EEB Articles Copyright (c) 2013 University of Connecticut All rights reserved. http://digitalcommons.uconn.edu/eeb_articles Recent documents in EEB Articles en-us Thu, 16 May 2013 01:59:03 PDT 3600 Euryhalinity in an Evolutionary Context http://digitalcommons.uconn.edu/eeb_articles/29 http://digitalcommons.uconn.edu/eeb_articles/29 Tue, 14 May 2013 13:33:33 PDT This chapter focuses on the evolutionary importance and taxonomic distribution of euryhalinity. Euryhalinity refers to broad halotolerance and broad halohabitat distribution. Salinity exposure experiments have demonstrated that species vary tenfold in their range of tolerable salinity levels, primarily because of differences in upper limits. Halotolerance breadth varies with the species’ evolutionary history, as represented by its ordinal classification, and with the species’ halohabitat. Freshwater and seawater species tolerate brackish water; their empirically-determined fundamental haloniche is broader than their realized haloniche, as revealed by the halohabitats they occupy. With respect to halohabitat distribution, a minority of species (<10%) are euryhaline. Habitat-euryhalinity is prevalent among basal actinopterygian fishes, is largely absent from orders arising from intermediate nodes, and reappears in the most derived taxa. There is pronounced family-level variability in the tendency to be halohabitat-euryhaline, which may have arisen during a burst of diversification following the Cretaceous-Palaeogene extinction. Low prevalence notwithstanding, euryhaline species are potent sources of evolutionary diversity. Euryhalinity is regarded as a key innovation trait whose evolution enables exploitation of new adaptive zone, triggering cladogenesis. We review phylogenetically-informed studies that demonstrate freshwater species diversifying from euryhaline ancestors through processes such as landlocking. These studies indicate that some euryhaline taxa are particularly susceptible to changes in halohabitat and subsequent diversification, and some geographic regions have been hotspots for transitions to freshwater. Comparative studies on mechanisms among multiple taxa and at multiple levels of biological integration are needed to clarify evolutionary pathways to, and from, euryhalinity.

]]> Eric T. Schultz et al. Integrating Ecology and Economics for Restoration: Using Ecological Indicators in Valuation of Ecosystem Services http://digitalcommons.uconn.edu/eeb_articles/28 http://digitalcommons.uconn.edu/eeb_articles/28 Wed, 25 Apr 2012 07:07:45 PDT Because it can uniquely furnish insights into nonuse values for ecosystem services, survey-based Stated Preference (SP) valuation is widely used to estimate the benefits of ecological restoration. SP surveys ask respondents to select among restoration options yielding different ecological outcomes. This review examines the representation of ecological outcomes in SP studies seeking to quantify values for restoration of aquatic ecosystems. To promote the validity of ecological indicators used in SP valuation, we identified four standards: indicators should be measurable, interpretable, applicable, and comprehensive. We reviewed recent SP studies estimating the value of aquatic ecosystem services to assess whether ecological indicators in current use had these desirable properties. More than half of the 54 indicators reviewed were measurable, meaning referable to potentially precise quantification. About one third were interpretable, i.e., presented in a way that facilitates understanding the effects of restoration. About three quarters of the indicators were applicable; SP valuation practitioners typically consult with natural scientists to ensure that indicators represent the effect of stressors on ecological systems, and with focus groups to ensure that indicators have a connection with ecosystem services that contribute to public well-being. While most of the SP studies employed diverse and potentially comprehensive indicators that could capture direct and indirect effects of restoration, and six of twenty studies used indicators that met all standards, shortcomings in the indicators were common. These problems can be rectified with attention to how natural scientists measure change, and to relationships between restoration outcomes and characteristics of fully-restored reference ecosystems.

]]> Eric T. Schultz et al. Assessment of River Herring and Striped Bass in the Connecticut River: Abundance, Population Structure, and Predator/Prey Interactions http://digitalcommons.uconn.edu/eeb_articles/26 http://digitalcommons.uconn.edu/eeb_articles/26 Mon, 16 Apr 2012 11:42:18 PDT Populations of anadromous alewife Alosa pseudoharengus and blueback herring A. aestivalis, collectively referred to as river herring, have declined in the Connecticut River. An explanatory hypothesis for these declines is that predation pressures have increased as a result of recent increases in abundance of sympatric striped bass Morone saxatilis. We sampled river herring and striped bass from the stretch of the Connecticut River between Wethersfield, CT and Holyoke, MA during the vernal migration seasons of 2005-2008. The objectives of the sampling program were to assess abundance, temporal/spatial distribution, and population structure of both river herring and striped bass, as well as striped bass food habits. Blueback herring population structure has changed over recent decades. Contemporary runs feature younger, smaller fish that are less likely to complete multiple spawning runs over their lifetime. These temporal shifts are indicative of elevated mortality rates operating on older, larger herring. Striped bass predation is a significant source of mortality for adult blueback herring in the Connecticut River. River herring comprise a significant portion of striped bass diets in the Connecticut River during May-June, and striped bass congregate in locations where they are successful in capturing herring. The estimated seasonal consumption of blueback herring by striped bass in our study stretch is comparable to the numbers of herring passed annually at the Holyoke fish lift prior to the onset of recent declines. Future studies will incoporate estimates of predation mortality described here into structured population models that can be used to hindcast the impact of striped bass predation on river herring run size in recent decades, and examine the potential for amelioration of river herring mortality via changes to management of striped bass fisheries.

]]> Justin P. Davis et al. Angler Survey of the Connecticut River http://digitalcommons.uconn.edu/eeb_articles/25 http://digitalcommons.uconn.edu/eeb_articles/25 Wed, 29 Feb 2012 08:02:17 PST The Connecticut River is the largest and most diverse inland fishery resource in the State of Connecticut. Significant improvements in water quality over the past 30 years have led to progressive increases in recreational use, presumably increasing fishing pressure on some species and possibly decreasing overall fishing quality. To address this concern, the Inland Fisheries Division (IFD) of the Connecticut Department of Energy and Environmental Protection (CT DEEP) conducted an angler survey on the entire portion of the Connecticut River within the state during March-October of 2008-09. The survey used a similar design as a smaller-scale survey of the river’s fisheries conducted during 1997-98. The objectives of the 2008-09 survey were to assess contemporary angler effort, catch, and harvest, as well as to quantify changes in these quantities since the 1997-98 survey. In addition, the 2008-09 survey assessed angler demographics and attitudes towards harvesting fish. Anglers spent an estimated 263,264 hours annually fishing on the Connecticut River during March-October of 2008-09, catching 35 different fish species. Total angler effort declined by 29-32% between 1997-98 and 2008-09. Declines in effort were largely the result of declines in shore angling effort as well as reduced angling activity during July-August. Total catch of species typically targeted by shore anglers declined by 26-82% between 1997-98 and 2008-09; harvest rates for almost all species either decreased or did not change. Overall, there was no evidence that angler impacts to Connecticut River fish populations have increased over the last decade.

]]> Justin P. Davis Extreme environments select for reproductive assurance: evidence from evening primroses (Oenothera) http://digitalcommons.uconn.edu/eeb_articles/24 http://digitalcommons.uconn.edu/eeb_articles/24 Mon, 16 Jan 2012 07:44:06 PST • Competing evolutionary forces shape plant breeding systems (e.g. inbreeding depression, reproductive assurance). Which of these forces prevails in a given population or species is predicted to depend upon such factors as life history, eco- logical conditions, and geographical context. Here, we examined two such predictions: that self-compatibility should be associated with the annual life history or extreme climatic conditions.

• We analyzed data from a clade of plants remarkable for variation in breeding system, life history and climatic conditions (Oenothera, sections Anogra and Kleinia, Onagraceae). We used a phylogenetic comparative approach and Bayesian or hybrid Bayesian tests to account for phylogenetic uncertainty. Geographic information system (GIS)-based climate data and ecological niche modeling allowed us to quantify climatic conditions.

• Breeding system and reproductive life span are not correlated in Anogra and Kleinia. Instead, self-compatibility is associated with the extremes of temperature in the coldest part of the year and precipitation in the driest part of the year.

• In the 60 yr since this pattern was anticipated, this is the first demonstration of a relationship between the evolution of self-compatibility and climatic extremes. We discuss possible explanations for this pattern and possible implications with respect to anthropogenic climate change.

]]> Margaret E.K. Evans et al. Environmental and Endogenous Factors Influencing Emigration in Juvenile Anadromous Alewives http://digitalcommons.uconn.edu/eeb_articles/23 http://digitalcommons.uconn.edu/eeb_articles/23 Tue, 06 Jul 2010 05:28:43 PDT We analyzed juvenile anadromous alewife migration at Bride Lake, a coastal lake in Connecticut, during summer 2006 and found that migration on 24-hour and seasonal timescales was influenced by conditions of the environment and characteristics of the individual. To identify environmental cues of juvenile migration, we continuously video recorded fish at the lake outflow and employed information-theoretic model selection to identify the best predictors of daily migration rate. More than 80% of the approximately 320,000 juveniles that migrated from mid-June to mid-August departed in three pulses lasting one or two days. Pulses of migration were associated with precipitation events, transient decreases in water temperature and transient increases in stream discharge. Diel timing of migration shifted over the summer. Early in the season most migration occurred around dawn; late in the season migration occurred at night. To identify individual characteristics associated with migratory behavior, we compared migrating juveniles that we collected as they were exiting Bride Lake to non-migrating juveniles that we collected from the center of the lake. Migrants were a non-random subset of the population; they were on average 1 – 12 mm larger, 2 – 14 d older, had grown more rapidly (11% greater length-at-age), and were in better condition (14% greater mass-at-length) than non-migrant fish. We infer that the amount of accumulated energy has a positive effect on the net benefit of migration at any time in the migratory season.

]]> Benjamin I. Gahagan et al. "Genetics in geographically structured populations: defining, estimating and interpreting FST." http://digitalcommons.uconn.edu/eeb_articles/22 http://digitalcommons.uconn.edu/eeb_articles/22 Mon, 15 Mar 2010 07:28:05 PDT Wright's F-statistics, and especially F(ST), provide important insights into the evolutionary processes that influence the structure of genetic variation within and among populations, and they are among the most widely used descriptive statistics in population and evolutionary genetics. Estimates of F(ST) can identify regions of the genome that have been the target of selection, and comparisons of F(ST) from different parts of the genome can provide insights into the demographic history of populations. For these reasons and others, F(ST) has a central role in population and evolutionary genetics and has wide applications in fields that range from disease association mapping to forensic science. This Review clarifies how F(ST) is defined, how it should be estimated, how it is related to similar statistics and how estimates of F(ST) should be interpreted.

]]> Kent E. Holsinger et al. Estimating Predation on Declining River Herring: Tag-recapture Study of Striped Bass in the Connecticut River http://digitalcommons.uconn.edu/eeb_articles/21 http://digitalcommons.uconn.edu/eeb_articles/21 Mon, 17 Aug 2009 06:55:44 PDT Populations of anadromous alewife Alosa pseudoharengus and blueback herring Alosa aestivalis, collectively referred to as river herring, have declined in the Connecticut River. A hypothesis for why river herring have declined is that predation pressures have increased associated with recent increases in abundance of striped bass Morone saxatilis. Information on striped bass abundance, size structure, and consumption rates are required to test this hypothesis. This study was designed to provide estimates of striped bass population size in the Connecticut River during the spring migration season, via an intensive mark-recapture exercise and either an open or robust mark-recapture model. Striped bass were sampled between Wethersfield, CT and Holyoke, MA in May-June 2007 and 2008 by night-time boat electrofishing. All fish ≥ 300 mm TL were tagged with a uniquely-coded internal anchor FLOY tag. Reports of tagged striped bass were solicited from recreational anglers. Monetary rewards were offered for tag reports. Connecticut Department of Environmental Protection (CDEP) conducted a creel survey of the Connecticut River in 2008, providing estimates of angler catch of striped bass. A total of 662 striped bass was tagged in 2007. Anglers reported 34 tag recaptures and an additional 7 recaptures were made during electrofishing operations. A total of 535 striped bass was tagged in 2008. Anglers reported 23 tag recaptures, and an additional 3 recaptures were made during electrofishing operations. Population size was estimated in 2008 using a Schnabel mark-recapture model; 65,744 (95% CI = 2,434 – 109,573) striped bass ≥ 300 mm TL were in the Connecticut River between Hartford and the MA/CT border during May 2008. Estimates were unavailable for 2007 because CDEP did not conduct a creel survey in that year. The Schnabel model population size estimate is biased to an unknown degree due to violation of underlying assumptions of the model. However, this population size estimate will still serve as a valuable reference point for quantifying predation in the Connecticut River. Future efforts to apply an open population model will require a much more extensive tagging and recapture effort. Alternately, telemetry studies of striped bass movement could elucidate the magnitude and direction of bias in closed population model estimates.

]]> Eric T. Schultz et al. Assessment of Anadromous Alewife and Blueback Herring Populations in Connecticut Coastal Streams and Connecticut River Tributaries http://digitalcommons.uconn.edu/eeb_articles/20 http://digitalcommons.uconn.edu/eeb_articles/20 Mon, 01 Jun 2009 08:04:16 PDT Alewife (Alosa pseudoharengus) and blueback herring (A. aestivalis) occur in anadromous populations that have a largely overlapping distribution from Florida to Newfoundland (Loesch 1987). Anadromous populations of these species are commonly collectively referred to as “river herring”. Adults inhabit coastal shelf waters until sexual maturity is reached at age 3-5 (Neves 1981). Sexually mature individuals make spawning migrations, commonly referred to as “runs”, into freshwater systems during spring months (Loesch 1987). Spawners can survive and return to spawn in subsequent years (Mullen et al. 1986). Juveniles reside in freshwater for 3-7 months, at which time they undertake a gradual migration to estuarine and marine waters (Loesch 1987).

Many freshwater systems within the State of Connecticut support river herring runs. These fish have historically been taken for use as bait by recreational anglers in Connecticut waters. These species also have ecological significance. Throughout all phases of their life cycle, river herring provide an important source of forage for a wide variety of predators (Loesch 1987). River herring runs can also serve as a vector for nutrient transport from the marine environment to freshwater systems (Durbin et al. 1979). There is also evidence that the seasonal presence of river herring in freshwater systems may benefit sport-fish species (McCaig 1980; Yako et al. 2000).

There is compelling evidence that river herring populations in Connecticut are declining. Annual passage of blueback herring at Holyoke Dam on the Connecticut River has declined three orders of magnitude over the previous 15 years (Savoy and Crecco 2004). Available data from other sites in Connecticut provide strong evidence of declines in the majority of streams surveyed, with the worst declines being noted in large river watersheds (Gephard et al. 2004). In response to these declines, an emergency fishery closure for inland waters was instituted by the Connecticut Department of Environmental Protection (CDEP) in 2001; this closure is still in effect.

The purposes of this project were to assess river herring population structure at study sites within Connecticut, make inter-watershed and temporal comparisons of population structure, and develop quantitative sampling strategies for estimation of river herring run size. Current data on population structure of river herring in Connecticut are largely unavailable. Collection of these data is crucial to the development of management strategies for amelioration of current population declines and will serve as valuable baseline data for future managers. Comparisons of contemporary population structure data to historic data will help to characterize decade-scale temporal shifts in population structure. Inter-watershed comparisons of population structure data may provide insight into processes driving the disproportionately precipitous declines within large river watersheds. Quantitative estimates of abundance are not available for many runs in Connecticut due to the prohibitive amount of cost and effort required to perform a census. Assessment of candidate quantitative sampling strategies will elucidate levels of sampling effort at which reasonably accurate and precise estimates of run size can be obtained.

]]> Justin P. Davis et al. Determining Winter flounder Spawning Sites in Two Connecticut Estuaries http://digitalcommons.uconn.edu/eeb_articles/19 http://digitalcommons.uconn.edu/eeb_articles/19 Mon, 01 Jun 2009 08:04:14 PDT Winter flounder (Pseudopleuronectes americanus) come inshore during the late winter and early spring to lay their eggs in shallow bays and estuaries along the coast. Unlike most fish eggs, which are buoyant, these eggs are demersal and sink to the seafloor. This makes them vulnerable to burial from various types of natural and human caused disturbances (e.g., storms, mobile fishing gear, maintenance dredging). Our objective was to map spawning areas in two harbors and search for generalities among these sites that would allow us to predict where winter flounder might spawn in other areas. This would allow managers to avoid permitting activities for those times and locations where winter flounder spawn.

We used a modified demersal plankton net (a benthic sled) to collect winter flounder eggs in New Haven and Milford harbors and map their distributions. Most of the eggs were collected at the end of March, when water temperatures were 4-6° C. This could vary from year to year depending on temperature. The distributions of eggs were not correlated with sediment type or depth but were related to the prevailing tidal currents in the area sampled. Since the eggs are present in low-current depositional areas, they are vulnerable to burial. Our observations suggest that winter flounder either do not deposit eggs in high current areas, or if eggs are deposited there, they are swept away.

Since early stage embryos (morula, blastula, gastrula) were found in low current areas, it seems unlikely that they were transported there from some other location. These findings have important management implications because any activities (dredging, building breakwaters, installing docks) near spawning areas could have adverse effects if they change the prevailing currents in the area.

]]> Eric T. Schultz et al. Anadromous Rainbow Smelt and Tomcod in Connecticut: Assessment of populations, conservation status, and need for restoration plan http://digitalcommons.uconn.edu/eeb_articles/18 http://digitalcommons.uconn.edu/eeb_articles/18 Mon, 01 Jun 2009 08:02:54 PDT (beginning of rainbow smelt executive summary)

Evidence indicates that anadromous rainbow smelt (Osmerus mordax) populations in Connecticut and elsewhere in the northeast United States have severely declined. Several sampling programs have documented declines in Connecticut’s smelt populations over the last three decades (Marcy 1976a, Marcy 1976b, Millstone Environmental Laboratory 2005). Similar declines have also been documented in the Hudson River (ASA Analysis & Communication 2005) and in Massachusetts (personal communication, Brad Chase, MA Division of Marine Fisheries 2004). Recreational and commercial fisheries in the region for this species have virtually ceased (Blake and Smith 1984). The Connecticut Fish Advisory Committee of the Endangered Species Program has recommended that rainbow smelt be listed as threatened in Connecticut, and the National Marine Fisheries Service (2004) has recently listed rainbow smelt as a Federal Species of Concern.

The purpose of this project is to develop an environmental history of rainbow smelt in Connecticut and surrounding regions, and document the current status of populations in Connecticut waters. An environmental history that assesses trends in abundance, environmental threats and historical efforts to ameliorate the threats will contribute to regional efforts to conserve these fish. Comprehensive review of the regional literature and trends associated with rainbow smelt has not been undertaken since Kendall (1926). Assessment of current abundance, distribution, areas of critical habitat, and whether the species is presently reproducing in state waters is critical for clarifying conservation status, designing a monitoring program and developing a recovery or enhancement plan, if this appears to be necessary.

(beginning of tomcod executive summary)

Atlantic tomcod (Microgadus tomcod) are believed to have declined significantly in Connecticut and other estuaries of the Northeast and Middle Atlantic states. Several monitoring programs indicate that the species is scarce and/or declining in the region’s estuaries (Gottschall and Pacileo 2004, Molnar 2004, Millstone Environmental Laboratory 2005, ASA Analysis and Communication 2005). Once-active recreational (NMFS MRFSS 2005, http://www.st.nmfs.gov) and commercial fisheries for this species in Connecticut are now dormant. For the past 10 years, the Connecticut Fish Advisory Committee of the Endangered Species Program has recommended that studies be undertaken to quantify the status of tomcod populations and to determine if conservation actions should be initiated.

The purpose of this project is to develop an environmental history of Atlantic tomcod in Connecticut and surrounding regions, and document the current status of populations in Connecticut waters. An environmental history that assesses trends in abundance, environmental threats and historical efforts to ameliorate the threats will contribute to regional efforts to conserve these fish. Assessment of current abundance, distribution, areas of critical habitat, and whether the species is presently reproducing in state waters is critical for determining conservation status, designing a monitoring program and developing a recovery or enhancement plan, if this appears to be necessary.

]]> Heather A. Fried et al. Temporal Shifts in Demography and Life History of an Anadromous Alewife Population in Connecticut http://digitalcommons.uconn.edu/eeb_articles/17 http://digitalcommons.uconn.edu/eeb_articles/17 Mon, 01 Jun 2009 05:30:21 PDT Populations of anadromous alewives (Alosa pseudoharengus) are declining throughout much of their range, particularly in southern New England where fishery moratoriums have recently been instituted in three states. The alewife run at Bride Brook, a coastal stream in East Lyme, Connecticut, was studied from 2003-06 to assess shifts in demography and life history. Annual censuses of abundance, along with sampling for size, age, and spawning history structure were conducted. These data were compared to similar data in 1966-67 at this site. Recent alewife runs at Bride Brook featured lower abundance and younger, smaller fish that were less likely to be repeat-spawners. The 1966 spawning run was dominated by age 5–7 repeat-spawners, while runs in 2003-06 were dominated by age 3 and 4 first-spawn fish. Mean length declined by 10% between 1966 and 2006. Alewives are also recruiting to the spawning run at younger ages and smaller sizes, indicating a shift in life history. The first-spawn portion of the 1966 spawning run was dominated by age 5 fish, while recent first-time spawners were primarily age 3. The shifts in demography and life history observed at Bride Brook are consistent with exploitation or predation concentrated on older, larger individuals in the population. The results of this study suggest recent increases in predatory pressure or bycatch mortality as promising hypotheses that merit further investigation.

]]> Justin P. Davis et al. Mechanisms promoting upriver transport of two species of larval fish in the Hudson River Estuary (USA) http://digitalcommons.uconn.edu/eeb_articles/16 http://digitalcommons.uconn.edu/eeb_articles/16 Mon, 06 Oct 2008 15:27:35 PDT Bay anchovy Anchoa mitchilli and naked goby Gobiosoma bosc larvae have been reported to move up-estuary. In the present study, we examined depth preferences and periodic vertical movements that might promote such along-estuary transport in these 2 species. We conducted 2 cruises of 3 d each in the Hudson River estuary, USA. The cruises were 1 wk apart, coinciding with spring and neap tides. We sampled every 2 h with an ichthyoplankton trawl to permit tests of time, depth, and lateral position on larval concentration. We also collected data on water-column structure with a CTD, and current velocity with an acoustic Doppler current profiler (ADCP). We briefly sampled at several sites over a distance of 25 km along the river, and found that larvae of both species were uniformly abundant along this section although salinity decreased sharply with increasing distance upriver. Bay anchovy larvae were more abundant than goby larvae (median concentration 234 vs 6.6 ind. 100 m–3). Most sampling was conducted at an oligohaline location (mean salinity = 3 to 5 psu). Larvae were typically more concentrated at greater depths; among anchovy larvae during neap tide conditions, and goby larvae during neap and spring tide conditions, larvae were more concentrated at 6 and 8 m than at the surface by a factor of 2 to 9. Large larvae showed a stronger depth preference than small larvae. During spring tide, the water column was less stratified, and anchovy larvae under these conditions were uniformly distributed vertically. There were slight lateral differences in larval concentration, with fewer larvae in shallow water over the shoals than in similar depths in the main channel. We evaluated periodic cycles in flow and larval distributions via harmonic regression. Tidal constituents of the depth-averaged current flow included the K1 (period = 23.9 h), M2 (period = 12.4 h), and the M4 (period = 6.2 h) tides. Harmonic regression explained >95% of the observed variability in mean flow. Diel periodicity in depth-averaged larvae concentration was evident, particularly among large anchovy and goby larvae during neap tide conditions. Larvae were more abundant in the sampled depths at night than during the day by a factor of 3 to 10. There was also diel periodicity in the mean depth of goby larvae, such that larvae were about 2 m shallower at night than during the day. There was no periodic variability in the mean depth of anchovy larvae. We suggest that diel periodicity in larval concentration and mean depth reflects diel migration to shallower water at night, noting that temporal variability in net avoidance may also contribute to the periodicity. We conclude that anchovy and goby larvae exhibit a depth distribution and vertical migration behavior that promotes upriver transport. Transport should be most rapid during neap tide periods.

]]> Eric T. Schultz et al. Recruitment of coral reef fishes to Bermuda: Local retention or long-distance transport? http://digitalcommons.uconn.edu/eeb_articles/15 http://digitalcommons.uconn.edu/eeb_articles/15 Mon, 06 Oct 2008 15:27:24 PDT The benthic marine fauna of isolated oceanic islands may be self-seeding, or alternatively may be continually supplied with recruits advected from elsewhere by ocean currents. Estimates of the time required for transport of larvae from elsewhere was combined with information on the larval durations of fishes inhabiting the reefs of Bermuda, to test the hypothesis that other populations are sources for recruits to Bermuda. Specifically, we tested the prediction that transport occurs frequently enough to sustain local populations of reef fishes. Transport of larvae was modelled as a 2-step process in several numerical simulations. The first step of transport was assumed to occur via the Gulf Stream. The second step, in which larvae are transported across the northern Sargasso Sea to Bermuda, was modelled in several different ways, Involving either cold-core rings thrown off by the Stream, or mixtures of Gulf Stream and Sargasso water entrained by cold-core rings. Travel distances and speeds were estimated from a variety of sources, focusing on satellite imagery of sea-surface temperature. Pelagic larval durations (PLDs) for reef fish on Bermuda were analyzed from the daily age record in the otoliths of 6 wrasse and 1 parrotfish species. When PLDs were compared with transport times, it was determined that transport events would occur too infrequently to sustain Bermudian populations of reef fishes. The PLDs for most of these species are similar to results obtained elsewhere in their geographic range. It is evident that these populations must be mainly replenished via a pool of larvae that are spawned locally and retained in the vicinity of the Bermuda islands.

]]> Eric T. Schultz et al. Decreased reproductive investment of female threespine stickleback <i>Gasterosteus aculeatus</i> infected with the cestode <i>Schistocephalus solidus</i>: parasite adaptation, host adaptation, or side effect? http://digitalcommons.uconn.edu/eeb_articles/14 http://digitalcommons.uconn.edu/eeb_articles/14 Mon, 06 Oct 2008 15:27:21 PDT Parasitic infections may cause alterations in host life history, including changes in reproductive investment (absolute amount of energy allocated to reproduction) and reproductive effort (proportion of available energy allocated to reproduction). Such changes in host life history may reflect: 1) a parasite tactic: the parasite adaptively manipulates energy flow within the host so that the host is induced to make a reduction in reproductive effort and reproductive investment, making more energy available to the parasite; 2) no tactic: there is no change in host reproductive effort and reproductive investment simply decreases as a side effect of the parasite depleting host energy stores; 3) a host tactic: the host adaptively increases reproductive effort in the face of infection and loss of body condition, reproductive investment possibly being reduced despite the increased reproductive effort. Females in Alaskan lake populations of threespine sticklebacks (Gasterosteus aculeatus) are capable of clutch production when parasitized by the cestode Schistocephalus solidus despite large relative parasite masses. We analyzed the somatic energy reserves, maturation stage and ovarian mass of female sticklebacks collected from an Alaska lake during a single reproductive season. We found that parasitized females were less likely to carry fully-matured gametes, had smaller ovarian masses, and had lower somatic energy stores than unparasitized females. The relationship between reproductive investment and energy storage did not differ between parasitized and unparasitized females. Thus, reproductive effort did not change in response to parasitic infection. We conclude there was no indication of either a parasite tactic or a host tactic. Simple nutrient theft is involved in the parasite's influence on host reproduction, consistent with an earlier hypothesis that reproductive curtailment in threespine sticklebacks is a side effect.

]]> Eric T. Schultz et al. A sex difference in seasonal timing of birth in a livebearing fish http://digitalcommons.uconn.edu/eeb_articles/13 http://digitalcommons.uconn.edu/eeb_articles/13 Mon, 06 Oct 2008 15:27:16 PDT Sex differences in seasonal timing include differences in hatch- or birth-date distribution and differences in the timing of migration or maturation such as protandrous arrival timing (PAT), which is early male arrival at breeding sites. I describe a novel form of protandrous arrival timing, as a sex difference in birth-date distribution in a live-bearing fish (Dwarf Perch, Micrometrus minimus). In this species, birth coincides with arrival at breeding sites because newborn males are sexually active. A series of samples of pregnant females and young of year was collected in Tomales Bay, CA. I analyzed the daily age record in otoliths to estimate the conception date of broods and the age that young-of-year individuals were born. Males were born at a younger age than females, as indicated by the daily age record and also by the predominance of females in broods from which some young had already been born, which was a common occurrence in pregnant females with older embryos. Sex ratio of broods varied with conception date such that early-season broods were predominantly male, possibly as a result of temperature-dependent sex determination. The combined effects of the sex difference in age at birth and seasonal shift in sex ratio were to shift the mean birth date of males relative to females by five days. The most likely ultimate explanation for PAT in the Dwarf Perch is that it arises from exploitation (scramble) competition for mating opportunities among recently-born young-of-year males.

]]> Eric T. Schultz Polytomies and bayesian phylogenetic inference http://digitalcommons.uconn.edu/eeb_articles/12 http://digitalcommons.uconn.edu/eeb_articles/12 Mon, 06 Oct 2008 15:25:59 PDT Bayesian phylogenetic analyses are now very popular in systematics and molecular evolution because they allow the use of much more realistic models than currently possible with maximum likelihood methods. There are, however, a growing number of examples in which large Bayesian posterior clade probabilities are associated with very short edge lengths and low values for non-Bayesian measures of support such as nonparametric bootstrapping. For the four-taxon case when the true tree is the star phylogeny, Bayesian analyses become increasingly unpredictable in their preference for one of the three possible resolved tree topologies as data set size increases. This leads to the prediction that hard (or near-hard) polytomies in nature will cause unpredictable behavior in Bayesian analyses, with arbitrary resolutions of the polytomy receiving very high posterior probabilities in some cases. We present a simple solution to this problem involving a reversible-jump Markov chain Monte Carlo (MCMC) algorithm that allows exploration of all of tree space, including unresolved tree topologies with one or more polytomies. The reversible-jump MCMC approach allows prior distributions to place some weight on less-resolved tree topologies, which eliminates misleadingly high posteriors associated with arbitrary resolutions of hard polytomies. Fortunately, assigning some prior probability to polytomous tree topologies does not appear to come with a significant cost in terms of the ability to assess the level of support for edges that do exist in the true tree. Methods are discussed for applying arbitrary prior distributions to tree topologies of varying resolution, and an empirical example showing evidence of polytomies is analyzed and discussed.

]]> Paul O. Lewis et al. A Bayesian hierarchical model for analysis of SNP diversity in multilocus, multipopulation samples http://digitalcommons.uconn.edu/eeb_articles/11 http://digitalcommons.uconn.edu/eeb_articles/11 Mon, 30 Jun 2008 11:22:45 PDT The distribution of genetic variation among populations is conveniently measured by Wright’s FST , which is a scaled variance taking on values in [0,1]. For certain types of genetic markers, and for single-nucleotide polymorphisms (SNPs) in particular, it is reasonable to presume that allelic differences at most loci are selectively neutral. For such loci, the distribution of genetic variation among populations is determined by the size of local populations, the pattern and rate of migration among those populations, and the rate of mutation. Because the demographic parameters (population sizes and igration rates)are common across all autosomal loci, locus-specific estimates of FST will depart from a common distribution only for loci with unusually high or low rates of mutation or for loci that are closely associated with genomic regions having a relationship with fitness. Thus, loci that are statistical outliers showing significantly more among-population differentiation than others may mark genomic regions subject to diversifying selection among the sample populations. Similarly, statistical outliers showing significantly less differentiation among populations than others may mark genomic regions subject to stabilizing selection across the sample populations. We propose several Bayesian hierarchical models to estimate locus-specific effects on FST , and we apply these models to single nucleotide polymorphism data from the HapMap project. Because loci that are physically associated with one another are likely to show similar patterns of variation, we introduce conditional autoregressive models to incorporate the local correlation among loci for high-resolution genomic data. We estimate the posterior distributions of model parameters using Markov chain Monte Carlo (MCMC) simulations. Model comparison using several criteria, including DIC and LPML, reveals that a model with locus- and population-specific effects is superior to other models for the data used in the analysis. To detect statistical outliers we propose an approach that measures divergence between the posterior distributions of locus-specific effects and the common FST with the Kullback-Leibler divergence measure. We calibrate this measure by comparing values with those produced from the divergence between a biased and a fair 3 coin. We conduct a simulation study to illustrate the performance of our approach for detecting loci subject to stabilizing/divergent selection, and we apply the proposed models to low- and high-resolution SNP data from the HapMap project. Model comparison using DIC and LPML reveals that CAR models are superior to alternative models for the high resolution data. For both low and high resolution data, we identify statistical outliers that are associated with known genes.

]]> Feng Guo et al. Annual Fecundity of Tautog in Long Island Sound: Size Effects and Long-Term Changes in a Harvested Population http://digitalcommons.uconn.edu/eeb_articles/10 http://digitalcommons.uconn.edu/eeb_articles/10 Tue, 20 Nov 2007 06:15:48 PST Abstract.—Few studies estimate the impact of individual size on annual reproductive output, which is an important consideration where size-selective harvest may truncate size distributions and sharply reduce populationwide reproductive potential. We conducted a 2-year study of reproduction in field-collected and captive tautog Tautoga onitis from Long Island Sound to investigate the influence of individual size on components that constitute annual fecundity: batch fecundity, spawning frequency, and season duration. Estimates of spawning frequency in field-caught females relied on time-varying features of postovulatory follicles that we validated in experiments conducted on captive spawners.Mature females collected in the wild demonstrated midseason peaks in spawning frequency and batch size. Both spawning frequency and batch fecundity increased significantly with size. As a result, annual fecundity increased sharply with size: large (500-mm) females produced 24–86 times as many eggs as did small (250-mm) females. Average (400-mm) females spawned 10–16 million eggs over a season, or about 10,000 eggs/g of whole body mass. We estimated temporal changes in populationwide egg production with data from a 22-year trawl survey in Long Island Sound. Over this period, an index of abundance declined by a factor of six and size distributions shifted to smaller fish. Despite the shift in size distribution, estimated annual egg production declined no more than the index of abundance because the sex ratio of the population has become female biased. Estimates of tautog annual fecundity were higher than those reported previously in the southern portion of the species’ range, reflecting genetic differentiation or phenotypic responses to environmental effects. Given the relatively large reproductive output of large females, their abundance is likely to influence the rate of population recovery in Long Island Sound.

]]> Lori H. LaPlante et al. Polytomies and bayesian phylogenetic inference http://digitalcommons.uconn.edu/eeb_articles/9 http://digitalcommons.uconn.edu/eeb_articles/9 Mon, 19 Feb 2007 12:27:04 PST Bayesian phylogenetic analyses are now very popular in systematics and molecular evolution because they allow the use of much more realistic models than currently possible with maximum likelihood methods. There are, however, a growing number of examples in which large Bayesian posterior clade probabilities are associated with very short edge lengths and low values for non-Bayesian measures of support such as nonparametric bootstrapping. For the four-taxon case when the true tree is the star phylogeny, Bayesian analyses become increasingly unpredictable in their preference for one of the three possible resolved tree topologies as data set size increases. This leads to the prediction that hard (or near-hard) polytomies in nature will cause unpredictable behavior in Bayesian analyses, with arbitrary resolutions of the polytomy receiving very high posterior probabilities in some cases. We present a simple solution to this problem involving a reversible-jump Markov chain Monte Carlo (MCMC) algorithm that allows exploration of all of tree space, including unresolved tree topologies with one or more polytomies. The reversible-jump MCMC approach allows prior distributions to place some weight on less-resolved tree topologies, which eliminates misleadingly high posteriors associated with arbitrary resolutions of hard polytomies. Fortunately, assigning some prior probability to polytomous tree topologies does not appear to come with a significant cost in terms of the ability to assess the level of support for edges that do exist in the true tree. Methods are discussed for applying arbitrary prior distributions to tree topologies of varying resolution, and an empirical example showing evidence of polytomies is analyzed and discussed.

]]> Paul O. Lewis et al.