio multi-scala, per questo motivi sono state prese in considerazione tre scale spaziali. A scala locale è stato compiuto un campionamento stagionale su sette sorgenti (quattro temporanee e tre permanenti) del Monte Prinzera, un affioramento ofiolitico vicino alla città di Parma. In questa area sono stati valutati l’efficacia e l’impatto ambientale di diversi metodi di campionamento e sono stati analizzati i drivers ecologici che influenzano le comunità. A scala più ampia sono state campionate per due volte 15 sorgenti della regione Emilia Romagna, al fine di identificare il ruolo della dispersione e la possibile presenza di un effetto di niche-filtering. A scala continentale sono state raccolte informazioni di letteratura riguardanti sorgenti dell’area Paleartica occidentale, e sono stati studiati i pattern biogeografici e l’influenza dei fattori climatici sulle comunità. Sono stati presi in considerazione differenti taxa di invertebrati (macroinvertebrati, ostracodi, acari acquatici e copepodi), scegliendo tra quelli che si prestavano meglio allo studio dei diversi processi in base alle loro caratteristiche biologiche e all’approfondimento tassonomico raggiungibile. I campionamenti biologici in sorgente sono caratterizzati da diversi problemi metodologici e possono causare impatti sugli ambienti. In questo lavoro sono stati paragonati due diversi metodi: l’utilizzo del retino con un approccio multi-habitat proporzionale e l’uso combinato di trappole e lavaggio di campioni di vegetazione. Il retino fornisce dati più accurati e completi, ma anche significativi disturbi sulle componenti biotiche e abiotiche delle sorgenti. Questo metodo è quindi raccomandato solo se il campionamento ha come scopo un’approfondita analisi della biodiversità. D’altra parte l’uso delle trappole e il lavaggio della vegetazione sono metodi affidabili che presentano minori impatti sull’ecosistema, quindi sono adatti a studi ecologici finalizzati all’analisi della struttura delle comunità. Questo lavoro ha confermato che i processi niche-based sono determinanti nello strutturare le comunità di ambienti sorgentizi, e che i driver ambientali spiegano una rilevante percentuale della variabilità delle comunità. Infatti le comunità di invertebrati del Monte Prinzera sono influenzate da fattori legati al chimismo delle acque, alla composizione e all’eterogeneità dell’habitat, all’idroperiodo e alle fluttuazioni della portata. Le sorgenti permanenti mostrano variazioni stagionali per quanto riguarda le concentrazioni dei principali ioni, mentre la conduttività, il pH e la temperatura dell’acqua sono più stabili. È probabile che sia la stabilità termica di questi ambienti a spiegare l’assenza di variazioni stagionali nella struttura delle comunità di macroinvertebrati. L’azione di niche-filtering delle sorgenti è stata analizzata tramite lo studio della diversità funzionale delle comunità di ostracodi dell’Emilia-Romagna. Le sorgenti ospitano più del 50% del pool di specie regionale, e numerose specie sono state rinvenute esclusivamente in questi habitat. Questo è il primo studio che analizza la diversità funzionale degli ostracodi, è stato quindi necessario stilare una lista di tratti funzionali. Analizzando il pool di specie regionale, la diversità funzionale nelle sorgenti non è significativamente diversa da quella misurata in comunità assemblate in maniera casuale. Le sorgenti non limitano quindi la diversità funzionale tra specie coesistenti, ma si può concludere che, data la soddisfazione delle esigenze ecologiche delle diverse specie, i processi di assembly in sorgente potrebbero essere influenzati da fattori stocastici come la dispersione, la speciazione e le estinzioni locali. In aggiunta, tutte le comunità studiate presentano pattern spaziali riconoscibili, rivelando una limitazione della dispersione tra le sorgenti, almeno per alcuni taxa. Il caratteristico isolamento delle sorgenti potrebbe essere la causa di questa limitazione, influenzando maggiormente i taxa a dispersione passiva rispetto a quelli a dispersione attiva. In ogni caso nelle comunità emiliano-romagnole i fattori spaziali spiegano solo una ridotta percentuale della variabilità biologica totale, mentre tutte le comunità risultano influenzate maggiormente dalle variabili ambientali. Il controllo ambientale è quindi prevalente rispetto a quello attuato dai fattori spaziali. Questo risultato dimostra che, nonostante le dinamiche stocastiche siano importanti in tutte le comunità studiate, a questa scala spaziale i fattori deterministici ricoprono un ruolo prevalente. I processi stocastici diventano più influenti invece nei climi aridi, dove il disturbo collegato ai frequenti eventi di disseccamento delle sorgenti provoca una dinamica source-sink tra le diverse comunità. Si è infatti notato che la variabilità spiegata dai fattori ambientali diminuisce all’aumentare dell’aridità del clima. Disturbi frequenti potrebbero provocare estinzioni locali seguite da ricolonizzazioni di specie provenienti dai siti vicini, riducendo la corrispondenza tra gli organismi e le loro richieste ambientali e quindi diminuendo la quantità di variabilità spiegata dai fattori ambientali. Si può quindi concludere che processi deterministici e stocastici non si escludono mutualmente, ma contribuiscono contemporaneamente a strutturare le comunità di invertebrati sorgentizi. Infine, a scala continentale, le comunità di ostracodi sorgentizi mostrano chiari pattern biogeografici e sono organizzate lungo gradienti ambientali principalmente collegati altitudine, latitudine, temperatura dell’acqua e conducibilità. Anche la tipologia di sorgente (elocrena, reocrena o limnocrena) è influente sulla composizione delle comunità. La presenza di specie rare ed endemiche inoltre caratterizza specifiche regioni geografiche.

The Roles of Phenotypic Plasticity and Plant-Microbe Interactions in the Evolution of Complex Traits in Boechera stricta

All organisms live in complex habitats that shape the course of their evolution by altering the phenotype expressed by a given genotype (a phenomenon known as phenotypic plasticity) and simultaneously by determining the evolutionary fitness of that phenotype. In some cases, phenotypic evolution may alter the environment experienced by future generations. This dissertation describes how genetic and environmental variation act synergistically to affect the evolution of glucosinolate defensive chemistry and flowering time in Boechera stricta, a wild perennial herb. I focus particularly on plant-associated microbes as a part of the plant’s environment that may alter trait evolution and in turn be affected by the evolution of those traits. In the first chapter I measure glucosinolate production and reproductive fitness of over 1,500 plants grown in common gardens in four diverse natural habitats, to describe how patterns of plasticity and natural selection intersect and may influence glucosinolate evolution. I detected extensive genetic variation for glucosinolate plasticity and determined that plasticity may aid colonization of new habitats by moving phenotypes in the same direction as natural selection. In the second chapter I conduct a greenhouse experiment to test whether naturally-occurring soil microbial communities contributed to the differences in phenotype and selection that I observed in the field experiment. I found that soil microbes cause plasticity of flowering time but not glucosinolate production, and that they may contribute to natural selection on both traits; thus, non-pathogenic plant-associated microbes are an environmental feature that could shape plant evolution. In the third chapter, I combine a multi-year, multi-habitat field experiment with high-throughput amplicon sequencing to determine whether B. stricta-associated microbial communities are shaped by plant genetic variation. I found that plant genotype predicts the diversity and composition of leaf-dwelling bacterial communities, but not root-associated bacterial communities. Furthermore, patterns of host genetic control over associated bacteria were largely site-dependent, indicating an important role for genotype-by-environment interactions in microbiome assembly. Together, my results suggest that soil microbes influence the evolution of plant functional traits and, because they are sensitive to plant genetic variation, this trait evolution may alter the microbial neighborhood of future B. stricta generations. Complex patterns of plasticity, selection, and symbiosis in natural habitats may impact the evolution of glucosinolate profiles in Boechera stricta.