Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols Used xiii 1. The Importance of Islands 3 2. Area and Number of Speicies 8 3. Further Explanations of the Area-Diversity Pattern 19 4. The Strategy of Colonization 68 5. Invasibility and the Variable Niche 94 6. Stepping Stones and Biotic Exchange 123 7. Evolutionary Changes Following Colonization 145 8. Prospect 181 Glossary 185 References 193 Index 201

The Theory of Island Biogeography

Many criteria for statistical parameter estimation, such as maximum likelihood, are formulated as a nonlinear optimization problem. Automatic Differentiation Model Builder (ADMB) is a programming framework based on automatic differentiation, aimed at highly nonlinear models with a large number of parameters. The benefits of using AD are computational efficiency and high numerical accuracy, both crucial in many practical problems. We describe the basic components and the underlying philosophy of ADMB, with an emphasis on functionality found in no other statistical software. One example of such a feature is the generic implementation of Laplace approximation of high-dimensional integrals for use in latent variable models. We also review the literature in which ADMB has been used, and discuss future development of ADMB as an open source project. Overall, the main advantages of ADMB are flexibility, speed, precision, stability and built-in methods to quantify uncertainty.

/pdf/ad-model-builder-using-automatic-differentiation-for-18b5wunetc.pdf

AD Model Builder: using automatic differentiation for statistical inference of highly parameterized complex nonlinear models

We show that globally declining fisheries catch trends cannot be explained by random processes and are consistent with declining stock abundance trends. Future projections are inherently uncertain but may provide a benchmark against which to assess the effectiveness of conservation measures. Marine reserves and fisheries closures are among those measures and can be equally effective in tropical and temperate areas—but must be combined with catch-, effort-, and gear restrictions to meet global conservation objectives.

https://science.sciencemag.org/content/sci/316/5829/1285.4.full.pdf

Response to Comments on "Impacts of Biodiversity Loss on Ocean Ecosystem Services"

BACKGROUND: Comparing patterns of ter- restrial and marine defaunation helps to place human impacts on marine fauna in context and to navigate toward recovery. De- faunation began in ear- nest tens of thousands of years later in the oceans than it did on land. Al- though defaunation has been less severe in the oceans than on land, our effects on marine animals are increasing in pace and impact. Humans have caused few complete extinctions in the sea, but we are responsible for many ecological, commercial, and local extinctions. Despite our late start, humans have already powerfully changed virtually all major marine ecosystems. ADVANCES: Humans have profoundly de- creased the abundance of both large (e.g., whales) and small (e.g., anchovies) marine fauna. Such declines can generate waves of ecological change that travel both up and down marine food webs and can alter ocean ecosystem functioning. Human harvesters have also been a major force of evolutionary change in the oceans and have reshaped the genetic structure of marine animal popula- tions. Climate change threatens toaccelerate marine defaunation over the next century. The high mobility of many marine animals offers some increased, though limited, ca- pacity for marine species to respond to cli- mate stress, but it also exposes many species to increased risk from other stressors. Be- cause humans are intensely reliant on ocean ecosystems for food and other ecosystem ser- vices, we are deeply affected by all of these forecasted changes. Three lessons emerge when comparing the marine and terrestrial defaunation ex-

/pdf/marine-defaunation-animal-loss-in-the-global-ocean-1ru8fpvwmg.pdf

Marine defaunation: Animal loss in the global ocean

Summary 1. Top-down control can be an important determinant of ecosystem structure and function, but in oceanic ecosystems, where cascading effects of predator depletions, recoveries, and invasions could be significant, such effects had rarely been demonstrated until recently. 2. Here we synthesize the evidence for oceanic top-down control that has emerged over the last decade, focusing on large, high trophic-level predators inhabiting continental shelves, seas, and the open ocean. 3. In these ecosystems, where controlled manipulations are largely infeasible, ‘pseudo-experimental’ analyses of predator‐prey interactions that treat independent predator populations as ‘replicates’, and temporal or spatial contrasts in predator populations and climate as ‘treatments’, are increasingly employed to help disentangle predator effects from environmental variation and noise. 4. Substantial reductions in marine mammals, sharks, and piscivorous fishes have led to mesopredator and invertebrate predator increases. Conversely, abundant oceanic predators have suppressed prey abundances. Predation has also inhibited recovery of depleted species, sometimes through predator‐prey role reversals. Trophic cascades have been initiated by oceanic predators linking to neritic food webs, but seem inconsistent in the pelagic realm with effects often attenuating at plankton. 5. Top-down control is not uniformly strong in the ocean, and appears contingent on the intensity and nature of perturbations to predator abundances. Predator diversity may dampen cascading effects except where nonselective fisheries deplete entire predator functional groups. In other cases, simultaneous exploitation of predator and prey can inhibit prey responses. Explicit consideration of anthropogenic modifications to oceanic foodwebs should help inform predictions about trophic control. 6. Synthesis and applications . Oceanic top-down control can have important socio-economic, conservation, and management implications as mesopredators and invertebrates assume dominance, and recovery of overexploited predators is impaired. Continued research aimed at integrating across trophic levels is needed to understand and forecast the ecosystem effects of changing oceanic predator abundances, the relative strength of top-down and bottom-up control, and interactions with intensifying anthropogenic stressors such as climate change.

/pdf/cascading-top-down-effects-of-changing-oceanic-predator-3vcmppik3q.pdf

Cascading top-down effects of changing oceanic predator abundances

▪ Abstract The total world catch from marine and freshwater wild stocks has peaked and may be slightly declining. There appear to be few significant resources to be developed, and the majority of the world's fish stocks are intensively exploited. Many marine ecosystems have been profoundly changed by fishing and other human activities. Although most of the world's major fisheries continue to produce substantial sustainable yield, a number have been severely overfished, and many more stocks appear to be heading toward depletion. The world's fisheries continue to be heavily subsidized, which encourages overfishing and provides society with a small fraction of the potential economic benefits. In most of the world's fisheries there is a “race for fish” in which boats compete to catch the fish before a quota is achieved or the fish are caught by someone else. The race for fish leads to economic inefficiency, poor quality product, and pressure to extract every fish for short-term gain. A number of countries hav...

State of the World’s Fisheries

Size at 50% maturity is commonly evaluated for wild popula- tions, but the uncertainty involved in such computation has been frequently overlooked in the application to marine fisheries. Here we evaluate three pro- cedures to obtain a confidence interval for size at 50% maturity, and in gen- eral for P% maturity: Fieller's analyti- cal method, nonparametric bootstrap, and a Monte Carlo algorithm. The three methods are compared in estimating size at 50% maturity (l 50% ) by using simulated data from an age-structured population, with von Bertalanffy growth and constant natural mortality, for sample sizes of 500 to 10,000 indi- viduals. Performance was assessed by using four criteria: 1) the proportion of times that the confidence interval did contain the true and known size at 50% maturity, 2) bias in estimating l 50% , 3) length and 4) shape of the confidence interval around l 50% . Judging from cri- teria 2-4, the three methods performed equally well, but in criterion 1, the Monte Carlo method outperformed the bootstrap and Fieller methods with a frequency remaining very close to the nominal 95% at all sample sizes. The Monte Carlo method was also robust to variations in natural mortality rate (M), although with lengthier and more asymmetric confidence intervals as M increased. This method was applied to two sets of real data. First, we used data from the squat lobster Pleuron- codes monodon with several levels of proportion mature, so that a confidence interval for the whole maturity curve could be outlined. Second, we compared two samples of the anchovy Engraulis ringens from different localities in cen- tral Chile to test the hypothesis that they differed in size at 50% maturity and concluded that they were not sta- tistically different. statistical uncertainty of the model- based l 50% is ignored (Table 1). In this work, we show three alterna- tive procedures: an analytical method derived from generalized linear models (McCullagh and Nelder, 1989), nonparametric boot- strap (Efron and Tibshirani, 1993), and a Monte Carlo algorithm devel- oped in our study. We show by simu- lation the behavior of the three methods for sample sizes of 500 to 10,000 individuals, concluding that they are similar in terms of bias, length, and shape of confidence inter- vals but that the Monte Carlo method outperforms the other two methods in percentage of times that the confi- dence interval contains the true pa- rameter, which remained close to the nominal 95% at all sample sizes.

Estimation of size at sexual maturity: an evaluation of analytical and resampling procedures

Snow crab (Chionoecetes opilio) migrations in the eastern Bering Sea have long been ignored. Based on preliminary information, we hypothesized that females undergo an extensive ontogenetic migratio...

Spatial dynamics of female snow crab (Chionoecetes opilio) in the Eastern Bering Sea

We investigated geographic variation in size and stage (instar) at maturity of snow crab (Chionoecetes opilio) on the eastern Bering Sea shelf. Size-frequency distribution analysis showed that females can reach maturity at four different instars, presumably Instars VIII to XI. Geographic variation in instar structure generates clinal variation in size at maturity, from small size at high latitudes (colder) to large size at low latitudes (warmer). Different pieces of evidence support the hypothesis that geographic variation in mature female size is a phenotypic response to environmental conditions governed by a single reaction norm. Clinal variation conforms to the “inverse Bergmann's rule”. We argue that a single macroecological rule should not be expected to explain all latitudinal size gradients observed in marine invertebrates. Size at maturity fluctuated cyclically, and was negatively and significantly cross-correlated with strength in the recruitment of females to the mature population. Cycl...

/pdf/variation-of-female-size-and-stage-at-maturity-in-snow-crab-3g2gvg4zkn.pdf

Variation of female size and stage at maturity in snow crab (chionoecetes opilio) (brachyura: majidae) from the eastern bering sea

Landings of the snow crab Chionoecetes opilio (J. C. Fabricius, 1788), which supports a lucrative fishery in the eastern Bering Sea (EBS), dropped to historical lows by 2000, and the geographic range of reproductive females contracted to the north-west. Resilience of the mature female range through larval advection may be hampered because hatching now occurs downstream. These changes have been punctuated by four pulses of recruitment, with a remarkably regular period of 6-7 yrs. Major pulses of the fishery, during the 1990s, were sustained by recruitment pulses that originated in regions of the northwest section of the EBS shelf beyond the reach of the fishery. Here we present, for the first time, a conceptual model of snow-crab spatial dynamics that integrates empirical information with new results from modeling of circulation and larval transport. The geographic region of interest, defined by means of biophysical modeling and tracking ontogenetic migrations, consists of the middle and outer domains of the EBS shelf, bounded by the 50- and 200-m isobaths. Connectivity analysis highlights the significance of subsystems in the southeast and northwest sections of the EBS's middle domain. Predicted settlement regions match historical regions of abundance of immature crabs and are consistent with observed fields of suitable near-bottom temperature. Our study, together with others, highlights the significance of climate change for the fate of important high-latitude fisheries.

Billy Ernst

Papers

State of the World’s Fisheries

Estimation of size at sexual maturity: an evaluation of analytical and resampling procedures

Spatial dynamics of female snow crab (Chionoecetes opilio) in the Eastern Bering Sea

Variation of female size and stage at maturity in snow crab (chionoecetes opilio) (brachyura: majidae) from the eastern bering sea

Spatial dynamics of snow crab (Chionoecetes opilio) in the eastern Bering Sea-putting together the pieces of the puzzle