Age of cichlids: new dates for ancient lake fish radiations

Timing divergence events allow us to infer the conditions under which biodiversity has evolved and gain important insights into the mechanisms driving evolution. Cichlid fishes are a model system for studying speciation and adaptive radiation, yet, we have lacked reliable timescales for their evolution. Phylogenetic reconstructions are consistent with cichlid origins prior to Gondwanan landmass fragmentation 121-165 MYA, considerably earlier than the first known fossil cichlids (Eocene). We examined the timing of cichlid evolution using a relaxed molecular clock calibrated with geological estimates for the ages of 1) Gondwanan fragmentation and 2) cichlid fossils. Timescales of cichlid evolution derived from fossil-dated phylogenies of other bony fishes most closely matched those suggested by Gondwanan breakup calibrations, suggesting the Eocene origins and marine dispersal implied by the cichlid fossil record may be due to its incompleteness. Using Gondwanan calibrations, we found accumulation of genetic diversity within the radiating lineages of the African Lakes Malawi, Victoria and Barombi Mbo, and Palaeolake Makgadikgadi began around or after the time of lake basin formation. These calibrations also suggest Lake Tanganyika was colonized independently by the major radiating cichlid tribes that then began to accumulate genetic diversity thereafter. These results contrast with the widely accepted theory that diversification into major lineages took place within the Tanganyika basin. Together, this evidence suggests that ancient lake habitats have played a key role in generating and maintaining diversity within radiating lineages and also that lakes may have captured preexisting cichlid diversity from multiple sources from which adaptive radiations have evolved.

Preference polymorphism for coloration but no speciation in a population of Lake Victoria cichlids

Female mating preference based on male nuptial coloration has been suggested to be an important source of diversifying selection in the radiation of Lake Victoria cichlid fish. Initial variation in female preference is a prerequisite for diversifying selection; however, it is rarely studied in natural populations. In clear water areas of Lake Victoria, the sibling species Pundamilia pundamilia with blue males and Pundamilia nyererei with red males coexist, intermediate phenotypes are rare, and most females have species-assortative mating preferences. Here, we study a population of Pundamilia that inhabits turbid water where male coloration is variable from reddish to blue with most males intermediate. We investigated male phenotype distribution and female mating preferences. Male phenotype was unimodally distributed with a mode on intermediate color in 1 year and more blue-shifted in 2 other years. In mate choice experiments with females of the turbid water population and males from a clearer water population, we found females with a significant and consistent preference for P. pundamilia (blue) males, females with such preferences for P. nyererei (red) males, and many females without a preference. Hence, female mating preferences in this population could cause disruptive selection on male coloration that is probably constrained by the low signal transduction of the turbid water environment. We suggest that if environmental signal transduction was improved and the preference/color polymorphism was stabilized by negative frequency-dependent selection, divergent sexual selection might separate the 2 morphs into reproductively isolated species resembling the clear water species P. pundamilia and P. nyererei.

Parallel evolution of facial stripe patterns in the Neolamprologus brichardilpulcher species complex endemic to Lake Tanganyika

Colour pattern diversity can be due to random processes or to natural or sexual selection. Consequently, similarities in colour patterns are not always correlated with common ancestry, but may result from convergent evolution under shared selection pressures or drift. Neolamprologus brichardi and Neolamprologus pulcher have been described as two distinct species based on differences in the arrangement of two dark bars on the operculum. Our study uses DNA sequences of the mitochondrial control region to show that relatedness of haplotypes disagrees with species assignment based on head colour pattern. This suggests repeated parallel evolution of particular stripe patterns. The complete lack of shared haplotypes between populations of the same or different phenotypes reflects strong philopatric behaviour, possibly induced by the cooperative breeding mode in which offspring remain in their natal territory and serve as helpers until they disperse to nearby territories or take over a breeding position. Concordant phylogeographic patterns between N. brichardi/N. pulcher populations and other rock-dwelling cichlids suggest that the same colonization routes have been taken by sympatric species and that these routes were affected by lake level fluctuations in the past. (C) 2007 Elsevier Inc. All rights reserved.

Characterization of legacy organic carbon in a culturally eutrophic lake : the role of the historic carbon deposition in the time course and extent of lake recovery

The time course of lake recovery after a reduction in external loading of nutrients is often controlled by conditions in the sediment. Remediation of eutrophication is hindered by the presence of legacy organic carbon deposits, that exert a demand on the terminal electron acceptors of the lake and contribute to problems such as internal nutrient recycling, absence of sediment macrofauna, and flux of toxic metal species into the water column. Being able to quantify the timing of a lake’s response requires determination of the magnitude and lability, i.e., the susceptibility to biodegradation, of the organic carbon within the legacy deposit. This characterization is problematic for organic carbon in sediments because of the presence of different fractions of carbon, which vary from highly labile to refractory. The lability of carbon under varied conditions was tested with a bioassay approach. It was found that the majority of the organic material found in the sediments is conditionally-labile, where mineralization potential is dependent on prevailing conditions. High labilities were noted under oxygenated conditions and a favorable temperature of 30 °C. Lability decreased when oxygen was removed, and was further reduced when the temperature was dropped to the hypolimnetic average of 8° C . These results indicate that reversible preservation mechanisms exist in the sediment, and are able to protect otherwise labile material from being mineralized under in situ conditions. The concept of an active sediment layer, a region in the sediments in which diagenetic reactions occur (with nothing occurring below it), was examined through three lines of evidence. Initially, porewater profiles of oxygen, nitrate, sulfate/total sulfide, ETSA (Electron Transport System Activity- the activity of oxygen, nitrate, iron/manganese, and sulfate), and methane were considered. It was found through examination of the porewater profiles that the edge of diagenesis occurred around 15-20 cm. Secondly, historical and contemporary TOC profiles were compared to find the point at which the profiles were coincident, indicating the depth at which no change has occurred over the (13 year) interval between core collections. This analysis suggested that no diagenesis has occurred in Onondaga Lake sediment below a depth of 15 cm. Finally, the time to 99% mineralization, the t99, was viewed by using a literature estimate of the kinetic rate constant for diagenesis. A t99 of 34 years, or approximately 30 cm of sediment depth, resulted for the slowly decaying carbon fraction. Based on these three lines of evidence , an active sediment layer of 15-20 cm is proposed for Onondaga Lake, corresponding to a time since deposition of 15-20 years. While a large legacy deposit of conditionally-labile organic material remains in the sediments of Onondaga Lake, it becomes clear that preservation, mechanisms that act to shield labile organic carbon from being degraded, protects this material from being mineralized and exerting a demand on the terminal electron acceptors of the lake. This has major implications for management of the lake, as it defines the time course of lake recovery following a reduction in nutrient loading.

Tracing the source of groundwater for three different coastal peatlands along Lake Superior

The goal of this project was to investigate the influence of a large inland lake on adjacent coastal freshwater peatlands. The specific aim was to determine the source of groundwater for three differently formed peatlands located on the southern shore of Lake Superior. The groundwater study was conducted at Bete Grise, a peatland complex in a dune-swale system; Pequaming, a peatland developed in the swale of a tombolo; and Lightfoot Bay, a peatland developed in a barrier beach wetland complex. To determine the source of groundwater in the peatlands, transects of six groundwater monitoring wells were established at each study site, covering distinctly different vegetation zones. At Pequaming and Lightfoot Bay the transects monitored two vegetation zones: transition zone from upland and open fen. At Bete Grise, the transects monitored dunes and swales. Additionally, at all three sites, upland groundwater was monitored using three wells that were installed into the adjacent upland forest. Biweekly measurements of well water pH and specific conductance were carried out from May to October of 2010. At each site, vegetation cover, peat depths and surface elevations were determined and compared to Lake Superior water levels. From June 14 – 17, July 20 – 21 and September 10 – 12, stable isotopes of oxygen (18O/16O) ratios were measured in all the wells and for Lake Superior water. A mixing model was used to estimate the percentage of lake water influencing each site based on the oxygen isotope ratios. During the sampling period, groundwater at all three sites was supported primarily by upland groundwater. Pequaming was approximately 80 % upland groundwater supported and up to 20 % Lake water supported in the uppermost 1 m layer of peat column of the transition zone and open fen. Bete Grise and Lightfoot Bay were 100 % upland groundwater supported throughout the season. The height of Lake Superior was near typical levels in 2010. In years when the lake level is higher, Lake water could intrude into the adjacent peatlands. However, under typical hydrologic conditions, these coastal peatlands are primarily supported by upland groundwater.

Ecology of larval fishes and large zooplankton in the Keweenaw Current region of Lake Superior, with special focus on lake herring, Coregonus artedi

I assessed the influence of the Keweenaw Current and spring thermal bar on the distribution of larval fishes and large zooplankton in Lake Superior. In 1998 and 1999, samples were collected from inshore (0.2 – 3.0 km from shore) and offshore (5.0 – 9.0 km from shore) locations on three transects off the western coast of the Keweenaw Peninsula, Michigan. For larval fishes, density and size distribution patterns of lake herring (Coregonus artedi), rainbow smelt (Osmerus mordax), burbot (Lota lota), deepwater sculpin (Myoxocephalus thompsoni), and spoonhead sculpin (Cottus ricei) suggest a seasonal inshore to offshore movement. For zooplankton, seasonal warming appeared to be the major factor that limited planktonic catches of the primarily benthic Mysisrelicta and Diporeia spp., while simultaneously stimulated growth and reproduction of the cladocerans Daphnia spp., Holopedium gibberum, and Bythotrephes cederstroemi. In contrast, calanoid copepods as a group were abundant throughout the entire sampling season. The greatest abundances of zooplankton were generally encountered offshore, even for the cladocerans, which apparently expanded from inshore to offshore locations with seasonal warming. In 2000, sampling efforts focused on lake herring. Samples were collected from surface waters at 0.1 – 17.0 km from shore on two transects. Lake herring larvae were also reared in the laboratory from eggs in order to validate the use of otolith microstructure for aging. Increment deposition was not statistically different from a daily rate starting from 28 days after hatching, near the time of yolk-sac absorption, but larvae with lower growth rates could not be aged as accurately. In Lake Superior, lake herring tended to be slightly more abundant, larger, and older at inshore locations, but a dense patch of younger larvae was also encountered 7 – 13 km from shore. The distribution iiipatterns suggest that larvae were transported by prevailing currents into the study region, possibly from the more productive spawning regions in western Lake Superior. Growth rates were suppressed at offshore locations where temperatures were less than 8°C. These results indicate that lake herring larvae may be transported far distances from spawning concentrations by longshore currents, and water temperatures may largely control their growth.

Glomerular filtration rate estimates decrease during high altitude expedition but increase with Lake Louise acute mountain sickness scores

AIM: Acute mountain sickness (AMS) can result in pulmonary and cerebral oedema with overperfusion of microvascular beds, elevated hydrostatic capillary pressure, capillary leakage and consequent oedema as pathogenetic mechanisms. Data on changes in glomerular filtration rate (GFR) at altitudes above 5000 m are very limited. METHODS: Thirty-four healthy mountaineers, who were randomized to two acclimatization protocols, undertook an expedition on Muztagh Ata Mountain (7549 m) in China. Tests were performed at five altitudes: Zurich pre-expedition (PE, 450 m), base camp (BC, 4497 m), Camp 1 (C1, 5533 m), Camp 2 (C2, 6265 m) and Camp 3 (C3, 6865 m). Cystatin C- and creatinine-based (Mayo Clinic quadratic equation) GFR estimates (eGFR) were assessed together with Lake Louise AMS score and other tests. RESULTS: eGFR significantly decreased from PE to BC (P < 0.01). However, when analysing at changes between BC and C3, only cystatin C-based estimates indicated a significant decrease in GFR (P = 0.02). There was a linear decrease in eGFR from PE to C3, with a decrease of approx. 3.1 mL min(-1) 1.73 m(-2) per 1000 m increase in altitude. No differences between eGFR of the two groups with different acclimatization protocols could be observed. There was a significant association between eGFR and haematocrit (P = 0.01), whereas no significant association between eGFR and aldosterone, renin and brain natriuretic peptide could be observed. Finally, higher AMS scores were significantly associated with higher eGFR (P = 0.01). CONCLUSIONS: Renal function declines when ascending from low to high altitude. Cystatin C-based eGFR decreases during ascent in high altitude expedition but increases with AMS scores. For individuals with eGFR <40 mL min(-1) 1.73 m(-2), caution may be necessary when planning trips to high altitude above 4500 m above sea level.

Paleomagnetic Study of the Portage Lake Volcanics exposed in the Quincy Mine

A detailed paleomagnetic and rock-magnetic investigation was conducted on thirty six basaltic flows of the ~1095 Ma Portage Lake Volcanics. The flows were sampled along the East Adit of the Quincy Mine (Hancock, MI). Thirty two flows yielded well-defined primary magnetization directions carried by magnetite. A secondary magnetization component carried by hematite was also found in twenty nine flows. After correction for serial correlation between the flows, nineteen independent mean directions were calculated. The corresponding paleomagnetic pole is located at 25.5 °N, 182.1 °W (A95 = 3.5°). The new pole overlaps with the pole from the ~1087 Ma Lake Shore Traps suggesting a standstill of the North American plate during that time period. The low angular dispersion of virtual geomagnetic poles (S = 7.9°) suggests that the flows were erupted within a short time period, or that the strength of geomagnetic secular variation was lower than that of the recent field.

Isolation of plant growth promoting bacteria from torch lake sediments and their role in phytoremediation of metal contaminated soil

In this study, we isolated eight copper-resistant bacteria from Torch Lake sediment contaminated by copper mine tailings (stamp sand). Sequence analysis of gyrB and rpoD genes revealed that these organisms are closer to various Pseudomonas species. These eight bacterial isolates were also resistant to zinc, cesium, lead, arsenate and mercury. Further characterization showed that all the strains produced plant growth promoting indole-3-acetic acid (IAA), iron chelating siderophore and solubilized mineral phosphate and metals. The effect of bacterial inoculation on plant growth and copper uptake by maize (Zea mays) and sunflower (Helianthus annuus) was investigated using one of the isolates (Pseudomonas sp. TLC 6-6.5-4) with higher IAA production and phosphate and metal soubilization, which resulted in a significant increase in copper accumulation in maize and sunflower, and an increase in the total biomass of maize. Genes involved in copper resistance of Pseudomonas sp. TLC 6-6.5-4 was analyzed by transposon mutational analysis. Two copper sensitive mutants with significant reduction in copper resistance were identified: CSM1, a mutant disrupted in trp A gene (tryptophan synthase alpha subunit); CSM2, a mutant disrupted in clpA gene (ATP-dependent Clp protease). Proteomic and metabolomic analysis were performed to identify biochemical and molecular mechanisms involved in copper resistance using CSM2 due to its lower minimum inhibitory concentration compared with CSM1 and the wild type. The effect of different bacterial inoculation methods on plant growth, copper uptake and soil enzyme activities was investigated. Four different delivery methods were used including soil inoculation (before or after plant emergence), seed coating and root dipping. Soil inoculation before sowing seeds and coating seeds with PGPB led to better growth of maize, higher copper uptake and an increase in soil invertase and dehydrogenase activities. Proteomic and metabolomic analyses were performed to investigate the effect of bacterial inoculation on maize grown in normal soil and stamp sand. Our results revealed that bacterial inoculation led to environment-dependent effects on maize proteome and metabolome.

Critical evaluation of diameter increment modelling in the Great Lakes region

Simulations of forest stand dynamics in a modelling framework including Forest Vegetation Simulator (FVS) are diameter driven, thus the diameter or basal area increment model needs a special attention. This dissertation critically evaluates diameter or basal area increment models and modelling approaches in the context of the Great Lakes region of the United States and Canada. A set of related studies are presented that critically evaluate the sub-model for change in individual tree basal diameter used in the Forest Vegetation Simulator (FVS), a dominant forestry model in the Great Lakes region. Various historical implementations of the STEMS (Stand and Tree Evaluation and Modeling System) family of diameter increment models, including the current public release of the Lake States variant of FVS (LS-FVS), were tested for the 30 most common tree species using data from the Michigan Forest Inventory and Analysis (FIA) program. The results showed that current public release of the LS-FVS diameter increment model over-predicts 10-year diameter increment by 17% on average. Also the study affirms that a simple adjustment factor as a function of a single predictor, dbh (diameter at breast height) used in the past versions, provides an inadequate correction of model prediction bias. In order to re-engineer the basal diameter increment model, the historical, conceptual and philosophical differences among the individual tree increment model families and their modelling approaches were analyzed and discussed. Two underlying conceptual approaches toward diameter or basal area increment modelling have been often used: the potential-modifier (POTMOD) and composite (COMP) approaches, which are exemplified by the STEMS/TWIGS and Prognosis models, respectively. It is argued that both approaches essentially use a similar base function and neither is conceptually different from a biological perspective, even though they look different in their model forms. No matter what modelling approach is used, the base function is the foundation of an increment model. Two base functions – gamma and Box-Lucas – were identified as candidate base functions for forestry applications. The results of a comparative analysis of empirical fits showed that quality of fit is essentially similar, and both are sufficiently detailed and flexible for forestry applications. The choice of either base function in order to model diameter or basal area increment is dependent upon personal preference; however, the gamma base function may be preferred over the Box-Lucas, as it fits the periodic increment data in both a linear and nonlinear composite model form. Finally, the utility of site index as a predictor variable has been criticized, as it has been widely used in models for complex, mixed species forest stands though not well suited for this purpose. An alternative to site index in an increment model was explored, using site index and a combination of climate variables and Forest Ecosystem Classification (FEC) ecosites and data from the Province of Ontario, Canada. The results showed that a combination of climate and FEC ecosites variables can replace site index in the diameter increment model.